Starting phenix.real_space_refine on Mon Feb 26 19:25:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jt3_22472/02_2024/7jt3_22472.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jt3_22472/02_2024/7jt3_22472.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jt3_22472/02_2024/7jt3_22472.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jt3_22472/02_2024/7jt3_22472.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jt3_22472/02_2024/7jt3_22472.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jt3_22472/02_2024/7jt3_22472.pdb" } resolution = 3.7 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= 0.100 sd= 0.580 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 4648 5.49 5 S 156 5.16 5 C 75067 2.51 5 N 27698 2.21 5 O 41034 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "b GLU 34": "OE1" <-> "OE2" Residue "b ASP 65": "OD1" <-> "OD2" Residue "b ASP 83": "OD1" <-> "OD2" Residue "b TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 263": "OD1" <-> "OD2" Residue "c ARG 13": "NH1" <-> "NH2" Residue "c GLU 28": "OE1" <-> "OE2" Residue "c ARG 33": "NH1" <-> "NH2" Residue "c ARG 59": "NH1" <-> "NH2" Residue "c ARG 77": "NH1" <-> "NH2" Residue "c ARG 83": "NH1" <-> "NH2" Residue "c GLU 86": "OE1" <-> "OE2" Residue "c GLU 99": "OE1" <-> "OE2" Residue "c ASP 108": "OD1" <-> "OD2" Residue "c PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 169": "NH1" <-> "NH2" Residue "c GLU 183": "OE1" <-> "OE2" Residue "c ARG 184": "NH1" <-> "NH2" Residue "d ARG 21": "NH1" <-> "NH2" Residue "d ASP 22": "OD1" <-> "OD2" Residue "d ARG 44": "NH1" <-> "NH2" Residue "d ARG 49": "NH1" <-> "NH2" Residue "d ARG 61": "NH1" <-> "NH2" Residue "d ARG 88": "NH1" <-> "NH2" Residue "d ARG 102": "NH1" <-> "NH2" Residue "d GLU 122": "OE1" <-> "OE2" Residue "d ASP 140": "OD1" <-> "OD2" Residue "d GLU 144": "OE1" <-> "OE2" Residue "d ASP 145": "OD1" <-> "OD2" Residue "d GLU 155": "OE1" <-> "OE2" Residue "d ARG 162": "NH1" <-> "NH2" Residue "d ASP 168": "OD1" <-> "OD2" Residue "d ARG 170": "NH1" <-> "NH2" Residue "d ASP 176": "OD1" <-> "OD2" Residue "d ASP 191": "OD1" <-> "OD2" Residue "d GLU 198": "OE1" <-> "OE2" Residue "e GLU 10": "OE1" <-> "OE2" Residue "e ARG 70": "NH1" <-> "NH2" Residue "e ARG 79": "NH1" <-> "NH2" Residue "e ARG 91": "NH1" <-> "NH2" Residue "e ARG 101": "NH1" <-> "NH2" Residue "e ARG 109": "NH1" <-> "NH2" Residue "e ARG 111": "NH1" <-> "NH2" Residue "e ARG 114": "NH1" <-> "NH2" Residue "e ARG 132": "NH1" <-> "NH2" Residue "e ASP 146": "OD1" <-> "OD2" Residue "e ASP 162": "OD1" <-> "OD2" Residue "f ARG 2": "NH1" <-> "NH2" Residue "f ASP 46": "OD1" <-> "OD2" Residue "f ASP 55": "OD1" <-> "OD2" Residue "f PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 123": "OE1" <-> "OE2" Residue "f ASP 146": "OD1" <-> "OD2" Residue "f ARG 152": "NH1" <-> "NH2" Residue "f GLU 154": "OE1" <-> "OE2" Residue "f ARG 162": "NH1" <-> "NH2" Residue "f ARG 169": "NH1" <-> "NH2" Residue "g GLU 60": "OE1" <-> "OE2" Residue "g ASP 86": "OD1" <-> "OD2" Residue "g ASP 101": "OD1" <-> "OD2" Residue "h GLU 17": "OE1" <-> "OE2" Residue "h GLU 47": "OE1" <-> "OE2" Residue "h TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 65": "OE1" <-> "OE2" Residue "h PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 114": "OE1" <-> "OE2" Residue "h GLU 116": "OE1" <-> "OE2" Residue "h ASP 124": "OD1" <-> "OD2" Residue "i ASP 46": "OD1" <-> "OD2" Residue "i GLU 107": "OE1" <-> "OE2" Residue "i ASP 120": "OD1" <-> "OD2" Residue "j ARG 13": "NH1" <-> "NH2" Residue "j ARG 37": "NH1" <-> "NH2" Residue "j ASP 49": "OD1" <-> "OD2" Residue "j ASP 60": "OD1" <-> "OD2" Residue "j ARG 96": "NH1" <-> "NH2" Residue "j ARG 120": "NH1" <-> "NH2" Residue "j ASP 141": "OD1" <-> "OD2" Residue "k GLU 4": "OE1" <-> "OE2" Residue "k ASP 56": "OD1" <-> "OD2" Residue "k GLU 110": "OE1" <-> "OE2" Residue "l ARG 21": "NH1" <-> "NH2" Residue "l ARG 33": "NH1" <-> "NH2" Residue "l ARG 41": "NH1" <-> "NH2" Residue "l ARG 47": "NH1" <-> "NH2" Residue "l ARG 60": "NH1" <-> "NH2" Residue "l ARG 78": "NH1" <-> "NH2" Residue "l 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 ASP 70": "OD1" <-> "OD2" Residue "m GLU 75": "OE1" <-> "OE2" Residue "m ARG 114": "NH1" <-> "NH2" Residue "n ARG 8": "NH1" <-> "NH2" Residue "n ARG 12": "NH1" <-> "NH2" Residue "n ARG 17": "NH1" <-> "NH2" Residue "n ARG 22": "NH1" <-> "NH2" Residue "n ARG 46": "NH1" <-> "NH2" Residue "n GLU 49": "OE1" <-> "OE2" Residue "n ARG 63": "NH1" <-> "NH2" Residue "n ARG 64": "NH1" <-> "NH2" Residue "n ARG 69": "NH1" <-> "NH2" Residue "n ARG 71": "NH1" <-> "NH2" Residue "n ASP 72": "OD1" <-> "OD2" Residue "n ARG 96": "NH1" <-> "NH2" Residue "n ASP 117": "OD1" <-> "OD2" Residue "n ARG 118": "NH1" <-> "NH2" Residue "o ARG 10": "NH1" <-> "NH2" Residue "o ARG 16": "NH1" <-> "NH2" Residue "o GLU 20": "OE1" <-> "OE2" Residue "o ARG 25": "NH1" <-> "NH2" Residue "o GLU 80": "OE1" <-> "OE2" Residue "o ARG 81": "NH1" <-> "NH2" Residue "o GLU 84": "OE1" <-> "OE2" Residue "o ARG 94": "NH1" <-> "NH2" Residue "o ARG 102": "NH1" <-> "NH2" Residue "o ARG 111": "NH1" <-> "NH2" Residue "p ASP 15": "OD1" <-> "OD2" Residue "p ARG 20": "NH1" <-> "NH2" Residue "p ARG 38": "NH1" <-> "NH2" Residue "p ARG 61": "NH1" <-> "NH2" Residue "p ARG 88": "NH1" <-> "NH2" Residue "p ARG 100": "NH1" <-> "NH2" Residue "p GLU 101": "OE1" <-> "OE2" Residue "p ARG 108": "NH1" <-> "NH2" Residue "q ARG 2": "NH1" <-> "NH2" Residue "q ARG 5": "NH1" <-> "NH2" Residue "q ARG 12": "NH1" <-> "NH2" Residue "q ARG 32": "NH1" <-> "NH2" Residue "q ARG 47": "NH1" <-> "NH2" Residue "q ARG 69": "NH1" <-> "NH2" Residue "r ARG 21": "NH1" <-> "NH2" Residue "r GLU 34": "OE1" <-> "OE2" Residue "r GLU 62": "OE1" <-> "OE2" Residue "r ARG 68": "NH1" <-> "NH2" Residue "r GLU 70": "OE1" <-> "OE2" Residue "r ARG 78": "NH1" <-> "NH2" Residue "r ARG 79": "NH1" <-> "NH2" Residue "r ARG 84": "NH1" <-> "NH2" Residue "s GLU 52": "OE1" <-> "OE2" Residue "s GLU 59": "OE1" <-> "OE2" Residue "s ASP 65": "OD1" <-> "OD2" Residue "s ASP 68": "OD1" <-> "OD2" Residue "s ASP 77": "OD1" <-> "OD2" Residue "s GLU 78": "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 GLU 42": "OE1" <-> "OE2" Residue "t PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t ARG 73": "NH1" <-> "NH2" Residue "t ASP 79": "OD1" <-> "OD2" 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 ARG 81": "NH1" <-> "NH2" Residue "u ARG 85": "NH1" <-> "NH2" Residue "u ASP 88": "OD1" <-> "OD2" Residue "u ARG 93": "NH1" <-> "NH2" Residue "v GLU 11": "OE1" <-> "OE2" Residue "v ASP 76": "OD1" <-> "OD2" Residue "v ASP 90": "OD1" <-> "OD2" Residue "w ASP 11": "OD1" <-> "OD2" Residue "w GLU 25": "OE1" <-> "OE2" Residue "w PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w GLU 79": "OE1" <-> "OE2" Residue "y GLU 17": "OE1" <-> "OE2" Residue "y ARG 29": "NH1" <-> "NH2" Residue "y ARG 47": "NH1" <-> "NH2" Residue "y ARG 52": "NH1" <-> "NH2" Residue "y GLU 59": "OE1" <-> "OE2" Residue "z ARG 10": "NH1" <-> "NH2" Residue "z ARG 29": "NH1" <-> "NH2" Residue "z ARG 44": "NH1" <-> "NH2" Residue "z GLU 57": "OE1" <-> "OE2" 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 PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 43": "NH1" <-> "NH2" Residue "C TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 3": "NH1" <-> "NH2" Residue "D ARG 12": "NH1" <-> "NH2" Residue "D ARG 14": "NH1" <-> "NH2" Residue "D ARG 19": "NH1" <-> "NH2" Residue "D ARG 21": "NH1" <-> "NH2" Residue "D ARG 33": "NH1" <-> "NH2" Residue "D ARG 41": "NH1" <-> "NH2" Residue "E ARG 12": "NH1" <-> "NH2" Residue "E 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 ASP 7": "OD1" <-> "OD2" Residue "G ASP 115": "OD1" <-> "OD2" Residue "G ASP 126": "OD1" <-> "OD2" Residue "G GLU 168": "OE1" <-> "OE2" Residue "G ASP 204": "OD1" <-> "OD2" Residue "G ARG 224": "NH1" <-> "NH2" Residue "H GLU 45": "OE1" <-> "OE2" Residue "H ASP 82": "OD1" <-> "OD2" Residue "H ASP 92": "OD1" <-> "OD2" Residue "H ARG 106": "NH1" <-> "NH2" Residue "H GLU 109": "OE1" <-> "OE2" Residue "H ASP 111": "OD1" <-> "OD2" Residue "H ARG 130": "NH1" <-> "NH2" Residue "H GLU 169": "OE1" <-> "OE2" Residue "I GLU 14": "OE1" <-> "OE2" Residue "I ASP 17": "OD1" <-> "OD2" Residue "I ASP 28": "OD1" <-> "OD2" Residue "I ASP 49": "OD1" <-> "OD2" Residue "I GLU 56": "OE1" <-> "OE2" Residue "I TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 140": "OD1" <-> "OD2" Residue "I GLU 159": "OE1" <-> "OE2" Residue "J PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 54": "OE1" <-> "OE2" Residue "J GLU 144": "OE1" <-> "OE2" Residue "J ARG 156": "NH1" <-> "NH2" Residue "K PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 16": "OE1" <-> "OE2" Residue "K GLU 23": "OE1" <-> "OE2" Residue "K ASP 41": "OD1" <-> "OD2" Residue "K TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 65": "OE1" <-> "OE2" Residue "K GLU 73": "OE1" <-> "OE2" Residue "K PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 98": "OE1" <-> "OE2" Residue "L PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 57": "OE1" <-> "OE2" Residue "L GLU 62": "OE1" <-> "OE2" Residue "L ASP 139": "OD1" <-> "OD2" Residue "M GLU 59": "OE1" <-> "OE2" Residue "N ASP 90": "OD1" <-> "OD2" Residue "N GLU 96": "OE1" <-> "OE2" Residue "N PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 123": "NH1" <-> "NH2" Residue "O GLU 27": "OE1" <-> "OE2" Residue "O GLU 47": "OE1" <-> "OE2" Residue "O ASP 60": "OD1" <-> "OD2" Residue "O GLU 78": "OE1" <-> "OE2" Residue "O ASP 85": "OD1" <-> "OD2" Residue "Q GLU 24": "OE1" <-> "OE2" Residue "Q ARG 55": "NH1" <-> "NH2" Residue "R GLU 49": "OE1" <-> "OE2" Residue "R GLU 58": "OE1" <-> "OE2" Residue "S ASP 17": "OD1" <-> "OD2" Residue "S ASP 32": "OD1" <-> "OD2" Residue "U ASP 23": "OD1" <-> "OD2" Residue "U ARG 28": "NH1" <-> "NH2" Residue "U PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 47": "OE1" <-> "OE2" Residue "U ASP 55": "OD1" <-> "OD2" Residue "U ASP 69": "OD1" <-> "OD2" Residue "V GLU 48": "OE1" <-> "OE2" Residue "W ARG 11": "NH1" <-> "NH2" Residue "W TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 26": "OD1" <-> "OD2" Residue "X ASP 63": "OD1" <-> "OD2" Residue "X GLU 64": "OE1" <-> "OE2" Residue "Y GLU 14": "OE1" <-> "OE2" Residue "Z ASP 12": "OD1" <-> "OD2" Residue "Z PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 66": "NH1" <-> "NH2" Residue "a ARG 7": "NH1" <-> "NH2" Residue "a ARG 12": "NH1" <-> "NH2" Residue "a GLU 25": "OE1" <-> "OE2" Residue "a PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 43": "OD1" <-> "OD2" Residue "a ARG 162": "NH1" <-> "NH2" Residue "a TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 GLU 16": "OE1" <-> "OE2" Residue "8 ARG 78": "NH1" <-> "NH2" Residue "8 GLU 85": "OE1" <-> "OE2" Residue "8 ARG 117": "NH1" <-> "NH2" Residue "9 GLU 16": "OE1" <-> "OE2" Residue "9 PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 GLU 50": "OE1" <-> "OE2" Residue "9 TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 GLU 54": "OE1" <-> "OE2" Residue "9 ARG 78": "NH1" <-> "NH2" Residue "9 GLU 81": "OE1" <-> "OE2" 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: 148603 Number of models: 1 Model: "" Number of chains: 58 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: 988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 988 Classifications: {'peptide': 131} 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: 1026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1026 Classifications: {'peptide': 134} 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': 91, 'rna2p_pyr': 49, 'rna3p_pur': 783, 'rna3p_pyr': 616} Link IDs: {'rna2p': 140, 'rna3p': 1398} Chain: "1" Number of atoms: 62311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2903, 62311 Classifications: {'RNA': 2903} Modifications used: {'5*END': 1, 'rna2p_pur': 216, 'rna2p_pyr': 94, 'rna3p_pur': 1456, 'rna3p_pyr': 1134} Link IDs: {'rna2p': 310, 'rna3p': 2592} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 3 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': 3, 'rna3p_pur': 61, 'rna3p_pyr': 52} Link IDs: {'rna2p': 7, 'rna3p': 112} Chain: "5" Number of atoms: 1618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1618 Classifications: {'RNA': 76} Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 31, 'rna3p_pyr': 32} Link IDs: {'rna2p': 12, 'rna3p': 63} Chain: "4" Number of atoms: 309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 309 Classifications: {'RNA': 14} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 11, 'rna3p_pyr': 2} Link IDs: {'rna3p': 13} Chain: "8" Number of atoms: 1016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1016 Classifications: {'peptide': 130} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 125} Chain: "9" Number of atoms: 754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 754 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Time building chain proxies: 55.05, per 1000 atoms: 0.37 Number of scatterers: 148603 At special positions: 0 Unit cell: (266.752, 243.828, 242.786, 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 156 16.00 P 4648 15.00 O 41034 8.00 N 27698 7.00 C 75067 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: 56.05 Conformation dependent library (CDL) restraints added in 8.1 seconds 12284 Ramachandran restraints generated. 