Starting phenix.real_space_refine on Sun Feb 25 16:03:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wd1_21620/02_2024/6wd1_21620.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wd1_21620/02_2024/6wd1_21620.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wd1_21620/02_2024/6wd1_21620.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wd1_21620/02_2024/6wd1_21620.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wd1_21620/02_2024/6wd1_21620.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wd1_21620/02_2024/6wd1_21620.pdb" } resolution = 3.3 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= 0.109 sd= 0.889 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 4652 5.49 5 S 153 5.16 5 C 74016 2.51 5 N 27371 2.21 5 O 40750 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "b GLU 78": "OE1" <-> "OE2" Residue "b ASP 167": "OD1" <-> "OD2" Residue "b GLU 198": "OE1" <-> "OE2" Residue "c ARG 13": "NH1" <-> "NH2" Residue "c GLU 17": "OE1" <-> "OE2" Residue "c ARG 33": "NH1" <-> "NH2" Residue "c ARG 59": "NH1" <-> "NH2" Residue "c GLU 74": "OE1" <-> "OE2" Residue "c ARG 77": "NH1" <-> "NH2" Residue "c PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 83": "NH1" <-> "NH2" Residue "c ASP 108": "OD1" <-> "OD2" Residue "c ARG 169": "NH1" <-> "NH2" Residue "c ARG 184": "NH1" <-> "NH2" Residue "d ARG 21": "NH1" <-> "NH2" Residue "d ARG 44": "NH1" <-> "NH2" Residue "d ARG 49": "NH1" <-> "NH2" Residue "d ARG 61": "NH1" <-> "NH2" Residue "d ARG 88": "NH1" <-> "NH2" Residue "d ASP 91": "OD1" <-> "OD2" Residue "d ARG 102": "NH1" <-> "NH2" Residue "d ASP 140": "OD1" <-> "OD2" Residue "d ASP 145": "OD1" <-> "OD2" Residue "d ARG 162": "NH1" <-> "NH2" Residue "d ASP 168": "OD1" <-> "OD2" Residue "d ARG 170": "NH1" <-> "NH2" Residue "e ASP 45": "OD1" <-> "OD2" Residue "e ARG 70": "NH1" <-> "NH2" Residue "e ARG 79": "NH1" <-> "NH2" Residue "e TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 ARG 132": "NH1" <-> "NH2" Residue "e GLU 133": "OE1" <-> "OE2" Residue "e TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ASP 143": "OD1" <-> "OD2" Residue "f ARG 2": "NH1" <-> "NH2" Residue "f ASP 59": "OD1" <-> "OD2" Residue "f ASP 136": "OD1" <-> "OD2" Residue "f ARG 152": "NH1" <-> "NH2" Residue "f ARG 162": "NH1" <-> "NH2" Residue "f ARG 169": "NH1" <-> "NH2" Residue "g GLU 45": "OE1" <-> "OE2" Residue "g GLU 53": "OE1" <-> "OE2" Residue "g GLU 127": "OE1" <-> "OE2" Residue "h ASP 29": "OD1" <-> "OD2" Residue "h ASP 74": "OD1" <-> "OD2" Residue "h GLU 98": "OE1" <-> "OE2" Residue "h PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 107": "OE1" <-> "OE2" Residue "h PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i GLU 36": "OE1" <-> "OE2" Residue "i ASP 46": "OD1" <-> "OD2" Residue "i GLU 49": "OE1" <-> "OE2" Residue "i ASP 95": "OD1" <-> "OD2" Residue "i GLU 107": "OE1" <-> "OE2" Residue "i GLU 122": "OE1" <-> "OE2" Residue "i GLU 140": "OE1" <-> "OE2" Residue "j GLU 9": "OE1" <-> "OE2" Residue "j ARG 13": "NH1" <-> "NH2" Residue "j GLU 31": "OE1" <-> "OE2" Residue "j ARG 37": "NH1" <-> "NH2" Residue "j ASP 49": "OD1" <-> "OD2" Residue "j ASP 71": "OD1" <-> "OD2" Residue "j GLU 91": "OE1" <-> "OE2" Residue "j ARG 96": "NH1" <-> "NH2" Residue "j GLU 98": "OE1" <-> "OE2" Residue "j ARG 120": "NH1" <-> "NH2" Residue "j GLU 129": "OE1" <-> "OE2" Residue "k PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k GLU 106": "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 PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ARG 78": "NH1" <-> "NH2" Residue "l ARG 126": "NH1" <-> "NH2" Residue "m ARG 10": "NH1" <-> "NH2" Residue "m ARG 18": "NH1" <-> "NH2" Residue "m 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 TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ASP 106": "OD1" <-> "OD2" 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 ARG 63": "NH1" <-> "NH2" Residue "n ARG 64": "NH1" <-> "NH2" Residue "n ARG 69": "NH1" <-> "NH2" Residue "n ARG 71": "NH1" <-> "NH2" Residue "n ARG 96": "NH1" <-> "NH2" Residue "n PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ASP 117": "OD1" <-> "OD2" Residue "n ARG 118": "NH1" <-> "NH2" Residue "o ASP 2": "OD1" <-> "OD2" 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 GLU 112": "OE1" <-> "OE2" Residue "p PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ARG 20": "NH1" <-> "NH2" Residue "p GLU 26": "OE1" <-> "OE2" Residue "p ARG 38": "NH1" <-> "NH2" Residue "p ARG 61": "NH1" <-> "NH2" Residue "p GLU 67": "OE1" <-> "OE2" Residue "p GLU 70": "OE1" <-> "OE2" Residue "p ARG 88": "NH1" <-> "NH2" Residue "p TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ARG 100": "NH1" <-> "NH2" Residue "p ARG 108": "NH1" <-> "NH2" Residue "q ARG 2": "NH1" <-> "NH2" Residue "q ARG 5": "NH1" <-> "NH2" Residue "q ARG 12": "NH1" <-> "NH2" Residue "q ARG 32": "NH1" <-> "NH2" Residue "q ARG 47": "NH1" <-> "NH2" Residue "q ASP 48": "OD1" <-> "OD2" Residue "q ARG 69": "NH1" <-> "NH2" Residue "q ASP 96": "OD1" <-> "OD2" Residue "q ASP 101": "OD1" <-> "OD2" Residue "r ARG 21": "NH1" <-> "NH2" Residue "r GLU 23": "OE1" <-> "OE2" Residue "r ASP 26": "OD1" <-> "OD2" Residue "r GLU 34": "OE1" <-> "OE2" Residue "r GLU 37": "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 GLU 59": "OE1" <-> "OE2" Residue "s ARG 84": "NH1" <-> "NH2" Residue "s ARG 88": "NH1" <-> "NH2" Residue "s ASP 94": "OD1" <-> "OD2" Residue "s ARG 95": "NH1" <-> "NH2" Residue "s ARG 110": "NH1" <-> "NH2" Residue "t ASP 37": "OD1" <-> "OD2" Residue "t GLU 52": "OE1" <-> "OE2" Residue "t ARG 73": "NH1" <-> "NH2" Residue "u ARG 5": "NH1" <-> "NH2" Residue "u ARG 6": "NH1" <-> "NH2" Residue "u GLU 9": "OE1" <-> "OE2" Residue "u ASP 17": "OD1" <-> "OD2" Residue "u ASP 80": "OD1" <-> "OD2" Residue "u ARG 81": "NH1" <-> "NH2" Residue "u ARG 85": "NH1" <-> "NH2" Residue "u ARG 93": "NH1" <-> "NH2" Residue "u PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v GLU 11": "OE1" <-> "OE2" Residue "v TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v GLU 59": "OE1" <-> "OE2" Residue "v ASP 66": "OD1" <-> "OD2" Residue "v ASP 90": "OD1" <-> "OD2" Residue "w ASP 11": "OD1" <-> "OD2" Residue "w GLU 13": "OE1" <-> "OE2" Residue "w PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x ASP 59": "OD1" <-> "OD2" Residue "y GLU 13": "OE1" <-> "OE2" Residue "y ARG 29": "NH1" <-> "NH2" Residue "y ARG 47": "NH1" <-> "NH2" Residue "y ASP 49": "OD1" <-> "OD2" Residue "y ARG 52": "NH1" <-> "NH2" Residue "z ARG 10": "NH1" <-> "NH2" Residue "z ARG 29": "NH1" <-> "NH2" Residue "z ARG 44": "NH1" <-> "NH2" Residue "B ARG 9": "NH1" <-> "NH2" Residue "B ARG 15": "NH1" <-> "NH2" Residue "B ARG 39": "NH1" <-> "NH2" Residue "B ARG 51": "NH1" <-> "NH2" Residue "C ARG 43": "NH1" <-> "NH2" Residue "C TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 3": "NH1" <-> "NH2" Residue "D ARG 12": "NH1" <-> "NH2" Residue "D ARG 14": "NH1" <-> "NH2" Residue "D ARG 19": "NH1" <-> "NH2" Residue "D ARG 21": "NH1" <-> "NH2" Residue "D ARG 33": "NH1" <-> "NH2" Residue "D ARG 41": "NH1" <-> "NH2" Residue "E ARG 12": "NH1" <-> "NH2" Residue "E 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 "G GLU 51": "OE1" <-> "OE2" Residue "G GLU 77": "OE1" <-> "OE2" Residue "G ASP 81": "OD1" <-> "OD2" Residue "G ASP 87": "OD1" <-> "OD2" Residue "G PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 139": "OE1" <-> "OE2" Residue "G ARG 224": "NH1" <-> "NH2" Residue "H GLU 27": "OE1" <-> "OE2" Residue "H ASP 33": "OD1" <-> "OD2" Residue "H GLU 81": "OE1" <-> "OE2" Residue "H ASP 92": "OD1" <-> "OD2" Residue "H ARG 106": "NH1" <-> "NH2" Residue "H GLU 124": "OE1" <-> "OE2" Residue "H ARG 130": "NH1" <-> "NH2" Residue "H GLU 151": "OE1" <-> "OE2" Residue "H GLU 165": "OE1" <-> "OE2" Residue "I ASP 17": "OD1" <-> "OD2" Residue "I GLU 34": "OE1" <-> "OE2" Residue "I ASP 49": "OD1" <-> "OD2" Residue "I TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 94": "OE1" <-> "OE2" Residue "I GLU 159": "OE1" <-> "OE2" Residue "I GLU 162": "OE1" <-> "OE2" Residue "I ASP 193": "OD1" <-> "OD2" Residue "J PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 115": "OE1" <-> "OE2" Residue "J GLU 144": "OE1" <-> "OE2" Residue "J GLU 150": "OE1" <-> "OE2" Residue "J ARG 156": "NH1" <-> "NH2" Residue "K GLU 23": "OE1" <-> "OE2" Residue "K GLU 98": "OE1" <-> "OE2" Residue "L GLU 39": "OE1" <-> "OE2" Residue "L ASP 125": "OD1" <-> "OD2" Residue "M GLU 41": "OE1" <-> "OE2" Residue "M ASP 53": "OD1" <-> "OD2" Residue "M GLU 59": "OE1" <-> "OE2" Residue "M GLU 72": "OE1" <-> "OE2" Residue "M GLU 90": "OE1" <-> "OE2" Residue "N PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 90": "OD1" <-> "OD2" Residue "N GLU 91": "OE1" <-> "OE2" Residue "N GLU 111": "OE1" <-> "OE2" Residue "N ARG 123": "NH1" <-> "NH2" Residue "O ASP 14": "OD1" <-> "OD2" Residue "O ASP 63": "OD1" <-> "OD2" Residue "O ASP 75": "OD1" <-> "OD2" Residue "O ASP 85": "OD1" <-> "OD2" Residue "Q ARG 55": "NH1" <-> "NH2" Residue "R ASP 41": "OD1" <-> "OD2" Residue "R GLU 49": "OE1" <-> "OE2" Residue "R ASP 57": "OD1" <-> "OD2" Residue "R GLU 65": "OE1" <-> "OE2" Residue "S GLU 9": "OE1" <-> "OE2" Residue "S GLU 38": "OE1" <-> "OE2" Residue "S ASP 39": "OD1" <-> "OD2" Residue "S PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 91": "OE1" <-> "OE2" Residue "T PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 44": "OE1" <-> "OE2" Residue "T ASP 73": "OD1" <-> "OD2" Residue "U ASP 23": "OD1" <-> "OD2" Residue "U ARG 28": "NH1" <-> "NH2" Residue "U GLU 47": "OE1" <-> "OE2" Residue "U ASP 53": "OD1" <-> "OD2" Residue "V PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 59": "OE1" <-> "OE2" Residue "W ARG 11": "NH1" <-> "NH2" Residue "W ASP 21": "OD1" <-> "OD2" Residue "Z PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 66": "NH1" <-> "NH2" Residue "a ARG 7": "NH1" <-> "NH2" Residue "a ARG 12": "NH1" <-> "NH2" Residue "a ARG 162": "NH1" <-> "NH2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 146942 Number of models: 1 Model: "" Number of chains: 56 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': 89, 'rna2p_pyr': 48, 'rna3p_pur': 785, 'rna3p_pyr': 617} Link IDs: {'rna2p': 137, 'rna3p': 1401} Chain: "1" Number of atoms: 62317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2903, 62317 Classifications: {'RNA': 2903} Modifications used: {'5*END': 1, 'rna2p_pur': 212, 'rna2p_pyr': 95, 'rna3p_pur': 1462, 'rna3p_pyr': 1134} Link IDs: {'rna2p': 307, 'rna3p': 2595} 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': 7, 'rna2p_pyr': 6, 'rna3p_pur': 32, 'rna3p_pyr': 32} Link IDs: {'rna2p': 13, 'rna3p': 63} 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} Time building chain proxies: 56.36, per 1000 atoms: 0.38 Number of scatterers: 146942 At special positions: 0 Unit cell: (279.93, 263.934, 246.605, 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 153 16.00 P 4652 15.00 O 40750 8.00 N 27371 7.00 C 74016 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 61.10 Conformation dependent library (CDL) restraints added in 8.3 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: 11072 Finding SS restraints... Secondary structure from input PDB file: 188 helices and 76 sheets defined 33.9% alpha, 16.4% beta 1385 base pairs and 2713 stacking pairs defined. Time for finding SS restraints: 51.74 Creating SS restraints... Processing helix chain 'b' and resid 29 through 31 No H-bonds generated for 'chain 'b' and resid 29 through 31' Processing helix chain 'b' and resid 206 through 214 removed outlier: 4.017A pdb=" N ALA b 210 " --> pdb=" O LYS b 206 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG b 211 " --> pdb=" O ALA b 207 " (cutoff:3.500A) Processing helix chain 'b' and resid 220 through 224 removed outlier: 3.686A pdb=" N ALA b 223 " --> pdb=" O ARG b 220 " (cutoff:3.500A) Processing helix chain 'c' and resid 39 through 44 Processing helix chain 'c' and resid 61 through 72 removed outlier: 3.653A pdb=" N ALA c 71 " --> pdb=" O HIS c 67 " (cutoff:3.500A) Processing helix chain 'c' and resid 97 through 102 removed outlier: 3.603A pdb=" N LEU c 100 " --> pdb=" O SER c 97 " (cutoff:3.500A) Processing helix chain 'c' and resid 120 through 125 Processing helix chain 'd' and resid 15 through 20 Processing helix chain 'd' and resid 24 through 39 removed outlier: 3.626A pdb=" N ALA d 36 " --> pdb=" O VAL d 32 " (cutoff:3.500A) Processing helix chain 'd' and resid 97 through 113 Processing helix chain 'd' and resid 130 through 140 removed outlier: 3.681A pdb=" N LEU d 134 " --> pdb=" O LYS d 130 " (cutoff:3.500A) Processing helix chain 'd' and resid 154 through 159 Processing helix chain 'd' and resid 160 through 162 No H-bonds generated for 'chain 'd' and resid 160 through 162' Processing helix chain 'd' and resid 176 through 183 Processing helix chain 'd' and resid 190 through 200 removed outlier: 3.572A pdb=" N LYS d 194 " --> pdb=" O ALA d 190 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLN d 195 " --> pdb=" O ASP d 191 " (cutoff:3.500A) Processing helix chain 'e' and resid 2 through 8 Processing helix chain 'e' and resid 9 through 15 removed outlier: 3.663A pdb=" N LYS e 13 " --> pdb=" O ASP e 9 " (cutoff:3.500A) Processing helix chain 'e' and resid 40 through 44 removed outlier: 3.731A pdb=" N ILE e 43 " --> pdb=" O GLY e 40 " (cutoff:3.500A) Processing helix chain 'e' and resid 45 through 60 removed outlier: 3.733A pdb=" N LEU e 49 " --> pdb=" O ASP e 45 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE e 59 " --> pdb=" O ASP e 55 " (cutoff:3.500A) Processing helix chain 'e' and resid 93 through 105 removed outlier: 3.772A pdb=" N GLU e 97 " --> pdb=" O GLU e 93 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE e 98 " --> pdb=" O ARG e 94 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE e 105 " --> pdb=" O ARG e 101 " (cutoff:3.500A) Processing helix chain 'e' and resid 161 through 172 removed outlier: 3.842A pdb=" N ALA e 167 " --> pdb=" O GLU e 163 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU e 168 " --> pdb=" O GLU e 164 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA e 171 " --> pdb=" O ALA e 167 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE e 172 " --> pdb=" O LEU e 168 " (cutoff:3.500A) Processing helix chain 'f' and resid 59 through 78 Processing helix chain 'f' and resid 136 through 151 removed outlier: 3.589A pdb=" N TYR f 150 " --> pdb=" O ASP f 146 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ARG f 151 " --> pdb=" O LEU f 147 " (cutoff:3.500A) Processing helix chain 'g' and resid 22 through 28 Processing helix chain 'g' and resid 40 through 49 Processing helix chain 'g' and resid 54 through 71 removed outlier: 3.625A pdb=" N LEU g 58 " --> pdb=" O LEU g 54 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA g 59 " --> pdb=" O GLU g 55 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLU g 60 " --> pdb=" O ALA g 56 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL g 61 " --> pdb=" O LYS g 57 " (cutoff:3.500A) Processing helix chain 'g' and resid 95 through 103 removed outlier: 3.759A pdb=" N ILE g 99 " --> pdb=" O GLY g 95 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASP g 101 " --> pdb=" O ARG g 97 " (cutoff:3.500A) Processing helix chain 'g' and resid 111 through 113 No H-bonds generated for 'chain 'g' and resid 111 through 113' Processing helix chain 'h' and resid 3 through 19 Processing helix chain 'h' and resid 33 through 48 removed outlier: 3.544A pdb=" N LYS h 37 " --> pdb=" O VAL h 33 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N THR h 39 " --> pdb=" O VAL h 35 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU h 40 " --> pdb=" O ASP h 36 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N ARG h 42 " --> pdb=" O MET h 38 " (cutoff:3.500A) Processing helix chain 'h' and resid 63 through 67 Processing helix chain 'h' and resid 73 through 78 removed outlier: 4.020A pdb=" N VAL h 77 " --> pdb=" O LYS h 73 " (cutoff:3.500A) Processing helix chain 'h' and resid 96 through 101 Processing helix chain 'h' and resid 102 through 105 Processing helix chain 'h' and resid 110 through 114 removed outlier: 3.823A pdb=" N GLU h 114 " --> pdb=" O ALA h 111 " (cutoff:3.500A) Processing helix chain 'i' and resid 23 through 27 Processing helix chain 'i' and resid 33 through 46 removed outlier: 3.640A pdb=" N ALA i 40 " --> pdb=" O GLU i 36 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA i 43 " --> pdb=" O LYS i 39 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS i 44 " --> pdb=" O ALA i 40 " (cutoff:3.500A) Processing helix chain 'i' and resid 74 through 83 removed outlier: 4.072A pdb=" N LYS i 80 " --> pdb=" O ALA i 76 " (cutoff:3.500A) Processing helix chain 'i' and resid 101 through 112 removed outlier: 3.502A pdb=" N GLU i 107 " --> pdb=" O ALA i 103 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ILE i 108 " --> pdb=" O GLN i 104 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N THR i 111 " --> pdb=" O GLU i 107 " (cutoff:3.500A) Processing helix chain 'i' and resid 120 through 135 removed outlier: 3.631A pdb=" N SER i 127 " --> pdb=" O ALA i 123 " (cutoff:3.500A) Processing helix chain 'j' and resid 24 through 38 removed outlier: 3.759A pdb=" N GLU j 31 " --> pdb=" O ARG j 27 " (cutoff:3.500A) Processing helix chain 'j' and resid 59 through 62 Processing helix chain 'j' and resid 67 through 72 Processing helix chain 'j' and resid 89 through 96 Processing helix chain 'j' and resid 97 through 107 removed outlier: 4.195A pdb=" N ILE j 101 " --> pdb=" O PRO j 97 " (cutoff:3.500A) Processing helix chain 'j' and resid 112 through 118 Processing helix chain 'k' and resid 104 through 108 Processing helix chain 'k' and resid 112 through 119 Processing helix chain 'l' and resid 37 through 41 removed outlier: 3.660A pdb=" N ARG l 41 " --> pdb=" O GLN l 38 " (cutoff:3.500A) Processing helix chain 'l' and resid 56 through 61 removed outlier: 3.601A pdb=" N LEU l 61 " --> pdb=" O LEU l 57 " (cutoff:3.500A) Processing helix chain 'l' and resid 69 through 72 Processing helix chain 'l' and resid 80 through 85 removed outlier: 4.902A pdb=" N ALA l 83 " --> pdb=" O SER l 80 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS l 84 " --> pdb=" O ASP l 81 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N VAL l 85 " --> pdb=" O LEU l 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 80 through 85' Processing helix chain 'l' and resid 128 through 139 Processing helix chain 'm' and resid 43 through 55 removed outlier: 3.671A pdb=" N ARG m 51 " --> pdb=" O GLU m 47 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N MET m 53 " --> pdb=" O ALA m 49 " (cutoff:3.500A) Processing helix chain 'm' and resid 109 through 122 removed outlier: 3.523A pdb=" N ALA m 116 " --> pdb=" O LEU m 112 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA m 122 " --> pdb=" O LYS m 118 " (cutoff:3.500A) Processing helix chain 'n' and resid 13 through 32 Processing helix chain 'n' and resid 38 through 57 removed outlier: 3.682A pdb=" N ARG n 45 " --> pdb=" O ALA n 41 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ARG n 46 " --> pdb=" O LYS n 42 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N VAL n 47 " --> pdb=" O GLU n 43 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU n 49 " --> pdb=" O ARG n 45 " (cutoff:3.500A) Proline residue: n 50 - end of helix removed outlier: 3.596A pdb=" N LYS n 56 " --> pdb=" O ILE n 52 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N THR n 57 " --> pdb=" O THR n 53 " (cutoff:3.500A) Processing helix chain 'n' and resid 60 through 69 Processing helix chain 'n' and resid 72 through 79 Processing helix chain 'n' and resid 82 through 87 Processing helix chain 'o' and resid 3 through 22 removed outlier: 4.608A pdb=" N ARG o 13 " --> pdb=" O ARG o 9 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ALA o 14 " --> pdb=" O ARG o 10 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS o 17 " --> pdb=" O ARG o 13 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU o 21 " --> pdb=" O LYS o 17 " (cutoff:3.500A) Processing helix chain 'o' and resid 55 through 60 removed outlier: 4.304A pdb=" N GLU o 60 " --> pdb=" O LYS o 56 " (cutoff:3.500A) Processing helix chain 'o' and resid 69 through 86 removed outlier: 3.520A pdb=" N ALA o 73 " --> pdb=" O ASP o 69 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA o 82 " --> pdb=" O VAL o 78 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N LEU o 83 " --> pdb=" O ALA o 79 " (cutoff:3.500A) Processing helix chain 'o' and resid 101 through 112 Processing helix chain 'p' and resid 2 through 7 Processing helix chain 'p' and resid 52 through 55 Processing helix chain 'p' and resid 96 through 101 removed outlier: 3.699A pdb=" N LEU p 99 " --> pdb=" O LEU p 96 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG p 100 " --> pdb=" O TYR p 97 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU p 101 " --> pdb=" O TYR p 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 96 through 101' Processing helix chain 'p' and resid 103 through 108 removed outlier: 3.631A pdb=" N ARG p 108 " --> pdb=" O LYS p 105 " (cutoff:3.500A) Processing helix chain 'q' and resid 6 through 19 removed outlier: 3.837A pdb=" N ALA q 11 " --> pdb=" O VAL q 7 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE q 16 " --> pdb=" O ARG q 12 " (cutoff:3.500A) Processing helix chain 'q' and resid 24 through 29 removed outlier: 3.676A pdb=" N SER q 28 " --> pdb=" O GLY q 25 " (cutoff:3.500A) Processing helix chain 'q' and resid 30 through 71 removed outlier: 4.370A pdb=" N GLN q 36 " --> pdb=" O ARG q 32 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ARG q 50 " --> pdb=" O TYR q 46 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N LYS q 53 " --> pdb=" O ARG q 49 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG q 54 " --> pdb=" O ARG q 50 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG q 57 " --> pdb=" O LYS q 53 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASN q 71 " --> pdb=" O ALA q 67 " (cutoff:3.500A) Processing helix chain 'q' and resid 75 through 85 removed outlier: 3.593A pdb=" N GLY q 81 " --> pdb=" O LYS q 77 " (cutoff:3.500A) Processing helix chain 'q' and resid 90 through 101 removed outlier: 3.523A pdb=" N ASP q 96 " --> pdb=" O LYS q 92 " (cutoff:3.500A) Processing helix chain 'q' and resid 101 through 117 removed outlier: 3.540A pdb=" N ALA q 107 " --> pdb=" O VAL q 103 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA q 117 " --> pdb=" O LYS q 113 " (cutoff:3.500A) Processing helix chain 's' and resid 13 through 19 removed outlier: 3.510A pdb=" N VAL s 17 " --> pdb=" O SER s 13 " (cutoff:3.500A) Processing helix chain 's' and resid 28 through 39 removed outlier: 3.673A pdb=" N LEU s 33 " --> pdb=" O VAL s 29 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ASP s 34 " --> pdb=" O SER s 30 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE s 35 " --> pdb=" O GLN s 31 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU s 36 " --> pdb=" O ALA s 32 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N TYR s 38 " --> pdb=" O ASP s 34 " (cutoff:3.500A) Processing helix chain 's' and resid 41 through 62 removed outlier: 3.525A pdb=" N SER s 53 " --> pdb=" O LYS s 49 " (cutoff:3.500A) Processing helix chain 's' and resid 88 through 92 removed outlier: 3.962A pdb=" N GLY s 91 " --> pdb=" O ARG s 88 " (cutoff:3.500A) Processing helix chain 't' and resid 2 through 8 removed outlier: 3.887A pdb=" N ARG t 6 " --> pdb=" O ILE t 2 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU t 7 " --> pdb=" O ARG t 3 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU t 8 " --> pdb=" O GLU t 4 " (cutoff:3.500A) No H-bonds generated for 'chain 't' and resid 2 through 8' Processing helix chain 't' and resid 18 through 28 Processing helix chain 't' and resid 39 through 51 removed outlier: 3.524A pdb=" N ALA t 45 " --> pdb=" O ALA t 41 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLN t 48 " --> pdb=" O LYS t 44 " (cutoff:3.500A) Processing helix chain 'v' and resid 13 through 22 removed outlier: 3.618A pdb=" N SER v 17 " --> pdb=" O GLY v 13 " (cutoff:3.500A) Processing helix chain 'v' and resid 44 through 51 Processing helix chain 'v' and resid 53 through 58 Processing helix chain 'x' and resid 52 through 61 removed outlier: 3.618A pdb=" N ARG x 56 " --> pdb=" O ALA x 52 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASP x 59 " --> pdb=" O MET x 55 " (cutoff:3.500A) Processing helix chain 'x' and resid 62 through 73 Processing helix chain 'y' and resid 9 through 22 Processing helix chain 'y' and resid 23 through 34 removed outlier: 3.532A pdb=" N GLN y 31 " --> pdb=" O ASN y 27 " (cutoff:3.500A) Processing helix chain 'y' and resid 40 through 61 removed outlier: 3.853A pdb=" N LYS y 44 " --> pdb=" O SER y 40 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA y 51 " --> pdb=" O ARG y 47 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU y 56 " --> pdb=" O ARG y 52 " (cutoff:3.500A) Processing helix chain 'z' and resid 16 through 27 removed outlier: 3.502A pdb=" N LYS z 20 " --> pdb=" O LEU z 16 " (cutoff:3.500A) Processing helix chain 'z' and resid 42 through 48 Processing helix chain 'B' and resid 8 through 15 Processing helix chain 'D' and resid 8 through 14 Processing helix chain 'D' and resid 17 through 22 Processing helix chain 'D' and resid 24 through 38 removed outlier: 3.592A pdb=" N ARG D 35 " --> pdb=" O LEU D 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 8 through 12 removed outlier: 3.556A pdb=" N LYS E 11 " --> pdb=" O GLY E 8 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 43 removed outlier: 3.547A pdb=" N HIS E 42 " --> pdb=" O LYS E 38 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU E 43 " --> pdb=" O ARG E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 61 removed outlier: 4.723A pdb=" N GLY E 55 " --> pdb=" O LYS E 51 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N LEU E 56 " --> pdb=" O GLY E 52 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL E 57 " --> pdb=" O ASP E 53 " (cutoff:3.500A) Processing helix chain 'F' and resid 18 through 22 removed outlier: 3.927A pdb=" N GLY F 21 " --> pdb=" O LYS F 18 " (cutoff:3.500A) Processing helix chain 'G' and resid 4 through 12 removed outlier: 3.501A pdb=" N MET G 8 " --> pdb=" O SER G 4 " (cutoff:3.500A) Processing helix chain 'G' and resid 23 through 28 removed outlier: 3.519A pdb=" N LYS G 27 " --> pdb=" O PRO G 24 " (cutoff:3.500A) Proline residue: G 28 - end of helix Processing helix chain 'G' and resid 41 through 62 removed outlier: 3.747A pdb=" N THR G 45 " --> pdb=" O ASN G 41 " (cutoff:3.500A) Proline residue: G 47 - end of helix removed outlier: 3.564A pdb=" N GLU G 51 " --> pdb=" O PRO G 47 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 87 Processing helix chain 'G' and resid 102 through 122 removed outlier: 4.312A pdb=" N GLN G 108 " --> pdb=" O LYS G 104 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU G 116 " --> pdb=" O ARG G 112 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASP G 122 " --> pdb=" O THR G 118 " (cutoff:3.500A) Processing helix chain 'G' and resid 129 through 143 removed outlier: 3.772A pdb=" N LEU G 140 " --> pdb=" O ARG G 136 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU G 143 " --> pdb=" O GLU G 139 " (cutoff:3.500A) Processing helix chain 'G' and resid 143 through 148 Processing helix chain 'G' and resid 150 through 154 removed outlier: 4.038A pdb=" N MET G 153 " --> pdb=" O ILE G 150 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N GLY G 154 " --> pdb=" O LYS G 151 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 150 through 154' Processing helix chain 'G' and resid 168 through 178 removed outlier: 3.664A pdb=" N ILE G 172 " --> pdb=" O GLU G 168 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ASN G 177 " --> pdb=" O LYS G 173 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU G 178 " --> pdb=" O GLU G 174 " (cutoff:3.500A) Processing helix chain 'G' and resid 205 through 224 removed outlier: 3.631A pdb=" N ALA G 215 " --> pdb=" O LEU G 211 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA G 218 " --> pdb=" O GLY G 214 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR G 219 " --> pdb=" O ALA G 215 " (cutoff:3.500A) Processing helix chain 'H' and resid 27 through 46 removed outlier: 3.738A pdb=" N ASN H 31 " --> pdb=" O GLU H 27 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE H 36 " --> pdb=" O LEU H 32 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS H 44 " --> pdb=" O GLN H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 71 through 77 removed outlier: 3.502A pdb=" N VAL H 75 " --> pdb=" O ARG H 71 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE H 76 " --> pdb=" O PRO H 72 " (cutoff:3.500A) Processing helix chain 'H' and resid 80 through 95 removed outlier: 3.676A pdb=" N VAL H 89 " --> pdb=" O LYS H 85 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASP H 92 " --> pdb=" O LYS H 88 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ILE H 93 " --> pdb=" O VAL H 89 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ALA H 94 " --> pdb=" O VAL H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 107 through 110 Processing helix chain 'H' and resid 111 through 124 removed outlier: 3.578A pdb=" N VAL H 115 " --> pdb=" O ASP H 111 " (cutoff:3.500A) Processing helix chain 'H' and resid 128 through 145 removed outlier: 3.549A pdb=" N ARG H 135 " --> pdb=" O ARG H 131 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU H 143 " --> pdb=" O ASN H 139 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY H 144 " --> pdb=" O ALA H 140 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA H 145 " --> pdb=" O MET H 141 " (cutoff:3.500A) Processing helix chain 'H' and resid 155 through 159 removed outlier: 3.848A pdb=" N ALA H 159 " --> pdb=" O LEU H 156 " (cutoff:3.500A) Processing helix chain 'I' and resid 7 through 15 removed outlier: 3.931A pdb=" N SER I 11 " --> pdb=" O LYS I 7 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 65 removed outlier: 4.255A pdb=" N TYR I 64 " --> pdb=" O VAL I 60 " (cutoff:3.500A) Processing helix chain 'I' and resid 67 through 81 removed outlier: 3.561A pdb=" N GLU I 77 " --> pdb=" O ASN I 73 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA I 78 " --> pdb=" O TYR I 74 " (cutoff:3.500A) Processing helix chain 'I' and resid 84 through 94 removed outlier: 3.654A pdb=" N LEU I 89 " --> pdb=" O THR I 85 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N LEU I 90 " --> pdb=" O GLY I 86 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA I 91 " --> pdb=" O GLU I 87 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU I 92 " --> pdb=" O ASN I 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 96 through 105 Processing helix chain 'I' and resid 109 through 119 Processing helix chain 'I' and resid 145 through 149 Processing helix chain 'I' and resid 153 through 160 removed outlier: 3.512A pdb=" N ALA I 157 " --> pdb=" O ARG I 153 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU I 160 " --> pdb=" O ALA I 156 " (cutoff:3.500A) Processing helix chain 'I' and resid 161 through 164 Processing helix chain 'I' and resid 186 through 190 removed outlier: 3.566A pdb=" N LEU I 190 " --> pdb=" O ARG I 187 " (cutoff:3.500A) Processing helix chain 'I' and resid 196 through 203 removed outlier: 3.943A pdb=" N TYR I 203 " --> pdb=" O ILE I 199 " (cutoff:3.500A) Processing helix chain 'J' and resid 54 through 69 removed outlier: 3.506A pdb=" N GLN J 60 " --> pdb=" O PRO J 56 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS J 61 " --> pdb=" O ALA J 57 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LYS J 65 " --> pdb=" O LYS J 61 " (cutoff:3.500A) Processing helix chain 'J' and resid 109 through 116 removed outlier: 3.765A pdb=" N VAL J 116 " --> pdb=" O ALA J 112 " (cutoff:3.500A) Processing helix chain 'J' and resid 131 through 145 Processing helix chain 'J' and resid 148 through 156 removed outlier: 3.670A pdb=" N LYS J 155 " --> pdb=" O MET J 151 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG J 156 " --> pdb=" O VAL J 152 " (cutoff:3.500A) Processing helix chain 'J' and resid 159 through 165 removed outlier: 3.690A pdb=" N LEU J 164 " --> pdb=" O VAL J 160 " (cutoff:3.500A) Processing helix chain 'K' and resid 12 through 16 Processing helix chain 'K' and resid 17 through 32 removed outlier: 3.564A pdb=" N MET K 21 " --> pdb=" O GLN K 17 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG K 24 " --> pdb=" O GLY K 20 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA K 27 " --> pdb=" O GLU K 23 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA K 32 " --> pdb=" O ALA K 28 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 80 removed outlier: 3.632A pdb=" N ILE K 71 " --> pdb=" O PRO K 67 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N PHE K 78 " --> pdb=" O LEU K 74 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG K 79 " --> pdb=" O GLU K 75 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N PHE K 80 " --> pdb=" O THR K 76 " (cutoff:3.500A) Processing helix chain 'L' and resid 19 through 30 removed outlier: 3.838A pdb=" N PHE L 25 " --> pdb=" O LEU L 21 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASN L 27 " --> pdb=" O ALA L 23 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE L 28 " --> pdb=" O LYS L 24 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU L 29 " --> pdb=" O PHE L 25 " (cutoff:3.500A) Processing helix chain 'L' and resid 34 through 54 removed outlier: 4.251A pdb=" N ARG L 52 " --> pdb=" O THR L 48 " (cutoff:3.500A) Processing helix chain 'L' and resid 58 through 63 removed outlier: 3.581A pdb=" N GLU L 62 " --> pdb=" O LEU L 58 " (cutoff:3.500A) Processing helix chain 'L' and resid 91 through 108 removed outlier: 3.539A pdb=" N ASN L 96 " --> pdb=" O PRO L 92 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA L 97 " --> pdb=" O VAL L 93 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL L 104 " --> pdb=" O MET L 100 " (cutoff:3.500A) Processing helix chain 'L' and resid 114 through 128 removed outlier: 3.667A pdb=" N ASP L 125 " --> pdb=" O ASN L 121 " (cutoff:3.500A) Processing helix chain 'L' and resid 132 through 146 removed outlier: 3.534A pdb=" N ALA L 144 " --> pdb=" O VAL L 140 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA L 146 " --> pdb=" O ARG L 142 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 19 removed outlier: 3.523A pdb=" N ARG M 12 " --> pdb=" O ASP M 8 " (cutoff:3.500A) Processing helix chain 'M' and resid 29 through 43 removed outlier: 3.669A pdb=" N ASN M 37 " --> pdb=" O VAL M 33 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N VAL M 38 " --> pdb=" O ALA M 34 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU M 42 " --> pdb=" O VAL M 38 " (cutoff:3.500A) Processing helix chain 'M' and resid 111 through 119 Processing helix chain 'N' and resid 34 through 38 Processing helix chain 'N' and resid 48 through 52 Processing helix chain 'N' and resid 70 through 86 removed outlier: 3.589A pdb=" N THR N 83 " --> pdb=" O ARG N 79 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU N 86 " --> pdb=" O ILE N 82 " (cutoff:3.500A) Processing helix chain 'N' and resid 90 through 95 Processing helix chain 'O' and resid 14 through 26 removed outlier: 3.711A pdb=" N GLN O 20 " --> pdb=" O ARG O 16 " (cutoff:3.500A) Processing helix chain 'O' and resid 26 through 33 Processing helix chain 'P' and resid 53 through 57 Processing helix chain 'P' and resid 58 through 71 Processing helix chain 'P' and resid 93 through 103 removed outlier: 3.595A pdb=" N ARG P 97 " --> pdb=" O GLU P 93 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASN P 100 " --> pdb=" O ILE P 96 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 9 Processing helix chain 'R' and resid 13 through 20 Processing helix chain 'R' and resid 25 through 37 Processing helix chain 'R' and resid 48 through 59 removed outlier: 3.521A pdb=" N ASP R 53 " --> pdb=" O GLU R 49 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N THR R 54 " --> pdb=" O GLY R 50 " (cutoff:3.500A) Processing helix chain 'R' and resid 60 through 62 No H-bonds generated for 'chain 'R' and resid 60 through 62' Processing helix chain 'R' and resid 64 through 83 removed outlier: 3.556A pdb=" N ARG R 70 " --> pdb=" O GLY R 66 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N SER R 73 " --> pdb=" O ARG R 69 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG R 78 " --> pdb=" O MET R 74 " (cutoff:3.500A) Processing helix chain 'R' and resid 84 through 92 removed outlier: 3.536A pdb=" N ARG R 92 " --> pdb=" O LEU R 88 " (cutoff:3.500A) Processing helix chain 'S' and resid 2 through 19 removed outlier: 3.506A pdb=" N TYR S 19 " --> pdb=" O LEU S 15 " (cutoff:3.500A) Processing helix chain 'S' and resid 23 through 27 removed outlier: 3.937A pdb=" N LEU S 26 " --> pdb=" O ARG S 23 " (cutoff:3.500A) Processing helix chain 'S' and resid 37 through 47 removed outlier: 3.670A pdb=" N VAL S 44 " --> pdb=" O ARG S 40 " (cutoff:3.500A) Processing helix chain 'S' and resid 55 through 59 Processing helix chain 'S' and resid 79 through 88 removed outlier: 3.578A pdb=" N ARG S 84 " --> pdb=" O ARG S 80 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLU S 85 " --> pdb=" O ILE S 81 " (cutoff:3.500A) Processing helix chain 'T' and resid 3 through 15 removed outlier: 3.705A pdb=" N LYS T 9 " --> pdb=" O GLU T 5 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE T 10 " --> pdb=" O ALA T 6 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER T 12 " --> pdb=" O ALA T 8 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU T 13 " --> pdb=" O LYS T 9 " (cutoff:3.500A) Processing helix chain 'T' and resid 23 through 42 removed outlier: 4.083A pdb=" N GLY T 40 " --> pdb=" O ASN T 36 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N HIS T 41 " --> pdb=" O HIS T 37 " (cutoff:3.500A) Processing helix chain 'T' and resid 48 through 73 removed outlier: 3.871A pdb=" N GLY T 54 " --> pdb=" O HIS T 50 " (cutoff:3.500A) Processing helix chain 'T' and resid 73 through 85 removed outlier: 3.576A pdb=" N GLU T 82 " --> pdb=" O THR T 78 " (cutoff:3.500A) Processing helix chain 'U' and resid 53 through 62 removed outlier: 3.667A pdb=" N TRP U 60 " --> pdb=" O ARG U 56 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL U 61 " --> pdb=" O ILE U 57 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY U 62 " --> pdb=" O ALA U 58 " (cutoff:3.500A) Processing helix chain 'U' and resid 68 through 78 removed outlier: 3.558A pdb=" N LEU U 74 " --> pdb=" O ARG U 70 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS U 76 " --> pdb=" O ALA U 72 " (cutoff:3.500A) Processing helix chain 'W' and resid 24 through 29 Processing helix chain 'W' and resid 30 through 32 No H-bonds generated for 'chain 'W' and resid 30 through 32' Processing helix chain 'W' and resid 40 through 45 removed outlier: 3.668A pdb=" N THR W 44 " --> pdb=" O PRO W 40 " (cutoff:3.500A) Processing helix chain 'W' and resid 47 through 64 removed outlier: 3.613A pdb=" N ARG W 56 " --> pdb=" O ARG W 52 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA W 57 " --> pdb=" O GLN W 53 " (cutoff:3.500A) Processing helix chain 'X' and resid 11 through 23 removed outlier: 3.605A pdb=" N GLU X 19 " --> pdb=" O LEU X 15 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU X 23 " --> pdb=" O GLU X 19 " (cutoff:3.500A) Processing helix chain 'X' and resid 40 through 44 Processing helix chain 'Y' and resid 4 through 6 No H-bonds generated for 'chain 'Y' and resid 4 through 6' Processing helix chain 'Y' and resid 7 through 41 removed outlier: 3.845A pdb=" N ILE Y 11 " --> pdb=" O LYS Y 7 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN Y 12 " --> pdb=" O LYS Y 8 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLU Y 14 " --> pdb=" O ALA Y 10 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LYS Y 18 " --> pdb=" O GLU Y 14 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N HIS Y 19 " --> pdb=" O LYS Y 15 " (cutoff:3.500A) Processing helix chain 'Y' and resid 42 through 63 removed outlier: 3.525A pdb=" N GLN Y 47 " --> pdb=" O LYS Y 43 " (cutoff:3.500A) Proline residue: Y 55 - end of helix removed outlier: 3.864A pdb=" N ARG Y 59 " --> pdb=" O PRO Y 55 " (cutoff:3.500A) Processing helix chain 'Y' and resid 68 through 86 removed outlier: 3.633A pdb=" N ALA Y 72 " --> pdb=" O LYS Y 68 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ASN Y 77 " --> pdb=" O ARG Y 73 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 23 removed outlier: 4.102A pdb=" N ARG Z 20 " --> pdb=" O ARG Z 16 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N CYS Z 22 " --> pdb=" O PHE Z 18 " (cutoff:3.500A) Processing helix chain 'Z' and resid 27 through 32 Processing helix chain 'Z' and resid 38 through 58 removed outlier: 3.519A pdb=" N LYS Z 45 " --> pdb=" O THR Z 41 " (cutoff:3.500A) Processing helix chain 'a' and resid 5 through 13 Processing helix chain 'a' and resid 22 through 30 removed outlier: 5.031A pdb=" N ALA a 28 " --> pdb=" O ASN a 24 " (cutoff:3.500A) Processing helix chain 'a' and resid 54 through 58 Processing helix chain 'a' and resid 181 through 197 removed outlier: 4.062A pdb=" N ASN a 188 " --> pdb=" O LYS a 184 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA a 195 " --> pdb=" O ALA a 191 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS a 197 " --> pdb=" O LEU a 193 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'b' and resid 2 through 4 Processing sheet with id=AA2, first strand: chain 'b' and resid 33 through 34 Processing sheet with id=AA3, first strand: chain 'b' and resid 100 through 104 removed outlier: 3.752A pdb=" N ARG b 79 " --> pdb=" O LEU b 92 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N LEU b 94 " --> pdb=" O VAL b 77 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N VAL b 77 " --> pdb=" O LEU b 94 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'b' and resid 128 through 130 removed outlier: 3.514A pdb=" N ALA b 189 " --> pdb=" O LEU b 129 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N ILE b 163 " --> pdb=" O ARG b 174 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ARG b 174 " --> pdb=" O ILE b 163 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N MET b 180 " --> pdb=" O VAL b 267 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'c' and resid 4 through 15 removed outlier: 3.753A pdb=" N GLY c 10 " --> pdb=" O VAL c 26 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL c 189 " --> pdb=" O THR c 25 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N LEU c 188 " --> pdb=" O VAL c 178 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ASP c 176 " --> pdb=" O LYS c 190 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N THR c 171 " --> pdb=" O GLY c 111 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N GLY c 111 " --> pdb=" O THR c 171 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N GLN c 173 " --> pdb=" O VAL c 109 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N VAL c 109 " --> pdb=" O GLN c 173 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE c 202 " --> pdb=" O THR c 110 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N THR c 112 " --> pdb=" O ASP c 200 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ASP c 200 " --> pdb=" O THR c 112 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'c' and resid 80 through 83 removed outlier: 6.533A pdb=" N ALA c 47 " --> pdb=" O VAL c 37 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N VAL c 37 " --> pdb=" O ALA c 47 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N GLN c 49 " --> pdb=" O THR c 35 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'c' and resid 117 through 119 removed outlier: 3.501A pdb=" N GLY c 117 " --> pdb=" O MET c 165 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'd' and resid 2 through 3 Processing sheet with id=AA9, first strand: chain 'd' and resid 118 through 121 removed outlier: 3.563A pdb=" N THR d 189 " --> pdb=" O ILE d 149 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N VAL d 146 " --> pdb=" O ASP d 168 " (cutoff:3.500A) removed outlier: 8.614A pdb=" N ARG d 170 " --> pdb=" O VAL d 146 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ILE d 148 " --> pdb=" O ARG d 170 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'e' and resid 65 through 67 removed outlier: 4.035A pdb=" N GLY e 85 " --> pdb=" O THR e 67 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N TYR e 127 " --> pdb=" O ILE e 155 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'f' and resid 8 through 9 removed outlier: 3.749A pdb=" N THR f 50 " --> pdb=" O LYS f 43 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'f' and resid 15 through 19 Processing sheet with id=AB4, first strand: chain 'f' and resid 120 through 126 removed outlier: 7.314A pdb=" N GLU f 129 " --> pdb=" O PRO f 125 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'f' and resid 95 through 98 removed outlier: 3.750A pdb=" N VAL f 112 " --> pdb=" O LEU f 104 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'g' and resid 4 through 5 Processing sheet with id=AB7, first strand: chain 'g' and resid 77 through 82 removed outlier: 7.207A pdb=" N VAL g 78 " --> pdb=" O ASN g 145 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N VAL g 147 " --> pdb=" O VAL g 78 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ILE g 80 " --> pdb=" O VAL g 147 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL g 142 " --> pdb=" O VAL g 130 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL g 130 " --> pdb=" O VAL g 142 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N SER g 131 " --> pdb=" O ARG g 116 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'i' and resid 7 through 10 removed outlier: 4.062A pdb=" N VAL i 8 " --> pdb=" O ILE i 58 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ILE i 58 " --> pdb=" O VAL i 8 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU i 10 " --> pdb=" O VAL i 56 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N VAL i 56 " --> pdb=" O LEU i 10 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL i 57 " --> pdb=" O VAL i 69 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL i 69 " --> pdb=" O VAL i 57 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'j' and resid 122 through 125 removed outlier: 5.947A pdb=" N ILE j 54 " --> pdb=" O LYS j 123 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N TYR j 125 " --> pdb=" O ILE j 54 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N VAL j 56 " --> pdb=" O TYR j 125 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N TYR j 16 " --> pdb=" O ILE j 55 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N LEU j 57 " --> pdb=" O TYR j 16 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N VAL j 18 " --> pdb=" O LEU j 57 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N TRP j 15 " --> pdb=" O GLN j 138 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'j' and resid 73 through 77 Processing sheet with id=AC2, first strand: chain 'k' and resid 6 through 10 removed outlier: 3.634A pdb=" N THR k 6 " --> pdb=" O CYS k 21 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL k 10 " --> pdb=" O ARG k 17 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ARG k 17 " --> pdb=" O VAL k 10 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N GLU k 45 " --> pdb=" O ARG k 17 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VAL k 19 " --> pdb=" O ILE k 43 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ILE k 43 " --> pdb=" O VAL k 19 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N CYS k 21 " --> pdb=" O ILE k 41 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ILE k 41 " --> pdb=" O CYS k 21 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N LYS k 23 " --> pdb=" O ILE k 39 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N ILE k 39 " --> pdb=" O LYS k 23 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ALA k 83 " --> pdb=" O VAL k 63 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N CYS k 84 " --> pdb=" O MET k 7 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N ASN k 9 " --> pdb=" O CYS k 84 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N LEU k 86 " --> pdb=" O ASN k 9 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'k' and resid 69 through 70 removed outlier: 3.664A pdb=" N VAL k 69 " --> pdb=" O ILE k 77 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N VAL k 76 " --> pdb=" O VAL p 72 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ALA p 57 " --> pdb=" O ILE p 49 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N ILE p 49 " --> pdb=" O ALA p 57 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N THR p 59 " --> pdb=" O ILE p 47 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ILE p 63 " --> pdb=" O GLU p 43 " (cutoff:3.500A) removed outlier: 9.425A pdb=" N GLU p 43 " --> pdb=" O ILE p 63 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS p 36 " --> pdb=" O GLU p 33 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N THR p 24 " --> pdb=" O LYS p 86 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER p 84 " --> pdb=" O GLU p 26 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N SER p 82 " --> pdb=" O LYS p 28 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N TRP p 30 " --> pdb=" O VAL p 80 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N VAL p 80 " --> pdb=" O TRP p 30 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'l' and resid 74 through 78 removed outlier: 6.589A pdb=" N ALA l 75 " --> pdb=" O LYS l 109 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N ILE l 111 " --> pdb=" O ALA l 75 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ILE l 77 " --> pdb=" O ILE l 111 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'l' and resid 89 through 90 removed outlier: 6.089A pdb=" N VAL l 122 " --> pdb=" O GLU l 143 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'm' and resid 62 through 65 removed outlier: 6.359A pdb=" N LEU m 33 " --> pdb=" O LEU m 102 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N GLU m 104 " --> pdb=" O PHE m 31 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N PHE m 31 " --> pdb=" O GLU m 104 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'm' and resid 41 through 42 removed outlier: 5.872A pdb=" N VAL m 89 " --> pdb=" O GLU m 75 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N GLU m 75 " --> pdb=" O VAL m 89 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N TYR m 91 " --> pdb=" O ILE m 73 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS m 71 " --> pdb=" O VAL m 93 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'n' and resid 33 through 37 removed outlier: 6.829A pdb=" N MET n 110 " --> pdb=" O CYS n 100 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'o' and resid 47 through 50 removed outlier: 3.597A pdb=" N VAL o 49 " --> pdb=" O VAL o 39 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N VAL o 28 " --> pdb=" O ASP o 93 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'p' and resid 89 through 90 removed outlier: 3.999A pdb=" N LYS p 110 " --> pdb=" O ALA p 90 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'r' and resid 11 through 14 removed outlier: 3.541A pdb=" N PHE r 5 " --> pdb=" O HIS r 12 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N TYR r 2 " --> pdb=" O ILE r 41 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ILE r 41 " --> pdb=" O TYR r 2 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N VAL r 4 " --> pdb=" O LEU r 39 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'r' and resid 19 through 22 removed outlier: 6.755A pdb=" N ASP r 95 " --> pdb=" O VAL r 64 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N LYS r 60 " --> pdb=" O THR r 99 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'r' and resid 72 through 78 removed outlier: 4.265A pdb=" N TYR r 83 " --> pdb=" O ARG r 78 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 's' and resid 4 through 10 removed outlier: 6.041A pdb=" N ILE s 4 " --> pdb=" O VAL s 107 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N VAL s 107 " --> pdb=" O ILE s 4 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N LYS s 6 " --> pdb=" O VAL s 105 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N VAL s 105 " --> pdb=" O LYS s 6 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N ARG s 8 " --> pdb=" O ILE s 103 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ILE s 103 " --> pdb=" O ARG s 8 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ILE s 96 " --> pdb=" O MET s 82 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N MET s 82 " --> pdb=" O ILE s 96 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N LYS s 98 " --> pdb=" O PRO s 80 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N THR s 100 " --> pdb=" O GLU s 78 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N GLU s 78 " --> pdb=" O THR s 100 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N HIS s 102 " --> pdb=" O VAL s 76 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N VAL s 76 " --> pdb=" O HIS s 102 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N THR s 104 " --> pdb=" O ILE s 74 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ILE s 74 " --> pdb=" O THR s 104 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N VAL s 106 " --> pdb=" O THR s 72 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 't' and resid 11 through 14 removed outlier: 3.554A pdb=" N LYS t 81 " --> pdb=" O VAL t 34 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 't' and resid 67 through 70 removed outlier: 3.664A pdb=" N HIS t 70 " --> pdb=" O ARG t 73 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ARG t 73 " --> pdb=" O HIS t 70 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'u' and resid 64 through 65 removed outlier: 6.282A pdb=" N LYS u 32 " --> pdb=" O VAL u 27 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N VAL u 27 " --> pdb=" O LYS u 32 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ILE u 34 " --> pdb=" O LYS u 25 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'u' and resid 40 through 44 Processing sheet with id=AE1, first strand: chain 'u' and resid 82 through 85 Processing sheet with id=AE2, first strand: chain 'v' and resid 3 through 8 removed outlier: 7.799A pdb=" N ASN v 5 " --> pdb=" O ASP v 43 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ASP v 43 " --> pdb=" O ASN v 5 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU v 38 " --> pdb=" O ILE v 30 " (cutoff:3.500A) removed outlier: 8.881A pdb=" N LYS v 25 " --> pdb=" O GLN v 87 " (cutoff:3.500A) removed outlier: 10.007A pdb=" N ILE v 89 " --> pdb=" O LYS v 25 " (cutoff:3.500A) removed outlier: 8.460A pdb=" N PHE v 91 " --> pdb=" O PRO v 27 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ILE v 29 " --> pdb=" O PHE v 91 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ARG v 93 " --> pdb=" O ILE v 29 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N TYR v 31 " --> pdb=" O ARG v 93 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASP v 76 " --> pdb=" O ASP v 90 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N VAL v 92 " --> pdb=" O ALA v 74 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N ALA v 74 " --> pdb=" O VAL v 92 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL v 65 " --> pdb=" O LYS v 68 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ILE v 4 " --> pdb=" O VAL v 64 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'w' and resid 18 through 19 removed outlier: 6.940A pdb=" N LEU w 55 " --> pdb=" O ILE w 33 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'w' and resid 26 through 27 removed outlier: 3.502A pdb=" N LYS w 62 " --> pdb=" O GLU w 79 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'x' and resid 12 through 15 Processing sheet with id=AE6, first strand: chain 'x' and resid 32 through 39 Processing sheet with id=AE7, first strand: chain 'z' and resid 34 through 38 Processing sheet with id=AE8, first strand: chain 'B' and resid 28 through 29 Processing sheet with id=AE9, first strand: chain 'C' and resid 6 through 11 Processing sheet with id=AF1, first strand: chain 'E' and resid 14 through 15 Processing sheet with id=AF2, first strand: chain 'F' and resid 15 through 17 Processing sheet with id=AF3, first strand: chain 'G' and resid 15 through 18 removed outlier: 6.689A pdb=" N PHE G 15 " --> pdb=" O ILE G 40 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N ILE G 40 " --> pdb=" O PHE G 15 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N HIS G 17 " --> pdb=" O HIS G 38 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N VAL G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ALA G 33 " --> pdb=" O VAL G 37 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ILE G 39 " --> pdb=" O PHE G 31 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'G' and resid 89 through 91 removed outlier: 5.722A pdb=" N ILE G 66 " --> pdb=" O PHE G 89 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N VAL G 91 " --> pdb=" O ILE G 66 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N PHE G 68 " --> pdb=" O VAL G 91 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N LEU G 67 " --> pdb=" O PHE G 161 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N ILE G 163 " --> pdb=" O LEU G 67 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL G 69 " --> pdb=" O ILE G 163 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N VAL G 182 " --> pdb=" O PHE G 197 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'H' and resid 19 through 20 removed outlier: 6.479A pdb=" N ILE H 63 " --> pdb=" O GLN H 99 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N ASN H 101 " --> pdb=" O ILE H 63 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N VAL H 65 " --> pdb=" O ASN H 101 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N ALA H 103 " --> pdb=" O VAL H 65 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N ILE H 67 " --> pdb=" O ALA H 103 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'H' and resid 163 through 170 removed outlier: 3.910A pdb=" N ARG H 163 " --> pdb=" O GLY H 154 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N GLY H 154 " --> pdb=" O ARG H 163 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU H 165 " --> pdb=" O VAL H 152 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL H 152 " --> pdb=" O GLU H 165 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY H 147 " --> pdb=" O PHE H 202 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N PHE H 202 " --> pdb=" O ASP H 182 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N ASP H 182 " --> pdb=" O PHE H 202 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLY H 204 " --> pdb=" O ASP H 180 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 189 through 190 Processing sheet with id=AF8, first strand: chain 'I' and resid 122 through 124 removed outlier: 4.680A pdb=" N ILE I 122 " --> pdb=" O VAL I 129 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'I' and resid 140 through 143 Processing sheet with id=AG1, first strand: chain 'J' and resid 19 through 21 Processing sheet with id=AG2, first strand: chain 'J' and resid 36 through 37 removed outlier: 3.576A pdb=" N GLY J 48 " --> pdb=" O THR J 36 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'J' and resid 44 through 45 Processing sheet with id=AG4, first strand: chain 'J' and resid 84 through 85 removed outlier: 3.538A pdb=" N VAL J 84 " --> pdb=" O MET J 95 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N MET J 95 " --> pdb=" O VAL J 84 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE J 94 " --> pdb=" O LYS J 125 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'K' and resid 2 through 3 removed outlier: 3.868A pdb=" N GLU K 65 " --> pdb=" O LYS K 35 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS K 35 " --> pdb=" O GLU K 65 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'K' and resid 58 through 61 removed outlier: 6.978A pdb=" N VAL K 7 " --> pdb=" O SER K 87 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N SER K 87 " --> pdb=" O VAL K 7 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'L' and resid 72 through 73 Processing sheet with id=AG8, first strand: chain 'M' and resid 74 through 76 removed outlier: 3.599A pdb=" N GLN M 75 " --> pdb=" O TYR M 127 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'M' and resid 74 through 76 removed outlier: 3.599A pdb=" N GLN M 75 " --> pdb=" O TYR M 127 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N VAL M 102 " --> pdb=" O ILE M 125 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'N' and resid 5 through 7 removed outlier: 3.508A pdb=" N TYR N 5 " --> pdb=" O ILE N 20 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE N 20 " --> pdb=" O TYR N 5 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLY N 7 " --> pdb=" O VAL N 18 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL N 18 " --> pdb=" O GLY N 7 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ARG N 11 " --> pdb=" O SER N 14 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'N' and resid 5 through 7 removed outlier: 3.508A pdb=" N TYR N 5 " --> pdb=" O ILE N 20 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE N 20 " --> pdb=" O TYR N 5 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLY N 7 " --> pdb=" O VAL N 18 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL N 18 " --> pdb=" O GLY N 7 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N VAL N 28 " --> pdb=" O ILE N 64 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N VAL N 66 " --> pdb=" O VAL N 28 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'O' and resid 45 through 52 removed outlier: 3.616A pdb=" N ARG O 45 " --> pdb=" O THR O 69 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR O 69 " --> pdb=" O ARG O 45 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLU O 47 " --> pdb=" O ILE O 67 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'O' and resid 45 through 52 removed outlier: 3.616A pdb=" N ARG O 45 " --> pdb=" O THR O 69 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR O 69 " --> pdb=" O ARG O 45 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLU O 47 " --> pdb=" O ILE O 67 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLU O 66 " --> pdb=" O LYS S 96 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LYS S 96 " --> pdb=" O GLU O 66 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'P' and resid 40 through 44 removed outlier: 6.769A pdb=" N ILE P 33 " --> pdb=" O LEU P 41 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N TRP P 43 " --> pdb=" O VAL P 31 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N VAL P 31 " --> pdb=" O TRP P 43 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N GLY P 18 " --> pdb=" O GLU P 82 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N MET P 84 " --> pdb=" O GLY P 18 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ALA P 20 " --> pdb=" O MET P 84 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N LYS P 86 " --> pdb=" O ALA P 20 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N ILE P 22 " --> pdb=" O LYS P 86 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N LEU P 81 " --> pdb=" O ILE P 106 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N ASN P 108 " --> pdb=" O LEU P 81 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE P 109 " --> pdb=" O VAL Z 5 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL Z 5 " --> pdb=" O ILE P 109 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'Q' and resid 29 through 30 Processing sheet with id=AH7, first strand: chain 'Q' and resid 34 through 39 removed outlier: 5.059A pdb=" N ARG Q 35 " --> pdb=" O ARG Q 53 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG Q 53 " --> pdb=" O ARG Q 35 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'U' and resid 34 through 35 removed outlier: 3.982A pdb=" N GLU U 34 " --> pdb=" O VAL U 21 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'U' and resid 8 through 11 Processing sheet with id=AI1, first strand: chain 'V' and resid 10 through 13 removed outlier: 7.007A pdb=" N VAL V 21 " --> pdb=" O VAL V 12 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N TRP V 72 " --> pdb=" O HIS V 44 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU V 74 " --> pdb=" O HIS V 46 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N GLU V 59 " --> pdb=" O VAL V 75 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'X' and resid 31 through 32 removed outlier: 7.737A pdb=" N THR X 32 " --> pdb=" O HIS X 51 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'a' and resid 20 through 21 removed outlier: 7.917A pdb=" N TYR a 21 " --> pdb=" O GLY a 221 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ALA a 223 " --> pdb=" O TYR a 21 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N VAL a 212 " --> pdb=" O VAL a 224 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LYS a 211 " --> pdb=" O ASN a 47 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N VAL a 42 " --> pdb=" O ILE a 175 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE a 175 " --> pdb=" O VAL a 42 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N THR a 173 " --> pdb=" O VAL a 44 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL a 46 " --> pdb=" O ILE a 171 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'a' and resid 60 through 63 1560 hydrogen bonds defined for protein. 