6142 Oldfield, 0 Emsley, 6142 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11504 Finding SS restraints... Secondary structure from input PDB file: 196 helices and 80 sheets defined 32.2% alpha, 14.6% beta 1280 base pairs and 2790 stacking pairs defined. Time for finding SS restraints: 49.00 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 198 through 202 Processing helix chain 'b' and resid 206 through 212 removed outlier: 4.038A pdb=" N ALA b 210 " --> pdb=" O LYS b 206 " (cutoff:3.500A) Processing helix chain 'b' and resid 261 through 265 removed outlier: 3.919A pdb=" N LYS b 264 " --> pdb=" O ARG b 261 " (cutoff:3.500A) Processing helix chain 'c' and resid 61 through 69 Processing helix chain 'c' and resid 98 through 103 removed outlier: 3.507A pdb=" N ALA c 102 " --> pdb=" O GLU c 99 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ASP c 103 " --> pdb=" O LEU c 100 " (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 38 removed outlier: 3.853A pdb=" N GLN d 30 " --> pdb=" O ALA d 26 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL d 31 " --> pdb=" O LEU d 27 " (cutoff:3.500A) Processing helix chain 'd' and resid 97 through 115 removed outlier: 3.500A pdb=" N SER d 110 " --> pdb=" O LYS d 106 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ARG d 114 " --> pdb=" O SER d 110 " (cutoff:3.500A) Processing helix chain 'd' and resid 130 through 140 removed outlier: 3.686A pdb=" N LEU d 134 " --> pdb=" O LYS d 130 " (cutoff:3.500A) Processing helix chain 'd' and resid 154 through 161 removed outlier: 3.826A pdb=" N ALA d 160 " --> pdb=" O ASN d 156 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA d 161 " --> pdb=" O LEU d 157 " (cutoff:3.500A) Processing helix chain 'd' and resid 176 through 183 removed outlier: 3.547A pdb=" N ILE d 181 " --> pdb=" O PRO d 177 " (cutoff:3.500A) Processing helix chain 'd' and resid 189 through 198 removed outlier: 3.549A pdb=" N LYS d 194 " --> pdb=" O ALA d 190 " (cutoff:3.500A) Processing helix chain 'e' and resid 2 through 15 removed outlier: 3.824A pdb=" N VAL e 11 " --> pdb=" O TYR e 7 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N VAL e 12 " --> pdb=" O LYS e 8 " (cutoff:3.500A) Processing helix chain 'e' and resid 47 through 56 Processing helix chain 'e' and resid 73 through 77 removed outlier: 4.075A pdb=" N PHE e 76 " --> pdb=" O VAL e 73 " (cutoff:3.500A) Processing helix chain 'e' and resid 93 through 104 removed outlier: 3.650A pdb=" N GLU e 97 " --> pdb=" O GLU e 93 " (cutoff:3.500A) Processing helix chain 'e' and resid 161 through 171 Processing helix chain 'f' and resid 59 through 78 removed outlier: 3.529A pdb=" N ALA f 69 " --> pdb=" O GLY f 65 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE f 76 " --> pdb=" O ASN f 72 " (cutoff:3.500A) Processing helix chain 'f' and resid 136 through 150 removed outlier: 3.553A pdb=" N GLY f 141 " --> pdb=" O LYS f 137 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL f 143 " --> pdb=" O VAL f 139 " (cutoff:3.500A) Processing helix chain 'g' and resid 22 through 29 removed outlier: 3.820A pdb=" N PHE g 29 " --> pdb=" O TYR g 25 " (cutoff:3.500A) Processing helix chain 'g' and resid 29 through 34 removed outlier: 3.534A pdb=" N GLN g 33 " --> pdb=" O PHE g 29 " (cutoff:3.500A) Processing helix chain 'g' and resid 40 through 48 removed outlier: 3.551A pdb=" N GLU g 45 " --> pdb=" O LYS g 41 " (cutoff:3.500A) Processing helix chain 'g' and resid 49 through 54 Processing helix chain 'g' and resid 54 through 59 Processing helix chain 'g' and resid 60 through 71 removed outlier: 4.404A pdb=" N ALA g 67 " --> pdb=" O ALA g 63 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG g 68 " --> pdb=" O ALA g 64 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS g 71 " --> pdb=" O ALA g 67 " (cutoff:3.500A) Processing helix chain 'g' and resid 98 through 104 removed outlier: 3.584A pdb=" N ALA g 102 " --> pdb=" O ASP g 98 " (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 removed outlier: 3.624A pdb=" N ILE h 11 " --> pdb=" O ASP h 7 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N SER h 16 " --> pdb=" O VAL h 12 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N GLU h 17 " --> pdb=" O ALA h 13 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ALA h 19 " --> pdb=" O VAL h 15 " (cutoff:3.500A) Processing helix chain 'h' and resid 33 through 48 removed outlier: 4.145A pdb=" N THR h 39 " --> pdb=" O VAL h 35 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLU h 40 " --> pdb=" O ASP h 36 " (cutoff:3.500A) Processing helix chain 'h' and resid 93 through 105 removed outlier: 4.146A pdb=" N LYS h 97 " --> pdb=" O ALA h 93 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N PHE h 99 " --> pdb=" O LEU h 95 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ALA h 100 " --> pdb=" O PHE h 96 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LYS h 101 " --> pdb=" O LYS h 97 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA h 104 " --> pdb=" O ALA h 100 " (cutoff:3.500A) Processing helix chain 'h' and resid 110 through 114 removed outlier: 3.726A pdb=" N GLU h 114 " --> pdb=" O ALA h 111 " (cutoff:3.500A) Processing helix chain 'i' and resid 12 through 16 removed outlier: 4.283A pdb=" N GLY i 15 " --> pdb=" O VAL i 12 " (cutoff:3.500A) Processing helix chain 'i' and resid 23 through 29 removed outlier: 3.595A pdb=" N LEU i 27 " --> pdb=" O VAL i 23 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLY i 28 " --> pdb=" O GLY i 24 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N GLN i 29 " --> pdb=" O PRO i 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 23 through 29' Processing helix chain 'i' and resid 35 through 45 removed outlier: 3.578A pdb=" N LYS i 39 " --> pdb=" O MET i 35 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ALA i 40 " --> pdb=" O GLU i 36 " (cutoff:3.500A) Processing helix chain 'i' and resid 74 through 82 Processing helix chain 'i' and resid 101 through 114 removed outlier: 3.579A pdb=" N THR i 111 " --> pdb=" O GLU i 107 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS i 112 " --> pdb=" O ILE i 108 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ALA i 114 " --> pdb=" O GLN i 110 " (cutoff:3.500A) Processing helix chain 'i' and resid 120 through 135 removed outlier: 4.153A pdb=" N SER i 127 " --> pdb=" O ALA i 123 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ILE i 128 " --> pdb=" O MET i 124 " (cutoff:3.500A) Processing helix chain 'j' and resid 24 through 38 removed outlier: 3.684A pdb=" N GLU j 31 " --> pdb=" O ARG j 27 " (cutoff:3.500A) Processing helix chain 'j' and resid 58 through 62 removed outlier: 3.931A pdb=" N VAL j 62 " --> pdb=" O ALA j 59 " (cutoff:3.500A) Processing helix chain 'j' and resid 67 through 72 Processing helix chain 'j' and resid 89 through 95 Processing helix chain 'j' and resid 98 through 107 removed outlier: 3.613A pdb=" N ALA j 104 " --> pdb=" O VAL j 100 " (cutoff:3.500A) Processing helix chain 'j' and resid 112 through 118 Processing helix chain 'j' and resid 132 through 136 Processing helix chain 'k' and resid 112 through 118 Processing helix chain 'l' and resid 37 through 41 removed outlier: 3.624A pdb=" N SER l 40 " --> pdb=" O GLY l 37 " (cutoff:3.500A) Processing helix chain 'l' and resid 56 through 61 Processing helix chain 'l' and resid 68 through 72 Processing helix chain 'l' and resid 80 through 82 No H-bonds generated for 'chain 'l' and resid 80 through 82' Processing helix chain 'l' and resid 128 through 139 removed outlier: 3.759A pdb=" N ILE l 135 " --> pdb=" O ALA l 131 " (cutoff:3.500A) Processing helix chain 'm' and resid 43 through 58 removed outlier: 3.501A pdb=" N ARG m 55 " --> pdb=" O ARG m 51 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA m 56 " --> pdb=" O ALA m 52 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL m 57 " --> pdb=" O MET m 53 " (cutoff:3.500A) Processing helix chain 'm' and resid 109 through 122 removed outlier: 3.948A 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 54 removed outlier: 4.799A pdb=" N ARG n 46 " --> pdb=" O LYS n 42 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL n 47 " --> pdb=" O GLU n 43 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU n 49 " --> pdb=" O ARG n 45 " (cutoff:3.500A) Proline residue: n 50 - end of helix Processing helix chain 'n' and resid 59 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 20 removed outlier: 3.609A pdb=" N ARG o 9 " --> pdb=" O SER o 5 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ARG o 10 " --> pdb=" O ALA o 6 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA o 11 " --> pdb=" O ARG o 7 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ARG o 13 " --> pdb=" O ARG o 9 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ALA o 14 " --> pdb=" O ARG o 10 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LYS o 17 " --> pdb=" O ARG o 13 " (cutoff:3.500A) Processing helix chain 'o' and resid 55 through 60 Processing helix chain 'o' and resid 67 through 85 removed outlier: 3.651A pdb=" N GLU o 80 " --> pdb=" O LYS o 76 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG o 81 " --> pdb=" O ALA o 77 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU o 83 " --> pdb=" O ALA o 79 " (cutoff:3.500A) Processing helix chain 'o' and resid 101 through 114 removed outlier: 3.525A pdb=" N ALA o 109 " --> pdb=" O ALA o 105 " (cutoff:3.500A) Processing helix chain 'p' and resid 2 through 9 removed outlier: 3.945A pdb=" N GLN p 6 " --> pdb=" O ASN p 2 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU p 7 " --> pdb=" O ILE p 3 " (cutoff:3.500A) Processing helix chain 'p' and resid 52 through 56 removed outlier: 3.598A pdb=" N SER p 56 " --> pdb=" O GLY p 53 " (cutoff:3.500A) Processing helix chain 'p' and resid 96 through 101 removed outlier: 4.098A pdb=" N GLU p 101 " --> pdb=" O TYR p 98 " (cutoff:3.500A) Processing helix chain 'q' and resid 6 through 18 Processing helix chain 'q' and resid 24 through 29 removed outlier: 3.995A pdb=" N SER q 28 " --> pdb=" O GLY q 25 " (cutoff:3.500A) Processing helix chain 'q' and resid 30 through 69 removed outlier: 4.480A pdb=" N GLN q 36 " --> pdb=" O ARG q 32 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ARG q 50 " --> pdb=" O TYR q 46 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N LYS q 53 " --> pdb=" O ARG q 49 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG q 54 " --> pdb=" O ARG q 50 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ARG q 63 " --> pdb=" O LEU q 59 " (cutoff:3.500A) Processing helix chain 'q' and resid 74 through 85 Processing helix chain 'q' and resid 90 through 101 removed outlier: 3.870A pdb=" N ASP q 96 " --> pdb=" O LYS q 92 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL q 99 " --> pdb=" O ALA q 95 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N PHE q 100 " --> pdb=" O ASP q 96 " (cutoff:3.500A) Processing helix chain 'q' and resid 101 through 117 removed outlier: 3.563A pdb=" N GLU q 110 " --> pdb=" O THR q 106 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LYS q 111 " --> pdb=" O ALA q 107 " (cutoff:3.500A) Processing helix chain 's' and resid 14 through 25 removed outlier: 3.511A pdb=" N ARG s 18 " --> pdb=" O ALA s 14 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL s 20 " --> pdb=" O LYS s 16 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N LEU s 23 " --> pdb=" O LEU s 19 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ILE s 24 " --> pdb=" O VAL s 20 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ARG s 25 " --> pdb=" O ALA s 21 " (cutoff:3.500A) Processing helix chain 's' and resid 28 through 37 removed outlier: 3.595A pdb=" N ASP s 34 " --> pdb=" O SER s 30 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU s 36 " --> pdb=" O ALA s 32 " (cutoff:3.500A) Processing helix chain 's' and resid 41 through 61 removed outlier: 4.035A pdb=" N VAL s 45 " --> pdb=" O LYS s 41 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS s 48 " --> pdb=" O ALA s 44 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS s 49 " --> pdb=" O VAL s 45 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASN s 57 " --> pdb=" O SER s 53 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA s 58 " --> pdb=" O ALA s 54 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU s 59 " --> pdb=" O ILE s 55 " (cutoff:3.500A) Processing helix chain 's' and resid 88 through 92 removed outlier: 3.737A pdb=" N GLY s 91 " --> pdb=" O ARG s 88 " (cutoff:3.500A) Processing helix chain 't' and resid 2 through 10 removed outlier: 3.624A pdb=" N LYS t 9 " --> pdb=" O GLU t 5 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL t 10 " --> pdb=" O ARG t 6 " (cutoff:3.500A) Processing helix chain 't' and resid 17 through 