4344 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3448 hydrogen bonds 5594 hydrogen bond angles 0 basepair planarities 1385 basepair parallelities 2713 stacking parallelities Total time for adding SS restraints: 236.59 Time building geometry restraints manager: 66.41 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: 29272 1.34 - 1.46: 63622 1.46 - 1.58: 57084 1.58 - 1.70: 9304 1.70 - 1.82: 276 Bond restraints: 159558 Sorted by residual: bond pdb=" CA THR h 80 " pdb=" CB THR h 80 " ideal model delta sigma weight residual 1.532 1.572 -0.040 1.36e-02 5.41e+03 8.64e+00 bond pdb=" CA ILE Q 66 " pdb=" CB ILE Q 66 " ideal model delta sigma weight residual 1.530 1.557 -0.027 1.05e-02 9.07e+03 6.57e+00 bond pdb=" N GLY H 1 " pdb=" CA GLY H 1 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.36e+00 bond pdb=" N GLY C 3 " pdb=" CA GLY C 3 " ideal model delta sigma weight residual 1.451 1.490 -0.039 1.60e-02 3.91e+03 5.99e+00 bond pdb=" N GLY a 159 " pdb=" CA GLY a 159 " ideal model delta sigma weight residual 1.451 1.490 -0.039 1.60e-02 3.91e+03 5.81e+00 ... (remaining 159553 not shown) Histogram of bond angle deviations from ideal: 99.70 - 106.56: 28527 106.56 - 113.41: 94124 113.41 - 120.27: 58793 120.27 - 127.12: 45936 127.12 - 133.98: 11126 Bond angle restraints: 238506 Sorted by residual: angle pdb=" C LEU E 61 " pdb=" N PRO E 62 " pdb=" CA PRO E 62 " ideal model delta sigma weight residual 118.85 128.56 -9.71 1.09e+00 8.42e-01 7.94e+01 angle pdb=" N ARG b 12 " pdb=" CA ARG b 12 " pdb=" C ARG b 12 " ideal model delta sigma weight residual 114.31 103.50 10.81 1.29e+00 6.01e-01 7.02e+01 angle pdb=" N THR S 49 " pdb=" CA THR S 49 " pdb=" C THR S 49 " ideal model delta sigma weight residual 113.18 103.06 10.12 1.21e+00 6.83e-01 7.00e+01 angle pdb=" N GLY r 50 " pdb=" CA GLY r 50 " pdb=" C GLY r 50 " ideal model delta sigma weight residual 112.49 102.40 10.09 1.21e+00 6.83e-01 6.96e+01 angle pdb=" N ILE V 32 " pdb=" CA ILE V 32 " pdb=" C ILE V 32 " ideal model delta sigma weight residual 110.53 118.06 -7.53 9.40e-01 1.13e+00 6.41e+01 ... (remaining 238501 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.72: 91280 35.72 - 71.44: 9689 71.44 - 107.16: 1225 107.16 - 142.89: 11 142.89 - 178.61: 17 Dihedral angle restraints: 102222 sinusoidal: 85064 harmonic: 17158 Sorted by residual: dihedral pdb=" C4' U 11130 " pdb=" C3' U 11130 " pdb=" C2' U 11130 " pdb=" C1' U 11130 " ideal model delta sinusoidal sigma weight residual -35.00 31.40 -66.40 1 8.00e+00 1.56e-02 9.00e+01 dihedral pdb=" C5' U 11130 " pdb=" C4' U 11130 " pdb=" C3' U 11130 " pdb=" O3' U 11130 " ideal model delta sinusoidal sigma weight residual 147.00 81.63 65.37 1 8.00e+00 1.56e-02 8.75e+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 39.66 160.34 1 1.50e+01 4.44e-03 8.28e+01 ... (remaining 102219 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 22202 0.088 - 0.177: 7552 0.177 - 0.265: 644 0.265 - 0.353: 65 0.353 - 0.442: 8 Chirality restraints: 30471 Sorted by residual: chirality pdb=" C3' U 11130 " pdb=" C4' U 11130 " pdb=" O3' U 11130 " pdb=" C2' U 11130 " both_signs ideal model delta sigma weight residual False -2.74 -2.30 -0.44 2.00e-01 2.50e+01 4.87e+00 chirality pdb=" CA ASN Z 8 " pdb=" N ASN Z 8 " pdb=" C ASN Z 8 " pdb=" CB ASN Z 8 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.34e+00 chirality pdb=" CA GLU Q 75 " pdb=" N GLU Q 75 " pdb=" C GLU Q 75 " pdb=" CB GLU Q 75 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.89e+00 ... (remaining 30468 not shown) Planarity restraints: 12929 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G 1 775 " 0.109 2.00e-02 2.50e+03 4.50e-02 6.09e+01 pdb=" N9 G 1 775 " -0.007 2.00e-02 2.50e+03 pdb=" C8 G 1 775 " -0.045 2.00e-02 2.50e+03 pdb=" N7 G 1 775 " -0.042 2.00e-02 2.50e+03 pdb=" C5 G 1 775 " -0.023 2.00e-02 2.50e+03 pdb=" C6 G 1 775 " 0.020 2.00e-02 2.50e+03 pdb=" O6 G 1 775 " 0.068 2.00e-02 2.50e+03 pdb=" N1 G 1 775 " 0.018 2.00e-02 2.50e+03 pdb=" C2 G 1 775 " -0.011 2.00e-02 2.50e+03 pdb=" N2 G 1 775 " -0.019 2.00e-02 2.50e+03 pdb=" N3 G 1 775 " -0.033 2.00e-02 2.50e+03 pdb=" C4 G 1 775 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G 12061 " -0.100 2.00e-02 2.50e+03 4.22e-02 5.33e+01 pdb=" N9 G 12061 " 0.006 2.00e-02 2.50e+03 pdb=" C8 G 12061 " 0.050 2.00e-02 2.50e+03 pdb=" N7 G 12061 " 0.043 2.00e-02 2.50e+03 pdb=" C5 G 12061 " 0.017 2.00e-02 2.50e+03 pdb=" C6 G 12061 " -0.020 2.00e-02 2.50e+03 pdb=" O6 G 12061 " -0.064 2.00e-02 2.50e+03 pdb=" N1 G 12061 " -0.016 2.00e-02 2.50e+03 pdb=" C2 G 12061 " 0.010 2.00e-02 2.50e+03 pdb=" N2 G 12061 " 0.027 2.00e-02 2.50e+03 pdb=" N3 G 12061 " 0.022 2.00e-02 2.50e+03 pdb=" C4 G 12061 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U 12629 " 0.079 2.00e-02 2.50e+03 4.21e-02 3.98e+01 pdb=" N1 U 12629 " -0.005 2.00e-02 2.50e+03 pdb=" C2 U 12629 " -0.014 2.00e-02 2.50e+03 pdb=" O2 U 12629 " -0.032 2.00e-02 2.50e+03 pdb=" N3 U 12629 " -0.009 2.00e-02 2.50e+03 pdb=" C4 U 12629 " -0.010 2.00e-02 2.50e+03 pdb=" O4 U 12629 " 0.071 2.00e-02 2.50e+03 pdb=" C5 U 12629 " -0.040 2.00e-02 2.50e+03 pdb=" C6 U 12629 " -0.040 2.00e-02 2.50e+03 ... (remaining 12926 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 17564 2.75 - 3.29: 134204 3.29 - 3.83: 292109 3.83 - 4.36: 370554 4.36 - 4.90: 500051 Nonbonded interactions: 1314482 Sorted by model distance: nonbonded pdb=" OG SER k 28 " pdb=" N1 A 12566 " model vdw 2.219 2.520 nonbonded pdb=" O LYS l 29 " pdb=" OG1 THR l 30 " model vdw 2.241 2.440 nonbonded pdb=" O ASN l 93 " pdb=" OG1 THR l 94 " model vdw 2.276 2.440 nonbonded pdb=" O LYS R 26 " pdb=" OG SER R 29 " model vdw 2.296 2.440 nonbonded pdb=" O2' G 12391 " pdb=" O5' A 12392 " model vdw 2.313 2.440 ... (remaining 1314477 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.110 Extract box with map and model: 11.640 Check model and map are aligned: 1.560 Set scattering table: 1.090 Process input model: 512.410 Find NCS groups from input model: 3.150 Set up NCS constraints: 0.350 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:2.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 533.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 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 0.040 159558 Z= 0.366 Angle : 0.936 12.080 238506 Z= 0.625 Chirality : 0.079 0.442 30471 Planarity : 0.007 0.064 12929 Dihedral : 22.095 178.607 91150 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 1.52 % Allowed : 10.56 % Favored : 87.92 % Rotamer: Outliers : 0.55 % Allowed : 6.09 % Favored : 93.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.05 (0.08), residues: 5919 helix: -3.91 (0.07), residues: 1800 sheet: -2.75 (0.14), residues: 1010 loop : -3.24 (0.09), residues: 3109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.006 TRP G 95 HIS 0.002 0.000 HIS E 30 PHE 0.029 0.005 PHE X 73 TYR 0.050 0.006 TYR N 6 ARG 0.007 0.001 ARG r 80 *********************** 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 1854 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 1827 time to evaluate : 6.295 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 83 ASP cc_start: 0.8465 (t0) cc_final: 0.8061 (t0) REVERT: c 30 GLU cc_start: 0.7148 (mt-10) cc_final: 0.6799 (mt-10) REVERT: c 59 ARG cc_start: 0.7582 (tpp-160) cc_final: 0.6690 (tpp-160) REVERT: c 99 GLU cc_start: 0.7960 (pp20) cc_final: 0.7637 (pp20) REVERT: c 168 GLU cc_start: 0.6752 (pm20) cc_final: 0.6287 (pm20) REVERT: c 181 ASP cc_start: 0.8066 (t70) cc_final: 0.7859 (t0) REVERT: d 133 LEU cc_start: 0.8330 (tp) cc_final: 0.8125 (tp) REVERT: d 183 PHE cc_start: 0.7965 (m-80) cc_final: 0.7749 (m-80) REVERT: e 70 ARG cc_start: 0.8798 (ttp80) cc_final: 0.8571 (ttp80) REVERT: e 84 ILE cc_start: 0.9050 (tp) cc_final: 0.8681 (mm) REVERT: e 95 MET cc_start: 0.8519 (ptt) cc_final: 0.8157 (ptm) REVERT: e 97 GLU cc_start: 0.9070 (tm-30) cc_final: 0.8800 (tm-30) REVERT: e 119 LYS cc_start: 0.8251 (tppt) cc_final: 0.8037 (ttpp) REVERT: e 137 PHE cc_start: 0.8405 (m-80) cc_final: 0.8019 (m-80) REVERT: f 2 ARG cc_start: 0.8127 (tpp80) cc_final: 0.7618 (tpp-160) REVERT: f 74 MET cc_start: 0.7265 (mtp) cc_final: 0.6996 (ttm) REVERT: f 151 ARG cc_start: 0.8396 (tpp-160) cc_final: 0.8130 (mmm160) REVERT: g 134 VAL cc_start: 0.6230 (m) cc_final: 0.5668 (m) REVERT: h 1 MET cc_start: 0.1792 (ppp) cc_final: 0.1300 (ppp) REVERT: h 33 VAL cc_start: 0.8416 (t) cc_final: 0.8146 (p) REVERT: j 16 TYR cc_start: 0.8463 (m-80) cc_final: 0.7984 (m-10) REVERT: j 31 GLU cc_start: 0.7477 (tp30) cc_final: 0.6926 (tp30) REVERT: j 54 ILE cc_start: 0.9211 (mt) cc_final: 0.8944 (mt) REVERT: j 58 ASN cc_start: 0.8939 (m110) cc_final: 0.8343 (m-40) REVERT: j 99 ARG cc_start: 0.8559 (mmm160) cc_final: 0.8307 (mmm-85) REVERT: j 103 ILE cc_start: 0.9249 (mt) cc_final: 0.9039 (mm) REVERT: k 44 LYS cc_start: 0.8768 (mmtt) cc_final: 0.8432 (mmtt) REVERT: k 71 ARG cc_start: 0.8070 (mmm-85) cc_final: 0.7851 (mmt-90) REVERT: k 73 ASP cc_start: 0.8055 (p0) cc_final: 0.7727 (p0) REVERT: k 111 LYS cc_start: 0.8793 (mtmm) cc_final: 0.8515 (tptt) REVERT: k 116 ILE cc_start: 0.8995 (pt) cc_final: 0.8597 (mt) REVERT: l 59 ARG cc_start: 0.8751 (mtp180) cc_final: 0.8523 (mtp180) REVERT: l 122 VAL cc_start: 0.8997 (p) cc_final: 0.8583 (m) REVERT: m 11 LYS cc_start: 0.8328 (mttp) cc_final: 0.7792 (mttp) REVERT: m 47 GLU cc_start: 0.8880 (tm-30) cc_final: 0.7939 (tm-30) REVERT: m 51 ARG cc_start: 0.7852 (mtt90) cc_final: 0.7549 (mtt90) REVERT: m 55 ARG cc_start: 0.8452 (ttm-80) cc_final: 0.7923 (ttp80) REVERT: m 76 LYS cc_start: 0.9051 (mmmm) cc_final: 0.8632 (mmmm) REVERT: n 73 ASN cc_start: 0.8946 (m-40) cc_final: 0.8511 (t0) REVERT: o 13 ARG cc_start: 0.8268 (tpt170) cc_final: 0.8012 (tpp80) REVERT: o 16 ARG cc_start: 0.7763 (mmt-90) cc_final: 0.7547 (tpp80) REVERT: o 24 THR cc_start: 0.8768 (m) cc_final: 0.8232 (p) REVERT: o 38 GLN cc_start: 0.8600 (pt0) cc_final: 0.8373 (pt0) REVERT: o 68 LYS cc_start: 0.8630 (mttm) cc_final: 0.8212 (mttm) REVERT: o 104 GLN cc_start: 0.8874 (tt0) cc_final: 0.8135 (tm-30) REVERT: p 7 LEU cc_start: 0.9292 (mt) cc_final: 0.8885 (mm) REVERT: p 23 ASP cc_start: 0.7778 (m-30) cc_final: 0.7432 (m-30) REVERT: p 30 TRP cc_start: 0.8273 (m100) cc_final: 0.8040 (m100) REVERT: p 54 LEU cc_start: 0.9363 (tp) cc_final: 0.8808 (tp) REVERT: q 65 ASN cc_start: 0.8746 (t0) cc_final: 0.8389 (t0) REVERT: r 11 GLN cc_start: 0.8737 (mt0) cc_final: 0.8496 (mt0) REVERT: r 21 ARG cc_start: 0.8408 (ttm170) cc_final: 0.8007 (mtt-85) REVERT: r 34 GLU cc_start: 0.8235 (pt0) cc_final: 0.8006 (pm20) REVERT: r 78 ARG cc_start: 0.8413 (ttm-80) cc_final: 0.8188 (ttp80) REVERT: s 3 THR cc_start: 0.8534 (m) cc_final: 0.8328 (p) REVERT: s 65 ASP cc_start: 0.7584 (t70) cc_final: 0.6616 (t0) REVERT: s 107 VAL cc_start: 0.9271 (m) cc_final: 0.9068 (m) REVERT: t 49 LYS cc_start: 0.8867 (mptt) cc_final: 0.8586 (tptm) REVERT: t 52 GLU cc_start: 0.8432 (mp0) cc_final: 0.8172 (mp0) REVERT: t 69 ARG cc_start: 0.8077 (mtt180) cc_final: 0.7708 (mtt90) REVERT: u 13 LEU cc_start: 0.9262 (mt) cc_final: 0.9014 (mp) REVERT: u 39 ASN cc_start: 0.8267 (t0) cc_final: 0.7572 (t0) REVERT: u 40 LEU cc_start: 0.9193 (mt) cc_final: 0.8732 (mm) REVERT: u 80 ASP cc_start: 0.7915 (m-30) cc_final: 0.7484 (m-30) REVERT: u 101 THR cc_start: 0.7885 (m) cc_final: 0.7615 (m) REVERT: v 31 TYR cc_start: 0.8539 (p90) cc_final: 0.8184 (p90) REVERT: v 48 MET cc_start: 0.8292 (tpt) cc_final: 0.7771 (tpt) REVERT: v 63 ILE cc_start: 0.8088 (mm) cc_final: 0.7048 (mm) REVERT: v 70 ILE cc_start: 0.8649 (mt) cc_final: 0.8351 (tp) REVERT: v 78 GLN cc_start: 0.8330 (mt0) cc_final: 0.7881 (mt0) REVERT: w 16 ARG cc_start: 0.9214 (mpt180) cc_final: 0.8958 (mpt90) REVERT: w 36 GLN cc_start: 0.8736 (pt0) cc_final: 0.8476 (pt0) REVERT: w 64 LYS cc_start: 0.8529 (tptm) cc_final: 0.7831 (tppt) REVERT: w 66 GLU cc_start: 0.7679 (mm-30) cc_final: 0.7048 (mm-30) REVERT: w 77 SER cc_start: 0.8969 (m) cc_final: 0.8416 (p) REVERT: x 16 ASN cc_start: 0.8199 (t0) cc_final: 0.7993 (m-40) REVERT: x 43 LYS cc_start: 0.8797 (mttp) cc_final: 0.8563 (mmtt) REVERT: x 44 ARG cc_start: 0.8356 (ptt90) cc_final: 0.7963 (ptt90) REVERT: y 1 MET cc_start: 0.7189 (ttm) cc_final: 0.6427 (ttm) REVERT: y 15 ASN cc_start: 0.9163 (t0) cc_final: 0.8944 (t0) REVERT: y 19 LEU cc_start: 0.7893 (mt) cc_final: 0.7148 (mt) REVERT: y 45 GLN cc_start: 0.8482 (pt0) cc_final: 0.8069 (pt0) REVERT: z 3 THR cc_start: 0.7961 (p) cc_final: 0.7749 (p) REVERT: z 29 ARG cc_start: 0.8454 (mtt-85) cc_final: 0.8050 (mmm-85) REVERT: z 38 GLU cc_start: 0.7821 (mm-30) cc_final: 0.7447 (mm-30) REVERT: B 8 THR cc_start: 0.9300 (p) cc_final: 0.9050 (t) REVERT: C 37 LYS cc_start: 0.8356 (mttm) cc_final: 0.8154 (mtpp) REVERT: D 6 GLN cc_start: 0.8898 (mm-40) cc_final: 0.8540 (mm110) REVERT: E 39 ARG cc_start: 0.8572 (ttt180) cc_final: 0.8033 (ttt-90) REVERT: E 63 TYR cc_start: 0.8267 (m-80) cc_final: 0.7954 (m-80) REVERT: F 8 LYS cc_start: 0.7661 (mtpt) cc_final: 0.7402 (mmmm) REVERT: F 11 CYS cc_start: 0.7710 (m) cc_final: 0.7318 (p) REVERT: G 23 ASN cc_start: 0.8269 (t0) cc_final: 0.8039 (t0) REVERT: G 26 MET cc_start: 0.7284 (ttm) cc_final: 0.6262 (tmm) REVERT: G 41 ASN cc_start: 0.6818 (t0) cc_final: 0.6187 (t0) REVERT: G 43 GLU cc_start: 0.8546 (pp20) cc_final: 0.8218 (pm20) REVERT: G 51 GLU cc_start: 0.9365 (tp30) cc_final: 0.8686 (tp30) REVERT: G 57 ASN cc_start: 0.9279 (t0) cc_final: 0.9003 (t0) REVERT: G 65 LYS cc_start: 0.7283 (mppt) cc_final: 0.6887 (tppt) REVERT: G 67 LEU cc_start: 0.7865 (OUTLIER) cc_final: 0.7568 (mm) REVERT: G 73 ARG cc_start: 0.8212 (mmp80) cc_final: 0.7957 (mmp80) REVERT: G 92 ASN cc_start: 0.7996 (p0) cc_final: 0.6764 (t0) REVERT: G 101 THR cc_start: 0.9052 (p) cc_final: 0.8814 (t) REVERT: G 111 LYS cc_start: 0.9323 (tppt) cc_final: 0.8772 (tptp) REVERT: G 112 ARG cc_start: 0.8754 (tpt90) cc_final: 0.8456 (tpm170) REVERT: G 113 LEU cc_start: 0.9275 (tp) cc_final: 0.9005 (tp) REVERT: G 158 ASP cc_start: 0.8185 (m-30) cc_final: 0.7392 (p0) REVERT: G 161 PHE cc_start: 0.8569 (t80) cc_final: 0.7868 (t80) REVERT: G 187 ASP cc_start: 0.6919 (t0) cc_final: 0.6632 (t0) REVERT: G 202 ASN cc_start: 0.8785 (t0) cc_final: 0.7854 (t0) REVERT: G 203 ASP cc_start: 0.7866 (p0) cc_final: 0.7400 (p0) REVERT: G 211 LEU cc_start: 0.8791 (tt) cc_final: 0.8580 (tp) REVERT: G 224 ARG cc_start: 0.6881 (tpm170) cc_final: 0.6677 (tpm170) REVERT: H 10 ARG cc_start: 0.7533 (mtt180) cc_final: 0.7111 (mtt180) REVERT: H 53 ARG cc_start: 0.8205 (ptm160) cc_final: 0.7919 (ptm160) REVERT: H 163 ARG cc_start: 0.6401 (ptt180) cc_final: 0.5322 (mtp180) REVERT: I 102 TYR cc_start: 0.8350 (t80) cc_final: 0.8068 (t80) REVERT: I 164 ARG cc_start: 0.3656 (ttm170) cc_final: 0.3420 (ptp-170) REVERT: J 42 ASN cc_start: 0.6401 (p0) cc_final: 0.5828 (m110) REVERT: J 69 ASN cc_start: 0.8781 (t0) cc_final: 0.8264 (p0) REVERT: J 82 HIS cc_start: 0.7333 (p90) cc_final: 0.6726 (p-80) REVERT: J 95 MET cc_start: 0.8029 (ptp) cc_final: 0.7769 (ppp) REVERT: J 131 ASN cc_start: 0.6736 (m-40) cc_final: 0.6399 (m-40) REVERT: K 35 LYS cc_start: 0.8294 (mtpp) cc_final: 0.7859 (pttp) REVERT: K 63 ASN cc_start: 0.7302 (t0) cc_final: 0.6351 (t0) REVERT: L 25 PHE cc_start: 0.8984 (t80) cc_final: 0.8536 (t80) REVERT: L 62 GLU cc_start: 0.5212 (tp30) cc_final: 0.3902 (mm-30) REVERT: L 100 MET cc_start: 0.6046 (mtm) cc_final: 0.5207 (mtm) REVERT: M 110 MET cc_start: 0.8868 (ptp) cc_final: 0.8559 (ptp) REVERT: N 87 MET cc_start: 0.8138 (mmp) cc_final: 0.6807 (pmm) REVERT: P 23 HIS cc_start: 0.7133 (t70) cc_final: 0.6804 (t70) REVERT: P 39 ASN cc_start: 0.8448 (m110) cc_final: 0.7925 (m-40) REVERT: P 58 THR cc_start: 0.7560 (t) cc_final: 0.7296 (p) REVERT: P 60 PHE cc_start: 0.6988 (t80) cc_final: 0.6497 (t80) REVERT: P 68 ARG cc_start: 0.8732 (mtp180) cc_final: 0.8178 (mtp180) REVERT: P 75 GLU cc_start: 0.8443 (mm-30) cc_final: 0.8065 (mp0) REVERT: P 112 VAL cc_start: 0.8987 (m) cc_final: 0.8762 (m) REVERT: P 127 ARG cc_start: 0.7991 (ttm110) cc_final: 0.7593 (ptp-170) REVERT: Q 5 GLN cc_start: 0.8779 (mt0) cc_final: 0.8570 (mt0) REVERT: Q 33 CYS cc_start: 0.8143 (t) cc_final: 0.7935 (t) REVERT: Q 37 TYR cc_start: 0.8025 (p90) cc_final: 0.7797 (p90) REVERT: Q 111 GLN cc_start: 0.7690 (mt0) cc_final: 0.7486 (mt0) REVERT: R 74 MET cc_start: 0.7831 (mmm) cc_final: 0.7348 (mmm) REVERT: S 5 MET cc_start: 0.4620 (mmm) cc_final: 0.3577 (mmm) REVERT: S 84 ARG cc_start: 0.6768 (ttp80) cc_final: 0.5570 (mtt180) REVERT: T 13 GLU cc_start: 0.8438 (tt0) cc_final: 0.8146 (tt0) REVERT: T 52 ARG cc_start: 0.9014 (tmm-80) cc_final: 0.8810 (tmm-80) REVERT: T 76 ARG cc_start: 0.8470 (ttm110) cc_final: 0.7439 (tpm170) REVERT: U 32 PHE cc_start: 0.7913 (p90) cc_final: 0.7457 (p90) REVERT: U 59 HIS cc_start: 0.8218 (t-90) cc_final: 0.7996 (t-170) REVERT: V 66 LEU cc_start: 0.7282 (mp) cc_final: 0.6520 (mp) REVERT: W 60 ARG cc_start: 0.8181 (mtt180) cc_final: 0.7888 (mtt-85) REVERT: W 63 TYR cc_start: 0.8677 (t80) cc_final: 0.7787 (t80) REVERT: X 61 VAL cc_start: 0.6001 (t) cc_final: 0.5749 (t) REVERT: Y 13 SER cc_start: 0.8335 (m) cc_final: 0.8038 (m) REVERT: Y 32 LYS cc_start: 0.9123 (pptt) cc_final: 0.8573 (pttt) REVERT: Y 53 MET cc_start: 0.8367 (tmm) cc_final: 0.8112 (tmm) REVERT: Y 58 ASP cc_start: 0.7533 (OUTLIER) cc_final: 0.7128 (m-30) REVERT: a 47 ASN cc_start: 0.8229 (t0) cc_final: 0.7983 (t0) outliers start: 27 outliers final: 7 residues processed: 1844 average time/residue: 1.5121 time to fit residues: 4720.5039 Evaluate side-chains 1438 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 1429 time to evaluate : 6.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 142 VAL Chi-restraints excluded: chain d residue 83 VAL Chi-restraints excluded: chain i residue 78 LEU Chi-restraints excluded: chain k residue 69 VAL Chi-restraints excluded: chain l residue 85 VAL Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain Y residue 58 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1043 random chunks: chunk 880 optimal weight: 10.0000 chunk 790 optimal weight: 8.9990 chunk 438 optimal weight: 30.0000 chunk 270 optimal weight: 7.9990 chunk 533 optimal weight: 0.0020 chunk 422 optimal weight: 7.9990 chunk 817 optimal weight: 10.0000 chunk 316 optimal weight: 9.9990 chunk 497 optimal weight: 50.0000 chunk 608 optimal weight: 20.0000 chunk 947 optimal weight: 50.0000 overall best weight: 6.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 24 HIS b 36 ASN b 162 GLN b 196 ASN b 199 HIS c 32 ASN c 36 GLN c 49 GLN ** c 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 164 GLN c 167 ASN ** d 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 41 GLN d 97 ASN d 115 GLN ** d 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 29 ASN f 37 ASN ** f 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 2 GLN ** g 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 103 ASN i 93 ASN ** j 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 58 ASN ** k 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 4 ASN l 104 GLN m 3 GLN ** n 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 62 ASN ** n 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 38 GLN o 98 GLN ** p 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 14 GLN p 76 HIS q 36 GLN ** q 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 18 GLN r 86 GLN r 87 GLN r 89 HIS ** s 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 57 ASN t 59 ASN ** u 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 8 ASN w 53 HIS x 16 ASN y 20 ASN ** y 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 35 GLN F 37 GLN G 57 ASN G 108 GLN ** G 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 167 HIS G 177 ASN ** H 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 138 GLN I 40 HIS ** I 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 125 ASN I 130 ASN J 72 ASN ** J 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 ASN L 147 ASN ** M 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 36 GLN N 125 GLN ** O 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 14 GLN ** P 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 72 ASN Q 111 GLN ** R 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 3 GLN ** T 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 36 ASN T 39 GLN ** U 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 26 ASN ** V 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 30 ASN ** W 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 53 GLN Y 19 HIS Y 20 ASN ** Y 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 81 GLN a 172 HIS ** a 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 66 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 159558 Z= 0.400 Angle : 0.766 11.802 238506 Z= 0.393 Chirality : 0.042 0.356 30471 Planarity : 0.006 0.077 12929 Dihedral : 22.945 176.603 79360 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 17.53 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.99 % Favored : 90.79 % Rotamer: Outliers : 4.54 % Allowed : 15.77 % Favored : 79.69 % 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: -3.61 (0.09), residues: 5919 helix: -2.04 (0.10), residues: 1812 sheet: -2.33 (0.14), residues: 1020 loop : -2.66 (0.10), residues: 3087 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP b 212 HIS 0.013 0.002 HIS P 117 PHE 0.034 0.002 PHE g 46 TYR 0.030 0.002 TYR G 212 ARG 0.014 0.001 ARG M 12 *********************** 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 1719 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 223 poor density : 1496 time to evaluate : 6.296 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: b 145 MET cc_start: 0.8016 (mmm) cc_final: 0.7792 (mmm) REVERT: b 235 GLU cc_start: 0.7398 (tm-30) cc_final: 0.6798 (tm-30) REVERT: b 260 LYS cc_start: 0.8866 (mtmm) cc_final: 0.8620 (ttmm) REVERT: b 270 ARG cc_start: 0.7958 (ttp-110) cc_final: 0.7734 (ttp80) REVERT: c 30 GLU cc_start: 0.7281 (mt-10) cc_final: 0.7054 (mt-10) REVERT: c 59 ARG cc_start: 0.7649 (tpp-160) cc_final: 0.6634 (tpp-160) REVERT: c 184 ARG cc_start: 0.7993 (mtt180) cc_final: 0.7755 (mtt180) REVERT: d 1 MET cc_start: 0.7751 (mmt) cc_final: 0.7401 (mmm) REVERT: d 28 VAL cc_start: 0.9405 (t) cc_final: 0.9159 (p) REVERT: e 31 GLU cc_start: 0.8700 (tm-30) cc_final: 0.8090 (pp20) REVERT: e 64 PRO cc_start: 0.9135 (Cg_exo) cc_final: 0.8835 (Cg_endo) REVERT: e 70 ARG cc_start: 0.8651 (ttp80) cc_final: 0.8443 (ttp80) REVERT: e 95 MET cc_start: 0.8695 (ptt) cc_final: 0.8412 (ptm) REVERT: e 137 PHE cc_start: 0.8465 (m-80) cc_final: 0.8146 (m-80) REVERT: e 139 GLU cc_start: 0.8934 (pm20) cc_final: 0.8523 (pm20) REVERT: f 2 ARG cc_start: 0.8098 (tpp80) cc_final: 0.7489 (tpp-160) REVERT: f 34 ARG cc_start: 0.7880 (mmm160) cc_final: 0.7646 (mmm160) REVERT: f 68 ARG cc_start: 0.8509 (tmt170) cc_final: 0.8138 (ttp80) REVERT: f 74 MET cc_start: 0.7566 (mtp) cc_final: 0.7287 (ttm) REVERT: f 140 ILE cc_start: 0.8582 (tt) cc_final: 0.8191 (tt) REVERT: f 151 ARG cc_start: 0.8324 (tpp-160) cc_final: 0.8077 (mmm160) REVERT: g 1 MET cc_start: 0.7929 (OUTLIER) cc_final: 0.7687 (tpt) REVERT: g 19 VAL cc_start: 0.9251 (OUTLIER) cc_final: 0.9046 (t) REVERT: g 25 TYR cc_start: 0.9179 (t80) cc_final: 0.8952 (t80) REVERT: h 1 MET cc_start: 0.1868 (ppp) cc_final: 0.1396 (ppp) REVERT: h 33 VAL cc_start: 0.8204 (t) cc_final: 0.7924 (p) REVERT: h 38 MET cc_start: 0.1678 (mmt) cc_final: 0.0009 (mmt) REVERT: j 41 LYS cc_start: 0.9137 (OUTLIER) cc_final: 0.8871 (mptt) REVERT: j 54 ILE cc_start: 0.9209 (mt) cc_final: 0.8985 (mt) REVERT: j 140 LEU cc_start: 0.8396 (tp) cc_final: 0.8038 (mt) REVERT: k 3 GLN cc_start: 0.8829 (pt0) cc_final: 0.8593 (pt0) REVERT: k 73 ASP cc_start: 0.8112 (p0) cc_final: 0.7843 (p0) REVERT: k 89 ASN cc_start: 0.8015 (t0) cc_final: 0.7660 (t0) REVERT: l 4 ASN cc_start: 0.8794 (OUTLIER) cc_final: 0.8333 (p0) REVERT: m 16 ARG cc_start: 0.8564 (mmt-90) cc_final: 0.8338 (mmt-90) REVERT: m 127 LYS cc_start: 0.8822 (tppt) cc_final: 0.8559 (tppt) REVERT: n 32 GLU cc_start: 0.8749 (mp0) cc_final: 0.8087 (mp0) REVERT: n 73 ASN cc_start: 0.9027 (m-40) cc_final: 0.8568 (t0) REVERT: n 110 MET cc_start: 0.9220 (mmp) cc_final: 0.8925 (mmp) REVERT: o 9 ARG cc_start: 0.8079 (tmm160) cc_final: 0.7801 (tmm160) REVERT: o 13 ARG cc_start: 0.8465 (tpt170) cc_final: 0.8054 (tpp-160) REVERT: o 24 THR cc_start: 0.8980 (m) cc_final: 0.8650 (t) REVERT: o 38 GLN cc_start: 0.8694 (pt0) cc_final: 0.8477 (pt0) REVERT: o 76 LYS cc_start: 0.9292 (ttmm) cc_final: 0.8738 (ttmm) REVERT: o 94 ARG cc_start: 0.8565 (OUTLIER) cc_final: 0.7528 (ttp-110) REVERT: o 104 GLN cc_start: 0.8853 (tt0) cc_final: 0.8266 (tp40) REVERT: p 8 GLU cc_start: 0.8583 (mm-30) cc_final: 0.8227 (mm-30) REVERT: p 9 GLN cc_start: 0.7904 (tm-30) cc_final: 0.7556 (tp40) REVERT: p 54 LEU cc_start: 0.9517 (tp) cc_final: 0.9305 (tp) REVERT: p 65 ASN cc_start: 0.8177 (p0) cc_final: 0.7869 (p0) REVERT: q 65 ASN cc_start: 0.8818 (t0) cc_final: 0.8516 (t0) REVERT: r 1 MET cc_start: 0.8474 (tpp) cc_final: 0.8055 (tpp) REVERT: r 21 ARG cc_start: 0.8515 (ttm170) cc_final: 0.8209 (mtt-85) REVERT: r 34 GLU cc_start: 0.8234 (pt0) cc_final: 0.7911 (pm20) REVERT: r 85 LYS cc_start: 0.8573 (ttmt) cc_final: 0.8252 (ttmt) REVERT: s 3 THR cc_start: 0.8608 (m) cc_final: 0.8247 (p) REVERT: s 6 LYS cc_start: 0.9569 (ptpt) cc_final: 0.9255 (ptpp) REVERT: s 68 ASP cc_start: 0.8648 (p0) cc_final: 0.8418 (p0) REVERT: t 33 LYS cc_start: 0.8753 (ttmm) cc_final: 0.8246 (ttmm) REVERT: t 49 LYS cc_start: 0.9015 (mptt) cc_final: 0.8813 (tppt) REVERT: t 52 GLU cc_start: 0.8530 (mp0) cc_final: 0.7993 (mp0) REVERT: t 56 GLU cc_start: 0.8292 (tp30) cc_final: 0.7799 (tp30) REVERT: u 13 LEU cc_start: 0.9164 (mt) cc_final: 0.8688 (mp) REVERT: u 39 ASN cc_start: 0.8145 (t0) cc_final: 0.7660 (t0) REVERT: u 100 GLU cc_start: 0.7956 (mm-30) cc_final: 0.7735 (mp0) REVERT: v 9 ARG cc_start: 0.7514 (mtm180) cc_final: 0.7234 (mtm110) REVERT: v 11 GLU cc_start: 0.7850 (pm20) cc_final: 0.7633 (pm20) REVERT: v 46 LYS cc_start: 0.8683 (mmtm) cc_final: 0.8434 (mmtt) REVERT: v 48 MET cc_start: 0.8478 (tpt) cc_final: 0.8146 (tpt) REVERT: v 50 MET cc_start: 0.9084 (tpp) cc_final: 0.8881 (tpp) REVERT: v 53 LYS cc_start: 0.9094 (pttm) cc_final: 0.8524 (pttm) REVERT: v 64 VAL cc_start: 0.8509 (OUTLIER) cc_final: 0.8260 (m) REVERT: w 36 GLN cc_start: 0.8840 (pt0) cc_final: 0.8536 (pt0) REVERT: w 77 SER cc_start: 0.8933 (m) cc_final: 0.8387 (p) REVERT: x 10 ARG cc_start: 0.7835 (mtp-110) cc_final: 0.7631 (mtp-110) REVERT: x 43 LYS cc_start: 0.8994 (mttp) cc_final: 0.8785 (mmtt) REVERT: x 55 MET cc_start: 0.8255 (OUTLIER) cc_final: 0.7952 (mtm) REVERT: y 1 MET cc_start: 0.7107 (ttm) cc_final: 0.6750 (ttm) REVERT: y 12 GLU cc_start: 0.8927 (tt0) cc_final: 0.8681 (tt0) REVERT: y 17 GLU cc_start: 0.8972 (tm-30) cc_final: 0.8694 (tm-30) REVERT: y 39 GLN cc_start: 0.8569 (mt0) cc_final: 0.8293 (pt0) REVERT: y 40 SER cc_start: 0.9372 (m) cc_final: 0.8726 (t) REVERT: z 38 GLU cc_start: 0.7790 (mm-30) cc_final: 0.7240 (mm-30) REVERT: z 48 ASN cc_start: 0.8736 (t0) cc_final: 0.8371 (t0) REVERT: z 55 LYS cc_start: 0.8626 (tptp) cc_final: 0.8287 (tptp) REVERT: C 37 LYS cc_start: 0.8458 (mttm) cc_final: 0.8071 (mttt) REVERT: F 9 LYS cc_start: 0.8504 (mttt) cc_final: 0.8268 (mttp) REVERT: G 17 HIS cc_start: 0.8084 (t-90) cc_final: 0.7822 (t-90) REVERT: G 26 MET cc_start: 0.7489 (ttm) cc_final: 0.6056 (tmm) REVERT: G 55 GLU cc_start: 0.9468 (tp30) cc_final: 0.9214 (pt0) REVERT: G 57 ASN cc_start: 0.9213 (OUTLIER) cc_final: 0.8979 (t0) REVERT: G 92 ASN cc_start: 0.7886 (p0) cc_final: 0.7591 (p0) REVERT: G 111 LYS cc_start: 0.9302 (tppt) cc_final: 0.8615 (tptp) REVERT: G 112 ARG cc_start: 0.8772 (tpt90) cc_final: 0.8412 (tpm170) REVERT: G 161 PHE cc_start: 0.8371 (t80) cc_final: 0.7789 (t80) REVERT: G 168 GLU cc_start: 0.8363 (mp0) cc_final: 0.8133 (mp0) REVERT: G 169 HIS cc_start: 0.8468 (p-80) cc_final: 0.8256 (p-80) REVERT: G 197 PHE cc_start: 0.7829 (m-80) cc_final: 0.7029 (m-80) REVERT: H 10 ARG cc_start: 0.7395 (mtt180) cc_final: 0.7181 (mtt180) REVERT: H 163 ARG cc_start: 0.6415 (ptt180) cc_final: 0.5271 (mtt180) REVERT: I 64 TYR cc_start: 0.7166 (m-80) cc_final: 0.6588 (m-80) REVERT: I 102 TYR cc_start: 0.8353 (t80) cc_final: 0.8001 (t80) REVERT: I 104 MET cc_start: 0.0732 (mmt) cc_final: -0.0152 (mmm) REVERT: I 164 ARG cc_start: 0.3264 (ttm170) cc_final: 0.2848 (ptm-80) REVERT: J 42 ASN cc_start: 0.6296 (p0) cc_final: 0.5716 (m110) REVERT: J 67 ARG cc_start: 0.8639 (mmm160) cc_final: 0.8186 (mmm160) REVERT: J 72 ASN cc_start: 0.6635 (m-40) cc_final: 0.6057 (m-40) REVERT: J 82 HIS cc_start: 0.7522 (p90) cc_final: 0.7050 (p-80) REVERT: J 131 ASN cc_start: 0.6753 (m-40) cc_final: 0.6146 (m-40) REVERT: K 35 LYS cc_start: 0.8512 (mtpp) cc_final: 0.8036 (pttp) REVERT: K 63 ASN cc_start: 0.7022 (t0) cc_final: 0.6343 (t0) REVERT: K 78 PHE cc_start: 0.8104 (m-10) cc_final: 0.7860 (m-10) REVERT: L 25 PHE cc_start: 0.9133 (t80) cc_final: 0.8691 (t80) REVERT: L 62 GLU cc_start: 0.4855 (tp30) cc_final: 0.3568 (mm-30) REVERT: L 143 MET cc_start: 0.7450 (ppp) cc_final: 0.7249 (ppp) REVERT: M 87 ARG cc_start: 0.8309 (mmt90) cc_final: 0.8108 (ttm110) REVERT: M 110 MET cc_start: 0.8895 (ptp) cc_final: 0.8479 (ptp) REVERT: N 45 MET cc_start: 0.8046 (ppp) cc_final: 0.7469 (ppp) REVERT: N 87 MET cc_start: 0.8167 (mmp) cc_final: 0.6906 (pmm) REVERT: O 42 LEU cc_start: 0.6472 (tp) cc_final: 0.5943 (tp) REVERT: O 71 LEU cc_start: 0.7090 (mm) cc_final: 0.6759 (tp) REVERT: P 39 ASN cc_start: 0.8418 (m110) cc_final: 0.8031 (m-40) REVERT: P 55 ARG cc_start: 0.8307 (mpt180) cc_final: 0.8021 (mpp-170) REVERT: P 58 THR cc_start: 0.7008 (t) cc_final: 0.6646 (p) REVERT: P 75 GLU cc_start: 0.8641 (mm-30) cc_final: 0.8321 (mp0) REVERT: P 81 LEU cc_start: 0.8371 (mm) cc_final: 0.7804 (mm) REVERT: P 111 ASP cc_start: 0.8449 (OUTLIER) cc_final: 0.8198 (m-30) REVERT: P 117 HIS cc_start: 0.6383 (m90) cc_final: 0.5806 (m90) REVERT: P 127 ARG cc_start: 0.7994 (ttm110) cc_final: 0.7776 (ptp-170) REVERT: Q 5 GLN cc_start: 0.8813 (mt0) cc_final: 0.8576 (mt0) REVERT: Q 33 CYS cc_start: 0.7595 (t) cc_final: 0.6722 (t) REVERT: Q 37 TYR cc_start: 0.8327 (p90) cc_final: 0.7927 (p90) REVERT: S 5 MET cc_start: 0.4151 (mmm) cc_final: 0.3329 (mmm) REVERT: S 84 ARG cc_start: 0.6404 (ttp80) cc_final: 0.5202 (mtt180) REVERT: T 26 VAL cc_start: 0.8551 (p) cc_final: 0.8339 (m) REVERT: T 44 GLU cc_start: 0.8897 (pt0) cc_final: 0.8597 (pm20) REVERT: T 67 ASP cc_start: 0.8710 (OUTLIER) cc_final: 0.8388 (m-30) REVERT: T 76 ARG cc_start: 0.8459 (ttm110) cc_final: 0.7606 (tpp-160) REVERT: U 5 ARG cc_start: 0.6724 (mtm180) cc_final: 0.5986 (mpp80) REVERT: U 36 VAL cc_start: 0.6899 (OUTLIER) cc_final: 0.6620 (t) REVERT: U 51 ARG cc_start: 0.7710 (tmt-80) cc_final: 0.7103 (tpt170) REVERT: U 56 ARG cc_start: 0.8037 (mmm-85) cc_final: 0.7408 (mmm-85) REVERT: U 59 HIS cc_start: 0.8098 (t-90) cc_final: 0.7503 (t-90) REVERT: U 60 TRP cc_start: 0.7767 (m100) cc_final: 0.6704 (m100) REVERT: V 61 ARG cc_start: 0.7663 (OUTLIER) cc_final: 0.7291 (tmt170) REVERT: W 60 ARG cc_start: 0.8249 (mtt180) cc_final: 0.7605 (mmm-85) REVERT: W 63 TYR cc_start: 0.8636 (t80) cc_final: 0.7627 (t80) REVERT: Y 26 MET cc_start: 0.7802 (ppp) cc_final: 0.7601 (ppp) REVERT: a 210 LYS cc_start: 0.8393 (pttt) cc_final: 0.8175 (pttm) outliers start: 223 outliers final: 138 residues processed: 1588 average time/residue: 1.3432 time to fit residues: 3640.0985 Evaluate side-chains 1491 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 1341 time to evaluate : 6.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 5 CYS Chi-restraints excluded: chain b residue 8 THR Chi-restraints excluded: chain b residue 48 ILE Chi-restraints excluded: chain b residue 50 THR Chi-restraints excluded: chain b residue 117 SER Chi-restraints excluded: chain b residue 119 VAL Chi-restraints excluded: chain b residue 156 SER Chi-restraints excluded: chain b residue 159 THR Chi-restraints excluded: chain b residue 200 MET Chi-restraints excluded: chain c residue 2 ILE Chi-restraints excluded: chain c residue 35 THR Chi-restraints excluded: chain c residue 139 SER Chi-restraints excluded: chain c residue 142 VAL Chi-restraints excluded: chain c residue 170 VAL Chi-restraints excluded: chain c residue 177 VAL Chi-restraints excluded: chain c residue 207 VAL Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 33 VAL Chi-restraints excluded: chain d residue 84 THR Chi-restraints excluded: chain d residue 105 LEU Chi-restraints excluded: chain d residue 148 ILE Chi-restraints excluded: chain d residue 150 THR Chi-restraints excluded: chain d residue 159 LEU Chi-restraints excluded: chain d residue 164 LEU Chi-restraints excluded: chain e residue 30 VAL Chi-restraints excluded: chain e residue 56 LEU Chi-restraints excluded: chain e residue 111 ARG Chi-restraints excluded: chain e residue 144 LYS Chi-restraints excluded: chain e residue 173 ASP Chi-restraints excluded: chain f residue 8 VAL Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 19 ASN Chi-restraints excluded: chain f residue 72 ASN Chi-restraints excluded: chain f residue 76 ILE Chi-restraints excluded: chain g residue 1 MET Chi-restraints excluded: chain g residue 19 VAL Chi-restraints excluded: chain g residue 122 LEU Chi-restraints excluded: chain g residue 130 VAL Chi-restraints excluded: chain h residue 123 ILE Chi-restraints excluded: chain i residue 69 VAL Chi-restraints excluded: chain i residue 78 LEU Chi-restraints excluded: chain j residue 25 LEU Chi-restraints excluded: chain j residue 41 LYS Chi-restraints excluded: chain k residue 21 CYS Chi-restraints excluded: chain k residue 56 ASP Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 69 VAL Chi-restraints excluded: chain l residue 4 ASN Chi-restraints excluded: chain l residue 10 GLU Chi-restraints excluded: chain l residue 23 ILE Chi-restraints excluded: chain l residue 27 LEU Chi-restraints excluded: chain l residue 40 SER Chi-restraints excluded: chain l residue 68 SER Chi-restraints excluded: chain l residue 73 ILE Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain m residue 42 THR Chi-restraints excluded: chain m residue 54 THR Chi-restraints excluded: chain m residue 70 ASP Chi-restraints excluded: chain m residue 74 THR Chi-restraints excluded: chain m residue 80 VAL Chi-restraints excluded: chain n residue 14 SER Chi-restraints excluded: chain n residue 36 THR Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 53 THR Chi-restraints excluded: chain n residue 113 ILE Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain o residue 94 ARG Chi-restraints excluded: chain o residue 95 SER Chi-restraints excluded: chain p residue 31 VAL Chi-restraints excluded: chain p residue 40 GLN Chi-restraints excluded: chain p residue 64 SER Chi-restraints excluded: chain q residue 28 SER Chi-restraints excluded: chain r residue 22 LEU Chi-restraints excluded: chain r residue 64 VAL Chi-restraints excluded: chain s residue 1 MET Chi-restraints excluded: chain s residue 13 SER Chi-restraints excluded: chain s residue 20 VAL Chi-restraints excluded: chain s residue 39 THR Chi-restraints excluded: chain s residue 40 ASN Chi-restraints excluded: chain s residue 66 ILE Chi-restraints excluded: chain s residue 67 ASP Chi-restraints excluded: chain s residue 77 ASP Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain t residue 60 THR Chi-restraints excluded: chain u residue 5 ARG Chi-restraints excluded: chain u residue 11 ILE Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain v residue 30 ILE Chi-restraints excluded: chain v residue 45 ASP Chi-restraints excluded: chain v residue 64 VAL Chi-restraints excluded: chain v residue 92 VAL Chi-restraints excluded: chain x residue 55 MET Chi-restraints excluded: chain x residue 66 VAL Chi-restraints excluded: chain y residue 11 VAL Chi-restraints excluded: chain y residue 50 VAL Chi-restraints excluded: chain y residue 55 THR Chi-restraints excluded: chain z residue 11 SER Chi-restraints excluded: chain z residue 15 ARG Chi-restraints excluded: chain z residue 40 THR Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain C residue 7 LYS Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain F residue 37 GLN Chi-restraints excluded: chain G residue 57 ASN Chi-restraints excluded: chain G residue 108 GLN Chi-restraints excluded: chain G residue 147 LEU Chi-restraints excluded: chain G residue 193 ASP Chi-restraints excluded: chain G residue 212 TYR Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 71 PHE Chi-restraints excluded: chain I residue 89 LEU Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain K residue 13 ASP Chi-restraints excluded: chain K residue 55 HIS Chi-restraints excluded: chain K residue 59 TYR Chi-restraints excluded: chain K residue 88 MET Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain M residue 13 ILE Chi-restraints excluded: chain M residue 33 VAL Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 105 THR Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 27 ASN Chi-restraints excluded: chain P residue 111 ASP Chi-restraints excluded: chain Q residue 34 THR Chi-restraints excluded: chain Q residue 62 VAL Chi-restraints excluded: chain Q residue 79 ILE Chi-restraints excluded: chain Q residue 96 THR Chi-restraints excluded: chain R residue 15 VAL Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain T residue 65 LEU Chi-restraints excluded: chain T residue 67 ASP Chi-restraints excluded: chain U residue 36 VAL Chi-restraints excluded: chain V residue 28 VAL Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain V residue 50 ASN Chi-restraints excluded: chain V residue 61 ARG Chi-restraints excluded: chain V residue 64 ARG Chi-restraints excluded: chain W residue 25 ILE Chi-restraints excluded: chain W residue 70 THR Chi-restraints excluded: chain X residue 68 HIS Chi-restraints excluded: chain Z residue 15 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1043 random chunks: chunk 526 optimal weight: 7.9990 chunk 293 optimal weight: 5.9990 chunk 788 optimal weight: 8.9990 chunk 644 optimal weight: 20.0000 chunk 261 optimal weight: 0.1980 chunk 948 optimal weight: 50.0000 chunk 1025 optimal weight: 20.0000 chunk 845 optimal weight: 10.0000 chunk 940 optimal weight: 3.9990 chunk 323 optimal weight: 3.9990 chunk 761 optimal weight: 30.0000 overall best weight: 4.