25 removed outlier: 3.570A pdb=" N ALA t 23 " --> pdb=" O LYS t 19 " (cutoff:3.500A) Processing helix chain 't' and resid 39 through 50 Processing helix chain 'v' and resid 14 through 22 removed outlier: 3.541A pdb=" N ARG v 18 " --> pdb=" O LYS v 14 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ARG v 19 " --> pdb=" O GLY v 15 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU v 20 " --> pdb=" O ALA v 16 " (cutoff:3.500A) Processing helix chain 'v' and resid 44 through 51 removed outlier: 3.949A pdb=" N ASN v 49 " --> pdb=" O ASP v 45 " (cutoff:3.500A) Processing helix chain 'v' and resid 52 through 58 removed outlier: 6.220A pdb=" N GLU v 55 " --> pdb=" O ALA v 52 " (cutoff:3.500A) Processing helix chain 'x' and resid 52 through 61 removed outlier: 3.745A pdb=" N ARG x 56 " --> pdb=" O ALA x 52 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP x 59 " --> pdb=" O MET x 55 " (cutoff:3.500A) Processing helix chain 'x' and resid 62 through 74 Processing helix chain 'y' and resid 9 through 23 removed outlier: 3.570A pdb=" N THR y 16 " --> pdb=" O GLU y 12 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU y 21 " --> pdb=" O GLU y 17 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG y 23 " --> pdb=" O LEU y 19 " (cutoff:3.500A) Processing helix chain 'y' and resid 25 through 34 removed outlier: 3.714A pdb=" N ALA y 32 " --> pdb=" O LEU y 28 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER y 34 " --> pdb=" O MET y 30 " (cutoff:3.500A) Processing helix chain 'y' and resid 40 through 60 removed outlier: 3.845A pdb=" N LYS y 44 " --> pdb=" O SER y 40 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN y 45 " --> pdb=" O HIS y 41 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG y 47 " --> pdb=" O LEU y 43 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN y 58 " --> pdb=" O LYS y 54 " (cutoff:3.500A) Processing helix chain 'z' and resid 16 through 26 removed outlier: 3.544A pdb=" N LEU z 23 " --> pdb=" O HIS z 19 " (cutoff:3.500A) Processing helix chain 'z' and resid 40 through 50 removed outlier: 3.753A pdb=" N MET z 46 " --> pdb=" O ALA z 42 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE z 47 " --> pdb=" O ILE z 43 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL z 50 " --> pdb=" O MET z 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 16 Processing helix chain 'D' and resid 8 through 17 Processing helix chain 'D' and resid 17 through 23 Processing helix chain 'D' and resid 24 through 37 removed outlier: 3.503A pdb=" N ARG D 33 " --> pdb=" O GLN D 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 11 removed outlier: 3.551A pdb=" N LYS E 11 " --> pdb=" O ARG E 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 43 Processing helix chain 'E' and resid 50 through 58 removed outlier: 4.360A pdb=" N GLY E 55 " --> pdb=" O LYS E 51 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N LEU E 56 " --> pdb=" O GLY E 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 18 through 22 removed outlier: 4.156A pdb=" N GLY F 21 " --> pdb=" O LYS F 18 " (cutoff:3.500A) Processing helix chain 'G' and resid 4 through 11 removed outlier: 3.683A pdb=" N ALA G 11 " --> pdb=" O ASP G 7 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 30 removed outlier: 4.120A pdb=" N ILE G 30 " --> pdb=" O LYS G 27 " (cutoff:3.500A) Processing helix chain 'G' and resid 41 through 43 No H-bonds generated for 'chain 'G' and resid 41 through 43' Processing helix chain 'G' and resid 44 through 54 removed outlier: 3.910A pdb=" N MET G 48 " --> pdb=" O LYS G 44 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASN G 50 " --> pdb=" O VAL G 46 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ALA G 52 " --> pdb=" O MET G 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 61 removed outlier: 3.730A pdb=" N SER G 61 " --> pdb=" O ASN G 57 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 84 removed outlier: 3.527A pdb=" N LEU G 84 " --> pdb=" O LYS G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 122 removed outlier: 3.689A pdb=" N THR G 118 " --> pdb=" O LYS G 114 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ASP G 122 " --> pdb=" O THR G 118 " (cutoff:3.500A) Processing helix chain 'G' and resid 129 through 146 removed outlier: 4.024A pdb=" N MET G 135 " --> pdb=" O LYS G 131 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ARG G 138 " --> pdb=" O LEU G 134 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU G 140 " --> pdb=" O ARG G 136 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU G 143 " --> pdb=" O GLU G 139 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N SER G 146 " --> pdb=" O LYS G 142 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 177 removed outlier: 4.270A pdb=" N GLU G 174 " --> pdb=" O ILE G 170 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ALA G 175 " --> pdb=" O ALA G 171 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN G 176 " --> pdb=" O ILE G 172 " (cutoff:3.500A) Processing helix chain 'G' and resid 205 through 207 No H-bonds generated for 'chain 'G' and resid 205 through 207' Processing helix chain 'G' and resid 208 through 222 removed outlier: 3.877A pdb=" N GLY G 214 " --> pdb=" O THR G 210 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA G 215 " --> pdb=" O LEU G 211 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL G 216 " --> pdb=" O TYR G 212 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ALA G 218 " --> pdb=" O GLY G 214 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N THR G 219 " --> pdb=" O ALA G 215 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL G 220 " --> pdb=" O VAL G 216 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG G 221 " --> pdb=" O ALA G 217 " (cutoff:3.500A) Processing helix chain 'H' and resid 27 through 47 removed outlier: 3.597A pdb=" N SER H 34 " --> pdb=" O ASP H 30 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE H 36 " --> pdb=" O LEU H 32 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG H 39 " --> pdb=" O ASP H 35 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR H 41 " --> pdb=" O LYS H 37 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU H 42 " --> pdb=" O VAL H 38 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR H 43 " --> pdb=" O ARG H 39 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LYS H 44 " --> pdb=" O GLN H 40 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU H 45 " --> pdb=" O TYR H 41 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU H 46 " --> pdb=" O LEU H 42 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ALA H 47 " --> pdb=" O THR H 43 " (cutoff:3.500A) Processing helix chain 'H' and resid 72 through 77 Processing helix chain 'H' and resid 80 through 90 Processing helix chain 'H' and resid 90 through 95 removed outlier: 3.618A pdb=" N ALA H 94 " --> pdb=" O VAL H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 107 through 110 removed outlier: 3.764A pdb=" N LEU H 110 " --> pdb=" O LYS H 107 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 107 through 110' Processing helix chain 'H' and resid 111 through 124 removed outlier: 3.525A pdb=" N ALA H 116 " --> pdb=" O ALA H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 128 through 142 removed outlier: 3.583A pdb=" N ARG H 135 " --> pdb=" O ARG H 131 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA H 140 " --> pdb=" O ALA H 136 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N MET H 141 " --> pdb=" O VAL H 137 " (cutoff:3.500A) Processing helix chain 'I' and resid 6 through 15 removed outlier: 4.131A pdb=" N LEU I 10 " --> pdb=" O PRO I 6 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N SER I 11 " --> pdb=" O LYS I 7 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU I 14 " --> pdb=" O LEU I 10 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 65 removed outlier: 3.556A pdb=" N ARG I 55 " --> pdb=" O GLY I 51 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU I 56 " --> pdb=" O VAL I 52 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL I 60 " --> pdb=" O GLU I 56 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG I 61 " --> pdb=" O LYS I 57 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE I 63 " --> pdb=" O LYS I 59 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N TYR I 64 " --> pdb=" O VAL I 60 " (cutoff:3.500A) Processing helix chain 'I' and resid 67 through 77 Processing helix chain 'I' and resid 84 through 94 removed outlier: 4.246A pdb=" N LEU I 90 " --> pdb=" O GLY I 86 " (cutoff:3.500A) Processing helix chain 'I' and resid 96 through 101 Processing helix chain 'I' and resid 109 through 118 removed outlier: 3.612A pdb=" N LEU I 116 " --> pdb=" O GLU I 112 " (cutoff:3.500A) Processing helix chain 'I' and resid 155 through 160 Processing helix chain 'I' and resid 161 through 164 removed outlier: 3.642A pdb=" N ARG I 164 " --> pdb=" O ALA I 161 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 161 through 164' Processing helix chain 'I' and resid 196 through 205 removed outlier: 3.513A pdb=" N GLU I 201 " --> pdb=" O HIS I 197 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N TYR I 203 " --> pdb=" O ILE I 199 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SER I 204 " --> pdb=" O VAL I 200 " (cutoff:3.500A) Processing helix chain 'J' and resid 54 through 59 Processing helix chain 'J' and resid 60 through 67 removed outlier: 4.081A pdb=" N GLU J 64 " --> pdb=" O GLN J 60 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N LYS J 65 " --> pdb=" O LYS J 61 " (cutoff:3.500A) Processing helix chain 'J' and resid 111 through 116 removed outlier: 4.130A pdb=" N VAL J 116 " --> pdb=" O ALA J 112 " (cutoff:3.500A) Processing helix chain 'J' and resid 131 through 144 removed outlier: 4.009A pdb=" N VAL J 136 " --> pdb=" O PRO J 132 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ARG J 137 " --> pdb=" O ILE J 133 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE J 140 " --> pdb=" O VAL J 136 " (cutoff:3.500A) Processing helix chain 'J' and resid 151 through 155 removed outlier: 3.551A pdb=" N ALA J 154 " --> pdb=" O MET J 151 " (cutoff:3.500A) Processing helix chain 'K' and resid 11 through 16 removed outlier: 3.627A pdb=" N GLU K 16 " --> pdb=" O ASP K 13 " (cutoff:3.500A) Processing helix chain 'K' and resid 17 through 31 removed outlier: 3.623A pdb=" N MET K 21 " --> pdb=" O GLN K 17 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE K 29 " --> pdb=" O TYR K 25 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 80 removed outlier: 3.928A pdb=" N GLU K 73 " --> pdb=" O GLU K 69 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU K 74 " --> pdb=" O VAL K 70 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N THR K 76 " --> pdb=" O ASP K 72 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N THR K 77 " --> pdb=" O GLU K 73 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N PHE K 78 " --> pdb=" O LEU K 74 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ARG K 79 " --> pdb=" O GLU K 75 " (cutoff:3.500A) Processing helix chain 'L' and resid 21 through 26 removed outlier: 3.526A pdb=" N VAL L 26 " --> pdb=" O LEU L 22 " (cutoff:3.500A) Processing helix chain 'L' and resid 36 through 46 removed outlier: 3.551A pdb=" N SER L 40 " --> pdb=" O SER L 36 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE L 41 " --> pdb=" O THR L 37 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL L 42 " --> pdb=" O ALA L 38 " (cutoff:3.500A) Processing helix chain 'L' and resid 46 through 54 removed outlier: 3.577A pdb=" N ALA L 50 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLN L 51 " --> pdb=" O GLU L 47 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N ARG L 52 " --> pdb=" O THR L 48 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER L 53 " --> pdb=" O LEU L 49 " (cutoff:3.500A) Processing helix chain 'L' and resid 56 through 61 Processing helix chain 'L' and resid 62 through 65 Processing helix chain 'L' and resid 91 through 109 removed outlier: 3.718A pdb=" N ASN L 96 " --> pdb=" O PRO L 92 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ALA L 97 " --> pdb=" O VAL L 93 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA L 99 " --> pdb=" O ARG L 95 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TRP L 102 " --> pdb=" O LEU L 98 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE L 103 " --> pdb=" O ALA L 99 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL L 104 " --> pdb=" O MET L 100 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LYS L 109 " --> pdb=" O GLU L 105 " (cutoff:3.500A) Processing helix chain 'L' and resid 114 through 127 removed outlier: 3.619A pdb=" N ALA L 120 " --> pdb=" O ALA L 116 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP L 125 " --> pdb=" O ASN L 121 " (cutoff:3.500A) Processing helix chain 'L' and resid 131 through 146 removed outlier: 3.983A pdb=" N LYS L 135 " --> pdb=" O GLY L 131 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LYS L 136 " --> pdb=" O THR L 132 