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 20 ASN ** c 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 167 ASN ** d 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 115 GLN d 165 HIS ** f 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 63 GLN ** g 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 40 HIS ** k 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 4 ASN l 54 GLN m 3 GLN n 3 HIS ** o 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 6 GLN q 55 GLN q 71 ASN ** r 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 87 GLN ** s 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 8 GLN ** D 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 35 GLN F 37 GLN ** G 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 119 GLN ** H 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 7 ASN ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 72 ASN ** J 77 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 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 51 GLN ** Y 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 159558 Z= 0.260 Angle : 0.623 11.097 238506 Z= 0.323 Chirality : 0.037 0.316 30471 Planarity : 0.005 0.058 12929 Dihedral : 23.001 176.450 79352 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.28 % Favored : 90.56 % Rotamer: Outliers : 5.05 % Allowed : 20.01 % Favored : 74.94 % 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: -2.97 (0.10), residues: 5919 helix: -1.25 (0.11), residues: 1827 sheet: -2.10 (0.15), residues: 1024 loop : -2.39 (0.10), residues: 3068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP b 212 HIS 0.011 0.001 HIS o 34 PHE 0.021 0.002 PHE Y 50 TYR 0.034 0.002 TYR G 212 ARG 0.012 0.001 ARG G 20 *********************** 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 1677 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 248 poor density : 1429 time to evaluate : 6.318 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: b 145 MET cc_start: 0.7979 (mmm) cc_final: 0.7729 (mmm) REVERT: b 180 MET cc_start: 0.8591 (mmm) cc_final: 0.8258 (mmm) REVERT: b 235 GLU cc_start: 0.7345 (tm-30) cc_final: 0.6801 (tm-30) REVERT: b 260 LYS cc_start: 0.8860 (mtmm) cc_final: 0.8653 (ttmm) REVERT: d 28 VAL cc_start: 0.9357 (t) cc_final: 0.9081 (p) REVERT: d 163 ASN cc_start: 0.5957 (m110) cc_final: 0.5723 (m-40) REVERT: e 41 GLU cc_start: 0.9320 (tp30) cc_final: 0.9075 (tp30) REVERT: e 62 GLN cc_start: 0.8013 (pp30) cc_final: 0.7443 (pp30) REVERT: e 70 ARG cc_start: 0.8696 (ttp80) cc_final: 0.8492 (ttp80) REVERT: e 84 ILE cc_start: 0.8484 (pt) cc_final: 0.7782 (mm) REVERT: e 95 MET cc_start: 0.8611 (ptt) cc_final: 0.8339 (ptm) REVERT: e 111 ARG cc_start: 0.8499 (OUTLIER) cc_final: 0.7782 (ttp-170) REVERT: e 137 PHE cc_start: 0.8526 (m-80) cc_final: 0.8203 (m-80) REVERT: e 142 TYR cc_start: 0.8135 (t80) cc_final: 0.7915 (t80) REVERT: f 2 ARG cc_start: 0.8023 (tpp80) cc_final: 0.7226 (tpp-160) REVERT: f 151 ARG cc_start: 0.8420 (tpp-160) cc_final: 0.8059 (mtp-110) REVERT: g 11 ASN cc_start: 0.7131 (t0) cc_final: 0.6878 (m-40) REVERT: g 33 GLN cc_start: 0.8424 (mt0) cc_final: 0.7937 (mt0) REVERT: h 1 MET cc_start: 0.2322 (ppp) cc_final: 0.1842 (ppp) REVERT: h 33 VAL cc_start: 0.8197 (t) cc_final: 0.7920 (p) REVERT: h 38 MET cc_start: 0.1210 (mmt) cc_final: -0.0490 (mmt) REVERT: h 86 MET cc_start: 0.1275 (ppp) cc_final: 0.0999 (ppp) REVERT: h 88 HIS cc_start: 0.5500 (OUTLIER) cc_final: 0.4350 (t70) REVERT: j 41 LYS cc_start: 0.9023 (OUTLIER) cc_final: 0.8806 (mmtm) REVERT: j 98 GLU cc_start: 0.7761 (pm20) cc_final: 0.7458 (pm20) REVERT: j 140 LEU cc_start: 0.8280 (tp) cc_final: 0.7965 (mt) REVERT: k 3 GLN cc_start: 0.8819 (pt0) cc_final: 0.8586 (pt0) REVERT: k 73 ASP cc_start: 0.8174 (p0) cc_final: 0.7908 (p0) REVERT: m 82 MET cc_start: 0.7620 (mmm) cc_final: 0.7366 (mmm) REVERT: m 127 LYS cc_start: 0.8836 (tppt) cc_final: 0.8566 (tppt) REVERT: n 32 GLU cc_start: 0.8782 (mp0) cc_final: 0.8180 (mp0) REVERT: n 73 ASN cc_start: 0.8935 (m-40) cc_final: 0.8491 (t0) REVERT: o 9 ARG cc_start: 0.8041 (tmm160) cc_final: 0.7833 (tmm160) REVERT: o 46 GLU cc_start: 0.7423 (mm-30) cc_final: 0.7126 (mm-30) REVERT: o 94 ARG cc_start: 0.8470 (OUTLIER) cc_final: 0.7599 (ttp-110) REVERT: o 104 GLN cc_start: 0.8795 (tt0) cc_final: 0.8267 (tp40) REVERT: p 8 GLU cc_start: 0.8619 (mm-30) cc_final: 0.8338 (mm-30) REVERT: p 9 GLN cc_start: 0.7921 (tm-30) cc_final: 0.7477 (tm-30) REVERT: p 70 GLU cc_start: 0.7164 (tp30) cc_final: 0.6408 (tp30) REVERT: q 65 ASN cc_start: 0.8798 (t0) cc_final: 0.8460 (t0) REVERT: r 1 MET cc_start: 0.8545 (tpp) cc_final: 0.8172 (tpp) REVERT: r 21 ARG cc_start: 0.8695 (ttm170) cc_final: 0.8230 (mtt-85) REVERT: r 34 GLU cc_start: 0.8165 (pt0) cc_final: 0.7917 (pm20) REVERT: r 85 LYS cc_start: 0.8515 (ttmt) cc_final: 0.8239 (ttmt) REVERT: s 3 THR cc_start: 0.8601 (m) cc_final: 0.8241 (p) REVERT: s 6 LYS cc_start: 0.9549 (ptpt) cc_final: 0.9222 (ptpp) REVERT: t 3 ARG cc_start: 0.6388 (mtp85) cc_final: 0.6053 (ttm110) REVERT: t 33 LYS cc_start: 0.8811 (ttmm) cc_final: 0.8566 (ttmm) REVERT: t 52 GLU cc_start: 0.8512 (mp0) cc_final: 0.7978 (mp0) REVERT: t 56 GLU cc_start: 0.8265 (tp30) cc_final: 0.7737 (tp30) REVERT: u 6 ARG cc_start: 0.7913 (tpp80) cc_final: 0.7579 (tpp80) REVERT: u 13 LEU cc_start: 0.9205 (mt) cc_final: 0.8874 (mp) REVERT: u 39 ASN cc_start: 0.8047 (t0) cc_final: 0.7659 (t0) REVERT: u 88 ASP cc_start: 0.8164 (p0) cc_final: 0.7852 (p0) REVERT: u 100 GLU cc_start: 0.8001 (mm-30) cc_final: 0.7743 (mp0) REVERT: v 53 LYS cc_start: 0.9078 (pttm) cc_final: 0.8466 (pttm) REVERT: v 76 ASP cc_start: 0.8086 (OUTLIER) cc_final: 0.7775 (m-30) REVERT: w 36 GLN cc_start: 0.8804 (pt0) cc_final: 0.8501 (pt0) REVERT: w 74 LYS cc_start: 0.8581 (mptt) cc_final: 0.8336 (mttp) REVERT: w 77 SER cc_start: 0.9042 (m) cc_final: 0.8572 (p) REVERT: w 79 GLU cc_start: 0.6848 (OUTLIER) cc_final: 0.6100 (pm20) REVERT: x 61 LYS cc_start: 0.8276 (mttt) cc_final: 0.7820 (mmtt) REVERT: y 39 GLN cc_start: 0.8590 (mt0) cc_final: 0.8194 (pt0) REVERT: y 40 SER cc_start: 0.9319 (m) cc_final: 0.8647 (t) REVERT: y 49 ASP cc_start: 0.8302 (m-30) cc_final: 0.8087 (m-30) REVERT: z 38 GLU cc_start: 0.7776 (mm-30) cc_final: 0.7238 (mm-30) REVERT: z 48 ASN cc_start: 0.8698 (t0) cc_final: 0.8305 (t0) REVERT: z 55 LYS cc_start: 0.8481 (tptp) cc_final: 0.8192 (tptp) REVERT: B 45 ASP cc_start: 0.8817 (t0) cc_final: 0.8527 (t0) REVERT: C 37 LYS cc_start: 0.8399 (mttm) cc_final: 0.8013 (mttt) REVERT: F 9 LYS cc_start: 0.8687 (mttt) cc_final: 0.8467 (mttp) REVERT: F 33 HIS cc_start: 0.7744 (m170) cc_final: 0.7505 (m170) REVERT: G 17 HIS cc_start: 0.8154 (t-90) cc_final: 0.7804 (t-90) REVERT: G 26 MET cc_start: 0.7438 (ttm) cc_final: 0.5978 (tmm) REVERT: G 48 MET cc_start: 0.8861 (ptt) cc_final: 0.8580 (ptt) REVERT: G 55 GLU cc_start: 0.9406 (tp30) cc_final: 0.9203 (pt0) REVERT: G 111 LYS cc_start: 0.9263 (tppt) cc_final: 0.8631 (tptp) REVERT: G 112 ARG cc_start: 0.8680 (tpt90) cc_final: 0.8315 (tpm170) REVERT: G 114 LYS cc_start: 0.8461 (mmtt) cc_final: 0.8255 (mmtm) REVERT: G 158 ASP cc_start: 0.8043 (m-30) cc_final: 0.7791 (m-30) REVERT: G 161 PHE cc_start: 0.8413 (t80) cc_final: 0.7867 (t80) REVERT: G 168 GLU cc_start: 0.8364 (mp0) cc_final: 0.7974 (mp0) REVERT: G 169 HIS cc_start: 0.8583 (p-80) cc_final: 0.8350 (p-80) REVERT: G 197 PHE cc_start: 0.7827 (m-80) cc_final: 0.7364 (t80) REVERT: H 10 ARG cc_start: 0.7579 (mtt180) cc_final: 0.7128 (mtt180) REVERT: H 15 LYS cc_start: 0.2949 (tmtt) cc_final: 0.2647 (tptm) REVERT: H 163 ARG cc_start: 0.6410 (ptt180) cc_final: 0.5355 (mtp180) REVERT: I 64 TYR cc_start: 0.7107 (m-80) cc_final: 0.6786 (m-80) REVERT: I 102 TYR cc_start: 0.7976 (t80) cc_final: 0.7737 (t80) REVERT: I 104 MET cc_start: 0.0585 (mmt) cc_final: -0.0324 (mmm) REVERT: I 164 ARG cc_start: 0.3294 (ttm170) cc_final: 0.2799 (ptm-80) REVERT: J 42 ASN cc_start: 0.6455 (p0) cc_final: 0.6034 (m110) REVERT: J 95 MET cc_start: 0.8288 (ptp) cc_final: 0.8012 (ptp) REVERT: J 151 MET cc_start: 0.8910 (tpp) cc_final: 0.8704 (tpp) REVERT: K 24 ARG cc_start: 0.8124 (ttm110) cc_final: 0.7923 (ptt-90) REVERT: K 35 LYS cc_start: 0.8462 (mtpp) cc_final: 0.8023 (pttp) REVERT: K 78 PHE cc_start: 0.8024 (m-10) cc_final: 0.7727 (m-10) REVERT: K 90 MET cc_start: 0.8187 (mpp) cc_final: 0.7927 (mpp) REVERT: L 25 PHE cc_start: 0.9066 (t80) cc_final: 0.8673 (t80) REVERT: L 62 GLU cc_start: 0.4599 (tp30) cc_final: 0.3536 (mp0) REVERT: M 2 MET cc_start: 0.7072 (ptt) cc_final: 0.6691 (tpt) REVERT: M 87 ARG cc_start: 0.8366 (mmt90) cc_final: 0.7998 (mtm-85) REVERT: M 110 MET cc_start: 0.8823 (ptp) cc_final: 0.8359 (ptp) REVERT: N 45 MET cc_start: 0.8117 (ppp) cc_final: 0.7441 (ppp) REVERT: N 87 MET cc_start: 0.8181 (mmp) cc_final: 0.6547 (pmm) REVERT: P 28 ASN cc_start: 0.7107 (m-40) cc_final: 0.6746 (m-40) REVERT: P 39 ASN cc_start: 0.8451 (m110) cc_final: 0.8154 (m110) REVERT: P 43 TRP cc_start: 0.7137 (p-90) cc_final: 0.6256 (p-90) REVERT: P 55 ARG cc_start: 0.8383 (mpt180) cc_final: 0.8083 (mpp-170) REVERT: P 58 THR cc_start: 0.7431 (t) cc_final: 0.7040 (p) REVERT: P 75 GLU cc_start: 0.8605 (mm-30) cc_final: 0.8311 (mp0) REVERT: P 111 ASP cc_start: 0.8589 (OUTLIER) cc_final: 0.7848 (m-30) REVERT: P 117 HIS cc_start: 0.5759 (m90) cc_final: 0.5268 (m-70) REVERT: Q 33 CYS cc_start: 0.7399 (t) cc_final: 0.6598 (t) REVERT: Q 37 TYR cc_start: 0.8457 (p90) cc_final: 0.7991 (p90) REVERT: S 5 MET cc_start: 0.4086 (mmm) cc_final: 0.3255 (mmm) REVERT: S 84 ARG cc_start: 0.6258 (ttp80) cc_final: 0.5687 (ptt90) REVERT: S 88 MET cc_start: 0.7186 (mtp) cc_final: 0.6954 (mtp) REVERT: T 26 VAL cc_start: 0.8512 (p) cc_final: 0.8266 (m) REVERT: T 34 GLN cc_start: 0.8222 (OUTLIER) cc_final: 0.8006 (mp10) REVERT: T 44 GLU cc_start: 0.8920 (pt0) cc_final: 0.8574 (pm20) REVERT: T 52 ARG cc_start: 0.8726 (tmm-80) cc_final: 0.8283 (ttp-170) REVERT: T 67 ASP cc_start: 0.8670 (m-30) cc_final: 0.8465 (m-30) REVERT: T 70 LYS cc_start: 0.9308 (mmmt) cc_final: 0.9101 (mmtp) REVERT: T 76 ARG cc_start: 0.8511 (ttm110) cc_final: 0.7478 (tpp-160) REVERT: T 82 GLU cc_start: 0.9038 (mm-30) cc_final: 0.8800 (mp0) REVERT: U 5 ARG cc_start: 0.6801 (mtm180) cc_final: 0.5863 (mpp80) REVERT: U 16 PHE cc_start: 0.7392 (t80) cc_final: 0.7095 (t80) REVERT: U 36 VAL cc_start: 0.6834 (OUTLIER) cc_final: 0.6436 (t) REVERT: U 51 ARG cc_start: 0.7663 (tmt-80) cc_final: 0.7206 (tpt170) REVERT: U 56 ARG cc_start: 0.7885 (mmm-85) cc_final: 0.7411 (mmm-85) REVERT: U 59 HIS cc_start: 0.8146 (t-90) cc_final: 0.7791 (t-90) REVERT: U 60 TRP cc_start: 0.7666 (m100) cc_final: 0.6826 (m100) REVERT: V 72 TRP cc_start: 0.7031 (m100) cc_final: 0.6713 (m100) REVERT: W 60 ARG cc_start: 0.8234 (mtt180) cc_final: 0.7555 (mmm-85) REVERT: W 63 TYR cc_start: 0.8619 (t80) cc_final: 0.7505 (t80) REVERT: Y 32 LYS cc_start: 0.9065 (pptt) cc_final: 0.8510 (pttt) REVERT: a 210 LYS cc_start: 0.8459 (pttt) cc_final: 0.8202 (pttm) outliers start: 248 outliers final: 154 residues processed: 1524 average time/residue: 1.4252 time to fit residues: 3762.1032 Evaluate side-chains 1504 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 1341 time to evaluate : 6.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 5 CYS Chi-restraints excluded: chain b residue 20 ASN Chi-restraints excluded: chain b residue 23 LEU Chi-restraints excluded: chain b residue 48 ILE Chi-restraints excluded: chain b residue 50 THR Chi-restraints excluded: chain b residue 52 HIS Chi-restraints excluded: chain b residue 104 LEU Chi-restraints excluded: chain b residue 117 SER Chi-restraints excluded: chain b residue 119 VAL Chi-restraints excluded: chain b residue 156 SER Chi-restraints excluded: chain b residue 179 GLU Chi-restraints excluded: chain b residue 200 MET Chi-restraints excluded: chain b residue 222 THR Chi-restraints excluded: chain c residue 2 ILE Chi-restraints excluded: chain c residue 12 THR Chi-restraints excluded: chain c residue 35 THR Chi-restraints excluded: chain c residue 97 SER Chi-restraints excluded: chain c residue 142 VAL Chi-restraints excluded: chain c residue 170 VAL Chi-restraints excluded: chain c residue 176 ASP Chi-restraints excluded: chain c residue 177 VAL Chi-restraints excluded: chain c residue 207 VAL Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 105 LEU Chi-restraints excluded: chain d residue 148 ILE Chi-restraints excluded: chain d residue 150 THR Chi-restraints excluded: chain d residue 159 LEU Chi-restraints excluded: chain d residue 200 LEU Chi-restraints excluded: chain e residue 111 ARG Chi-restraints excluded: chain e residue 120 SER Chi-restraints excluded: chain e residue 144 LYS Chi-restraints excluded: chain f residue 19 ASN Chi-restraints excluded: chain f residue 72 ASN Chi-restraints excluded: chain f residue 112 VAL Chi-restraints excluded: chain g residue 130 VAL Chi-restraints excluded: chain h residue 88 HIS Chi-restraints excluded: chain h residue 123 ILE Chi-restraints excluded: chain i residue 57 VAL Chi-restraints excluded: chain i residue 69 VAL Chi-restraints excluded: chain i residue 78 LEU Chi-restraints excluded: chain j residue 25 LEU Chi-restraints excluded: chain j residue 41 LYS Chi-restraints excluded: chain k residue 19 VAL Chi-restraints excluded: chain k residue 21 CYS Chi-restraints excluded: chain k residue 44 LYS Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 69 VAL Chi-restraints excluded: chain k residue 122 VAL Chi-restraints excluded: chain l residue 23 ILE Chi-restraints excluded: chain l residue 40 SER Chi-restraints excluded: chain l residue 68 SER Chi-restraints excluded: chain l residue 73 ILE Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain m residue 42 THR Chi-restraints excluded: chain m residue 54 THR Chi-restraints excluded: chain m residue 80 VAL Chi-restraints excluded: chain m residue 119 LEU Chi-restraints excluded: chain n residue 36 THR Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 51 LEU Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain o residue 80 GLU Chi-restraints excluded: chain o residue 94 ARG Chi-restraints excluded: chain p residue 39 LEU Chi-restraints excluded: chain p residue 81 ASP Chi-restraints excluded: chain q residue 28 SER Chi-restraints excluded: chain q residue 79 ILE Chi-restraints excluded: chain q residue 97 ILE Chi-restraints excluded: chain q residue 109 VAL Chi-restraints excluded: chain r residue 22 LEU Chi-restraints excluded: chain r residue 64 VAL Chi-restraints excluded: chain s residue 20 VAL Chi-restraints excluded: chain s residue 39 THR Chi-restraints excluded: chain s residue 40 ASN Chi-restraints excluded: chain s residue 66 ILE Chi-restraints excluded: chain s residue 67 ASP Chi-restraints excluded: chain s residue 77 ASP Chi-restraints excluded: chain s residue 86 MET Chi-restraints excluded: chain t residue 22 THR Chi-restraints excluded: chain t residue 27 SER Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain t residue 60 THR Chi-restraints excluded: chain t residue 86 THR Chi-restraints excluded: chain u residue 5 ARG Chi-restraints excluded: chain u residue 11 ILE Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain u residue 64 ILE Chi-restraints excluded: chain v residue 30 ILE Chi-restraints excluded: chain v residue 61 LEU Chi-restraints excluded: chain v residue 72 VAL Chi-restraints excluded: chain v residue 76 ASP Chi-restraints excluded: chain v residue 92 VAL Chi-restraints excluded: chain w residue 62 LYS Chi-restraints excluded: chain w residue 79 GLU Chi-restraints excluded: chain x residue 58 ILE Chi-restraints excluded: chain x residue 66 VAL Chi-restraints excluded: chain y residue 11 VAL Chi-restraints excluded: chain y residue 55 THR Chi-restraints excluded: chain z residue 6 ILE Chi-restraints excluded: chain z residue 15 ARG Chi-restraints excluded: chain z residue 40 THR Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain C residue 7 LYS Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 147 LEU Chi-restraints excluded: chain G residue 193 ASP Chi-restraints excluded: chain G residue 198 VAL Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 71 PHE Chi-restraints excluded: chain I residue 89 LEU Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 199 ILE Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 91 SER Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain J residue 140 ILE Chi-restraints excluded: chain K residue 13 ASP Chi-restraints excluded: chain K residue 52 ASN Chi-restraints excluded: chain K residue 55 HIS Chi-restraints excluded: chain K residue 59 TYR Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 59 GLU Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 117 LEU Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 105 THR Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 27 ASN Chi-restraints excluded: chain P residue 108 ASN Chi-restraints excluded: chain P residue 109 ILE Chi-restraints excluded: chain P residue 111 ASP Chi-restraints excluded: chain Q residue 96 THR Chi-restraints excluded: chain R residue 15 VAL Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain S residue 26 LEU Chi-restraints excluded: chain T residue 31 LEU Chi-restraints excluded: chain T residue 34 GLN Chi-restraints excluded: chain T residue 65 LEU Chi-restraints excluded: chain U residue 2 VAL Chi-restraints excluded: chain U residue 20 VAL Chi-restraints excluded: chain U residue 36 VAL Chi-restraints excluded: chain V residue 28 VAL Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain W residue 25 ILE Chi-restraints excluded: chain W residue 28 LEU Chi-restraints excluded: chain W residue 70 THR Chi-restraints excluded: chain Y residue 13 SER Chi-restraints excluded: chain Z residue 15 LEU Chi-restraints excluded: chain a residue 196 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1043 random chunks: chunk 937 optimal weight: 7.9990 chunk 713 optimal weight: 50.0000 chunk 492 optimal weight: 20.0000 chunk 105 optimal weight: 4.9990 chunk 452 optimal weight: 6.9990 chunk 637 optimal weight: 10.0000 chunk 952 optimal weight: 10.0000 chunk 1008 optimal weight: 10.0000 chunk 497 optimal weight: 10.0000 chunk 902 optimal weight: 8.9990 chunk 271 optimal weight: 10.0000 overall best weight: 7.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 142 ASN ** c 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 167 ASN ** d 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 33 ASN ** k 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 29 HIS ** k 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 3 GLN ** n 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 6 GLN q 55 GLN ** r 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 87 GLN s 31 GLN ** t 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 8 GLN F 35 GLN G 108 GLN ** G 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 81 GLN ** J 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 15 ASN ** M 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 30 ASN ** O 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 108 ASN Q 5 GLN Q 28 GLN ** T 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 55 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.3782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.088 159558 Z= 0.428 Angle : 0.757 12.769 238506 Z= 0.385 Chirality : 0.042 0.337 30471 Planarity : 0.006 0.072 12929 Dihedral : 23.303 178.342 79352 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 20.27 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.36 % Favored : 89.49 % Rotamer: Outliers : 6.66 % Allowed : 20.99 % Favored : 72.35 % 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: -2.82 (0.10), residues: 5919 helix: -1.06 (0.11), residues: 1841 sheet: -1.99 (0.15), residues: 1032 loop : -2.36 (0.10), residues: 3046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP b 212 HIS 0.010 0.002 HIS K 11 PHE 0.033 0.002 PHE D 18 TYR 0.036 0.002 TYR G 212 ARG 0.015 0.001 ARG L 91 *********************** 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 1689 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 327 poor density : 1362 time to evaluate : 6.352 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: b 142 ASN cc_start: 0.8733 (OUTLIER) cc_final: 0.8425 (t0) REVERT: b 145 MET cc_start: 0.8103 (mmm) cc_final: 0.7812 (mmm) REVERT: b 193 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.8090 (mt-10) REVERT: b 235 GLU cc_start: 0.7194 (tm-30) cc_final: 0.6646 (tm-30) REVERT: b 260 LYS cc_start: 0.8850 (mtmm) cc_final: 0.8649 (ttmm) REVERT: b 270 ARG cc_start: 0.7940 (ttp-110) cc_final: 0.7689 (ttp80) REVERT: d 28 VAL cc_start: 0.9417 (t) cc_final: 0.9176 (p) REVERT: d 141 MET cc_start: 0.8669 (mmm) cc_final: 0.8407 (mmm) REVERT: d 163 ASN cc_start: 0.6401 (m110) cc_final: 0.6108 (m-40) REVERT: e 70 ARG cc_start: 0.8732 (ttp80) cc_final: 0.8507 (ttp80) REVERT: e 95 MET cc_start: 0.8644 (ptt) cc_final: 0.8250 (ptm) REVERT: e 111 ARG cc_start: 0.8549 (OUTLIER) cc_final: 0.7827 (ptt-90) REVERT: e 126 ASN cc_start: 0.8450 (m-40) cc_final: 0.8123 (m-40) REVERT: e 137 PHE cc_start: 0.8604 (m-80) cc_final: 0.8301 (m-80) REVERT: f 2 ARG cc_start: 0.8024 (tpp80) cc_final: 0.7274 (tpp-160) REVERT: f 68 ARG cc_start: 0.8889 (ttp80) cc_final: 0.8580 (ttp80) REVERT: f 100 ASN cc_start: 0.6875 (p0) cc_final: 0.6661 (p0) REVERT: f 151 ARG cc_start: 0.8384 (tpp-160) cc_final: 0.7866 (mtp-110) REVERT: g 2 GLN cc_start: 0.8351 (mm-40) cc_final: 0.8123 (mm-40) REVERT: g 7 ASP cc_start: 0.7619 (t0) cc_final: 0.7295 (t0) REVERT: h 1 MET cc_start: 0.2576 (ppp) cc_final: 0.1882 (ppp) REVERT: h 33 VAL cc_start: 0.7966 (OUTLIER) cc_final: 0.7716 (p) REVERT: h 38 MET cc_start: 0.1313 (mmt) cc_final: 0.0667 (mmt) REVERT: h 88 HIS cc_start: 0.6221 (OUTLIER) cc_final: 0.4586 (t70) REVERT: j 41 LYS cc_start: 0.9038 (OUTLIER) cc_final: 0.8553 (mttp) REVERT: j 98 GLU cc_start: 0.7929 (pm20) cc_final: 0.7586 (pm20) REVERT: k 73 ASP cc_start: 0.8248 (p0) cc_final: 0.7974 (p0) REVERT: m 31 PHE cc_start: 0.7952 (m-80) cc_final: 0.7566 (m-80) REVERT: m 127 LYS cc_start: 0.8815 (tppt) cc_final: 0.8571 (tppt) REVERT: n 32 GLU cc_start: 0.8817 (mp0) cc_final: 0.8070 (mp0) REVERT: n 73 ASN cc_start: 0.9013 (m-40) cc_final: 0.8544 (t0) REVERT: o 9 ARG cc_start: 0.8115 (tmm160) cc_final: 0.7722 (tmm160) REVERT: o 24 THR cc_start: 0.8943 (OUTLIER) cc_final: 0.8520 (p) REVERT: o 94 ARG cc_start: 0.8654 (OUTLIER) cc_final: 0.7600 (ttp-110) REVERT: o 104 GLN cc_start: 0.8902 (tt0) cc_final: 0.8421 (tp40) REVERT: p 8 GLU cc_start: 0.8667 (mm-30) cc_final: 0.8063 (mm-30) REVERT: p 9 GLN cc_start: 0.8096 (tm-30) cc_final: 0.7490 (tm-30) REVERT: p 15 ASP cc_start: 0.7325 (OUTLIER) cc_final: 0.6902 (p0) REVERT: p 23 ASP cc_start: 0.7860 (m-30) cc_final: 0.7362 (m-30) REVERT: p 70 GLU cc_start: 0.7125 (tp30) cc_final: 0.6578 (tp30) REVERT: p 79 VAL cc_start: 0.9338 (OUTLIER) cc_final: 0.9117 (t) REVERT: p 92 ARG cc_start: 0.8759 (OUTLIER) cc_final: 0.7674 (ptm-80) REVERT: q 56 PHE cc_start: 0.9281 (OUTLIER) cc_final: 0.8876 (m-10) REVERT: q 65 ASN cc_start: 0.8829 (t0) cc_final: 0.8449 (t0) REVERT: r 1 MET cc_start: 0.8469 (tpp) cc_final: 0.7998 (tpp) REVERT: r 21 ARG cc_start: 0.8664 (ttm170) cc_final: 0.8135 (mtt-85) REVERT: r 85 LYS cc_start: 0.8544 (ttmt) cc_final: 0.8278 (ttmt) REVERT: s 3 THR cc_start: 0.8679 (m) cc_final: 0.8324 (p) REVERT: t 3 ARG cc_start: 0.6779 (OUTLIER) cc_final: 0.5934 (ttp-170) REVERT: t 52 GLU cc_start: 0.8315 (mp0) cc_final: 0.8059 (mp0) REVERT: t 56 GLU cc_start: 0.8314 (tp30) cc_final: 0.7781 (tp30) REVERT: u 6 ARG cc_start: 0.7871 (tpp80) cc_final: 0.7630 (tpp80) REVERT: u 11 ILE cc_start: 0.9265 (OUTLIER) cc_final: 0.8924 (pt) REVERT: u 13 LEU cc_start: 0.9233 (mt) cc_final: 0.8887 (mp) REVERT: u 39 ASN cc_start: 0.8091 (t0) cc_final: 0.7792 (t0) REVERT: u 88 ASP cc_start: 0.8347 (p0) cc_final: 0.8069 (p0) REVERT: u 100 GLU cc_start: 0.8154 (mm-30) cc_final: 0.7882 (mp0) REVERT: v 53 LYS cc_start: 0.8957 (pttm) cc_final: 0.8351 (pttm) REVERT: v 69 GLU cc_start: 0.8465 (mm-30) cc_final: 0.7753 (tp30) REVERT: v 76 ASP cc_start: 0.8202 (m-30) cc_final: 0.7802 (m-30) REVERT: w 66 GLU cc_start: 0.7689 (mm-30) cc_final: 0.7252 (mm-30) REVERT: w 77 SER cc_start: 0.9044 (m) cc_final: 0.8570 (p) REVERT: x 43 LYS cc_start: 0.8901 (mmtt) cc_final: 0.8071 (mmmt) REVERT: y 39 GLN cc_start: 0.8550 (mt0) cc_final: 0.8223 (pt0) REVERT: y 40 SER cc_start: 0.9392 (m) cc_final: 0.8909 (t) REVERT: y 49 ASP cc_start: 0.8315 (m-30) cc_final: 0.8012 (m-30) REVERT: z 9 THR cc_start: 0.8491 (p) cc_final: 0.8212 (p) REVERT: z 38 GLU cc_start: 0.7763 (mm-30) cc_final: 0.7204 (mm-30) REVERT: z 48 ASN cc_start: 0.8807 (t0) cc_final: 0.8338 (t0) REVERT: z 55 LYS cc_start: 0.8559 (tptp) cc_final: 0.8306 (tptp) REVERT: C 37 LYS cc_start: 0.8544 (mttm) cc_final: 0.8193 (mttt) REVERT: F 9 LYS cc_start: 0.8385 (mttt) cc_final: 0.8008 (mttp) REVERT: G 17 HIS cc_start: 0.8099 (t-90) cc_final: 0.7769 (t-90) REVERT: G 26 MET cc_start: 0.7392 (ttm) cc_final: 0.6010 (tmm) REVERT: G 48 MET cc_start: 0.8954 (ptt) cc_final: 0.8618 (ptt) REVERT: G 51 GLU cc_start: 0.9496 (tp30) cc_final: 0.8786 (tp30) REVERT: G 55 GLU cc_start: 0.9444 (tp30) cc_final: 0.9134 (pt0) REVERT: G 77 GLU cc_start: 0.9207 (tp30) cc_final: 0.8489 (tm-30) REVERT: G 81 ASP cc_start: 0.8567 (p0) cc_final: 0.7407 (p0) REVERT: G 89 PHE cc_start: 0.6903 (m-80) cc_final: 0.6643 (m-80) REVERT: G 111 LYS cc_start: 0.9287 (tppt) cc_final: 0.8754 (tptp) REVERT: G 158 ASP cc_start: 0.8005 (m-30) cc_final: 0.7791 (m-30) REVERT: G 168 GLU cc_start: 0.8321 (mp0) cc_final: 0.8008 (mp0) REVERT: G 169 HIS cc_start: 0.8601 (p-80) cc_final: 0.8227 (p-80) REVERT: G 170 ILE cc_start: 0.8230 (OUTLIER) cc_final: 0.7946 (tt) REVERT: G 197 PHE cc_start: 0.7888 (m-80) cc_final: 0.6683 (t80) REVERT: H 10 ARG cc_start: 0.7625 (mtt180) cc_final: 0.7206 (mtt180) REVERT: H 15 LYS cc_start: 0.2764 (tmtt) cc_final: 0.2475 (tptm) REVERT: H 141 MET cc_start: 0.8360 (mmm) cc_final: 0.7969 (mmm) REVERT: H 163 ARG cc_start: 0.6394 (ptt180) cc_final: 0.5171 (ttt180) REVERT: I 53 GLN cc_start: 0.7305 (mt0) cc_final: 0.6723 (mm-40) REVERT: I 56 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7451 (pp20) REVERT: I 104 MET cc_start: 0.1033 (mmt) cc_final: 0.0474 (mtt) REVERT: I 164 ARG cc_start: 0.3497 (ttm170) cc_final: 0.2931 (ptm-80) REVERT: I 197 HIS cc_start: 0.8073 (m-70) cc_final: 0.7711 (m90) REVERT: I 201 GLU cc_start: 0.8463 (pt0) cc_final: 0.8134 (pt0) REVERT: J 95 MET cc_start: 0.8274 (ptp) cc_final: 0.8008 (ptp) REVERT: K 1 MET cc_start: 0.7823 (tpp) cc_final: 0.7508 (tpp) REVERT: K 36 ILE cc_start: 0.8931 (mm) cc_final: 0.8730 (mm) REVERT: K 56 LYS cc_start: 0.7543 (mtmm) cc_final: 0.7328 (mppt) REVERT: K 78 PHE cc_start: 0.8137 (m-10) cc_final: 0.7876 (m-10) REVERT: K 90 MET cc_start: 0.8336 (mpp) cc_final: 0.7947 (mpp) REVERT: K 92 THR cc_start: 0.7318 (OUTLIER) cc_final: 0.7075 (p) REVERT: L 100 MET cc_start: 0.5622 (mtm) cc_final: 0.4476 (mmt) REVERT: L 115 MET cc_start: 0.7163 (OUTLIER) cc_final: 0.6637 (pmm) REVERT: M 2 MET cc_start: 0.7121 (ptt) cc_final: 0.6538 (tpt) REVERT: M 95 MET cc_start: 0.7929 (tpt) cc_final: 0.7640 (tpt) REVERT: M 110 MET cc_start: 0.8878 (ptp) cc_final: 0.8375 (ptp) REVERT: N 45 MET cc_start: 0.8217 (ppp) cc_final: 0.7438 (ppp) REVERT: N 87 MET cc_start: 0.8168 (mmp) cc_final: 0.6919 (pmm) REVERT: N 108 ARG cc_start: 0.4937 (OUTLIER) cc_final: 0.4662 (ptt-90) REVERT: P 43 TRP cc_start: 0.7220 (p-90) cc_final: 0.6537 (p-90) REVERT: P 55 ARG cc_start: 0.8546 (mpt180) cc_final: 0.8134 (mpp-170) REVERT: P 58 THR cc_start: 0.6954 (t) cc_final: 0.6522 (p) REVERT: P 68 ARG cc_start: 0.8524 (OUTLIER) cc_final: 0.8269 (mtm180) REVERT: P 75 GLU cc_start: 0.8537 (mm-30) cc_final: 0.8217 (mp0) REVERT: P 84 MET cc_start: 0.7624 (ttt) cc_final: 0.6932 (ppp) REVERT: P 111 ASP cc_start: 0.8680 (OUTLIER) cc_final: 0.8079 (m-30) REVERT: Q 33 CYS cc_start: 0.7539 (t) cc_final: 0.6721 (t) REVERT: Q 37 TYR cc_start: 0.8450 (p90) cc_final: 0.7908 (p90) REVERT: Q 101 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8843 (tp) REVERT: S 5 MET cc_start: 0.4164 (mmm) cc_final: 0.3346 (mmm) REVERT: T 26 VAL cc_start: 0.8642 (p) cc_final: 0.8314 (m) REVERT: T 44 GLU cc_start: 0.8879 (pt0) cc_final: 0.8520 (pm20) REVERT: T 67 ASP cc_start: 0.8695 (m-30) cc_final: 0.8469 (m-30) REVERT: T 76 ARG cc_start: 0.8405 (ttm110) cc_final: 0.7249 (tpp-160) REVERT: T 80 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7007 (mp) REVERT: U 32 PHE cc_start: 0.7793 (p90) cc_final: 0.7476 (p90) REVERT: U 36 VAL cc_start: 0.6796 (OUTLIER) cc_final: 0.6476 (t) REVERT: U 51 ARG cc_start: 0.7681 (tmt-80) cc_final: 0.7326 (tmt-80) REVERT: U 56 ARG cc_start: 0.8025 (mmm-85) cc_final: 0.7570 (mmm-85) REVERT: U 59 HIS cc_start: 0.8053 (t-90) cc_final: 0.7666 (t-90) REVERT: V 16 MET cc_start: 0.5985 (mmp) cc_final: 0.5483 (mmp) REVERT: V 17 GLU cc_start: 0.5076 (tt0) cc_final: 0.3713 (tm-30) REVERT: V 72 TRP cc_start: 0.7019 (m100) cc_final: 0.6513 (m100) REVERT: W 60 ARG cc_start: 0.8316 (mtt180) cc_final: 0.7869 (mtt-85) REVERT: W 63 TYR cc_start: 0.8571 (t80) cc_final: 0.7260 (t80) REVERT: Y 14 GLU cc_start: 0.9422 (mp0) cc_final: 0.8966 (mp0) outliers start: 327 outliers final: 222 residues processed: 1508 average time/residue: 1.3210 time to fit residues: 3422.4449 Evaluate side-chains 1545 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 246 poor density : 1299 time to evaluate : 6.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 5 CYS Chi-restraints excluded: chain b residue 8 THR Chi-restraints excluded: chain b residue 15 VAL Chi-restraints excluded: chain b residue 23 LEU Chi-restraints excluded: chain b residue 48 ILE Chi-restraints excluded: chain b residue 50 THR Chi-restraints excluded: chain b residue 52 HIS Chi-restraints excluded: chain b residue 104 LEU Chi-restraints excluded: chain b residue 117 SER Chi-restraints excluded: chain b residue 119 VAL Chi-restraints excluded: chain b residue 142 ASN Chi-restraints excluded: chain b residue 156 SER Chi-restraints excluded: chain b residue 159 THR Chi-restraints excluded: chain b residue 164 VAL Chi-restraints excluded: chain b residue 179 GLU Chi-restraints excluded: chain b residue 193 GLU Chi-restraints excluded: chain b residue 200 MET Chi-restraints excluded: chain b residue 203 VAL Chi-restraints excluded: chain b residue 222 THR Chi-restraints excluded: chain c residue 2 ILE Chi-restraints excluded: chain c residue 12 THR Chi-restraints excluded: chain c residue 35 THR Chi-restraints excluded: chain c residue 42 ASN Chi-restraints excluded: chain c residue 97 SER Chi-restraints excluded: chain c residue 99 GLU Chi-restraints excluded: chain c residue 126 ASN Chi-restraints excluded: chain c residue 142 VAL Chi-restraints excluded: chain c residue 170 VAL Chi-restraints excluded: chain c residue 177 VAL Chi-restraints excluded: chain c residue 193 VAL Chi-restraints excluded: chain c residue 207 VAL Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 33 VAL Chi-restraints excluded: chain d residue 73 ILE Chi-restraints excluded: chain d residue 83 VAL Chi-restraints excluded: chain d residue 105 LEU Chi-restraints excluded: chain d residue 148 ILE Chi-restraints excluded: chain d residue 150 THR Chi-restraints excluded: chain d residue 159 LEU Chi-restraints excluded: chain d residue 164 LEU Chi-restraints excluded: chain e residue 35 LEU Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 56 LEU Chi-restraints excluded: chain e residue 73 VAL Chi-restraints excluded: chain e residue 111 ARG Chi-restraints excluded: chain e residue 120 SER Chi-restraints excluded: chain e residue 144 LYS Chi-restraints excluded: chain e residue 169 LEU Chi-restraints excluded: chain e residue 173 ASP Chi-restraints excluded: chain f residue 3 VAL Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 19 ASN Chi-restraints excluded: chain f residue 33 THR Chi-restraints excluded: chain f residue 72 ASN Chi-restraints excluded: chain f residue 124 CYS Chi-restraints excluded: chain g residue 122 LEU Chi-restraints excluded: chain g residue 130 VAL Chi-restraints excluded: chain h residue 27 VAL Chi-restraints excluded: chain h residue 33 VAL Chi-restraints excluded: chain h residue 88 HIS Chi-restraints excluded: chain h residue 123 ILE Chi-restraints excluded: chain i residue 57 VAL Chi-restraints excluded: chain i residue 69 VAL Chi-restraints excluded: chain j residue 25 LEU Chi-restraints excluded: chain j residue 28 LEU Chi-restraints excluded: chain j residue 41 LYS Chi-restraints excluded: chain k residue 19 VAL Chi-restraints excluded: chain k residue 21 CYS Chi-restraints excluded: chain k residue 44 LYS Chi-restraints excluded: chain k residue 56 ASP Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 69 VAL Chi-restraints excluded: chain k residue 110 GLU Chi-restraints excluded: chain l residue 10 GLU Chi-restraints excluded: chain l residue 23 ILE Chi-restraints excluded: chain l residue 40 SER Chi-restraints excluded: chain l residue 46 VAL Chi-restraints excluded: chain l residue 68 SER Chi-restraints excluded: chain l residue 73 ILE Chi-restraints excluded: chain l residue 85 VAL Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain l residue 125 LEU Chi-restraints excluded: chain m residue 7 THR Chi-restraints excluded: chain m residue 42 THR Chi-restraints excluded: chain m residue 54 THR Chi-restraints excluded: chain m residue 74 THR Chi-restraints excluded: chain m residue 80 VAL Chi-restraints excluded: chain m residue 119 LEU Chi-restraints excluded: chain n residue 14 SER Chi-restraints excluded: chain n residue 24 MET Chi-restraints excluded: chain n residue 36 THR Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 51 LEU Chi-restraints excluded: chain n residue 53 THR Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain n residue 97 ILE Chi-restraints excluded: chain n residue 113 ILE Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain o residue 18 LEU Chi-restraints excluded: chain o residue 24 THR Chi-restraints excluded: chain o residue 35 ILE Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain o residue 94 ARG Chi-restraints excluded: chain p residue 15 ASP Chi-restraints excluded: chain p residue 31 VAL Chi-restraints excluded: chain p residue 39 LEU Chi-restraints excluded: chain p residue 40 GLN Chi-restraints excluded: chain p residue 79 VAL Chi-restraints excluded: chain p residue 81 ASP Chi-restraints excluded: chain p residue 83 ILE Chi-restraints excluded: chain p residue 92 ARG Chi-restraints excluded: chain q residue 28 SER Chi-restraints excluded: chain q residue 30 VAL Chi-restraints excluded: chain q residue 56 PHE Chi-restraints excluded: chain q residue 79 ILE Chi-restraints excluded: chain q residue 97 ILE Chi-restraints excluded: chain q residue 109 VAL Chi-restraints excluded: chain r residue 22 LEU Chi-restraints excluded: chain r residue 41 ILE Chi-restraints excluded: chain r residue 64 VAL Chi-restraints excluded: chain s residue 20 VAL Chi-restraints excluded: chain s residue 33 LEU Chi-restraints excluded: chain s residue 39 THR Chi-restraints excluded: chain s residue 40 ASN Chi-restraints excluded: chain s residue 66 ILE Chi-restraints excluded: chain s residue 67 ASP Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain s residue 77 ASP Chi-restraints excluded: chain t residue 3 ARG Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain t residue 60 THR Chi-restraints excluded: chain t residue 86 THR Chi-restraints excluded: chain u residue 5 ARG Chi-restraints excluded: chain u residue 11 ILE Chi-restraints excluded: chain u residue 28 LEU Chi-restraints excluded: chain u residue 64 ILE Chi-restraints excluded: chain u residue 80 ASP Chi-restraints excluded: chain u residue 102 ILE Chi-restraints excluded: chain v residue 1 MET Chi-restraints excluded: chain v residue 30 ILE Chi-restraints excluded: chain v residue 35 GLU Chi-restraints excluded: chain v residue 45 ASP Chi-restraints excluded: chain v residue 47 VAL Chi-restraints excluded: chain v residue 61 LEU Chi-restraints excluded: chain v residue 65 VAL Chi-restraints excluded: chain v residue 70 ILE Chi-restraints excluded: chain v residue 72 VAL Chi-restraints excluded: chain v residue 90 ASP Chi-restraints excluded: chain v residue 92 VAL Chi-restraints excluded: chain w residue 32 ILE Chi-restraints excluded: chain w residue 52 ASP Chi-restraints excluded: chain w residue 62 LYS Chi-restraints excluded: chain x residue 47 THR Chi-restraints excluded: chain x residue 53 LYS Chi-restraints excluded: chain x residue 58 ILE Chi-restraints excluded: chain y residue 50 VAL Chi-restraints excluded: chain y residue 55 THR Chi-restraints excluded: chain z residue 6 ILE Chi-restraints excluded: chain z residue 11 SER Chi-restraints excluded: chain z residue 40 THR Chi-restraints excluded: chain z residue 56 VAL Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain C residue 7 LYS Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 108 GLN Chi-restraints excluded: chain G residue 152 ASP Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 193 ASP Chi-restraints excluded: chain G residue 198 VAL Chi-restraints excluded: chain G residue 211 LEU Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 56 GLU Chi-restraints excluded: chain I residue 71 PHE Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 199 ILE Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 91 SER Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain J residue 140 ILE Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 52 ASN Chi-restraints excluded: chain K residue 55 HIS Chi-restraints excluded: chain K residue 59 TYR Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 115 MET Chi-restraints excluded: chain M residue 11 THR Chi-restraints excluded: chain M residue 35 ILE Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 105 THR Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain N residue 28 VAL Chi-restraints excluded: chain N residue 108 ARG Chi-restraints excluded: chain N residue 125 GLN Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 27 ASN Chi-restraints excluded: chain P residue 68 ARG Chi-restraints excluded: chain P residue 79 LYS Chi-restraints excluded: chain P residue 82 GLU Chi-restraints excluded: chain P residue 108 ASN Chi-restraints excluded: chain P residue 109 ILE Chi-restraints excluded: chain P residue 111 ASP Chi-restraints excluded: chain Q residue 30 ARG Chi-restraints excluded: chain Q residue 62 VAL Chi-restraints excluded: chain Q residue 96 THR Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain S residue 26 LEU Chi-restraints excluded: chain T residue 31 LEU Chi-restraints excluded: chain T residue 58 MET Chi-restraints excluded: chain T residue 65 LEU Chi-restraints excluded: chain T residue 80 LEU Chi-restraints excluded: chain U residue 2 VAL Chi-restraints excluded: chain U residue 20 VAL Chi-restraints excluded: chain U residue 33 ILE Chi-restraints excluded: chain U residue 36 VAL Chi-restraints excluded: chain V residue 28 VAL Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain V residue 50 ASN Chi-restraints excluded: chain W residue 25 ILE Chi-restraints excluded: chain W residue 28 LEU Chi-restraints excluded: chain W residue 58 ILE Chi-restraints excluded: chain W residue 70 THR Chi-restraints excluded: chain Y residue 13 SER Chi-restraints excluded: chain Z residue 15 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1043 random chunks: chunk 839 optimal weight: 50.0000 chunk 572 optimal weight: 50.0000 chunk 14 optimal weight: 2.9990 chunk 750 optimal weight: 10.0000 chunk 415 optimal weight: 0.6980 chunk 860 optimal weight: 6.9990 chunk 696 optimal weight: 40.0000 chunk 1 optimal weight: 0.9980 chunk 514 optimal weight: 40.0000 chunk 904 optimal weight: 10.0000 chunk 254 optimal weight: 0.9980 overall best weight: 2.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 142 ASN ** c 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 167 ASN ** d 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 115 GLN ** g 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 3 GLN ** o 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 38 GLN p 6 GLN q 55 GLN r 6 GLN r 11 GLN r 87 GLN ** s 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 87 GLN w 36 GLN x 22 ASN ** y 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 8 GLN G 41 ASN G 108 GLN ** G 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 39 GLN ** I 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 72 ASN ** J 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 15 ASN ** M 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 108 ASN ** P 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 5 GLN Q 71 HIS ** T 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.3843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 159558 Z= 0.180 Angle : 0.579 16.811 238506 Z= 0.298 Chirality : 0.034 0.298 30471 Planarity : 0.004 0.063 12929 Dihedral : 23.208 179.888 79350 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.31 % Favored : 91.55 % Rotamer: Outliers : 5.11 % Allowed : 23.23 % Favored : 71.66 % 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: -2.40 (0.10), residues: 5919 helix: -0.60 (0.12), residues: 1829 sheet: -1.79 (0.15), residues: 1018 loop : -2.17 (0.11), residues: 3072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP b 212 HIS 0.008 0.001 HIS P 117 PHE 0.036 0.001 PHE Z 18 TYR 0.036 0.001 TYR G 212 ARG 0.012 0.001 ARG v 93 *********************** 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 1660 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 251 poor density : 1409 time to evaluate : 6.314 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: b 142 ASN cc_start: 0.8603 (OUTLIER) cc_final: 0.8094 (t0) REVERT: b 156 SER cc_start: 0.9247 (OUTLIER) cc_final: 0.8748 (t) REVERT: b 193 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.8129 (mt-10) REVERT: c 59 ARG cc_start: 0.7500 (tpp-160) cc_final: 0.6497 (tpp-160) REVERT: d 163 ASN cc_start: 0.6254 (m110) cc_final: 0.5800 (m-40) REVERT: e 70 ARG cc_start: 0.8740 (ttp80) cc_final: 0.8449 (ttp80) REVERT: e 95 MET cc_start: 0.8598 (ptt) cc_final: 0.8280 (ptm) REVERT: e 111 ARG cc_start: 0.8505 (OUTLIER) cc_final: 0.7753 (ttp-170) REVERT: e 137 PHE cc_start: 0.8547 (m-80) cc_final: 0.8262 (m-80) REVERT: f 2 ARG cc_start: 0.8024 (tpp80) cc_final: 0.7150 (tpp-160) REVERT: f 68 ARG cc_start: 0.8855 (ttp80) cc_final: 0.8239 (ttp80) REVERT: f 151 ARG cc_start: 0.8445 (tpp-160) cc_final: 0.8056 (mtp-110) REVERT: g 11 ASN cc_start: 0.7120 (t0) cc_final: 0.6839 (m-40) REVERT: g 33 GLN cc_start: 0.8331 (mt0) cc_final: 0.7920 (mt0) REVERT: h 1 MET cc_start: 0.2418 (ppp) cc_final: 0.1623 (ppp) REVERT: h 33 VAL cc_start: 0.7911 (OUTLIER) cc_final: 0.7664 (p) REVERT: h 38 MET cc_start: 0.1374 (mmt) cc_final: 0.0894 (mmt) REVERT: h 88 HIS cc_start: 0.5742 (OUTLIER) cc_final: 0.4051 (t-90) REVERT: h 105 LYS cc_start: 0.7019 (OUTLIER) cc_final: 0.6578 (pptt) REVERT: j 25 LEU cc_start: 0.9319 (OUTLIER) cc_final: 0.9095 (tp) REVERT: j 98 GLU cc_start: 0.7691 (pm20) cc_final: 0.7449 (pm20) REVERT: j 103 ILE cc_start: 0.9334 (mt) cc_final: 0.9037 (mm) REVERT: j 118 MET cc_start: 0.8007 (ptp) cc_final: 0.7628 (ptp) REVERT: k 73 ASP cc_start: 0.8112 (p0) cc_final: 0.7861 (p0) REVERT: k 100 PHE cc_start: 0.8033 (m-80) cc_final: 0.7771 (m-10) REVERT: m 53 MET cc_start: 0.8492 (ttp) cc_final: 0.8118 (ptm) REVERT: m 82 MET cc_start: 0.7441 (mmm) cc_final: 0.7110 (mmm) REVERT: m 105 MET cc_start: 0.7878 (mtm) cc_final: 0.7183 (mtm) REVERT: m 117 PHE cc_start: 0.8684 (OUTLIER) cc_final: 0.8386 (m-10) REVERT: m 127 LYS cc_start: 0.8840 (tppt) cc_final: 0.8615 (tppt) REVERT: m 133 LYS cc_start: 0.8663 (OUTLIER) cc_final: 0.8391 (mttm) REVERT: n 32 GLU cc_start: 0.8871 (mp0) cc_final: 0.8200 (mp0) REVERT: n 73 ASN cc_start: 0.8846 (m-40) cc_final: 0.8430 (t0) REVERT: o 9 ARG cc_start: 0.8030 (tmm160) cc_final: 0.7774 (tmm160) REVERT: o 56 LYS cc_start: 0.8452 (mptt) cc_final: 0.8077 (mmtm) REVERT: o 104 GLN cc_start: 0.8577 (tt0) cc_final: 0.8328 (tp40) REVERT: p 8 GLU cc_start: 0.8603 (mm-30) cc_final: 0.8372 (mm-30) REVERT: p 9 GLN cc_start: 0.8029 (tm-30) cc_final: 0.7458 (tm-30) REVERT: p 23 ASP cc_start: 0.7877 (m-30) cc_final: 0.7542 (m-30) REVERT: p 70 GLU cc_start: 0.7264 (tp30) cc_final: 0.6547 (tp30) REVERT: q 65 ASN cc_start: 0.8782 (t0) cc_final: 0.8401 (t0) REVERT: r 1 MET cc_start: 0.8611 (tpp) cc_final: 0.8258 (tpp) REVERT: r 21 ARG cc_start: 0.8631 (ttm170) cc_final: 0.8158 (mtt-85) REVERT: s 3 THR cc_start: 0.8563 (m) cc_final: 0.8349 (p) REVERT: s 6 LYS cc_start: 0.9536 (ptpt) cc_final: 0.9195 (ptpp) REVERT: t 56 GLU cc_start: 0.8325 (tp30) cc_final: 0.7748 (tp30) REVERT: u 6 ARG cc_start: 0.7727 (tpp80) cc_final: 0.7323 (tpp80) REVERT: u 11 ILE cc_start: 0.9230 (OUTLIER) cc_final: 0.8977 (pt) REVERT: u 39 ASN cc_start: 0.7904 (t0) cc_final: 0.7383 (t0) REVERT: u 88 ASP cc_start: 0.8342 (p0) cc_final: 0.8092 (p0) REVERT: u 100 GLU cc_start: 0.8140 (mm-30) cc_final: 0.7882 (mp0) REVERT: v 50 MET cc_start: 0.9044 (tpp) cc_final: 0.8827 (tpp) REVERT: v 76 ASP cc_start: 0.8085 (OUTLIER) cc_final: 0.7851 (m-30) REVERT: v 80 HIS cc_start: 0.8911 (t-90) cc_final: 0.8134 (t-170) REVERT: w 51 ARG cc_start: 0.8382 (ttt-90) cc_final: 0.8119 (ptm160) REVERT: w 66 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7289 (mm-30) REVERT: w 77 SER cc_start: 0.9056 (m) cc_final: 0.8660 (p) REVERT: w 79 GLU cc_start: 0.6835 (OUTLIER) cc_final: 0.6048 (pm20) REVERT: x 43 LYS cc_start: 0.8906 (mmtt) cc_final: 0.8072 (mmmt) REVERT: x 53 LYS cc_start: 0.8877 (OUTLIER) cc_final: 0.8655 (ttpp) REVERT: x 61 LYS cc_start: 0.8261 (mttt) cc_final: 0.7926 (mmtt) REVERT: y 39 GLN cc_start: 0.8505 (mt0) cc_final: 0.8163 (pt0) REVERT: y 40 SER cc_start: 0.9275 (m) cc_final: 0.8720 (t) REVERT: y 49 ASP cc_start: 0.8270 (m-30) cc_final: 0.7860 (m-30) REVERT: z 38 GLU cc_start: 0.7820 (mm-30) cc_final: 0.7251 (mm-30) REVERT: z 47 ILE cc_start: 0.9332 (mm) cc_final: 0.9129 (mt) REVERT: z 48 ASN cc_start: 0.8705 (t0) cc_final: 0.8290 (t0) REVERT: z 55 LYS cc_start: 0.8495 (tptp) cc_final: 0.8197 (tptp) REVERT: C 7 LYS cc_start: 0.7579 (OUTLIER) cc_final: 0.7256 (mtmm) REVERT: C 37 LYS cc_start: 0.8431 (mttm) cc_final: 0.8045 (mttt) REVERT: D 26 ASN cc_start: 0.7913 (m-40) cc_final: 0.7411 (m-40) REVERT: G 17 HIS cc_start: 0.7998 (t-90) cc_final: 0.7708 (t-90) REVERT: G 26 MET cc_start: 0.7271 (ttm) cc_final: 0.5853 (tmm) REVERT: G 48 MET cc_start: 0.9123 (ptt) cc_final: 0.8674 (ptt) REVERT: G 51 GLU cc_start: 0.9472 (tp30) cc_final: 0.8758 (tp30) REVERT: G 55 GLU cc_start: 0.9438 (tp30) cc_final: 0.9130 (pt0) REVERT: G 84 LEU cc_start: 0.8786 (mt) cc_final: 0.8541 (pp) REVERT: G 111 LYS cc_start: 0.9425 (tppt) cc_final: 0.8845 (tptp) REVERT: G 161 PHE cc_start: 0.8424 (t80) cc_final: 0.7813 (t80) REVERT: G 168 GLU cc_start: 0.8204 (mp0) cc_final: 0.7738 (mp0) REVERT: G 173 LYS cc_start: 0.9243 (mmmm) cc_final: 0.8926 (mmtp) REVERT: G 197 PHE cc_start: 0.7895 (m-80) cc_final: 0.6605 (t80) REVERT: H 10 ARG cc_start: 0.7547 (mtt180) cc_final: 0.7125 (mtt180) REVERT: H 163 ARG cc_start: 0.6422 (ptt180) cc_final: 0.5342 (mtp180) REVERT: I 56 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.7157 (pp20) REVERT: I 64 TYR cc_start: 0.7022 (m-80) cc_final: 0.6461 (m-10) REVERT: I 164 ARG cc_start: 0.3414 (ttm170) cc_final: 0.2884 (ptm-80) REVERT: J 69 ASN cc_start: 0.8655 (t0) cc_final: 0.8023 (p0) REVERT: K 1 MET cc_start: 0.7814 (tpp) cc_final: 0.7526 (tpp) REVERT: K 11 HIS cc_start: 0.7941 (t-90) cc_final: 0.7624 (t-90) REVERT: K 62 MET cc_start: 0.6629 (ttt) cc_final: 0.6126 (ttt) REVERT: K 78 PHE cc_start: 0.8042 (m-10) cc_final: 0.7779 (m-10) REVERT: K 90 MET cc_start: 0.8284 (mpp) cc_final: 0.8075 (mpp) REVERT: L 25 PHE cc_start: 0.9145 (t80) cc_final: 0.8752 (t80) REVERT: M 59 GLU cc_start: 0.7460 (mp0) cc_final: 0.7070 (mp0) REVERT: M 110 MET cc_start: 0.8844 (ptp) cc_final: 0.8305 (ptp) REVERT: N 45 MET cc_start: 0.8354 (ppp) cc_final: 0.7599 (ppp) REVERT: N 87 MET cc_start: 0.8169 (mmp) cc_final: 0.6558 (pmm) REVERT: N 108 ARG cc_start: 0.4896 (OUTLIER) cc_final: 0.3792 (ttp-170) REVERT: P 43 TRP cc_start: 0.6888 (p-90) cc_final: 0.6622 (p-90) REVERT: P 55 ARG cc_start: 0.8464 (mpt180) cc_final: 0.8060 (mpp-170) REVERT: P 56 LYS cc_start: 0.8317 (tptp) cc_final: 0.8057 (tptp) REVERT: P 58 THR cc_start: 0.7268 (t) cc_final: 0.6806 (p) REVERT: P 68 ARG cc_start: 0.8571 (ttp-170) cc_final: 0.8137 (mtm180) REVERT: P 75 GLU cc_start: 0.8533 (mm-30) cc_final: 0.8215 (mp0) REVERT: P 84 MET cc_start: 0.7347 (ttt) cc_final: 0.6794 (ppp) REVERT: Q 37 TYR cc_start: 0.8293 (p90) cc_final: 0.8038 (p90) REVERT: Q 74 GLN cc_start: 0.8639 (mp10) cc_final: 0.8350 (mp10) REVERT: Q 101 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8699 (tp) REVERT: S 5 MET cc_start: 0.4001 (mmm) cc_final: 0.3318 (mmm) REVERT: T 9 LYS cc_start: 0.8148 (mtmt) cc_final: 0.7842 (pttt) REVERT: T 26 VAL cc_start: 0.8493 (p) cc_final: 0.8218 (m) REVERT: T 44 GLU cc_start: 0.8914 (pt0) cc_final: 0.8601 (pm20) REVERT: T 52 ARG cc_start: 0.8774 (tmm-80) cc_final: 0.8380 (ttp-170) REVERT: T 76 ARG cc_start: 0.8377 (ttm110) cc_final: 0.7559 (tpp-160) REVERT: U 3 THR cc_start: 0.7578 (OUTLIER) cc_final: 0.6546 (p) REVERT: U 5 ARG cc_start: 0.6699 (mtm180) cc_final: 0.6039 (mpp-170) REVERT: U 9 HIS cc_start: 0.8006 (m-70) cc_final: 0.7693 (m-70) REVERT: U 16 PHE cc_start: 0.7548 (t80) cc_final: 0.7215 (t80) REVERT: U 32 PHE cc_start: 0.7711 (p90) cc_final: 0.7083 (p90) REVERT: U 36 VAL cc_start: 0.7107 (OUTLIER) cc_final: 0.6758 (t) REVERT: U 51 ARG cc_start: 0.7714 (tmt-80) cc_final: 0.7305 (tpt170) REVERT: U 56 ARG cc_start: 0.8046 (mmm-85) cc_final: 0.7722 (mmm-85) REVERT: U 59 HIS cc_start: 0.8048 (t-90) cc_final: 0.7644 (t-90) REVERT: V 16 MET cc_start: 0.6117 (mmp) cc_final: 0.5436 (mmp) REVERT: V 17 GLU cc_start: 0.4559 (tt0) cc_final: 0.3351 (tm-30) REVERT: V 72 TRP cc_start: 0.6887 (m100) cc_final: 0.6614 (m100) REVERT: W 60 ARG cc_start: 0.8422 (mtt180) cc_final: 0.7803 (mmm-85) REVERT: W 63 TYR cc_start: 0.8587 (t80) cc_final: 0.7333 (t80) REVERT: W 64 LEU cc_start: 0.7976 (mt) cc_final: 0.7719 (mt) REVERT: W 69 TYR cc_start: 0.7572 (m-10) cc_final: 0.7351 (m-10) REVERT: Y 32 LYS cc_start: 0.9061 (pptt) cc_final: 0.8534 (pttt) REVERT: a 56 ASP cc_start: 0.8249 (OUTLIER) cc_final: 0.7864 (p0) REVERT: a 196 LEU cc_start: 0.1768 (OUTLIER) cc_final: 0.1421 (tp) outliers start: 251 outliers final: 148 residues processed: 1522 average time/residue: 1.3207 time to fit residues: 3446.6653 Evaluate side-chains 1515 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 1344 time to evaluate : 6.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 8 THR Chi-restraints excluded: chain b residue 48 ILE Chi-restraints excluded: chain b residue 50 THR Chi-restraints excluded: chain b residue 52 HIS Chi-restraints excluded: chain b residue 104 LEU Chi-restraints excluded: chain b residue 119 VAL Chi-restraints excluded: chain b residue 142 ASN Chi-restraints excluded: chain b residue 156 SER Chi-restraints excluded: chain b residue 164 VAL Chi-restraints excluded: chain b residue 179 GLU Chi-restraints excluded: chain b residue 193 GLU Chi-restraints excluded: chain b residue 222 THR Chi-restraints excluded: chain c residue 2 ILE Chi-restraints excluded: chain c residue 12 THR Chi-restraints excluded: chain c residue 35 THR Chi-restraints excluded: chain c residue 42 ASN Chi-restraints excluded: chain c residue 142 VAL Chi-restraints excluded: chain c residue 170 VAL Chi-restraints excluded: chain c residue 177 VAL Chi-restraints excluded: chain d residue 41 GLN Chi-restraints excluded: chain d residue 105 LEU Chi-restraints excluded: chain d residue 148 ILE Chi-restraints excluded: chain d residue 159 LEU Chi-restraints excluded: chain e residue 30 VAL Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 56 LEU Chi-restraints excluded: chain e residue 111 ARG Chi-restraints excluded: chain e residue 120 SER Chi-restraints excluded: chain e residue 144 LYS Chi-restraints excluded: chain e residue 173 ASP Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 19 ASN Chi-restraints excluded: chain f residue 42 VAL Chi-restraints excluded: chain f residue 124 CYS Chi-restraints excluded: chain f residue 154 GLU Chi-restraints excluded: chain g residue 12 LEU Chi-restraints excluded: chain g residue 130 VAL Chi-restraints excluded: chain h residue 27 VAL Chi-restraints excluded: chain h residue 33 VAL Chi-restraints excluded: chain h residue 88 HIS Chi-restraints excluded: chain h residue 105 LYS Chi-restraints excluded: chain i residue 57 VAL Chi-restraints excluded: chain i residue 69 VAL Chi-restraints excluded: chain i residue 78 LEU Chi-restraints excluded: chain j residue 25 LEU Chi-restraints excluded: chain j residue 28 LEU Chi-restraints excluded: chain k residue 19 VAL Chi-restraints excluded: chain k residue 21 CYS Chi-restraints excluded: chain k residue 35 VAL Chi-restraints excluded: chain k residue 44 LYS Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 69 VAL Chi-restraints excluded: chain k residue 106 GLU Chi-restraints excluded: chain l residue 3 LEU Chi-restraints excluded: chain l residue 40 SER Chi-restraints excluded: chain l residue 46 VAL Chi-restraints excluded: chain l residue 68 SER Chi-restraints excluded: chain l residue 73 ILE Chi-restraints excluded: chain l residue 76 GLU Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain l residue 144 GLU Chi-restraints excluded: chain m residue 42 THR Chi-restraints excluded: chain m residue 54 THR Chi-restraints excluded: chain m residue 74 THR Chi-restraints excluded: chain m residue 80 VAL Chi-restraints excluded: chain m residue 117 PHE Chi-restraints excluded: chain m residue 133 LYS Chi-restraints excluded: chain n residue 24 MET Chi-restraints excluded: chain n residue 51 LEU Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain n residue 113 ILE Chi-restraints excluded: chain o residue 24 THR Chi-restraints excluded: chain o residue 31 THR Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain p residue 6 GLN Chi-restraints excluded: chain p residue 31 VAL Chi-restraints excluded: chain p residue 40 GLN Chi-restraints excluded: chain p residue 81 ASP Chi-restraints excluded: chain p residue 83 ILE Chi-restraints excluded: chain q residue 28 SER Chi-restraints excluded: chain q residue 97 ILE Chi-restraints excluded: chain q residue 109 VAL Chi-restraints excluded: chain r residue 22 LEU Chi-restraints excluded: chain s residue 1 MET Chi-restraints excluded: chain s residue 20 VAL Chi-restraints excluded: chain s residue 30 SER Chi-restraints excluded: chain s residue 40 ASN Chi-restraints excluded: chain s residue 66 ILE Chi-restraints excluded: chain s residue 77 ASP Chi-restraints excluded: chain t residue 27 SER Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain t residue 60 THR Chi-restraints excluded: chain u residue 5 ARG Chi-restraints excluded: chain u residue 11 ILE Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain u residue 28 LEU Chi-restraints excluded: chain u residue 102 ILE Chi-restraints excluded: chain v residue 30 ILE Chi-restraints excluded: chain v residue 35 GLU Chi-restraints excluded: chain v residue 70 ILE Chi-restraints excluded: chain v residue 76 ASP Chi-restraints excluded: chain v residue 92 VAL Chi-restraints excluded: chain w residue 62 LYS Chi-restraints excluded: chain w residue 66 GLU Chi-restraints excluded: chain w residue 79 GLU Chi-restraints excluded: chain x residue 53 LYS Chi-restraints excluded: chain y residue 21 LEU Chi-restraints excluded: chain z residue 6 ILE Chi-restraints excluded: chain z residue 15 ARG Chi-restraints excluded: chain z residue 56 VAL Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain C residue 7 LYS Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 22 MET Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain G residue 108 GLN Chi-restraints excluded: chain G residue 193 ASP Chi-restraints excluded: chain G residue 198 VAL Chi-restraints excluded: chain G residue 211 LEU Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain I residue 56 GLU Chi-restraints excluded: chain I residue 71 PHE Chi-restraints excluded: chain I residue 89 LEU Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 199 ILE Chi-restraints excluded: chain J residue 91 SER Chi-restraints excluded: chain J residue 121 ASN Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain J residue 140 ILE Chi-restraints excluded: chain K residue 52 ASN Chi-restraints excluded: chain K residue 55 HIS Chi-restraints excluded: chain K residue 59 TYR Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 115 MET Chi-restraints excluded: chain M residue 9 MET Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 62 LEU Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 105 THR Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain N residue 28 VAL Chi-restraints excluded: chain N residue 108 ARG Chi-restraints excluded: chain P residue 27 ASN Chi-restraints excluded: chain P residue 79 LYS Chi-restraints excluded: chain P residue 108 ASN Chi-restraints excluded: chain P residue 109 ILE Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain S residue 26 LEU Chi-restraints excluded: chain T residue 31 LEU Chi-restraints excluded: chain T residue 65 LEU Chi-restraints excluded: chain U residue 2 VAL Chi-restraints excluded: chain U residue 3 THR Chi-restraints excluded: chain U residue 20 VAL Chi-restraints excluded: chain U residue 33 ILE Chi-restraints excluded: chain U residue 36 VAL Chi-restraints excluded: chain V residue 28 VAL Chi-restraints excluded: chain V residue 50 ASN Chi-restraints excluded: chain W residue 25 ILE Chi-restraints excluded: chain W residue 58 ILE Chi-restraints excluded: chain Y residue 13 SER Chi-restraints excluded: chain a residue 56 ASP Chi-restraints excluded: chain a residue 196 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1043 random chunks: chunk 339 optimal weight: 5.9990 chunk 907 optimal weight: 10.0000 chunk 199 optimal weight: 2.9990 chunk 591 optimal weight: 20.0000 chunk 248 optimal weight: 10.0000 chunk 1009 optimal weight: 10.0000 chunk 837 optimal weight: 30.0000 chunk 467 optimal weight: 20.0000 chunk 83 optimal weight: 6.9990 chunk 333 optimal weight: 0.0050 chunk 529 optimal weight: 30.0000 overall best weight: 5.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 142 ASN ** c 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 164 GLN c 167 ASN ** d 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 38 GLN ** p 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 43 GLN q 55 GLN r 6 GLN r 87 GLN ** s 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 68 ASN y 20 ASN ** y 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 8 GLN ** G 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 108 GLN ** G 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 HIS ** 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 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 108 ASN ** P 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 5 GLN ** T 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 55 HIS ** 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: 0.8241 moved from start: 0.4107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 159558 Z= 0.301 Angle : 0.641 13.187 238506 Z= 0.328 Chirality : 0.037 0.310 30471 Planarity : 0.005 0.057 12929 Dihedral : 23.255 176.188 79350 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 17.66 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.71 % Favored : 90.15 % Rotamer: Outliers : 6.03 % Allowed : 23.70 % Favored : 70.27 % 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: -2.34 (0.10), residues: 5919 helix: -0.51 (0.12), residues: 1824 sheet: -1.67 (0.15), residues: 1005 loop : -2.18 (0.11), residues: 3090 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.002 TRP b 212 HIS 0.007 0.001 HIS V 30 PHE 0.032 0.002 PHE D 18 TYR 0.038 0.002 TYR G 212 ARG 0.012 0.001 ARG v 93 *********************** 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 1654 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 296 poor density : 1358 time to evaluate : 6.390 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: b 124 LYS cc_start: 0.8850 (OUTLIER) cc_final: 0.8250 (ptpp) REVERT: b 142 ASN cc_start: 0.8653 (OUTLIER) cc_final: 0.8172 (t0) REVERT: b 180 MET cc_start: 0.8370 (mmm) cc_final: 0.8113 (mmm) REVERT: b 193 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.8194 (mt-10) REVERT: d 40 ARG cc_start: 0.8298 (OUTLIER) cc_final: 0.7390 (mtp85) REVERT: d 163 ASN cc_start: 0.6251 (m110) cc_final: 0.5749 (m-40) REVERT: e 3 LEU cc_start: 0.9189 (pt) cc_final: 0.8448 (pt) REVERT: e 31 GLU cc_start: 0.8843 (tm-30) cc_final: 0.8408 (pp20) REVERT: e 70 ARG cc_start: 0.8750 (ttp80) cc_final: 0.8457 (ttp80) REVERT: e 100 GLU cc_start: 0.8725 (tt0) cc_final: 0.8471 (mt-10) REVERT: e 111 ARG cc_start: 0.8518 (OUTLIER) cc_final: 0.7594 (ptt90) REVERT: e 137 PHE cc_start: 0.8585 (m-80) cc_final: 0.8293 (m-80) REVERT: f 2 ARG cc_start: 0.7986 (tpp80) cc_final: 0.7130 (tpp-160) REVERT: f 68 ARG cc_start: 0.8852 (ttp80) cc_final: 0.8454 (ttp80) REVERT: f 94 ARG cc_start: 0.7233 (mmp80) cc_final: 0.7026 (mmp80) REVERT: f 147 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8787 (mm) REVERT: f 151 ARG cc_start: 0.8461 (tpp-160) cc_final: 0.8078 (mtp-110) REVERT: g 7 ASP cc_start: 0.7732 (t0) cc_final: 0.7395 (t0) REVERT: g 33 GLN cc_start: 0.8352 (mt0) cc_final: 0.7954 (mt0) REVERT: h 1 MET cc_start: 0.2527 (ppp) cc_final: 0.1649 (ppp) REVERT: h 33 VAL cc_start: 0.7871 (OUTLIER) cc_final: 0.7624 (p) REVERT: h 38 MET cc_start: 0.1373 (mmt) cc_final: 0.0967 (mmt) REVERT: h 86 MET cc_start: 0.1161 (ppp) cc_final: 0.0858 (ppp) REVERT: h 88 HIS cc_start: 0.5815 (OUTLIER) cc_final: 0.4046 (t70) REVERT: h 105 LYS cc_start: 0.7093 (OUTLIER) cc_final: 0.6639 (pptt) REVERT: i 116 MET cc_start: -0.0846 (mtt) cc_final: -0.1441 (ptp) REVERT: j 74 TYR cc_start: 0.8314 (m-80) cc_final: 0.7912 (m-80) REVERT: j 98 GLU cc_start: 0.7848 (pm20) cc_final: 0.7491 (pm20) REVERT: k 73 ASP cc_start: 0.8151 (p0) cc_final: 0.7897 (p0) REVERT: m 31 PHE cc_start: 0.7970 (m-80) cc_final: 0.7578 (m-10) REVERT: m 64 TRP cc_start: 0.8385 (m-90) cc_final: 0.7649 (m-10) REVERT: m 82 MET cc_start: 0.7574 (mmm) cc_final: 0.6004 (mmt) REVERT: m 127 LYS cc_start: 0.8838 (tppt) cc_final: 0.8630 (tppt) REVERT: n 32 GLU cc_start: 0.8850 (mp0) cc_final: 0.8155 (mp0) REVERT: n 73 ASN cc_start: 0.8981 (m-40) cc_final: 0.8547 (t0) REVERT: o 9 ARG cc_start: 0.8072 (tmm160) cc_final: 0.7790 (tmm160) REVERT: o 104 GLN cc_start: 0.8545 (tt0) cc_final: 0.8290 (tp40) REVERT: p 8 GLU cc_start: 0.8699 (mm-30) cc_final: 0.8416 (mm-30) REVERT: p 9 GLN cc_start: 0.7970 (tm-30) cc_final: 0.7764 (tm-30) REVERT: p 23 ASP cc_start: 0.7843 (m-30) cc_final: 0.7490 (m-30) REVERT: p 70 GLU cc_start: 0.7313 (tp30) cc_final: 0.6779 (tp30) REVERT: q 56 PHE cc_start: 0.9260 (OUTLIER) cc_final: 0.8827 (m-10) REVERT: q 65 ASN cc_start: 0.8700 (t0) cc_final: 0.8332 (t0) REVERT: r 1 MET cc_start: 0.8626 (tpp) cc_final: 0.8289 (tpp) REVERT: r 21 ARG cc_start: 0.8655 (ttm170) cc_final: 0.8158 (mtt-85) REVERT: s 6 LYS cc_start: 0.9533 (ptpt) cc_final: 0.9193 (ptpp) REVERT: s 19 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8662 (mp) REVERT: t 3 ARG cc_start: 0.6288 (mtp85) cc_final: 0.5812 (ttm110) REVERT: t 56 GLU cc_start: 0.8212 (tp30) cc_final: 0.7804 (tp30) REVERT: u 6 ARG cc_start: 0.7683 (tpp80) cc_final: 0.7364 (tpp80) REVERT: u 39 ASN cc_start: 0.7705 (t0) cc_final: 0.7422 (t0) REVERT: u 45 GLN cc_start: 0.8518 (mt0) cc_final: 0.8186 (mp10) REVERT: v 7 GLU cc_start: 0.7916 (tp30) cc_final: 0.7618 (tp30) REVERT: v 79 ARG cc_start: 0.8999 (mmm-85) cc_final: 0.8683 (mmt-90) REVERT: v 80 HIS cc_start: 0.8941 (t-90) cc_final: 0.8154 (t-170) REVERT: w 66 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.7282 (mm-30) REVERT: w 77 SER cc_start: 0.8984 (m) cc_final: 0.8454 (p) REVERT: w 79 GLU cc_start: 0.6865 (OUTLIER) cc_final: 0.6345 (pm20) REVERT: x 10 ARG cc_start: 0.7666 (mtp-110) cc_final: 0.7447 (mtp180) REVERT: x 42 GLU cc_start: 0.8278 (mp0) cc_final: 0.8020 (mp0) REVERT: y 39 GLN cc_start: 0.8591 (mt0) cc_final: 0.8197 (pt0) REVERT: y 40 SER cc_start: 0.9354 (m) cc_final: 0.8815 (t) REVERT: y 49 ASP cc_start: 0.8336 (m-30) cc_final: 0.7890 (m-30) REVERT: z 38 GLU cc_start: 0.7809 (mm-30) cc_final: 0.7287 (mm-30) REVERT: z 48 ASN cc_start: 0.8796 (t0) cc_final: 0.8353 (t0) REVERT: z 55 LYS cc_start: 0.8510 (tptp) cc_final: 0.8229 (tptp) REVERT: C 37 LYS cc_start: 0.8464 (mttm) cc_final: 0.8098 (mttt) REVERT: D 1 MET cc_start: 0.6968 (OUTLIER) cc_final: 0.6708 (mmm) REVERT: G 17 HIS cc_start: 0.8045 (t-90) cc_final: 0.7786 (t-90) REVERT: G 48 MET cc_start: 0.9038 (ptt) cc_final: 0.8660 (ptt) REVERT: G 51 GLU cc_start: 0.9471 (tp30) cc_final: 0.9138 (tp30) REVERT: G 89 PHE cc_start: 0.6956 (m-80) cc_final: 0.6545 (m-80) REVERT: G 111 LYS cc_start: 0.9451 (tppt) cc_final: 0.8842 (tptp) REVERT: G 151 LYS cc_start: 0.8778 (pttt) cc_final: 0.8350 (ptmm) REVERT: G 161 PHE cc_start: 0.8317 (t80) cc_final: 0.7721 (t80) REVERT: G 168 GLU cc_start: 0.8242 (mp0) cc_final: 0.7975 (mp0) REVERT: G 173 LYS cc_start: 0.9247 (mmmm) cc_final: 0.8946 (mmtp) REVERT: G 197 PHE cc_start: 0.7938 (m-80) cc_final: 0.7410 (t80) REVERT: H 10 ARG cc_start: 0.7579 (mtt180) cc_final: 0.7141 (mtt180) REVERT: H 141 MET cc_start: 0.8538 (mmm) cc_final: 0.8168 (mmm) REVERT: H 163 ARG cc_start: 0.6416 (ptt180) cc_final: 0.5149 (ttt180) REVERT: I 56 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7238 (pp20) REVERT: I 98 ASP cc_start: 0.7375 (t0) cc_final: 0.7069 (p0) REVERT: I 123 MET cc_start: 0.8573 (tmm) cc_final: 0.8342 (tmm) REVERT: I 164 ARG cc_start: 0.3450 (ttm170) cc_final: 0.2655 (ptm-80) REVERT: J 67 ARG cc_start: 0.8366 (mmm160) cc_final: 0.8090 (mmm160) REVERT: J 69 ASN cc_start: 0.8694 (t0) cc_final: 0.8056 (p0) REVERT: K 17 GLN cc_start: 0.8807 (tm-30) cc_final: 0.8451 (pp30) REVERT: K 62 MET cc_start: 0.6802 (ttt) cc_final: 0.6406 (ttt) REVERT: K 78 PHE cc_start: 0.8118 (m-10) cc_final: 0.7910 (m-10) REVERT: K 90 MET cc_start: 0.8194 (mpp) cc_final: 0.7798 (mpp) REVERT: K 92 THR cc_start: 0.7457 (OUTLIER) cc_final: 0.7211 (p) REVERT: L 49 LEU cc_start: 0.6968 (mm) cc_final: 0.6727 (mm) REVERT: L 100 MET cc_start: 0.5660 (mtm) cc_final: 0.4982 (mmt) REVERT: M 8 ASP cc_start: 0.7972 (t0) cc_final: 0.7471 (m-30) REVERT: M 110 MET cc_start: 0.8884 (ptp) cc_final: 0.8337 (ptp) REVERT: N 11 ARG cc_start: 0.5362 (tpt170) cc_final: 0.4801 (tpt170) REVERT: N 45 MET cc_start: 0.8323 (ppp) cc_final: 0.7545 (ppp) REVERT: N 87 MET cc_start: 0.8160 (mmp) cc_final: 0.6542 (pmm) REVERT: N 108 ARG cc_start: 0.4992 (OUTLIER) cc_final: 0.4289 (ptt180) REVERT: P 55 ARG cc_start: 0.8555 (mpt180) cc_final: 0.8169 (mpp-170) REVERT: P 68 ARG cc_start: 0.8659 (ttp-170) cc_final: 0.8397 (ttm170) REVERT: P 75 GLU cc_start: 0.8552 (mm-30) cc_final: 0.8221 (mp0) REVERT: P 84 MET cc_start: 0.7238 (ttt) cc_final: 0.6500 (ppp) REVERT: P 111 ASP cc_start: 0.8795 (m-30) cc_final: 0.7959 (m-30) REVERT: Q 37 TYR cc_start: 0.8464 (p90) cc_final: 0.8129 (p90) REVERT: Q 101 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8699 (tp) REVERT: T 9 LYS cc_start: 0.8187 (mtmt) cc_final: 0.7864 (pttt) REVERT: T 44 GLU cc_start: 0.8920 (pt0) cc_final: 0.8567 (pm20) REVERT: T 52 ARG cc_start: 0.8872 (tmm-80) cc_final: 0.8517 (ttp-170) REVERT: T 63 ARG cc_start: 0.8056 (tpp80) cc_final: 0.7808 (tpp-160) REVERT: T 64 LYS cc_start: 0.7446 (ttmm) cc_final: 0.7137 (ttmm) REVERT: T 67 ASP cc_start: 0.8455 (m-30) cc_final: 0.8158 (m-30) REVERT: T 76 ARG cc_start: 0.8480 (ttm110) cc_final: 0.8228 (ttm110) REVERT: U 3 THR cc_start: 0.7565 (OUTLIER) cc_final: 0.6213 (p) REVERT: U 5 ARG cc_start: 0.6789 (mtm180) cc_final: 0.6210 (mpp-170) REVERT: U 9 HIS cc_start: 0.8175 (m-70) cc_final: 0.7878 (m-70) REVERT: U 16 PHE cc_start: 0.7403 (t80) cc_final: 0.7099 (t80) REVERT: U 32 PHE cc_start: 0.7580 (p90) cc_final: 0.6910 (p90) REVERT: U 36 VAL cc_start: 0.7061 (OUTLIER) cc_final: 0.6817 (t) REVERT: U 56 ARG cc_start: 0.8070 (mmm-85) cc_final: 0.7729 (mmm-85) REVERT: U 59 HIS cc_start: 0.8060 (t-90) cc_final: 0.7646 (t-90) REVERT: V 16 MET cc_start: 0.6399 (OUTLIER) cc_final: 0.5584 (mmp) REVERT: V 17 GLU cc_start: 0.4919 (tt0) cc_final: 0.3602 (tm-30) REVERT: V 72 TRP cc_start: 0.6860 (m100) cc_final: 0.6612 (m100) REVERT: W 31 TYR cc_start: 0.7465 (m-80) cc_final: 0.7059 (m-10) REVERT: W 60 ARG cc_start: 0.8386 (mtt180) cc_final: 0.7914 (mtt-85) REVERT: W 63 TYR cc_start: 0.8548 (t80) cc_final: 0.7284 (t80) REVERT: W 69 TYR cc_start: 0.7656 (m-10) cc_final: 0.7377 (m-10) REVERT: Y 14 GLU cc_start: 0.9475 (mp0) cc_final: 0.8985 (mp0) REVERT: a 56 ASP cc_start: 0.8205 (OUTLIER) cc_final: 0.7789 (p0) REVERT: a 196 LEU cc_start: 0.1782 (OUTLIER) cc_final: 0.1434 (tp) outliers start: 296 outliers final: 210 residues processed: 1489 average time/residue: 1.3246 time to fit residues: 3386.9281 Evaluate side-chains 1551 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 233 poor density : 1318 time to evaluate : 6.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 5 CYS Chi-restraints excluded: chain b residue 8 THR Chi-restraints excluded: chain b residue 48 ILE Chi-restraints excluded: chain b residue 50 THR Chi-restraints excluded: chain b residue 52 HIS Chi-restraints excluded: chain b residue 104 LEU Chi-restraints excluded: chain b residue 117 SER Chi-restraints excluded: chain b residue 119 VAL Chi-restraints excluded: chain b residue 124 LYS Chi-restraints excluded: chain b residue 142 ASN Chi-restraints excluded: chain b residue 156 SER Chi-restraints excluded: chain b residue 159 THR Chi-restraints excluded: chain b residue 164 VAL Chi-restraints excluded: chain b residue 179 GLU Chi-restraints excluded: chain b residue 193 GLU Chi-restraints excluded: chain b residue 200 MET Chi-restraints excluded: chain b residue 222 THR Chi-restraints excluded: chain c residue 2 ILE Chi-restraints excluded: chain c residue 12 THR Chi-restraints excluded: chain c residue 35 THR Chi-restraints excluded: chain c residue 42 ASN Chi-restraints excluded: chain c residue 97 SER Chi-restraints excluded: chain c residue 126 ASN Chi-restraints excluded: chain c residue 142 VAL Chi-restraints excluded: chain c residue 170 VAL Chi-restraints excluded: chain c residue 177 VAL Chi-restraints excluded: chain c residue 207 VAL Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 33 VAL Chi-restraints excluded: chain d residue 40 ARG Chi-restraints excluded: chain d residue 41 GLN Chi-restraints excluded: chain d residue 73 ILE Chi-restraints excluded: chain d residue 105 LEU Chi-restraints excluded: chain d residue 148 ILE Chi-restraints excluded: chain d residue 150 THR Chi-restraints excluded: chain d residue 159 LEU Chi-restraints excluded: chain d residue 164 LEU Chi-restraints excluded: chain d residue 200 LEU Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 30 VAL Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 56 LEU Chi-restraints excluded: chain e residue 65 LEU Chi-restraints excluded: chain e residue 111 ARG Chi-restraints excluded: chain e residue 120 SER Chi-restraints excluded: chain e residue 144 LYS Chi-restraints excluded: chain e residue 169 LEU Chi-restraints excluded: chain e residue 173 ASP Chi-restraints excluded: chain f residue 3 VAL Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 19 ASN Chi-restraints excluded: chain f residue 38 ASP Chi-restraints excluded: chain f residue 42 VAL Chi-restraints excluded: chain f residue 72 ASN Chi-restraints excluded: chain f residue 124 CYS Chi-restraints excluded: chain f residue 147 LEU Chi-restraints excluded: chain g residue 12 LEU Chi-restraints excluded: chain g residue 122 LEU Chi-restraints excluded: chain g residue 130 VAL Chi-restraints excluded: chain h residue 27 VAL Chi-restraints excluded: chain h residue 33 VAL Chi-restraints excluded: chain h residue 88 HIS Chi-restraints excluded: chain h residue 105 LYS Chi-restraints excluded: chain h residue 123 ILE Chi-restraints excluded: chain i residue 52 LEU Chi-restraints excluded: chain i residue 57 VAL Chi-restraints excluded: chain i residue 69 VAL Chi-restraints excluded: chain j residue 25 LEU Chi-restraints excluded: chain j residue 28 LEU Chi-restraints excluded: chain k residue 19 VAL Chi-restraints excluded: chain k residue 21 CYS Chi-restraints excluded: chain k residue 35 VAL Chi-restraints excluded: chain k residue 44 LYS Chi-restraints excluded: chain k residue 47 ILE Chi-restraints excluded: chain k residue 56 ASP Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 69 VAL Chi-restraints excluded: chain k residue 106 GLU Chi-restraints excluded: chain l residue 3 LEU Chi-restraints excluded: chain l residue 23 ILE Chi-restraints excluded: chain l residue 40 SER Chi-restraints excluded: chain l residue 68 SER Chi-restraints excluded: chain l residue 73 ILE Chi-restraints excluded: chain l residue 85 VAL Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain l residue 122 VAL Chi-restraints excluded: chain l residue 125 LEU Chi-restraints excluded: chain l residue 144 GLU Chi-restraints excluded: chain m residue 42 THR Chi-restraints excluded: chain m residue 54 THR Chi-restraints excluded: chain m residue 74 THR Chi-restraints excluded: chain m residue 119 LEU Chi-restraints excluded: chain m residue 136 MET Chi-restraints excluded: chain n residue 9 GLN Chi-restraints excluded: chain n residue 24 MET Chi-restraints excluded: chain n residue 51 LEU Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain n residue 65 LEU Chi-restraints excluded: chain n residue 113 ILE Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain o residue 18 LEU Chi-restraints excluded: chain o residue 24 THR Chi-restraints excluded: chain o residue 31 THR Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain p residue 7 LEU Chi-restraints excluded: chain p residue 31 VAL Chi-restraints excluded: chain p residue 40 GLN Chi-restraints excluded: chain p residue 81 ASP Chi-restraints excluded: chain q residue 28 SER Chi-restraints excluded: chain q residue 56 PHE Chi-restraints excluded: chain q residue 79 ILE Chi-restraints excluded: chain q residue 97 ILE Chi-restraints excluded: chain q residue 109 VAL Chi-restraints excluded: chain r residue 22 LEU Chi-restraints excluded: chain r residue 41 ILE Chi-restraints excluded: chain r residue 64 VAL Chi-restraints excluded: chain s residue 19 LEU Chi-restraints excluded: chain s residue 20 VAL Chi-restraints excluded: chain s residue 40 ASN Chi-restraints excluded: chain s residue 66 ILE Chi-restraints excluded: chain s residue 73 LYS Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain s residue 77 ASP Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain t residue 60 THR Chi-restraints excluded: chain t residue 86 THR Chi-restraints excluded: chain u residue 5 ARG Chi-restraints excluded: chain u residue 12 VAL Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain u residue 28 LEU Chi-restraints excluded: chain u residue 35 VAL Chi-restraints excluded: chain u residue 36 GLU Chi-restraints excluded: chain u residue 64 ILE Chi-restraints excluded: chain u residue 73 ASN Chi-restraints excluded: chain u residue 102 ILE Chi-restraints excluded: chain v residue 30 ILE Chi-restraints excluded: chain v residue 35 GLU Chi-restraints excluded: chain v residue 45 ASP Chi-restraints excluded: chain v residue 58 SER Chi-restraints excluded: chain v residue 64 VAL Chi-restraints excluded: chain v residue 65 VAL Chi-restraints excluded: chain v residue 70 ILE Chi-restraints excluded: chain v residue 85 LYS Chi-restraints excluded: chain v residue 92 VAL Chi-restraints excluded: chain w residue 52 ASP Chi-restraints excluded: chain w residue 62 LYS Chi-restraints excluded: chain w residue 66 GLU Chi-restraints excluded: chain w residue 79 GLU Chi-restraints excluded: chain x residue 51 SER Chi-restraints excluded: chain x residue 58 ILE Chi-restraints excluded: chain x residue 66 VAL Chi-restraints excluded: chain z residue 6 ILE Chi-restraints excluded: chain z residue 9 THR Chi-restraints excluded: chain z residue 40 THR Chi-restraints excluded: chain z residue 56 VAL Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain C residue 7 LYS Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 22 MET Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain G residue 108 GLN Chi-restraints excluded: chain G residue 193 ASP Chi-restraints excluded: chain G residue 198 VAL Chi-restraints excluded: chain G residue 211 LEU Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain I residue 56 GLU Chi-restraints excluded: chain I residue 71 PHE Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 199 ILE Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 91 SER Chi-restraints excluded: chain J residue 121 ASN Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain J residue 140 ILE Chi-restraints excluded: chain K residue 23 GLU Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 52 ASN Chi-restraints excluded: chain K residue 55 HIS Chi-restraints excluded: chain K residue 59 TYR Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 115 MET Chi-restraints excluded: chain M residue 9 MET Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 62 LEU Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 105 THR Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain N residue 28 VAL Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain N residue 108 ARG Chi-restraints excluded: chain O residue 91 ASP Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 27 ASN Chi-restraints excluded: chain P residue 79 LYS Chi-restraints excluded: chain P residue 80 ASN Chi-restraints excluded: chain P residue 108 ASN Chi-restraints excluded: chain P residue 109 ILE Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain S residue 26 LEU Chi-restraints excluded: chain T residue 31 LEU Chi-restraints excluded: chain T residue 58 MET Chi-restraints excluded: chain T residue 65 LEU Chi-restraints excluded: chain U residue 2 VAL Chi-restraints excluded: chain U residue 3 THR Chi-restraints excluded: chain U residue 20 VAL Chi-restraints excluded: chain U residue 33 ILE Chi-restraints excluded: chain U residue 36 VAL Chi-restraints excluded: chain V residue 16 MET Chi-restraints excluded: chain V residue 26 ARG Chi-restraints excluded: chain V residue 28 VAL Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain V residue 50 ASN Chi-restraints excluded: chain V residue 57 VAL Chi-restraints excluded: chain W residue 25 ILE Chi-restraints excluded: chain W residue 28 LEU Chi-restraints excluded: chain W residue 58 ILE Chi-restraints excluded: chain W residue 70 THR Chi-restraints excluded: chain Y residue 13 SER Chi-restraints excluded: chain a residue 56 ASP Chi-restraints excluded: chain a residue 196 LEU Chi-restraints excluded: chain a residue 216 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1043 random chunks: chunk 972 optimal weight: 8.9990 chunk 113 optimal weight: 50.0000 chunk 574 optimal weight: 1.9990 chunk 736 optimal weight: 10.0000 chunk 570 optimal weight: 0.3980 chunk 849 optimal weight: 10.0000 chunk 563 optimal weight: 0.9990 chunk 1005 optimal weight: 7.9990 chunk 629 optimal weight: 40.0000 chunk 612 optimal weight: 20.0000 chunk 464 optimal weight: 50.0000 overall best weight: 4.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 142 ASN ** c 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 164 GLN c 167 ASN ** d 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 29 ASN ** g 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 38 GLN p 6 GLN ** p 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 19 GLN q 55 GLN r 87 GLN ** s 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 22 ASN y 31 GLN z 8 GLN ** G 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 HIS ** 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 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 108 ASN ** P 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 5 GLN ** T 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 55 HIS ** 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: 0.8217 moved from start: 0.4272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 159558 Z= 0.244 Angle : 0.602 13.171 238506 Z= 0.308 Chirality : 0.035 0.313 30471 Planarity : 0.004 0.054 12929 Dihedral : 23.259 178.009 79350 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 16.83 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.29 % Favored : 90.59 % Rotamer: Outliers : 5.64 % Allowed : 25.06 % Favored : 69.30 % 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: -2.19 (0.11), residues: 5919 helix: -0.34 (0.12), residues: 1812 sheet: -1.55 (0.15), residues: 1016 loop : -2.13 (0.11), residues: 3091 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP b 212 HIS 0.009 0.001 HIS b 141 PHE 0.032 0.002 PHE D 18 TYR 0.036 0.002 TYR G 212 ARG 0.014 0.001 ARG v 93 *********************** 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 1636 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 277 poor density : 1359 time to evaluate : 6.248 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: b 124 LYS cc_start: 0.8856 (OUTLIER) cc_final: 0.8248 (ptpp) REVERT: b 142 ASN cc_start: 0.8576 (OUTLIER) cc_final: 0.8061 (t0) REVERT: b 180 MET cc_start: 0.8458 (mmm) cc_final: 0.8248 (mmt) REVERT: b 193 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.8174 (mt-10) REVERT: b 212 TRP cc_start: 0.7843 (p90) cc_final: 0.7324 (p-90) REVERT: d 40 ARG cc_start: 0.8128 (OUTLIER) cc_final: 0.7282 (mtp85) REVERT: d 163 ASN cc_start: 0.6224 (OUTLIER) cc_final: 0.5675 (m110) REVERT: e 3 LEU cc_start: 0.9054 (pt) cc_final: 0.8727 (pt) REVERT: e 70 ARG cc_start: 0.8757 (ttp80) cc_final: 0.8444 (ttp80) REVERT: e 100 GLU cc_start: 0.8725 (tt0) cc_final: 0.8514 (mt-10) REVERT: e 111 ARG cc_start: 0.8541 (OUTLIER) cc_final: 0.7583 (ttp-170) REVERT: e 126 ASN cc_start: 0.8464 (m-40) cc_final: 0.8208 (m-40) REVERT: e 137 PHE cc_start: 0.8589 (m-80) cc_final: 0.8281 (m-80) REVERT: e 144 LYS cc_start: 0.8190 (OUTLIER) cc_final: 0.7832 (mmtm) REVERT: f 2 ARG cc_start: 0.7996 (tpp80) cc_final: 0.7160 (tpp-160) REVERT: f 68 ARG cc_start: 0.8856 (ttp80) cc_final: 0.8442 (ttp80) REVERT: f 151 ARG cc_start: 0.8476 (tpp-160) cc_final: 0.8078 (mtp-110) REVERT: g 1 MET cc_start: 0.6941 (tpt) cc_final: 0.6630 (tpt) REVERT: g 33 GLN cc_start: 0.8172 (mt0) cc_final: 0.7901 (mt0) REVERT: h 1 MET cc_start: 0.2455 (ppp) cc_final: 0.1536 (ppp) REVERT: h 33 VAL cc_start: 0.7866 (OUTLIER) cc_final: 0.7624 (p) REVERT: h 38 MET cc_start: 0.1849 (mmt) cc_final: 0.1427 (mmt) REVERT: h 88 HIS cc_start: 0.5925 (OUTLIER) cc_final: 0.4047 (t-90) REVERT: i 116 MET cc_start: -0.0902 (mtt) cc_final: -0.1173 (ptp) REVERT: j 25 LEU cc_start: 0.9368 (OUTLIER) cc_final: 0.9141 (tp) REVERT: j 74 TYR cc_start: 0.8090 (m-80) cc_final: 0.7690 (m-80) REVERT: j 98 GLU cc_start: 0.7800 (pm20) cc_final: 0.7409 (pm20) REVERT: j 99 ARG cc_start: 0.8996 (tpp-160) cc_final: 0.8793 (tpp-160) REVERT: k 73 ASP cc_start: 0.8120 (p0) cc_final: 0.7878 (p0) REVERT: m 31 PHE cc_start: 0.7930 (m-80) cc_final: 0.7567 (m-80) REVERT: m 82 MET cc_start: 0.7542 (mmm) cc_final: 0.6013 (mmt) REVERT: m 117 PHE cc_start: 0.8877 (OUTLIER) cc_final: 0.8588 (m-10) REVERT: m 127 LYS cc_start: 0.8828 (tppt) cc_final: 0.8593 (tppt) REVERT: m 133 LYS cc_start: 0.8485 (OUTLIER) cc_final: 0.8022 (mttm) REVERT: n 32 GLU cc_start: 0.8812 (mp0) cc_final: 0.8150 (mp0) REVERT: n 73 ASN cc_start: 0.8907 (m-40) cc_final: 0.8484 (t0) REVERT: o 9 ARG cc_start: 0.7969 (tmm160) cc_final: 0.7738 (tmm160) REVERT: o 56 LYS cc_start: 0.8283 (mptt) cc_final: 0.8083 (mptt) REVERT: o 104 GLN cc_start: 0.8525 (tt0) cc_final: 0.8272 (tp40) REVERT: p 8 GLU cc_start: 0.8680 (mm-30) cc_final: 0.8427 (mm-30) REVERT: p 9 GLN cc_start: 0.7966 (tm-30) cc_final: 0.7704 (tm-30) REVERT: p 23 ASP cc_start: 0.7834 (m-30) cc_final: 0.7571 (m-30) REVERT: p 70 GLU cc_start: 0.7273 (tp30) cc_final: 0.6658 (tp30) REVERT: q 56 PHE cc_start: 0.9247 (OUTLIER) cc_final: 0.8773 (m-10) REVERT: q 65 ASN cc_start: 0.8689 (t0) cc_final: 0.8318 (t0) REVERT: r 1 MET cc_start: 0.8611 (tpp) cc_final: 0.8272 (tpp) REVERT: r 21 ARG cc_start: 0.8642 (ttm170) cc_final: 0.8171 (mtt-85) REVERT: s 6 LYS cc_start: 0.9532 (ptpt) cc_final: 0.9199 (ptpp) REVERT: s 19 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8666 (mp) REVERT: t 3 ARG cc_start: 0.6159 (mtp85) cc_final: 0.5827 (ttm110) REVERT: t 56 GLU cc_start: 0.8195 (tp30) cc_final: 0.7786 (tp30) REVERT: u 6 ARG cc_start: 0.7593 (tpp80) cc_final: 0.7324 (tpp80) REVERT: u 11 ILE cc_start: 0.9219 (OUTLIER) cc_final: 0.8954 (pt) REVERT: u 34 ILE cc_start: 0.8942 (mp) cc_final: 0.8649 (pt) REVERT: u 39 ASN cc_start: 0.7712 (t0) cc_final: 0.7444 (t0) REVERT: u 46 LYS cc_start: 0.8591 (tmtt) cc_final: 0.8390 (tmtt) REVERT: v 79 ARG cc_start: 0.8944 (mmm-85) cc_final: 0.8635 (mmt-90) REVERT: w 51 ARG cc_start: 0.8457 (ttt-90) cc_final: 0.7916 (ptm160) REVERT: w 66 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.7201 (mm-30) REVERT: w 77 SER cc_start: 0.9054 (m) cc_final: 0.8583 (p) REVERT: w 79 GLU cc_start: 0.6805 (OUTLIER) cc_final: 0.6279 (pm20) REVERT: x 10 ARG cc_start: 0.7668 (mtp-110) cc_final: 0.7444 (mtp180) REVERT: y 28 LEU cc_start: 0.9415 (mp) cc_final: 0.9195 (mp) REVERT: y 39 GLN cc_start: 0.8583 (mt0) cc_final: 0.8108 (pt0) REVERT: y 40 SER cc_start: 0.9278 (m) cc_final: 0.8727 (t) REVERT: y 49 ASP cc_start: 0.8303 (m-30) cc_final: 0.8023 (m-30) REVERT: z 38 GLU cc_start: 0.7840 (mm-30) cc_final: 0.7322 (mm-30) REVERT: z 48 ASN cc_start: 0.8848 (t0) cc_final: 0.8379 (t0) REVERT: z 55 LYS cc_start: 0.8490 (tptp) cc_final: 0.8189 (tptp) REVERT: C 7 LYS cc_start: 0.7639 (OUTLIER) cc_final: 0.7289 (mtmm) REVERT: C 37 LYS cc_start: 0.8439 (mttm) cc_final: 0.8079 (mttt) REVERT: D 1 MET cc_start: 0.6880 (OUTLIER) cc_final: 0.6622 (mmm) REVERT: D 26 ASN cc_start: 0.8369 (m-40) cc_final: 0.8123 (m-40) REVERT: G 17 HIS cc_start: 0.8038 (t-90) cc_final: 0.7803 (t-90) REVERT: G 51 GLU cc_start: 0.9513 (tp30) cc_final: 0.9182 (tp30) REVERT: G 77 GLU cc_start: 0.9251 (tp30) cc_final: 0.8708 (tp30) REVERT: G 84 LEU cc_start: 0.8812 (mt) cc_final: 0.8548 (pp) REVERT: G 89 PHE cc_start: 0.6953 (m-80) cc_final: 0.6517 (m-80) REVERT: G 111 LYS cc_start: 0.9427 (tppt) cc_final: 0.9050 (tptp) REVERT: G 151 LYS cc_start: 0.8691 (pttt) cc_final: 0.8184 (ptmm) REVERT: G 153 MET cc_start: 0.3692 (tpt) cc_final: 0.3124 (tpt) REVERT: G 161 PHE cc_start: 0.8305 (t80) cc_final: 0.7664 (t80) REVERT: G 168 GLU cc_start: 0.8372 (mp0) cc_final: 0.7969 (mp0) REVERT: G 197 PHE cc_start: 0.7908 (m-80) cc_final: 0.7349 (t80) REVERT: H 10 ARG cc_start: 0.7596 (mtt180) cc_final: 0.7030 (mtt180) REVERT: H 163 ARG cc_start: 0.6450 (ptt180) cc_final: 0.5332 (mtp180) REVERT: I 56 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.7234 (pp20) REVERT: I 64 TYR cc_start: 0.7073 (m-80) cc_final: 0.6513 (m-10) REVERT: I 104 MET cc_start: 0.0409 (mmt) cc_final: -0.0671 (mtt) REVERT: I 164 ARG cc_start: 0.3360 (ttm170) cc_final: 0.2882 (ptm-80) REVERT: J 69 ASN cc_start: 0.8609 (t0) cc_final: 0.8003 (p0) REVERT: J 145 ASN cc_start: 0.8908 (t0) cc_final: 0.8274 (m110) REVERT: K 1 MET cc_start: 0.7592 (tpp) cc_final: 0.7347 (tpp) REVERT: K 33 GLU cc_start: 0.8990 (mp0) cc_final: 0.8782 (pm20) REVERT: K 59 TYR cc_start: 0.8351 (OUTLIER) cc_final: 0.7517 (t80) REVERT: K 62 MET cc_start: 0.6792 (ttt) cc_final: 0.6339 (ttt) REVERT: K 78 PHE cc_start: 0.8075 (m-10) cc_final: 0.7864 (m-10) REVERT: K 92 THR cc_start: 0.7183 (OUTLIER) cc_final: 0.6919 (p) REVERT: L 49 LEU cc_start: 0.6981 (mm) cc_final: 0.6739 (mm) REVERT: L 100 MET cc_start: 0.5584 (mtm) cc_final: 0.4938 (mmt) REVERT: M 8 ASP cc_start: 0.7870 (t0) cc_final: 0.7346 (m-30) REVERT: M 66 GLN cc_start: 0.8729 (mm110) cc_final: 0.8505 (mp10) REVERT: M 76 ARG cc_start: 0.7464 (tpt90) cc_final: 0.7224 (tpt90) REVERT: M 110 MET cc_start: 0.8874 (ptp) cc_final: 0.8324 (ptp) REVERT: M 126 CYS cc_start: 0.7704 (m) cc_final: 0.7313 (m) REVERT: N 11 ARG cc_start: 0.5553 (tpt170) cc_final: 0.5036 (tpt170) REVERT: N 45 MET cc_start: 0.8287 (ppp) cc_final: 0.7485 (ppp) REVERT: N 87 MET cc_start: 0.8133 (mmp) cc_final: 0.6922 (pmm) REVERT: N 108 ARG cc_start: 0.4956 (OUTLIER) cc_final: 0.4262 (ptt180) REVERT: P 55 ARG cc_start: 0.8560 (mpt180) cc_final: 0.8143 (mpp-170) REVERT: P 68 ARG cc_start: 0.8547 (ttp-170) cc_final: 0.8282 (ttm170) REVERT: P 75 GLU cc_start: 0.8541 (mm-30) cc_final: 0.8220 (mp0) REVERT: P 84 MET cc_start: 0.7289 (ttt) cc_final: 0.6714 (ppp) REVERT: P 92 ARG cc_start: 0.4585 (tpt-90) cc_final: 0.4366 (tpt-90) REVERT: P 111 ASP cc_start: 0.8834 (m-30) cc_final: 0.7877 (m-30) REVERT: Q 37 TYR cc_start: 0.8257 (p90) cc_final: 0.8026 (p90) REVERT: Q 101 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8602 (tp) REVERT: T 9 LYS cc_start: 0.8269 (mtmt) cc_final: 0.8042 (pttt) REVERT: T 13 GLU cc_start: 0.8367 (tt0) cc_final: 0.7415 (tp30) REVERT: T 44 GLU cc_start: 0.8940 (pt0) cc_final: 0.8594 (pm20) REVERT: T 52 ARG cc_start: 0.8893 (tmm-80) cc_final: 0.8537 (ttp-170) REVERT: T 63 ARG cc_start: 0.8006 (tpp80) cc_final: 0.7729 (tpp-160) REVERT: T 64 LYS cc_start: 0.7424 (ttmm) cc_final: 0.7082 (ttmm) REVERT: T 67 ASP cc_start: 0.8551 (m-30) cc_final: 0.8279 (m-30) REVERT: T 70 LYS cc_start: 0.9241 (mmtp) cc_final: 0.8992 (mmmt) REVERT: T 76 ARG cc_start: 0.8745 (ttm110) cc_final: 0.8123 (ttm110) REVERT: T 79 GLN cc_start: 0.8662 (pt0) cc_final: 0.8211 (pm20) REVERT: U 3 THR cc_start: 0.7580 (OUTLIER) cc_final: 0.6451 (p) REVERT: U 5 ARG cc_start: 0.6704 (mtm180) cc_final: 0.6187 (mpp-170) REVERT: U 9 HIS cc_start: 0.8118 (m-70) cc_final: 0.7794 (m-70) REVERT: U 16 PHE cc_start: 0.7328 (t80) cc_final: 0.7027 (t80) REVERT: U 32 PHE cc_start: 0.7634 (p90) cc_final: 0.6995 (p90) REVERT: U 36 VAL cc_start: 0.7159 (OUTLIER) cc_final: 0.6894 (t) REVERT: U 56 ARG cc_start: 0.8067 (mmm-85) cc_final: 0.7719 (mmm-85) REVERT: U 59 HIS cc_start: 0.7999 (t-90) cc_final: 0.7561 (t-90) REVERT: V 16 MET cc_start: 0.6357 (OUTLIER) cc_final: 0.5619 (mmp) REVERT: V 17 GLU cc_start: 0.5093 (tt0) cc_final: 0.3712 (tm-30) REVERT: W 31 TYR cc_start: 0.7440 (m-80) cc_final: 0.7004 (m-10) REVERT: W 60 ARG cc_start: 0.8382 (mtt180) cc_final: 0.7773 (mmm-85) REVERT: W 63 TYR cc_start: 0.8456 (t80) cc_final: 0.7393 (t80) REVERT: a 56 ASP cc_start: 0.8298 (OUTLIER) cc_final: 0.7895 (p0) REVERT: a 196 LEU cc_start: 0.2393 (OUTLIER) cc_final: 0.2179 (tp) outliers start: 277 outliers final: 199 residues processed: 1486 average time/residue: 1.4262 time to fit residues: 3679.5912 Evaluate side-chains 1561 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 228 poor density : 1333 time to evaluate : 6.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 5 CYS Chi-restraints excluded: chain b residue 8 THR Chi-restraints excluded: chain b residue 48 ILE Chi-restraints excluded: chain b residue 50 THR Chi-restraints excluded: chain b residue 52 HIS Chi-restraints excluded: chain b residue 87 SER Chi-restraints excluded: chain b residue 104 LEU Chi-restraints excluded: chain b residue 119 VAL Chi-restraints excluded: chain b residue 124 LYS Chi-restraints excluded: chain b residue 142 ASN Chi-restraints excluded: chain b residue 156 SER Chi-restraints excluded: chain b residue 164 VAL Chi-restraints excluded: chain b residue 179 GLU Chi-restraints excluded: chain b residue 193 GLU Chi-restraints excluded: chain b residue 222 THR Chi-restraints excluded: chain c residue 2 ILE Chi-restraints excluded: chain c residue 12 THR Chi-restraints excluded: chain c residue 35 THR Chi-restraints excluded: chain c residue 42 ASN Chi-restraints excluded: chain c residue 64 GLU Chi-restraints excluded: chain c residue 97 SER Chi-restraints excluded: chain c residue 126 ASN Chi-restraints excluded: chain c residue 142 VAL Chi-restraints excluded: chain c residue 167 ASN Chi-restraints excluded: chain c residue 170 VAL Chi-restraints excluded: chain c residue 177 VAL Chi-restraints excluded: chain c residue 207 VAL Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 40 ARG Chi-restraints excluded: chain d residue 41 GLN Chi-restraints excluded: chain d residue 105 LEU Chi-restraints excluded: chain d residue 148 ILE Chi-restraints excluded: chain d residue 150 THR Chi-restraints excluded: chain d residue 159 LEU Chi-restraints excluded: chain d residue 163 ASN Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 30 VAL Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 56 LEU Chi-restraints excluded: chain e residue 65 LEU Chi-restraints excluded: chain e residue 111 ARG Chi-restraints excluded: chain e residue 120 SER Chi-restraints excluded: chain e residue 144 LYS Chi-restraints excluded: chain e residue 158 THR Chi-restraints excluded: chain e residue 173 ASP Chi-restraints excluded: chain f residue 3 VAL Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 19 ASN Chi-restraints excluded: chain f residue 38 ASP Chi-restraints excluded: chain f residue 42 VAL Chi-restraints excluded: chain f residue 72 ASN Chi-restraints excluded: chain f residue 124 CYS Chi-restraints excluded: chain f residue 130 ILE Chi-restraints excluded: chain f residue 154 GLU Chi-restraints excluded: chain g residue 130 VAL Chi-restraints excluded: chain h residue 27 VAL Chi-restraints excluded: chain h residue 33 VAL Chi-restraints excluded: chain h residue 88 HIS Chi-restraints excluded: chain h residue 123 ILE Chi-restraints excluded: chain i residue 52 LEU Chi-restraints excluded: chain i residue 57 VAL Chi-restraints excluded: chain i residue 69 VAL Chi-restraints excluded: chain i residue 78 LEU Chi-restraints excluded: chain j residue 25 LEU Chi-restraints excluded: chain j residue 28 LEU Chi-restraints excluded: chain j residue 80 HIS Chi-restraints excluded: chain j residue 81 ILE Chi-restraints excluded: chain k residue 19 VAL Chi-restraints excluded: chain k residue 21 CYS Chi-restraints excluded: chain k residue 35 VAL Chi-restraints excluded: chain k residue 44 LYS Chi-restraints excluded: chain k residue 56 ASP Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 69 VAL Chi-restraints excluded: chain k residue 106 GLU Chi-restraints excluded: chain l residue 3 LEU Chi-restraints excluded: chain l residue 23 ILE Chi-restraints excluded: chain l residue 40 SER Chi-restraints excluded: chain l residue 68 SER Chi-restraints excluded: chain l residue 73 ILE Chi-restraints excluded: chain l residue 85 VAL Chi-restraints excluded: chain l residue 110 VAL Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain l residue 144 GLU Chi-restraints excluded: chain m residue 42 THR Chi-restraints excluded: chain m residue 54 THR Chi-restraints excluded: chain m residue 74 THR Chi-restraints excluded: chain m residue 117 PHE Chi-restraints excluded: chain m residue 133 LYS Chi-restraints excluded: chain n residue 9 GLN Chi-restraints excluded: chain n residue 24 MET 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 n residue 65 LEU Chi-restraints excluded: chain n residue 113 ILE Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain o residue 18 LEU Chi-restraints excluded: chain o residue 24 THR Chi-restraints excluded: chain o residue 31 THR Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain o residue 103 VAL Chi-restraints excluded: chain p residue 6 GLN Chi-restraints excluded: chain p residue 31 VAL Chi-restraints excluded: chain p residue 40 GLN Chi-restraints excluded: chain p residue 81 ASP Chi-restraints excluded: chain p residue 101 GLU Chi-restraints excluded: chain q residue 28 SER Chi-restraints excluded: chain q residue 56 PHE Chi-restraints excluded: chain q residue 97 ILE Chi-restraints excluded: chain q residue 109 VAL Chi-restraints excluded: chain r residue 22 LEU Chi-restraints excluded: chain r residue 41 ILE Chi-restraints excluded: chain r residue 64 VAL Chi-restraints excluded: chain s residue 19 LEU Chi-restraints excluded: chain s residue 20 VAL Chi-restraints excluded: chain s residue 40 ASN Chi-restraints excluded: chain s residue 66 ILE Chi-restraints excluded: chain s residue 73 LYS Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain s residue 77 ASP Chi-restraints excluded: chain t residue 33 LYS Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain t residue 60 THR Chi-restraints excluded: chain t residue 86 THR Chi-restraints excluded: chain u residue 5 ARG Chi-restraints excluded: chain u residue 11 ILE Chi-restraints excluded: chain u residue 12 VAL Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain u residue 28 LEU Chi-restraints excluded: chain u residue 35 VAL Chi-restraints excluded: chain u residue 36 GLU Chi-restraints excluded: chain u residue 64 ILE Chi-restraints excluded: chain u residue 102 ILE Chi-restraints excluded: chain v residue 1 MET Chi-restraints excluded: chain v residue 30 ILE Chi-restraints excluded: chain v residue 35 GLU Chi-restraints excluded: chain v residue 45 ASP Chi-restraints excluded: chain v residue 58 SER Chi-restraints excluded: chain v residue 64 VAL Chi-restraints excluded: chain v residue 65 VAL Chi-restraints excluded: chain v residue 70 ILE Chi-restraints excluded: chain v residue 92 VAL Chi-restraints excluded: chain w residue 62 LYS Chi-restraints excluded: chain w residue 66 GLU Chi-restraints excluded: chain w residue 79 GLU Chi-restraints excluded: chain x residue 6 VAL Chi-restraints excluded: chain x residue 51 SER Chi-restraints excluded: chain x residue 58 ILE Chi-restraints excluded: chain z residue 6 ILE Chi-restraints excluded: chain z residue 40 THR Chi-restraints excluded: chain z residue 56 VAL Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain C residue 7 LYS Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 3 ARG Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 22 MET Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 60 CYS Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 193 ASP Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 56 GLU Chi-restraints excluded: chain I residue 71 PHE Chi-restraints excluded: chain I residue 89 LEU Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 199 ILE Chi-restraints excluded: chain I residue 201 GLU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 121 ASN Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain J residue 140 ILE Chi-restraints excluded: chain J residue 156 ARG Chi-restraints excluded: chain K residue 23 GLU Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 52 ASN Chi-restraints excluded: chain K residue 55 HIS Chi-restraints excluded: chain K residue 59 TYR Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 115 MET Chi-restraints excluded: chain M residue 9 MET Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 62 LEU Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 105 THR Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain N residue 28 VAL Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain N residue 108 ARG Chi-restraints excluded: chain O residue 91 ASP Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 79 LYS Chi-restraints excluded: chain P residue 80 ASN Chi-restraints excluded: chain P residue 109 ILE Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 73 LEU Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain S residue 26 LEU Chi-restraints excluded: chain T residue 31 LEU Chi-restraints excluded: chain T residue 65 LEU Chi-restraints excluded: chain U residue 2 VAL Chi-restraints excluded: chain U residue 3 THR Chi-restraints excluded: chain U residue 20 VAL Chi-restraints excluded: chain U residue 28 ARG Chi-restraints excluded: chain U residue 33 ILE Chi-restraints excluded: chain U residue 36 VAL Chi-restraints excluded: chain V residue 16 MET Chi-restraints excluded: chain V residue 26 ARG Chi-restraints excluded: chain V residue 28 VAL Chi-restraints excluded: chain V residue 50 ASN Chi-restraints excluded: chain W residue 25 ILE Chi-restraints excluded: chain W residue 28 LEU Chi-restraints excluded: chain W residue 58 ILE Chi-restraints excluded: chain Y residue 13 SER Chi-restraints excluded: chain a residue 56 ASP Chi-restraints excluded: chain a residue 196 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1043 random chunks: chunk 621 optimal weight: 50.0000 chunk 401 optimal weight: 10.0000 chunk 600 optimal weight: 50.0000 chunk 302 optimal weight: 6.9990 chunk 197 optimal weight: 2.9990 chunk 194 optimal weight: 1.9990 chunk 639 optimal weight: 30.0000 chunk 684 optimal weight: 50.0000 chunk 497 optimal weight: 50.0000 chunk 93 optimal weight: 1.9990 chunk 790 optimal weight: 8.