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU L 145 " --> pdb=" O HIS L 141 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 19 removed outlier: 3.584A pdb=" N LEU M 10 " --> pdb=" O ILE M 6 " (cutoff:3.500A) Processing helix chain 'M' and resid 29 through 43 removed outlier: 3.607A pdb=" N VAL M 33 " --> pdb=" O SER M 29 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ALA M 34 " --> pdb=" O LYS M 30 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL M 38 " --> pdb=" O ALA M 34 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LEU M 39 " --> pdb=" O ILE M 35 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU M 42 " --> pdb=" O VAL M 38 " (cutoff:3.500A) Processing helix chain 'M' and resid 112 through 119 removed outlier: 3.743A pdb=" N GLN M 117 " --> pdb=" O ARG M 113 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY M 119 " --> pdb=" O ALA M 115 " (cutoff:3.500A) Processing helix chain 'N' and resid 10 through 14 removed outlier: 3.889A pdb=" N SER N 13 " --> pdb=" O ARG N 10 " (cutoff:3.500A) Processing helix chain 'N' and resid 34 through 38 Processing helix chain 'N' and resid 44 through 48 removed outlier: 4.063A pdb=" N VAL N 47 " --> pdb=" O ARG N 44 " (cutoff:3.500A) Processing helix chain 'N' and resid 70 through 86 removed outlier: 3.615A pdb=" N ALA N 75 " --> pdb=" O ILE N 71 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR N 83 " --> pdb=" O ARG N 79 " (cutoff:3.500A) Processing helix chain 'N' and resid 94 through 99 Processing helix chain 'O' and resid 14 through 26 removed outlier: 3.636A pdb=" N ILE O 18 " --> pdb=" O ASP O 14 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N GLN O 20 " --> pdb=" O ARG O 16 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA O 23 " --> pdb=" O ASP O 19 " (cutoff:3.500A) Processing helix chain 'O' and resid 26 through 31 removed outlier: 3.587A pdb=" N ARG O 31 " --> pdb=" O GLU O 27 " (cutoff:3.500A) Processing helix chain 'O' and resid 83 through 88 Processing helix chain 'P' and resid 58 through 68 removed outlier: 3.593A pdb=" N ALA P 62 " --> pdb=" O THR P 58 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA P 66 " --> pdb=" O ALA P 62 " (cutoff:3.500A) Processing helix chain 'P' and resid 94 through 101 removed outlier: 4.042A pdb=" N ALA P 98 " --> pdb=" O SER P 94 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU P 99 " --> pdb=" O THR P 95 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 7 Processing helix chain 'Q' and resid 114 through 118 removed outlier: 3.617A pdb=" N GLY Q 117 " --> pdb=" O SER Q 114 " (cutoff:3.500A) Processing helix chain 'R' and resid 2 through 6 removed outlier: 3.707A pdb=" N GLY R 5 " --> pdb=" O ARG R 2 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE R 6 " --> pdb=" O ILE R 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 2 through 6' Processing helix chain 'R' and resid 13 through 19 Processing helix chain 'R' and resid 25 through 36 removed outlier: 3.816A pdb=" N ALA R 36 " --> pdb=" O ILE R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 48 through 60 removed outlier: 3.872A pdb=" N ASP R 53 " --> pdb=" O GLU R 49 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N THR R 54 " --> pdb=" O GLY R 50 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASP R 57 " --> pdb=" O ASP R 53 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU R 58 " --> pdb=" O THR R 54 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA R 60 " --> pdb=" O ARG R 56 " (cutoff:3.500A) Processing helix chain 'R' and resid 64 through 79 removed outlier: 3.549A pdb=" N ARG R 70 " --> pdb=" O GLY R 66 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE R 76 " --> pdb=" O ILE R 72 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LYS R 77 " --> pdb=" O SER R 73 " (cutoff:3.500A) Processing helix chain 'R' and resid 80 through 82 No H-bonds generated for 'chain 'R' and resid 80 through 82' Processing helix chain 'R' and resid 84 through 92 Processing helix chain 'S' and resid 2 through 17 removed outlier: 3.535A pdb=" N LYS S 6 " --> pdb=" O LYS S 2 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS S 11 " --> pdb=" O ALA S 7 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU S 15 " --> pdb=" O LYS S 11 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASP S 17 " --> pdb=" O VAL S 13 " (cutoff:3.500A) Processing helix chain 'S' and resid 37 through 46 Processing helix chain 'S' and resid 47 through 50 removed outlier: 3.755A pdb=" N LEU S 50 " --> pdb=" O LEU S 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 47 through 50' Processing helix chain 'S' and resid 55 through 59 removed outlier: 3.640A pdb=" N GLN S 59 " --> pdb=" O PRO S 56 " (cutoff:3.500A) Processing helix chain 'S' and resid 83 through 88 removed outlier: 3.517A pdb=" N MET S 88 " --> pdb=" O ARG S 84 " (cutoff:3.500A) Processing helix chain 'T' and resid 3 through 14 removed outlier: 3.559A pdb=" N THR T 7 " --> pdb=" O SER T 3 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU T 13 " --> pdb=" O LYS T 9 " (cutoff:3.500A) Processing helix chain 'T' and resid 23 through 44 removed outlier: 3.587A pdb=" N GLN T 27 " --> pdb=" O SER T 23 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL T 28 " --> pdb=" O THR T 24 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA T 33 " --> pdb=" O ALA T 29 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLN T 34 " --> pdb=" O LEU T 30 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE T 35 " --> pdb=" O LEU T 31 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN T 36 " --> pdb=" O THR T 32 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N GLY T 40 " --> pdb=" O ASN T 36 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N HIS T 41 " --> pdb=" O HIS T 37 " (cutoff:3.500A) Processing helix chain 'T' and resid 48 through 73 removed outlier: 3.799A pdb=" N GLY T 54 " --> pdb=" O HIS T 50 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS T 70 " --> pdb=" O LEU T 66 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ARG T 71 " --> pdb=" O ASP T 67 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS T 72 " --> pdb=" O TYR T 68 " (cutoff:3.500A) Processing helix chain 'T' and resid 73 through 84 removed outlier: 3.674A pdb=" N ILE T 81 " --> pdb=" O TYR T 77 " (cutoff:3.500A) Processing helix chain 'U' and resid 53 through 62 removed outlier: 3.594A pdb=" N HIS U 59 " --> pdb=" O ASP U 55 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N TRP U 60 " --> pdb=" O ARG U 56 