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 142 ASN ** c 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 164 GLN c 167 ASN ** d 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 88 HIS j 135 GLN ** k 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 38 GLN ** p 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 55 GLN r 87 GLN ** s 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 22 ASN y 20 ASN G 108 GLN ** H 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 55 HIS ** a 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.4429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 159558 Z= 0.271 Angle : 0.621 13.177 238506 Z= 0.317 Chirality : 0.036 0.317 30471 Planarity : 0.005 0.057 12929 Dihedral : 23.279 177.593 79350 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 17.71 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.92 % Favored : 89.96 % Rotamer: Outliers : 5.83 % Allowed : 25.33 % Favored : 68.85 % 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: -2.14 (0.11), residues: 5919 helix: -0.31 (0.12), residues: 1823 sheet: -1.47 (0.16), residues: 1008 loop : -2.12 (0.11), residues: 3088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP b 212 HIS 0.014 0.001 HIS b 141 PHE 0.032 0.002 PHE D 18 TYR 0.037 0.002 TYR G 212 ARG 0.015 0.001 ARG v 93 *********************** 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 1623 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 286 poor density : 1337 time to evaluate : 7.149 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: b 124 LYS cc_start: 0.8899 (OUTLIER) cc_final: 0.8304 (ptpp) REVERT: b 142 ASN cc_start: 0.8753 (OUTLIER) cc_final: 0.8165 (t0) REVERT: b 180 MET cc_start: 0.8382 (mmm) cc_final: 0.8118 (mmm) REVERT: b 193 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.8210 (mt-10) REVERT: b 212 TRP cc_start: 0.7886 (p90) cc_final: 0.7500 (p-90) REVERT: d 40 ARG cc_start: 0.8090 (OUTLIER) cc_final: 0.7219 (mtp85) REVERT: d 163 ASN cc_start: 0.6247 (OUTLIER) cc_final: 0.5700 (m110) REVERT: e 70 ARG cc_start: 0.8767 (ttp80) cc_final: 0.8447 (ttp80) REVERT: e 90 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8291 (tp) REVERT: e 111 ARG cc_start: 0.8572 (OUTLIER) cc_final: 0.7650 (ttp-170) REVERT: e 126 ASN cc_start: 0.8479 (m-40) cc_final: 0.8217 (m-40) REVERT: e 137 PHE cc_start: 0.8554 (m-80) cc_final: 0.8244 (m-80) REVERT: e 144 LYS cc_start: 0.8245 (OUTLIER) cc_final: 0.7905 (mmtm) REVERT: e 176 PHE cc_start: 0.5214 (m-10) cc_final: 0.4935 (m-80) REVERT: f 2 ARG cc_start: 0.7999 (tpp80) cc_final: 0.7093 (tpp-160) REVERT: f 68 ARG cc_start: 0.8813 (ttp80) cc_final: 0.8371 (ttp80) REVERT: f 87 GLN cc_start: 0.7249 (mp10) cc_final: 0.6580 (mp10) REVERT: f 151 ARG cc_start: 0.8472 (tpp-160) cc_final: 0.8080 (mtp-110) REVERT: f 154 GLU cc_start: 0.8745 (pt0) cc_final: 0.8099 (pm20) REVERT: g 1 MET cc_start: 0.6924 (tpt) cc_final: 0.6655 (tpt) REVERT: g 33 GLN cc_start: 0.8203 (mt0) cc_final: 0.7973 (mt0) REVERT: h 1 MET cc_start: 0.2535 (ppp) cc_final: 0.1584 (ppp) REVERT: h 33 VAL cc_start: 0.7808 (OUTLIER) cc_final: 0.7573 (p) REVERT: h 38 MET cc_start: 0.1747 (mmt) cc_final: 0.1196 (mmt) REVERT: h 88 HIS cc_start: 0.5779 (OUTLIER) cc_final: 0.4209 (t-90) REVERT: i 52 LEU cc_start: 0.5091 (OUTLIER) cc_final: 0.4429 (mt) REVERT: i 116 MET cc_start: -0.0909 (mtt) cc_final: -0.1496 (ptp) REVERT: j 74 TYR cc_start: 0.8262 (m-80) cc_final: 0.7966 (m-80) REVERT: j 98 GLU cc_start: 0.7835 (pm20) cc_final: 0.7442 (pm20) REVERT: j 99 ARG cc_start: 0.9015 (tpp-160) cc_final: 0.8812 (tpp-160) REVERT: k 73 ASP cc_start: 0.8122 (p0) cc_final: 0.7876 (p0) REVERT: m 31 PHE cc_start: 0.8073 (m-80) cc_final: 0.7682 (m-10) REVERT: m 64 TRP cc_start: 0.8278 (m-90) cc_final: 0.7788 (m-10) REVERT: m 82 MET cc_start: 0.7567 (mmm) cc_final: 0.5993 (mmt) REVERT: m 117 PHE cc_start: 0.8794 (OUTLIER) cc_final: 0.8491 (m-10) REVERT: m 127 LYS cc_start: 0.8832 (tppt) cc_final: 0.8605 (tppt) REVERT: m 133 LYS cc_start: 0.8470 (OUTLIER) cc_final: 0.8016 (mttm) REVERT: n 32 GLU cc_start: 0.8840 (mp0) cc_final: 0.8177 (mp0) REVERT: n 73 ASN cc_start: 0.8918 (m-40) cc_final: 0.8497 (t0) REVERT: o 9 ARG cc_start: 0.8018 (tmm160) cc_final: 0.7709 (tmm160) REVERT: o 104 GLN cc_start: 0.8537 (tt0) cc_final: 0.8284 (tp40) REVERT: p 8 GLU cc_start: 0.8791 (mm-30) cc_final: 0.8502 (mm-30) REVERT: p 9 GLN cc_start: 0.7871 (tm-30) cc_final: 0.7602 (tm-30) REVERT: p 23 ASP cc_start: 0.7733 (m-30) cc_final: 0.7471 (m-30) REVERT: p 70 GLU cc_start: 0.7287 (tp30) cc_final: 0.6715 (tp30) REVERT: p 79 VAL cc_start: 0.9259 (OUTLIER) cc_final: 0.9031 (t) REVERT: q 56 PHE cc_start: 0.9269 (OUTLIER) cc_final: 0.8813 (m-10) REVERT: q 65 ASN cc_start: 0.8700 (t0) cc_final: 0.8219 (t0) REVERT: r 1 MET cc_start: 0.8658 (tpp) cc_final: 0.8437 (tpp) REVERT: r 21 ARG cc_start: 0.8646 (ttm170) cc_final: 0.8148 (mtt-85) REVERT: r 31 GLU cc_start: 0.8771 (tp30) cc_final: 0.8498 (tp30) REVERT: s 6 LYS cc_start: 0.9532 (ptpt) cc_final: 0.9195 (ptpp) REVERT: s 19 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8657 (mp) REVERT: t 3 ARG cc_start: 0.6215 (mtp85) cc_final: 0.5802 (ttm110) REVERT: t 56 GLU cc_start: 0.8158 (tp30) cc_final: 0.7805 (tp30) REVERT: u 6 ARG cc_start: 0.7603 (tpp80) cc_final: 0.7318 (tpp80) REVERT: u 39 ASN cc_start: 0.7866 (t0) cc_final: 0.7639 (t0) REVERT: u 100 GLU cc_start: 0.7960 (mp0) cc_final: 0.7693 (mp0) REVERT: v 80 HIS cc_start: 0.8805 (t-90) cc_final: 0.8240 (t-90) REVERT: w 66 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7261 (mm-30) REVERT: w 77 SER cc_start: 0.8977 (m) cc_final: 0.8449 (p) REVERT: w 79 GLU cc_start: 0.6752 (OUTLIER) cc_final: 0.6226 (pm20) REVERT: x 10 ARG cc_start: 0.7661 (mtp-110) cc_final: 0.7432 (mtp180) REVERT: y 15 ASN cc_start: 0.8987 (t0) cc_final: 0.8778 (t0) REVERT: y 39 GLN cc_start: 0.8599 (mt0) cc_final: 0.8127 (pt0) REVERT: y 40 SER cc_start: 0.9286 (m) cc_final: 0.8745 (t) REVERT: y 49 ASP cc_start: 0.8318 (OUTLIER) cc_final: 0.8022 (m-30) REVERT: z 38 GLU cc_start: 0.7780 (mm-30) cc_final: 0.7165 (mm-30) REVERT: z 48 ASN cc_start: 0.8870 (t0) cc_final: 0.8399 (t0) REVERT: z 55 LYS cc_start: 0.8481 (tptp) cc_final: 0.8050 (tptp) REVERT: C 37 LYS cc_start: 0.8446 (mttm) cc_final: 0.8094 (mttt) REVERT: D 1 MET cc_start: 0.6920 (OUTLIER) cc_final: 0.6698 (mmm) REVERT: D 26 ASN cc_start: 0.8395 (m-40) cc_final: 0.8158 (m-40) REVERT: G 17 HIS cc_start: 0.8050 (t-90) cc_final: 0.7827 (t-90) REVERT: G 26 MET cc_start: 0.7144 (ttm) cc_final: 0.6565 (mmt) REVERT: G 51 GLU cc_start: 0.9525 (tp30) cc_final: 0.9188 (tp30) REVERT: G 89 PHE cc_start: 0.6958 (m-80) cc_final: 0.6488 (m-80) REVERT: G 111 LYS cc_start: 0.9421 (tppt) cc_final: 0.9054 (tptp) REVERT: G 151 LYS cc_start: 0.8565 (pttt) cc_final: 0.8146 (ptmm) REVERT: G 153 MET cc_start: 0.3432 (tpt) cc_final: 0.2906 (tpt) REVERT: G 161 PHE cc_start: 0.8192 (t80) cc_final: 0.7587 (t80) REVERT: G 168 GLU cc_start: 0.8322 (mp0) cc_final: 0.7999 (mp0) REVERT: G 197 PHE cc_start: 0.7908 (m-80) cc_final: 0.7359 (t80) REVERT: H 10 ARG cc_start: 0.7321 (mtt180) cc_final: 0.6926 (mtt180) REVERT: H 163 ARG cc_start: 0.6407 (ptt180) cc_final: 0.5231 (mtp180) REVERT: I 56 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7268 (pp20) REVERT: I 64 TYR cc_start: 0.7098 (m-80) cc_final: 0.6536 (m-10) REVERT: I 104 MET cc_start: 0.0352 (mmt) cc_final: -0.0638 (mtt) REVERT: I 164 ARG cc_start: 0.3437 (ttm170) cc_final: 0.2868 (ptm-80) REVERT: J 145 ASN cc_start: 0.8920 (t0) cc_final: 0.8276 (m110) REVERT: J 147 ASN cc_start: 0.3742 (OUTLIER) cc_final: 0.3126 (p0) REVERT: K 1 MET cc_start: 0.7604 (tpp) cc_final: 0.7190 (tpp) REVERT: K 56 LYS cc_start: 0.7275 (mtmm) cc_final: 0.7059 (mptt) REVERT: K 59 TYR cc_start: 0.8427 (OUTLIER) cc_final: 0.7505 (t80) REVERT: K 62 MET cc_start: 0.7009 (ttt) cc_final: 0.6679 (ttt) REVERT: K 92 THR cc_start: 0.7219 (OUTLIER) cc_final: 0.6958 (p) REVERT: L 49 LEU cc_start: 0.7009 (mm) cc_final: 0.6742 (mm) REVERT: L 100 MET cc_start: 0.5562 (mtm) cc_final: 0.4927 (mmt) REVERT: M 110 MET cc_start: 0.8869 (ptp) cc_final: 0.8318 (ptp) REVERT: N 11 ARG cc_start: 0.5561 (tpt170) cc_final: 0.5075 (tpt170) REVERT: N 45 MET cc_start: 0.8352 (ppp) cc_final: 0.7556 (ppp) REVERT: N 87 MET cc_start: 0.8116 (mmp) cc_final: 0.6895 (pmm) REVERT: N 108 ARG cc_start: 0.4953 (OUTLIER) cc_final: 0.4307 (ptt180) REVERT: P 55 ARG cc_start: 0.8574 (mpt180) cc_final: 0.8200 (mpp-170) REVERT: P 75 GLU cc_start: 0.8556 (mm-30) cc_final: 0.8231 (mp0) REVERT: P 84 MET cc_start: 0.7332 (ttt) cc_final: 0.6704 (ppp) REVERT: P 111 ASP cc_start: 0.8759 (m-30) cc_final: 0.7819 (m-30) REVERT: Q 37 TYR cc_start: 0.8262 (p90) cc_final: 0.8032 (p90) REVERT: Q 101 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8619 (tp) REVERT: R 80 MET cc_start: 0.8224 (ttp) cc_final: 0.7961 (tmm) REVERT: T 9 LYS cc_start: 0.8282 (mtmt) cc_final: 0.8056 (pttt) REVERT: T 13 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.7429 (tp30) REVERT: T 44 GLU cc_start: 0.8955 (pt0) cc_final: 0.8581 (pm20) REVERT: T 52 ARG cc_start: 0.8856 (tmm-80) cc_final: 0.8565 (ttp-170) REVERT: T 63 ARG cc_start: 0.8022 (tpp80) cc_final: 0.7731 (tpp-160) REVERT: T 64 LYS cc_start: 0.7481 (ttmm) cc_final: 0.7114 (ttmm) REVERT: T 67 ASP cc_start: 0.8592 (m-30) cc_final: 0.8223 (m-30) REVERT: T 70 LYS cc_start: 0.9236 (mmtp) cc_final: 0.9028 (mmmt) REVERT: T 79 GLN cc_start: 0.8734 (pt0) cc_final: 0.8294 (pm20) REVERT: U 3 THR cc_start: 0.7644 (OUTLIER) cc_final: 0.6432 (p) REVERT: U 5 ARG cc_start: 0.6777 (mtm180) cc_final: 0.6256 (mpp-170) REVERT: U 9 HIS cc_start: 0.8152 (m-70) cc_final: 0.7836 (m-70) REVERT: U 16 PHE cc_start: 0.7246 (t80) cc_final: 0.6927 (t80) REVERT: U 31 ARG cc_start: 0.6007 (tmm-80) cc_final: 0.5685 (tmm-80) REVERT: U 32 PHE cc_start: 0.7613 (p90) cc_final: 0.6984 (p90) REVERT: U 36 VAL cc_start: 0.7230 (OUTLIER) cc_final: 0.6961 (t) REVERT: U 56 ARG cc_start: 0.8071 (mmm-85) cc_final: 0.7727 (mmm-85) REVERT: U 59 HIS cc_start: 0.8002 (t-90) cc_final: 0.7562 (t-90) REVERT: V 16 MET cc_start: 0.6302 (OUTLIER) cc_final: 0.5663 (mmp) REVERT: V 17 GLU cc_start: 0.5005 (tt0) cc_final: 0.3606 (tm-30) REVERT: W 31 TYR cc_start: 0.7386 (m-80) cc_final: 0.6905 (m-10) REVERT: W 60 ARG cc_start: 0.8378 (mtt180) cc_final: 0.7974 (mtt-85) REVERT: W 63 TYR cc_start: 0.8435 (t80) cc_final: 0.7657 (t80) REVERT: X 79 TYR cc_start: 0.3992 (t80) cc_final: 0.3102 (t80) REVERT: Z 46 ARG cc_start: 0.6931 (tpt170) cc_final: 0.5952 (ttp80) REVERT: a 56 ASP cc_start: 0.8201 (OUTLIER) cc_final: 0.7773 (p0) REVERT: a 196 LEU cc_start: 0.1731 (OUTLIER) cc_final: 0.1476 (tp) outliers start: 286 outliers final: 208 residues processed: 1473 average time/residue: 1.3993 time to fit residues: 3549.9072 Evaluate side-chains 1565 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 240 poor density : 1325 time to evaluate : 6.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 5 CYS Chi-restraints excluded: chain b residue 8 THR Chi-restraints excluded: chain b residue 48 ILE Chi-restraints excluded: chain b residue 50 THR Chi-restraints excluded: chain b residue 52 HIS Chi-restraints excluded: chain b residue 104 LEU Chi-restraints excluded: chain b residue 117 SER Chi-restraints excluded: chain b residue 119 VAL Chi-restraints excluded: chain b residue 124 LYS Chi-restraints excluded: chain b residue 142 ASN Chi-restraints excluded: chain b residue 156 SER Chi-restraints excluded: chain b residue 159 THR Chi-restraints excluded: chain b residue 164 VAL Chi-restraints excluded: chain b residue 179 GLU Chi-restraints excluded: chain b residue 193 GLU Chi-restraints excluded: chain b residue 200 MET Chi-restraints excluded: chain b residue 222 THR Chi-restraints excluded: chain b residue 271 SER Chi-restraints excluded: chain c residue 2 ILE Chi-restraints excluded: chain c residue 12 THR Chi-restraints excluded: chain c residue 35 THR Chi-restraints excluded: chain c residue 42 ASN Chi-restraints excluded: chain c residue 126 ASN Chi-restraints excluded: chain c residue 142 VAL Chi-restraints excluded: chain c residue 170 VAL Chi-restraints excluded: chain c residue 177 VAL Chi-restraints excluded: chain c residue 183 GLU Chi-restraints excluded: chain c residue 207 VAL Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 40 ARG Chi-restraints excluded: chain d residue 41 GLN Chi-restraints excluded: chain d residue 105 LEU Chi-restraints excluded: chain d residue 148 ILE Chi-restraints excluded: chain d residue 150 THR Chi-restraints excluded: chain d residue 159 LEU Chi-restraints excluded: chain d residue 163 ASN Chi-restraints excluded: chain e residue 6 TYR Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 30 VAL Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 56 LEU Chi-restraints excluded: chain e residue 90 LEU Chi-restraints excluded: chain e residue 111 ARG Chi-restraints excluded: chain e residue 120 SER Chi-restraints excluded: chain e residue 144 LYS Chi-restraints excluded: chain e residue 154 THR Chi-restraints excluded: chain e residue 158 THR Chi-restraints excluded: chain e residue 173 ASP Chi-restraints excluded: chain f residue 3 VAL Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 19 ASN Chi-restraints excluded: chain f residue 38 ASP Chi-restraints excluded: chain f residue 42 VAL Chi-restraints excluded: chain f residue 72 ASN Chi-restraints excluded: chain f residue 124 CYS Chi-restraints excluded: chain g residue 130 VAL Chi-restraints excluded: chain h residue 27 VAL Chi-restraints excluded: chain h residue 33 VAL Chi-restraints excluded: chain h residue 88 HIS Chi-restraints excluded: chain h residue 123 ILE Chi-restraints excluded: chain i residue 52 LEU Chi-restraints excluded: chain i residue 57 VAL Chi-restraints excluded: chain i residue 69 VAL Chi-restraints excluded: chain i residue 78 LEU Chi-restraints excluded: chain j residue 25 LEU Chi-restraints excluded: chain j residue 28 LEU Chi-restraints excluded: chain j residue 80 HIS Chi-restraints excluded: chain j residue 81 ILE Chi-restraints excluded: chain k residue 19 VAL Chi-restraints excluded: chain k residue 21 CYS Chi-restraints excluded: chain k residue 35 VAL Chi-restraints excluded: chain k residue 44 LYS Chi-restraints excluded: chain k residue 47 ILE Chi-restraints excluded: chain k residue 56 ASP Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 69 VAL Chi-restraints excluded: chain k residue 106 GLU Chi-restraints excluded: chain l residue 3 LEU Chi-restraints excluded: chain l residue 23 ILE Chi-restraints excluded: chain l residue 40 SER Chi-restraints excluded: chain l residue 68 SER Chi-restraints excluded: chain l residue 73 ILE Chi-restraints excluded: chain l residue 110 VAL Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain l residue 125 LEU Chi-restraints excluded: chain l residue 144 GLU Chi-restraints excluded: chain m residue 42 THR Chi-restraints excluded: chain m residue 54 THR Chi-restraints excluded: chain m residue 74 THR Chi-restraints excluded: chain m residue 117 PHE Chi-restraints excluded: chain m residue 119 LEU Chi-restraints excluded: chain m residue 133 LYS Chi-restraints excluded: chain m residue 136 MET Chi-restraints excluded: chain n residue 9 GLN Chi-restraints excluded: chain n residue 24 MET Chi-restraints excluded: chain n residue 51 LEU Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain n residue 65 LEU Chi-restraints excluded: chain n residue 113 ILE Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain o residue 18 LEU Chi-restraints excluded: chain o residue 24 THR Chi-restraints excluded: chain o residue 31 THR Chi-restraints excluded: chain o residue 35 ILE Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain o residue 103 VAL Chi-restraints excluded: chain p residue 6 GLN Chi-restraints excluded: chain p residue 31 VAL Chi-restraints excluded: chain p residue 40 GLN Chi-restraints excluded: chain p residue 79 VAL Chi-restraints excluded: chain p residue 81 ASP Chi-restraints excluded: chain p residue 101 GLU Chi-restraints excluded: chain q residue 28 SER Chi-restraints excluded: chain q residue 56 PHE Chi-restraints excluded: chain q residue 79 ILE Chi-restraints excluded: chain q residue 97 ILE Chi-restraints excluded: chain r residue 22 LEU Chi-restraints excluded: chain r residue 41 ILE Chi-restraints excluded: chain r residue 64 VAL Chi-restraints excluded: chain s residue 19 LEU Chi-restraints excluded: chain s residue 20 VAL Chi-restraints excluded: chain s residue 39 THR Chi-restraints excluded: chain s residue 40 ASN Chi-restraints excluded: chain s residue 66 ILE Chi-restraints excluded: chain s residue 73 LYS Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain s residue 77 ASP Chi-restraints excluded: chain t residue 33 LYS Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain t residue 60 THR Chi-restraints excluded: chain t residue 86 THR Chi-restraints excluded: chain u residue 5 ARG Chi-restraints excluded: chain u residue 11 ILE Chi-restraints excluded: chain u residue 12 VAL Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain u residue 28 LEU Chi-restraints excluded: chain u residue 35 VAL Chi-restraints excluded: chain u residue 36 GLU Chi-restraints excluded: chain u residue 64 ILE Chi-restraints excluded: chain u residue 102 ILE Chi-restraints excluded: chain v residue 30 ILE Chi-restraints excluded: chain v residue 35 GLU Chi-restraints excluded: chain v residue 45 ASP Chi-restraints excluded: chain v residue 58 SER Chi-restraints excluded: chain v residue 64 VAL Chi-restraints excluded: chain v residue 65 VAL Chi-restraints excluded: chain v residue 70 ILE Chi-restraints excluded: chain v residue 85 LYS Chi-restraints excluded: chain v residue 92 VAL Chi-restraints excluded: chain w residue 62 LYS Chi-restraints excluded: chain w residue 66 GLU Chi-restraints excluded: chain w residue 79 GLU Chi-restraints excluded: chain x residue 6 VAL Chi-restraints excluded: chain x residue 51 SER Chi-restraints excluded: chain x residue 58 ILE Chi-restraints excluded: chain y residue 49 ASP Chi-restraints excluded: chain z residue 6 ILE Chi-restraints excluded: chain z residue 9 THR Chi-restraints excluded: chain z residue 40 THR Chi-restraints excluded: chain z residue 56 VAL Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain C residue 7 LYS Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 3 ARG Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 22 MET Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain G residue 108 GLN Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 193 ASP Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 148 ILE Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 56 GLU Chi-restraints excluded: chain I residue 71 PHE Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 199 ILE Chi-restraints excluded: chain I residue 201 GLU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 91 SER Chi-restraints excluded: chain J residue 121 ASN Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain J residue 140 ILE Chi-restraints excluded: chain J residue 147 ASN Chi-restraints excluded: chain J residue 156 ARG Chi-restraints excluded: chain K residue 23 GLU Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 52 ASN Chi-restraints excluded: chain K residue 55 HIS Chi-restraints excluded: chain K residue 59 TYR Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 115 MET Chi-restraints excluded: chain M residue 9 MET Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 62 LEU Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 105 THR Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain N residue 28 VAL Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain N residue 108 ARG Chi-restraints excluded: chain O residue 91 ASP Chi-restraints excluded: chain P residue 79 LYS Chi-restraints excluded: chain P residue 80 ASN Chi-restraints excluded: chain P residue 83 VAL Chi-restraints excluded: chain P residue 109 ILE Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain S residue 26 LEU Chi-restraints excluded: chain T residue 13 GLU Chi-restraints excluded: chain T residue 31 LEU Chi-restraints excluded: chain T residue 65 LEU Chi-restraints excluded: chain U residue 2 VAL Chi-restraints excluded: chain U residue 3 THR Chi-restraints excluded: chain U residue 20 VAL Chi-restraints excluded: chain U residue 33 ILE Chi-restraints excluded: chain U residue 36 VAL Chi-restraints excluded: chain V residue 16 MET Chi-restraints excluded: chain V residue 26 ARG Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain V residue 50 ASN Chi-restraints excluded: chain V residue 57 VAL Chi-restraints excluded: chain W residue 25 ILE Chi-restraints excluded: chain W residue 28 LEU Chi-restraints excluded: chain W residue 58 ILE Chi-restraints excluded: chain W residue 70 THR Chi-restraints excluded: chain Y residue 13 SER Chi-restraints excluded: chain a residue 56 ASP Chi-restraints excluded: chain a residue 196 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1043 random chunks: chunk 914 optimal weight: 7.9990 chunk 963 optimal weight: 30.0000 chunk 878 optimal weight: 10.0000 chunk 936 optimal weight: 7.9990 chunk 962 optimal weight: 10.0000 chunk 563 optimal weight: 8.9990 chunk 408 optimal weight: 50.0000 chunk 735 optimal weight: 8.9990 chunk 287 optimal weight: 6.9990 chunk 846 optimal weight: 8.9990 chunk 886 optimal weight: 30.0000 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 142 ASN ** c 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 167 ASN ** d 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 88 HIS ** k 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 38 GLN p 6 GLN ** p 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 55 GLN r 87 GLN ** s 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 22 ASN y 20 ASN ** G 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 108 GLN ** H 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 84 ASN ** I 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 72 ASN ** J 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 55 HIS ** a 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.4755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.087 159558 Z= 0.447 Angle : 0.760 13.372 238506 Z= 0.383 Chirality : 0.042 0.316 30471 Planarity : 0.006 0.070 12929 Dihedral : 23.486 179.178 79350 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 22.11 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.12 % Favored : 88.76 % Rotamer: Outliers : 6.21 % Allowed : 25.43 % Favored : 68.36 % 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: -2.35 (0.10), residues: 5919 helix: -0.53 (0.12), residues: 1841 sheet: -1.54 (0.16), residues: 993 loop : -2.25 (0.11), residues: 3085 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP b 212 HIS 0.028 0.002 HIS h 88 PHE 0.034 0.002 PHE D 18 TYR 0.036 0.002 TYR G 212 ARG 0.017 0.001 ARG v 93 *********************** 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 1635 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 305 poor density : 1330 time to evaluate : 6.305 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: b 124 LYS cc_start: 0.8880 (OUTLIER) cc_final: 0.8269 (ptpp) REVERT: b 193 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.8213 (mt-10) REVERT: b 212 TRP cc_start: 0.7876 (p90) cc_final: 0.7668 (p-90) REVERT: d 40 ARG cc_start: 0.8326 (OUTLIER) cc_final: 0.7396 (mtp85) REVERT: d 163 ASN cc_start: 0.6376 (OUTLIER) cc_final: 0.5855 (m110) REVERT: e 70 ARG cc_start: 0.8735 (ttp80) cc_final: 0.8446 (ttp80) REVERT: e 90 LEU cc_start: 0.8651 (tp) cc_final: 0.8376 (tp) REVERT: e 111 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.7757 (ptt-90) REVERT: e 126 ASN cc_start: 0.8497 (m-40) cc_final: 0.8192 (m-40) REVERT: e 137 PHE cc_start: 0.8611 (m-80) cc_final: 0.8274 (m-80) REVERT: f 2 ARG cc_start: 0.8138 (tpp80) cc_final: 0.7289 (tpp-160) REVERT: f 151 ARG cc_start: 0.8404 (tpp-160) cc_final: 0.7962 (mtp-110) REVERT: g 1 MET cc_start: 0.7115 (tpt) cc_final: 0.6811 (tpt) REVERT: g 33 GLN cc_start: 0.8299 (mt0) cc_final: 0.7979 (mt0) REVERT: h 1 MET cc_start: 0.3749 (ppp) cc_final: 0.3222 (pmm) REVERT: h 33 VAL cc_start: 0.7773 (OUTLIER) cc_final: 0.7533 (p) REVERT: h 38 MET cc_start: 0.2285 (mmt) cc_final: 0.1577 (mmt) REVERT: i 52 LEU cc_start: 0.5194 (OUTLIER) cc_final: 0.4589 (mt) REVERT: i 116 MET cc_start: -0.1692 (mtt) cc_final: -0.2057 (ptp) REVERT: j 74 TYR cc_start: 0.8490 (m-80) cc_final: 0.8232 (m-80) REVERT: j 98 GLU cc_start: 0.7962 (pm20) cc_final: 0.7493 (pm20) REVERT: k 73 ASP cc_start: 0.8100 (p0) cc_final: 0.7884 (p0) REVERT: l 59 ARG cc_start: 0.8835 (mtp180) cc_final: 0.8508 (mtp180) REVERT: m 24 THR cc_start: 0.9227 (p) cc_final: 0.8781 (t) REVERT: m 31 PHE cc_start: 0.8091 (m-80) cc_final: 0.7693 (m-10) REVERT: m 82 MET cc_start: 0.7714 (mmm) cc_final: 0.7073 (mmt) REVERT: m 117 PHE cc_start: 0.8869 (OUTLIER) cc_final: 0.8510 (m-10) REVERT: m 133 LYS cc_start: 0.8468 (OUTLIER) cc_final: 0.7988 (mttm) REVERT: n 32 GLU cc_start: 0.8824 (mp0) cc_final: 0.8117 (mp0) REVERT: n 73 ASN cc_start: 0.9018 (m-40) cc_final: 0.8577 (t0) REVERT: o 9 ARG cc_start: 0.7964 (tmm160) cc_final: 0.7725 (tmm160) REVERT: o 104 GLN cc_start: 0.8676 (tt0) cc_final: 0.8468 (tp40) REVERT: p 15 ASP cc_start: 0.7275 (OUTLIER) cc_final: 0.6863 (p0) REVERT: p 23 ASP cc_start: 0.7936 (m-30) cc_final: 0.7639 (m-30) REVERT: p 70 GLU cc_start: 0.7217 (tp30) cc_final: 0.6805 (tp30) REVERT: p 79 VAL cc_start: 0.9368 (OUTLIER) cc_final: 0.9156 (t) REVERT: q 56 PHE cc_start: 0.9303 (OUTLIER) cc_final: 0.8943 (m-10) REVERT: q 65 ASN cc_start: 0.8836 (t0) cc_final: 0.8431 (t0) REVERT: r 21 ARG cc_start: 0.8681 (ttm170) cc_final: 0.8058 (mtt-85) REVERT: r 31 GLU cc_start: 0.8993 (tp30) cc_final: 0.8669 (tp30) REVERT: r 98 ILE cc_start: 0.8707 (mm) cc_final: 0.8477 (tp) REVERT: s 6 LYS cc_start: 0.9489 (ptpt) cc_final: 0.9141 (ptpp) REVERT: s 19 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8678 (mp) REVERT: s 62 ASP cc_start: 0.8175 (p0) cc_final: 0.7964 (p0) REVERT: t 3 ARG cc_start: 0.6255 (mtp85) cc_final: 0.5589 (ttm110) REVERT: u 6 ARG cc_start: 0.7660 (tpp80) cc_final: 0.7291 (tpp80) REVERT: u 39 ASN cc_start: 0.8005 (t0) cc_final: 0.7680 (t0) REVERT: u 93 ARG cc_start: 0.7870 (mtm180) cc_final: 0.7363 (ptt-90) REVERT: u 100 GLU cc_start: 0.8010 (mp0) cc_final: 0.7671 (mp0) REVERT: v 80 HIS cc_start: 0.8940 (t-90) cc_final: 0.8428 (t-90) REVERT: w 66 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7231 (mm-30) REVERT: w 77 SER cc_start: 0.9021 (m) cc_final: 0.8450 (p) REVERT: w 79 GLU cc_start: 0.6589 (OUTLIER) cc_final: 0.6189 (pm20) REVERT: y 39 GLN cc_start: 0.8493 (mt0) cc_final: 0.7913 (pt0) REVERT: y 40 SER cc_start: 0.9383 (m) cc_final: 0.8836 (t) REVERT: y 49 ASP cc_start: 0.8347 (OUTLIER) cc_final: 0.8063 (m-30) REVERT: z 38 GLU cc_start: 0.7769 (mm-30) cc_final: 0.7153 (mm-30) REVERT: z 48 ASN cc_start: 0.8925 (t0) cc_final: 0.8671 (t0) REVERT: z 55 LYS cc_start: 0.8525 (tptp) cc_final: 0.8112 (tptp) REVERT: C 37 LYS cc_start: 0.8473 (mttm) cc_final: 0.8151 (mttt) REVERT: D 26 ASN cc_start: 0.8527 (m-40) cc_final: 0.8260 (m-40) REVERT: G 26 MET cc_start: 0.6996 (ttm) cc_final: 0.6733 (ttt) REVERT: G 51 GLU cc_start: 0.9506 (tp30) cc_final: 0.9195 (tp30) REVERT: G 89 PHE cc_start: 0.6949 (m-80) cc_final: 0.6537 (m-80) REVERT: G 111 LYS cc_start: 0.9458 (tppt) cc_final: 0.9099 (tptp) REVERT: G 151 LYS cc_start: 0.8454 (pttt) cc_final: 0.7945 (ptmt) REVERT: G 153 MET cc_start: 0.4186 (tpt) cc_final: 0.3801 (tpt) REVERT: G 161 PHE cc_start: 0.8334 (t80) cc_final: 0.7770 (t80) REVERT: G 168 GLU cc_start: 0.8467 (mp0) cc_final: 0.8112 (mp0) REVERT: G 197 PHE cc_start: 0.7948 (m-80) cc_final: 0.7446 (t80) REVERT: H 10 ARG cc_start: 0.7319 (mtt180) cc_final: 0.7113 (mtt180) REVERT: H 163 ARG cc_start: 0.6457 (ptt180) cc_final: 0.5093 (ttt180) REVERT: I 62 ARG cc_start: 0.8140 (mtt-85) cc_final: 0.7938 (mtt-85) REVERT: I 97 LEU cc_start: 0.8344 (mt) cc_final: 0.8098 (mt) REVERT: I 104 MET cc_start: 0.0757 (mmt) cc_final: -0.0132 (mtt) REVERT: J 70 MET cc_start: 0.8815 (pmm) cc_final: 0.7819 (tpp) REVERT: K 1 MET cc_start: 0.7660 (tpp) cc_final: 0.7276 (tpp) REVERT: K 17 GLN cc_start: 0.8938 (tm-30) cc_final: 0.8418 (pp30) REVERT: K 38 ARG cc_start: 0.7387 (mmm-85) cc_final: 0.7052 (mmm160) REVERT: K 56 LYS cc_start: 0.7238 (mtmm) cc_final: 0.6992 (mptt) REVERT: K 59 TYR cc_start: 0.8491 (OUTLIER) cc_final: 0.7461 (t80) REVERT: K 62 MET cc_start: 0.7103 (ttt) cc_final: 0.6787 (ttt) REVERT: K 92 THR cc_start: 0.7304 (OUTLIER) cc_final: 0.7057 (p) REVERT: L 49 LEU cc_start: 0.7044 (mm) cc_final: 0.6766 (mm) REVERT: L 100 MET cc_start: 0.5330 (mtm) cc_final: 0.4688 (mmt) REVERT: M 2 MET cc_start: 0.6277 (tpt) cc_final: 0.4821 (ptt) REVERT: M 66 GLN cc_start: 0.8816 (mm110) cc_final: 0.8616 (mp10) REVERT: M 110 MET cc_start: 0.8821 (ptp) cc_final: 0.8314 (ptp) REVERT: N 87 MET cc_start: 0.8051 (mmp) cc_final: 0.6735 (pmm) REVERT: P 55 ARG cc_start: 0.8418 (mpt180) cc_final: 0.8054 (mpp-170) REVERT: P 75 GLU cc_start: 0.8519 (mm-30) cc_final: 0.8147 (mp0) REVERT: P 84 MET cc_start: 0.7238 (ttt) cc_final: 0.6509 (ppp) REVERT: P 111 ASP cc_start: 0.8924 (m-30) cc_final: 0.8572 (m-30) REVERT: Q 37 TYR cc_start: 0.8421 (p90) cc_final: 0.8095 (p90) REVERT: R 80 MET cc_start: 0.8215 (ttp) cc_final: 0.7957 (tmm) REVERT: T 44 GLU cc_start: 0.8919 (pt0) cc_final: 0.8560 (pm20) REVERT: T 52 ARG cc_start: 0.8820 (tmm-80) cc_final: 0.8408 (ttp-170) REVERT: T 63 ARG cc_start: 0.8097 (tpp80) cc_final: 0.7767 (tpp-160) REVERT: T 67 ASP cc_start: 0.8638 (m-30) cc_final: 0.8319 (m-30) REVERT: T 70 LYS cc_start: 0.9266 (mmtp) cc_final: 0.9030 (mmmt) REVERT: U 3 THR cc_start: 0.7501 (OUTLIER) cc_final: 0.7298 (p) REVERT: U 32 PHE cc_start: 0.7646 (p90) cc_final: 0.6963 (p90) REVERT: U 36 VAL cc_start: 0.7076 (OUTLIER) cc_final: 0.6860 (t) REVERT: U 59 HIS cc_start: 0.8010 (t-90) cc_final: 0.7470 (t-90) REVERT: U 70 ARG cc_start: 0.5735 (tpt90) cc_final: 0.5053 (mmm160) REVERT: V 16 MET cc_start: 0.7036 (OUTLIER) cc_final: 0.6826 (mmm) REVERT: W 31 TYR cc_start: 0.7455 (m-80) cc_final: 0.6884 (m-10) REVERT: W 60 ARG cc_start: 0.8386 (mtt180) cc_final: 0.7935 (mtt-85) REVERT: W 63 TYR cc_start: 0.8494 (t80) cc_final: 0.7476 (t80) REVERT: Y 14 GLU cc_start: 0.9518 (mp0) cc_final: 0.8989 (mp0) REVERT: a 56 ASP cc_start: 0.8059 (OUTLIER) cc_final: 0.7719 (p0) outliers start: 305 outliers final: 245 residues processed: 1475 average time/residue: 1.3027 time to fit residues: 3293.4071 Evaluate side-chains 1541 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 267 poor density : 1274 time to evaluate : 6.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 5 CYS Chi-restraints excluded: chain b residue 8 THR Chi-restraints excluded: chain b residue 15 VAL Chi-restraints excluded: chain b residue 23 LEU Chi-restraints excluded: chain b residue 48 ILE Chi-restraints excluded: chain b residue 50 THR Chi-restraints excluded: chain b residue 52 HIS Chi-restraints excluded: chain b residue 86 ARG Chi-restraints excluded: chain b residue 87 SER Chi-restraints excluded: chain b residue 104 LEU Chi-restraints excluded: chain b residue 117 SER Chi-restraints excluded: chain b residue 119 VAL Chi-restraints excluded: chain b residue 124 LYS Chi-restraints excluded: chain b residue 156 SER Chi-restraints excluded: chain b residue 159 THR Chi-restraints excluded: chain b residue 164 VAL Chi-restraints excluded: chain b residue 179 GLU Chi-restraints excluded: chain b residue 193 GLU Chi-restraints excluded: chain b residue 200 MET Chi-restraints excluded: chain b residue 222 THR Chi-restraints excluded: chain b residue 271 SER Chi-restraints excluded: chain c residue 2 ILE Chi-restraints excluded: chain c residue 12 THR Chi-restraints excluded: chain c residue 35 THR Chi-restraints excluded: chain c residue 42 ASN Chi-restraints excluded: chain c residue 73 VAL Chi-restraints excluded: chain c residue 97 SER Chi-restraints excluded: chain c residue 126 ASN Chi-restraints excluded: chain c residue 142 VAL Chi-restraints excluded: chain c residue 170 VAL Chi-restraints excluded: chain c residue 177 VAL Chi-restraints excluded: chain c residue 183 GLU Chi-restraints excluded: chain c residue 193 VAL Chi-restraints excluded: chain c residue 207 VAL Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 40 ARG Chi-restraints excluded: chain d residue 41 GLN Chi-restraints excluded: chain d residue 73 ILE Chi-restraints excluded: chain d residue 105 LEU Chi-restraints excluded: chain d residue 150 THR Chi-restraints excluded: chain d residue 159 LEU Chi-restraints excluded: chain d residue 163 ASN Chi-restraints excluded: chain d residue 164 LEU Chi-restraints excluded: chain d residue 200 LEU Chi-restraints excluded: chain e residue 6 TYR Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 30 VAL Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 48 LEU Chi-restraints excluded: chain e residue 56 LEU Chi-restraints excluded: chain e residue 111 ARG Chi-restraints excluded: chain e residue 120 SER Chi-restraints excluded: chain e residue 144 LYS Chi-restraints excluded: chain e residue 154 THR Chi-restraints excluded: chain e residue 158 THR Chi-restraints excluded: chain e residue 173 ASP Chi-restraints excluded: chain f residue 3 VAL Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 19 ASN Chi-restraints excluded: chain f residue 38 ASP Chi-restraints excluded: chain f residue 42 VAL Chi-restraints excluded: chain f residue 72 ASN Chi-restraints excluded: chain f residue 124 CYS Chi-restraints excluded: chain f residue 147 LEU Chi-restraints excluded: chain f residue 154 GLU Chi-restraints excluded: chain g residue 108 VAL Chi-restraints excluded: chain g residue 122 LEU Chi-restraints excluded: chain g residue 130 VAL Chi-restraints excluded: chain h residue 27 VAL Chi-restraints excluded: chain h residue 33 VAL Chi-restraints excluded: chain h residue 58 THR Chi-restraints excluded: chain h residue 123 ILE Chi-restraints excluded: chain i residue 52 LEU Chi-restraints excluded: chain i residue 57 VAL Chi-restraints excluded: chain i residue 69 VAL Chi-restraints excluded: chain i residue 78 LEU Chi-restraints excluded: chain j residue 25 LEU Chi-restraints excluded: chain j residue 28 LEU Chi-restraints excluded: chain j residue 73 VAL Chi-restraints excluded: chain j residue 80 HIS Chi-restraints excluded: chain j residue 81 ILE Chi-restraints excluded: chain k residue 19 VAL Chi-restraints excluded: chain k residue 21 CYS Chi-restraints excluded: chain k residue 35 VAL Chi-restraints excluded: chain k residue 44 LYS Chi-restraints excluded: chain k residue 56 ASP Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 69 VAL Chi-restraints excluded: chain k residue 106 GLU Chi-restraints excluded: chain k residue 110 GLU Chi-restraints excluded: chain k residue 114 LYS Chi-restraints excluded: chain l residue 3 LEU Chi-restraints excluded: chain l residue 23 ILE Chi-restraints excluded: chain l residue 40 SER Chi-restraints excluded: chain l residue 68 SER Chi-restraints excluded: chain l residue 73 ILE Chi-restraints excluded: chain l residue 85 VAL Chi-restraints excluded: chain l residue 110 VAL Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain l residue 125 LEU Chi-restraints excluded: chain l residue 144 GLU Chi-restraints excluded: chain m residue 7 THR Chi-restraints excluded: chain m residue 42 THR Chi-restraints excluded: chain m residue 54 THR Chi-restraints excluded: chain m residue 74 THR Chi-restraints excluded: chain m residue 117 PHE Chi-restraints excluded: chain m residue 119 LEU Chi-restraints excluded: chain m residue 133 LYS Chi-restraints excluded: chain m residue 136 MET Chi-restraints excluded: chain n residue 24 MET Chi-restraints excluded: chain n residue 51 LEU Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain n residue 65 LEU Chi-restraints excluded: chain n residue 75 ILE Chi-restraints excluded: chain n residue 113 ILE Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain o residue 18 LEU Chi-restraints excluded: chain o residue 24 THR Chi-restraints excluded: chain o residue 35 ILE Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain o residue 53 THR Chi-restraints excluded: chain o residue 103 VAL Chi-restraints excluded: chain p residue 6 GLN Chi-restraints excluded: chain p residue 15 ASP Chi-restraints excluded: chain p residue 31 VAL Chi-restraints excluded: chain p residue 40 GLN Chi-restraints excluded: chain p residue 79 VAL Chi-restraints excluded: chain p residue 81 ASP Chi-restraints excluded: chain p residue 101 GLU Chi-restraints excluded: chain q residue 28 SER Chi-restraints excluded: chain q residue 30 VAL Chi-restraints excluded: chain q residue 56 PHE Chi-restraints excluded: chain q residue 79 ILE Chi-restraints excluded: chain q residue 97 ILE Chi-restraints excluded: chain r residue 22 LEU Chi-restraints excluded: chain r residue 41 ILE Chi-restraints excluded: chain r residue 64 VAL Chi-restraints excluded: chain s residue 19 LEU Chi-restraints excluded: chain s residue 20 VAL Chi-restraints excluded: chain s residue 39 THR Chi-restraints excluded: chain s residue 40 ASN Chi-restraints excluded: chain s residue 66 ILE Chi-restraints excluded: chain s residue 73 LYS Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain s residue 77 ASP Chi-restraints excluded: chain s residue 100 THR Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain t residue 33 LYS Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain t residue 60 THR Chi-restraints excluded: chain t residue 86 THR Chi-restraints excluded: chain u residue 5 ARG Chi-restraints excluded: chain u residue 11 ILE Chi-restraints excluded: chain u residue 12 VAL Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain u residue 28 LEU Chi-restraints excluded: chain u residue 35 VAL Chi-restraints excluded: chain u residue 36 GLU Chi-restraints excluded: chain u residue 64 ILE Chi-restraints excluded: chain u residue 73 ASN Chi-restraints excluded: chain u residue 102 ILE Chi-restraints excluded: chain v residue 30 ILE Chi-restraints excluded: chain v residue 35 GLU Chi-restraints excluded: chain v residue 45 ASP Chi-restraints excluded: chain v residue 58 SER Chi-restraints excluded: chain v residue 64 VAL Chi-restraints excluded: chain v residue 65 VAL Chi-restraints excluded: chain v residue 70 ILE Chi-restraints excluded: chain v residue 85 LYS Chi-restraints excluded: chain v residue 89 ILE Chi-restraints excluded: chain v residue 92 VAL Chi-restraints excluded: chain w residue 20 LYS Chi-restraints excluded: chain w residue 52 ASP Chi-restraints excluded: chain w residue 62 LYS Chi-restraints excluded: chain w residue 66 GLU Chi-restraints excluded: chain w residue 79 GLU Chi-restraints excluded: chain x residue 6 VAL Chi-restraints excluded: chain x residue 51 SER Chi-restraints excluded: chain x residue 58 ILE Chi-restraints excluded: chain y residue 49 ASP Chi-restraints excluded: chain z residue 6 ILE Chi-restraints excluded: chain z residue 9 THR Chi-restraints excluded: chain z residue 40 THR Chi-restraints excluded: chain z residue 56 VAL Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain C residue 7 LYS Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 22 MET Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 60 CYS Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain G residue 108 GLN Chi-restraints excluded: chain G residue 147 LEU Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 193 ASP Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 148 ILE Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 56 GLU Chi-restraints excluded: chain I residue 71 PHE Chi-restraints excluded: chain I residue 84 ASN Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 199 ILE Chi-restraints excluded: chain I residue 201 GLU Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 91 SER Chi-restraints excluded: chain J residue 121 ASN Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain J residue 140 ILE Chi-restraints excluded: chain J residue 156 ARG Chi-restraints excluded: chain K residue 23 GLU Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 52 ASN Chi-restraints excluded: chain K residue 55 HIS Chi-restraints excluded: chain K residue 59 TYR Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 115 MET Chi-restraints excluded: chain L residue 117 LEU Chi-restraints excluded: chain M residue 9 MET Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 62 LEU Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 105 THR Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain N residue 28 VAL Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain N residue 108 ARG Chi-restraints excluded: chain O residue 91 ASP Chi-restraints excluded: chain P residue 79 LYS Chi-restraints excluded: chain P residue 96 ILE Chi-restraints excluded: chain P residue 109 ILE Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain R residue 6 ILE Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain S residue 26 LEU Chi-restraints excluded: chain T residue 13 GLU Chi-restraints excluded: chain T residue 31 LEU Chi-restraints excluded: chain T residue 37 HIS Chi-restraints excluded: chain U residue 2 VAL Chi-restraints excluded: chain U residue 3 THR Chi-restraints excluded: chain U residue 20 VAL Chi-restraints excluded: chain U residue 33 ILE Chi-restraints excluded: chain U residue 36 VAL Chi-restraints excluded: chain V residue 16 MET Chi-restraints excluded: chain V residue 26 ARG Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain V residue 50 ASN Chi-restraints excluded: chain V residue 57 VAL Chi-restraints excluded: chain W residue 25 ILE Chi-restraints excluded: chain W residue 28 LEU Chi-restraints excluded: chain W residue 58 ILE Chi-restraints excluded: chain W residue 70 THR Chi-restraints excluded: chain X residue 12 LEU Chi-restraints excluded: chain Y residue 13 SER Chi-restraints excluded: chain Z residue 15 LEU Chi-restraints excluded: chain a residue 56 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1043 random chunks: chunk 933 optimal weight: 2.9990 chunk 615 optimal weight: 20.0000 chunk 990 optimal weight: 3.9990 chunk 604 optimal weight: 20.0000 chunk 469 optimal weight: 30.0000 chunk 688 optimal weight: 30.0000 chunk 1039 optimal weight: 40.0000 chunk 956 optimal weight: 4.9990 chunk 827 optimal weight: 3.9990 chunk 85 optimal weight: 0.0050 chunk 639 optimal weight: 30.0000 overall best weight: 3.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 32 ASN c 167 ASN ** d 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 94 GLN f 110 HIS ** g 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 103 ASN ** k 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 38 GLN ** p 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 19 GLN q 55 GLN r 87 GLN s 31 GLN s 61 ASN ** H 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 55 HIS ** a 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.4758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 159558 Z= 0.211 Angle : 0.610 13.168 238506 Z= 0.310 Chirality : 0.035 0.313 30471 Planarity : 0.005 0.070 12929 Dihedral : 23.375 179.037 79350 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 17.04 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.26 % Favored : 90.64 % Rotamer: Outliers : 4.71 % Allowed : 27.22 % Favored : 68.07 % 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: -2.14 (0.11), residues: 5919 helix: -0.28 (0.12), residues: 1832 sheet: -1.49 (0.16), residues: 1001 loop : -2.14 (0.11), residues: 3086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP b 212 HIS 0.009 0.001 HIS V 30 PHE 0.032 0.002 PHE D 18 TYR 0.038 0.002 TYR G 212 ARG 0.018 0.001 ARG Q 113 ********************** 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 1563 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 231 poor density : 1332 time to evaluate : 6.278 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: b 124 LYS cc_start: 0.8931 (OUTLIER) cc_final: 0.8340 (ptpp) REVERT: b 132 ARG cc_start: 0.8245 (tmm-80) cc_final: 0.8021 (ttp80) REVERT: b 193 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.8167 (mt-10) REVERT: b 212 TRP cc_start: 0.7869 (p90) cc_final: 0.7393 (p-90) REVERT: b 270 ARG cc_start: 0.8017 (ttp80) cc_final: 0.7772 (ttp80) REVERT: d 28 VAL cc_start: 0.9306 (t) cc_final: 0.9075 (p) REVERT: d 40 ARG cc_start: 0.7997 (OUTLIER) cc_final: 0.7201 (mtp85) REVERT: d 141 MET cc_start: 0.8701 (mmm) cc_final: 0.8467 (tpp) REVERT: d 163 ASN cc_start: 0.6281 (OUTLIER) cc_final: 0.5685 (m110) REVERT: e 25 MET cc_start: 0.9174 (mmm) cc_final: 0.8946 (tpp) REVERT: e 70 ARG cc_start: 0.8772 (ttp80) cc_final: 0.8469 (ttp80) REVERT: e 90 LEU cc_start: 0.8681 (tp) cc_final: 0.8363 (tp) REVERT: e 111 ARG cc_start: 0.8411 (OUTLIER) cc_final: 0.7700 (ptt-90) REVERT: e 126 ASN cc_start: 0.8478 (m-40) cc_final: 0.8228 (m-40) REVERT: e 129 MET cc_start: 0.6786 (pmm) cc_final: 0.6463 (pmm) REVERT: e 137 PHE cc_start: 0.8803 (m-80) cc_final: 0.8536 (m-80) REVERT: e 144 LYS cc_start: 0.8306 (OUTLIER) cc_final: 0.8006 (mmtm) REVERT: f 2 ARG cc_start: 0.8090 (tpp80) cc_final: 0.7148 (tpp-160) REVERT: f 68 ARG cc_start: 0.8861 (ttp80) cc_final: 0.8428 (ttp80) REVERT: f 87 GLN cc_start: 0.7341 (mp10) cc_final: 0.6752 (mp10) REVERT: f 151 ARG cc_start: 0.8453 (tpp-160) cc_final: 0.8078 (mtp-110) REVERT: f 154 GLU cc_start: 0.8760 (OUTLIER) cc_final: 0.8087 (pm20) REVERT: h 1 MET cc_start: 0.3610 (ppp) cc_final: 0.3152 (pmm) REVERT: h 33 VAL cc_start: 0.7744 (OUTLIER) cc_final: 0.7507 (p) REVERT: h 38 MET cc_start: 0.2073 (mmt) cc_final: 0.0862 (mmt) REVERT: i 52 LEU cc_start: 0.5175 (OUTLIER) cc_final: 0.4573 (mt) REVERT: i 56 VAL cc_start: 0.7212 (p) cc_final: 0.6946 (t) REVERT: i 116 MET cc_start: -0.0785 (mtt) cc_final: -0.1294 (ptp) REVERT: j 25 LEU cc_start: 0.9337 (OUTLIER) cc_final: 0.9098 (tp) REVERT: j 74 TYR cc_start: 0.8259 (m-80) cc_final: 0.7970 (m-80) REVERT: j 98 GLU cc_start: 0.7774 (pm20) cc_final: 0.7452 (pm20) REVERT: k 73 ASP cc_start: 0.8069 (p0) cc_final: 0.7809 (p0) REVERT: m 11 LYS cc_start: 0.8838 (mttt) cc_final: 0.8595 (mttp) REVERT: m 24 THR cc_start: 0.9148 (p) cc_final: 0.8662 (t) REVERT: m 31 PHE cc_start: 0.8099 (m-80) cc_final: 0.7712 (m-10) REVERT: m 64 TRP cc_start: 0.8272 (m-90) cc_final: 0.7860 (m-10) REVERT: m 82 MET cc_start: 0.7458 (mmm) cc_final: 0.5936 (mmt) REVERT: m 117 PHE cc_start: 0.8813 (OUTLIER) cc_final: 0.8519 (m-10) REVERT: m 133 LYS cc_start: 0.8518 (OUTLIER) cc_final: 0.8059 (mttm) REVERT: n 32 GLU cc_start: 0.8867 (mp0) cc_final: 0.8266 (mp0) REVERT: n 73 ASN cc_start: 0.8817 (m-40) cc_final: 0.8463 (t0) REVERT: o 9 ARG cc_start: 0.8039 (tmm160) cc_final: 0.7758 (tmm160) REVERT: o 104 GLN cc_start: 0.8535 (tt0) cc_final: 0.8300 (tp40) REVERT: p 8 GLU cc_start: 0.8737 (mm-30) cc_final: 0.8456 (mm-30) REVERT: p 9 GLN cc_start: 0.7746 (tm-30) cc_final: 0.7422 (tm-30) REVERT: p 23 ASP cc_start: 0.7674 (m-30) cc_final: 0.7444 (m-30) REVERT: p 70 GLU cc_start: 0.7189 (tp30) cc_final: 0.6568 (tp30) REVERT: q 65 ASN cc_start: 0.8806 (t0) cc_final: 0.8316 (t0) REVERT: r 21 ARG cc_start: 0.8647 (ttm170) cc_final: 0.8149 (mtt-85) REVERT: r 31 GLU cc_start: 0.8875 (tp30) cc_final: 0.8540 (tp30) REVERT: s 6 LYS cc_start: 0.9509 (ptpt) cc_final: 0.9177 (ptpp) REVERT: s 19 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8640 (mp) REVERT: s 31 GLN cc_start: 0.8611 (OUTLIER) cc_final: 0.8310 (pp30) REVERT: t 3 ARG cc_start: 0.5978 (mtp85) cc_final: 0.5696 (ttm110) REVERT: t 56 GLU cc_start: 0.8083 (tp30) cc_final: 0.7851 (tp30) REVERT: u 6 ARG cc_start: 0.7487 (tpp80) cc_final: 0.7070 (tpp80) REVERT: u 11 ILE cc_start: 0.9201 (OUTLIER) cc_final: 0.9001 (pt) REVERT: u 39 ASN cc_start: 0.8055 (t0) cc_final: 0.7706 (t0) REVERT: v 80 HIS cc_start: 0.8952 (t-90) cc_final: 0.8227 (t-90) REVERT: v 93 ARG cc_start: 0.8880 (ttm110) cc_final: 0.7908 (ttm110) REVERT: w 51 ARG cc_start: 0.8478 (ttt-90) cc_final: 0.7877 (ptm160) REVERT: w 66 GLU cc_start: 0.7689 (mm-30) cc_final: 0.7193 (mm-30) REVERT: w 77 SER cc_start: 0.8943 (m) cc_final: 0.8412 (p) REVERT: w 79 GLU cc_start: 0.6424 (OUTLIER) cc_final: 0.5907 (pm20) REVERT: x 10 ARG cc_start: 0.7672 (mtp-110) cc_final: 0.7442 (mtp180) REVERT: x 43 LYS cc_start: 0.8934 (mmtt) cc_final: 0.8555 (mmtp) REVERT: y 39 GLN cc_start: 0.8449 (mt0) cc_final: 0.8113 (pt0) REVERT: y 49 ASP cc_start: 0.8321 (OUTLIER) cc_final: 0.8032 (m-30) REVERT: z 38 GLU cc_start: 0.7797 (mm-30) cc_final: 0.7218 (mm-30) REVERT: z 47 ILE cc_start: 0.9334 (mm) cc_final: 0.9101 (mt) REVERT: z 55 LYS cc_start: 0.8491 (tptp) cc_final: 0.8250 (tptp) REVERT: C 7 LYS cc_start: 0.7623 (OUTLIER) cc_final: 0.7285 (mtmm) REVERT: C 37 LYS cc_start: 0.8414 (mttm) cc_final: 0.8091 (mttt) REVERT: G 26 MET cc_start: 0.7074 (ttm) cc_final: 0.6780 (mmt) REVERT: G 48 MET cc_start: 0.8632 (ppp) cc_final: 0.8355 (ppp) REVERT: G 51 GLU cc_start: 0.9488 (tp30) cc_final: 0.9210 (tp30) REVERT: G 89 PHE cc_start: 0.6934 (m-80) cc_final: 0.6499 (m-80) REVERT: G 111 LYS cc_start: 0.9427 (tppt) cc_final: 0.9011 (tptp) REVERT: G 151 LYS cc_start: 0.8454 (pttt) cc_final: 0.7979 (ptmt) REVERT: G 153 MET cc_start: 0.4161 (tpt) cc_final: 0.3761 (tpt) REVERT: G 161 PHE cc_start: 0.8234 (t80) cc_final: 0.7604 (t80) REVERT: G 168 GLU cc_start: 0.8397 (mp0) cc_final: 0.8032 (mp0) REVERT: G 173 LYS cc_start: 0.9341 (mmmm) cc_final: 0.9061 (mtmm) REVERT: G 197 PHE cc_start: 0.7834 (m-80) cc_final: 0.7366 (t80) REVERT: H 10 ARG cc_start: 0.7579 (mtt180) cc_final: 0.7108 (mtt180) REVERT: H 163 ARG cc_start: 0.6394 (ptt180) cc_final: 0.5062 (mtp180) REVERT: I 104 MET cc_start: -0.0389 (mmt) cc_final: -0.1207 (mtt) REVERT: J 68 ARG cc_start: 0.8645 (ttp-110) cc_final: 0.8137 (ttm110) REVERT: J 70 MET cc_start: 0.8741 (pmm) cc_final: 0.7770 (tpp) REVERT: J 156 ARG cc_start: 0.7695 (OUTLIER) cc_final: 0.7172 (ptt-90) REVERT: K 1 MET cc_start: 0.7558 (tpp) cc_final: 0.7210 (tpp) REVERT: K 59 TYR cc_start: 0.8357 (OUTLIER) cc_final: 0.7233 (t80) REVERT: K 62 MET cc_start: 0.6985 (OUTLIER) cc_final: 0.6645 (ttt) REVERT: K 92 THR cc_start: 0.7192 (OUTLIER) cc_final: 0.6932 (p) REVERT: L 49 LEU cc_start: 0.7023 (mm) cc_final: 0.6744 (mm) REVERT: L 100 MET cc_start: 0.5523 (mtm) cc_final: 0.4923 (mmt) REVERT: M 2 MET cc_start: 0.6023 (tpt) cc_final: 0.4590 (ptt) REVERT: M 66 GLN cc_start: 0.8737 (mm110) cc_final: 0.8536 (mp10) REVERT: M 100 ILE cc_start: 0.8958 (mp) cc_final: 0.8749 (mt) REVERT: M 110 MET cc_start: 0.8842 (ptp) cc_final: 0.8277 (ptp) REVERT: M 128 VAL cc_start: 0.9226 (t) cc_final: 0.8932 (m) REVERT: N 56 MET cc_start: 0.8155 (mpp) cc_final: 0.7947 (mmt) REVERT: N 87 MET cc_start: 0.8028 (mmp) cc_final: 0.6763 (pmm) REVERT: P 36 ARG cc_start: 0.8554 (mmm-85) cc_final: 0.8297 (mmm-85) REVERT: P 55 ARG cc_start: 0.8427 (mpt180) cc_final: 0.8066 (mpp-170) REVERT: P 75 GLU cc_start: 0.8560 (mm-30) cc_final: 0.8232 (mp0) REVERT: P 84 MET cc_start: 0.7213 (ttt) cc_final: 0.6765 (ppp) REVERT: P 111 ASP cc_start: 0.8895 (m-30) cc_final: 0.8502 (m-30) REVERT: Q 120 ARG cc_start: 0.8184 (ttt90) cc_final: 0.7942 (mtp85) REVERT: R 80 MET cc_start: 0.8098 (ttp) cc_final: 0.7851 (tmm) REVERT: T 9 LYS cc_start: 0.8287 (mtmt) cc_final: 0.8067 (pttt) REVERT: T 13 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.7431 (tp30) REVERT: T 44 GLU cc_start: 0.9009 (pt0) cc_final: 0.8643 (pm20) REVERT: T 52 ARG cc_start: 0.8846 (tmm-80) cc_final: 0.8547 (ttp-170) REVERT: T 63 ARG cc_start: 0.8005 (tpp80) cc_final: 0.7711 (tpp-160) REVERT: T 64 LYS cc_start: 0.7386 (ttmm) cc_final: 0.6985 (ttmm) REVERT: T 67 ASP cc_start: 0.8549 (m-30) cc_final: 0.8237 (m-30) REVERT: T 70 LYS cc_start: 0.9262 (mmtp) cc_final: 0.9040 (mmmt) REVERT: U 3 THR cc_start: 0.7580 (OUTLIER) cc_final: 0.6305 (p) REVERT: U 5 ARG cc_start: 0.7019 (mtm180) cc_final: 0.6116 (mpp-170) REVERT: U 9 HIS cc_start: 0.7958 (m-70) cc_final: 0.7661 (m-70) REVERT: U 32 PHE cc_start: 0.7613 (p90) cc_final: 0.7055 (p90) REVERT: U 36 VAL cc_start: 0.7204 (OUTLIER) cc_final: 0.6997 (t) REVERT: U 56 ARG cc_start: 0.8395 (mmm-85) cc_final: 0.7853 (mmm160) REVERT: U 59 HIS cc_start: 0.8147 (t-90) cc_final: 0.7897 (t-90) REVERT: U 70 ARG cc_start: 0.5594 (tpt90) cc_final: 0.4904 (mmm160) REVERT: V 26 ARG cc_start: 0.6021 (OUTLIER) cc_final: 0.5763 (mtm180) REVERT: W 31 TYR cc_start: 0.7339 (m-80) cc_final: 0.6867 (m-10) REVERT: W 60 ARG cc_start: 0.8365 (mtt180) cc_final: 0.7948 (mtt-85) REVERT: W 63 TYR cc_start: 0.8359 (t80) cc_final: 0.7600 (t80) REVERT: a 56 ASP cc_start: 0.8247 (OUTLIER) cc_final: 0.7865 (p0) outliers start: 231 outliers final: 178 residues processed: 1440 average time/residue: 1.2927 time to fit residues: 3196.9931 Evaluate side-chains 1513 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 205 poor density : 1308 time to evaluate : 6.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 5 CYS Chi-restraints excluded: chain b residue 8 THR Chi-restraints excluded: chain b residue 15 VAL Chi-restraints excluded: chain b residue 48 ILE Chi-restraints excluded: chain b residue 50 THR Chi-restraints excluded: chain b residue 52 HIS Chi-restraints excluded: chain b residue 86 ARG Chi-restraints excluded: chain b residue 104 LEU Chi-restraints excluded: chain b residue 119 VAL Chi-restraints excluded: chain b residue 124 LYS Chi-restraints excluded: chain b residue 159 THR Chi-restraints excluded: chain b residue 179 GLU Chi-restraints excluded: chain b residue 193 GLU Chi-restraints excluded: chain b residue 222 THR Chi-restraints excluded: chain b residue 271 SER Chi-restraints excluded: chain c residue 2 ILE Chi-restraints excluded: chain c residue 12 THR Chi-restraints excluded: chain c residue 35 THR Chi-restraints excluded: chain c residue 42 ASN Chi-restraints excluded: chain c residue 142 VAL Chi-restraints excluded: chain c residue 170 VAL Chi-restraints excluded: chain c residue 177 VAL Chi-restraints excluded: chain c residue 183 GLU Chi-restraints excluded: chain c residue 193 VAL Chi-restraints excluded: chain c residue 207 VAL Chi-restraints excluded: chain d residue 40 ARG Chi-restraints excluded: chain d residue 41 GLN Chi-restraints excluded: chain d residue 105 LEU Chi-restraints excluded: chain d residue 150 THR Chi-restraints excluded: chain d residue 159 LEU Chi-restraints excluded: chain d residue 163 ASN Chi-restraints excluded: chain d residue 200 LEU Chi-restraints excluded: chain e residue 6 TYR Chi-restraints excluded: chain e residue 30 VAL Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 56 LEU Chi-restraints excluded: chain e residue 111 ARG Chi-restraints excluded: chain e residue 120 SER Chi-restraints excluded: chain e residue 144 LYS Chi-restraints excluded: chain e residue 154 THR Chi-restraints excluded: chain e residue 158 THR Chi-restraints excluded: chain f residue 3 VAL Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 19 ASN Chi-restraints excluded: chain f residue 42 VAL Chi-restraints excluded: chain f residue 124 CYS Chi-restraints excluded: chain f residue 154 GLU Chi-restraints excluded: chain g residue 122 LEU Chi-restraints excluded: chain g residue 130 VAL Chi-restraints excluded: chain h residue 27 VAL Chi-restraints excluded: chain h residue 33 VAL Chi-restraints excluded: chain h residue 58 THR Chi-restraints excluded: chain h residue 123 ILE Chi-restraints excluded: chain i residue 52 LEU Chi-restraints excluded: chain i residue 57 VAL Chi-restraints excluded: chain i residue 69 VAL Chi-restraints excluded: chain i residue 78 LEU Chi-restraints excluded: chain j residue 25 LEU Chi-restraints excluded: chain j residue 28 LEU Chi-restraints excluded: chain j residue 81 ILE Chi-restraints excluded: chain k residue 19 VAL Chi-restraints excluded: chain k residue 21 CYS Chi-restraints excluded: chain k residue 35 VAL Chi-restraints excluded: chain k residue 44 LYS Chi-restraints excluded: chain k residue 56 ASP Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 69 VAL Chi-restraints excluded: chain k residue 106 GLU Chi-restraints excluded: chain l residue 3 LEU Chi-restraints excluded: chain l residue 40 SER Chi-restraints excluded: chain l residue 68 SER Chi-restraints excluded: chain l residue 73 ILE Chi-restraints excluded: chain l residue 85 VAL Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain l residue 125 LEU Chi-restraints excluded: chain l residue 144 GLU Chi-restraints excluded: chain m residue 42 THR Chi-restraints excluded: chain m residue 54 THR Chi-restraints excluded: chain m residue 74 THR Chi-restraints excluded: chain m residue 117 PHE Chi-restraints excluded: chain m residue 119 LEU Chi-restraints excluded: chain m residue 133 LYS Chi-restraints excluded: chain n residue 24 MET Chi-restraints excluded: chain n residue 51 LEU Chi-restraints excluded: chain n residue 113 ILE Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain o residue 24 THR Chi-restraints excluded: chain o residue 35 ILE Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain o residue 103 VAL Chi-restraints excluded: chain p residue 31 VAL Chi-restraints excluded: chain p residue 40 GLN Chi-restraints excluded: chain p residue 81 ASP Chi-restraints excluded: chain p residue 101 GLU Chi-restraints excluded: chain q residue 28 SER Chi-restraints excluded: chain r residue 22 LEU Chi-restraints excluded: chain r residue 41 ILE Chi-restraints excluded: chain r residue 64 VAL Chi-restraints excluded: chain s residue 19 LEU Chi-restraints excluded: chain s residue 20 VAL Chi-restraints excluded: chain s residue 31 GLN Chi-restraints excluded: chain s residue 40 ASN Chi-restraints excluded: chain s residue 66 ILE Chi-restraints excluded: chain s residue 67 ASP Chi-restraints excluded: chain s residue 73 LYS Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain t residue 33 LYS Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain t residue 60 THR Chi-restraints excluded: chain t residue 86 THR Chi-restraints excluded: chain u residue 5 ARG Chi-restraints excluded: chain u residue 11 ILE Chi-restraints excluded: chain u residue 12 VAL Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain u residue 28 LEU Chi-restraints excluded: chain u residue 35 VAL Chi-restraints excluded: chain u residue 36 GLU Chi-restraints excluded: chain u residue 64 ILE Chi-restraints excluded: chain u residue 102 ILE Chi-restraints excluded: chain v residue 1 MET Chi-restraints excluded: chain v residue 30 ILE Chi-restraints excluded: chain v residue 35 GLU Chi-restraints excluded: chain v residue 45 ASP Chi-restraints excluded: chain v residue 58 SER Chi-restraints excluded: chain v residue 64 VAL Chi-restraints excluded: chain v residue 65 VAL Chi-restraints excluded: chain v residue 70 ILE Chi-restraints excluded: chain v residue 85 LYS Chi-restraints excluded: chain v residue 92 VAL Chi-restraints excluded: chain w residue 62 LYS Chi-restraints excluded: chain w residue 79 GLU Chi-restraints excluded: chain x residue 6 VAL Chi-restraints excluded: chain x residue 41 SER Chi-restraints excluded: chain x residue 58 ILE Chi-restraints excluded: chain y residue 49 ASP Chi-restraints excluded: chain z residue 6 ILE Chi-restraints excluded: chain z residue 40 THR Chi-restraints excluded: chain z residue 56 VAL Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain C residue 7 LYS Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain D residue 3 ARG Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 22 MET Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain G residue 147 LEU Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 193 ASP Chi-restraints excluded: chain G residue 211 LEU Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 56 GLU Chi-restraints excluded: chain I residue 71 PHE Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 201 GLU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 91 SER Chi-restraints excluded: chain J residue 121 ASN Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain J residue 140 ILE Chi-restraints excluded: chain J residue 156 ARG Chi-restraints excluded: chain K residue 23 GLU Chi-restraints excluded: chain K residue 55 HIS Chi-restraints excluded: chain K residue 59 TYR Chi-restraints excluded: chain K residue 62 MET Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 115 MET Chi-restraints excluded: chain M residue 9 MET Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 62 LEU Chi-restraints excluded: chain M residue 105 THR Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain N residue 28 VAL Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain N residue 108 ARG Chi-restraints excluded: chain P residue 79 LYS Chi-restraints excluded: chain P residue 96 ILE Chi-restraints excluded: chain P residue 109 ILE Chi-restraints excluded: chain P residue 115 ILE Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain R residue 6 ILE Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain S residue 26 LEU Chi-restraints excluded: chain T residue 13 GLU Chi-restraints excluded: chain U residue 2 VAL Chi-restraints excluded: chain U residue 3 THR Chi-restraints excluded: chain U residue 33 ILE Chi-restraints excluded: chain U residue 36 VAL Chi-restraints excluded: chain V residue 26 ARG Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain V residue 57 VAL Chi-restraints excluded: chain W residue 25 ILE Chi-restraints excluded: chain W residue 28 LEU Chi-restraints excluded: chain W residue 58 ILE Chi-restraints excluded: chain W residue 70 THR Chi-restraints excluded: chain X residue 12 LEU Chi-restraints excluded: chain Y residue 13 SER Chi-restraints excluded: chain a residue 56 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1043 random chunks: chunk 507 optimal weight: 30.0000 chunk 657 optimal weight: 10.0000 chunk 881 optimal weight: 20.0000 chunk 253 optimal weight: 6.9990 chunk 762 optimal weight: 20.0000 chunk 122 optimal weight: 10.0000 chunk 229 optimal weight: 9.9990 chunk 828 optimal weight: 10.0000 chunk 346 optimal weight: 6.9990 chunk 850 optimal weight: 30.0000 chunk 104 optimal weight: 0.2980 overall best weight: 6.8590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 167 ASN ** d 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 38 GLN m 17 ASN ** o 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 38 GLN ** p 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 19 GLN q 55 GLN r 87 GLN ** u 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 22 ASN y 20 ASN ** H 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 55 HIS ** a 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.147678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.098016 restraints weight = 352082.932| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 1.56 r_work: 0.3264 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.4766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.267 159558 Z= 0.301 Angle : 0.639 59.196 238506 Z= 0.329 Chirality : 0.038 1.383 30471 Planarity : 0.005 0.066 12929 Dihedral : 23.374 179.073 79350 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 18.24 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.22 % Favored : 90.66 % Rotamer: Outliers : 4.81 % Allowed : 27.38 % Favored : 67.81 % Cbeta Deviations : 0.02 % 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: -2.14 (0.11), residues: 5919 helix: -0.28 (0.12), residues: 1832 sheet: -1.48 (0.16), residues: 1001 loop : -2.14 (0.11), residues: 3086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP b 212 HIS 0.020 0.001 HIS J 82 PHE 0.061 0.002 PHE r 53 TYR 0.036 0.002 TYR G 212 ARG 0.042 0.001 ARG n 12 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 51235.21 seconds wall clock time: 889 minutes 14.49 seconds (53354.49 seconds total)