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL U 61 " --> pdb=" O ILE U 57 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLY U 62 " --> pdb=" O ALA U 58 " (cutoff:3.500A) Processing helix chain 'U' and resid 68 through 78 removed outlier: 3.719A pdb=" N ALA U 72 " --> pdb=" O SER U 68 " (cutoff:3.500A) Processing helix chain 'W' and resid 24 through 29 removed outlier: 3.684A pdb=" N LYS W 29 " --> pdb=" O ILE W 25 " (cutoff:3.500A) Processing helix chain 'W' and resid 40 through 45 removed outlier: 3.538A pdb=" N THR W 44 " --> pdb=" O PRO W 40 " (cutoff:3.500A) Processing helix chain 'W' and resid 47 through 52 Processing helix chain 'W' and resid 52 through 64 removed outlier: 3.524A pdb=" N ARG W 56 " --> pdb=" O ARG W 52 " (cutoff:3.500A) Processing helix chain 'X' and resid 11 through 23 Processing helix chain 'X' and resid 40 through 44 removed outlier: 3.758A pdb=" N MET X 43 " --> pdb=" O PHE X 40 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ILE X 44 " --> pdb=" O PRO X 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 40 through 44' Processing helix chain 'X' and resid 69 through 74 removed outlier: 3.795A pdb=" N PHE X 73 " --> pdb=" O LEU X 70 " (cutoff:3.500A) Processing helix chain 'Y' and resid 7 through 41 removed outlier: 3.774A pdb=" N ILE Y 11 " --> pdb=" O LYS Y 7 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS Y 18 " --> pdb=" O GLU Y 14 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N HIS Y 19 " --> pdb=" O LYS Y 15 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR Y 29 " --> pdb=" O SER Y 25 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ILE Y 31 " --> pdb=" O MET Y 27 " (cutoff:3.500A) Processing helix chain 'Y' and resid 42 through 63 removed outlier: 3.628A pdb=" N GLN Y 54 " --> pdb=" O PHE Y 50 " (cutoff:3.500A) Proline residue: Y 55 - end of helix Processing helix chain 'Y' and resid 69 through 85 removed outlier: 3.545A pdb=" N LEU Y 78 " --> pdb=" O HIS Y 74 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR Y 79 " --> pdb=" O LYS Y 75 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA Y 80 " --> pdb=" O ALA Y 76 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLN Y 81 " --> pdb=" O ASN Y 77 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE Y 82 " --> pdb=" O LEU Y 78 " (cutoff:3.500A) Processing helix chain 'Z' and resid 18 through 23 removed outlier: 3.867A pdb=" N GLU Z 23 " --> pdb=" O LYS Z 19 " (cutoff:3.500A) Processing helix chain 'Z' and resid 27 through 33 removed outlier: 4.557A pdb=" N ARG Z 33 " --> pdb=" O ALA Z 29 " (cutoff:3.500A) Processing helix chain 'Z' and resid 38 through 57 removed outlier: 3.792A pdb=" N THR Z 42 " --> pdb=" O GLU Z 38 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYS Z 45 " --> pdb=" O THR Z 41 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA Z 49 " --> pdb=" O LYS Z 45 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS Z 57 " --> pdb=" O LYS Z 53 " (cutoff:3.500A) Processing helix chain 'a' and resid 181 through 189 removed outlier: 4.433A pdb=" N LYS a 186 " --> pdb=" O ALA a 182 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N GLU a 187 " --> pdb=" O ASP a 183 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN a 188 " --> pdb=" O LYS a 184 " (cutoff:3.500A) Processing helix chain '8' and resid 28 through 32 removed outlier: 3.603A pdb=" N ASN 8 31 " --> pdb=" O GLN 8 28 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS 8 32 " --> pdb=" O HIS 8 29 " (cutoff:3.500A) No H-bonds generated for 'chain '8' and resid 28 through 32' Processing helix chain '8' and resid 43 through 47 removed outlier: 3.563A pdb=" N SER 8 46 " --> pdb=" O ILE 8 43 " (cutoff:3.500A) Processing helix chain '8' and resid 51 through 59 removed outlier: 3.519A pdb=" N ARG 8 55 " --> pdb=" O TYR 8 51 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ALA 8 59 " --> pdb=" O ARG 8 55 " (cutoff:3.500A) Processing helix chain '8' and resid 79 through 99 removed outlier: 3.712A pdb=" N ASN 8 83 " --> pdb=" O SER 8 79 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU 8 85 " --> pdb=" O GLU 8 81 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU 8 91 " --> pdb=" O ALA 8 87 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL 8 92 " --> pdb=" O LEU 8 88 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N GLU 8 97 " --> pdb=" O ALA 8 93 " (cutoff:3.500A) Processing helix chain '8' and resid 112 through 115 removed outlier: 3.653A pdb=" N LYS 8 115 " --> pdb=" O ARG 8 112 " (cutoff:3.500A) No H-bonds generated for 'chain '8' and resid 112 through 115' Processing helix chain '8' and resid 116 through 124 removed outlier: 3.706A pdb=" N LYS 8 122 " --> pdb=" O ARG 8 118 " (cutoff:3.500A) Processing helix chain '8' and resid 125 through 130 removed outlier: 3.585A pdb=" N LYS 8 129 " --> pdb=" O SER 8 126 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ALA 8 130 " --> pdb=" O SER 8 127 " (cutoff:3.500A) Processing helix chain '9' and resid 52 through 58 removed outlier: 3.627A pdb=" N LEU 9 57 " --> pdb=" O LYS 9 53 " (cutoff:3.500A) Processing helix chain '9' and resid 79 through 98 removed outlier: 3.529A pdb=" N ARG 9 90 " --> pdb=" O ALA 9 86 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LYS 9 96 " --> pdb=" O VAL 9 92 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU 9 98 " --> pdb=" O MET 9 94 " (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: 6.578A pdb=" N ILE b 90 " --> pdb=" O LEU b 80 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N LEU b 80 " --> pdb=" O ILE b 90 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LEU b 92 " --> pdb=" O GLU b 78 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'b' and resid 128 through 130 removed outlier: 3.594A pdb=" N LEU b 129 " --> pdb=" O ALA b 189 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ALA b 189 " --> pdb=" O LEU b 129 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N THR b 172 " --> pdb=" O VAL b 164 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'c' and resid 4 through 15 removed outlier: 5.116A pdb=" N LYS c 8 " --> pdb=" O GLU c 28 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N GLU c 28 " --> pdb=" O LYS c 8 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY c 10 " --> pdb=" O VAL c 26 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LEU c 186 " --> pdb=" O VAL c 180 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N VAL c 180 " --> pdb=" O LEU c 186 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N LEU c 188 " --> pdb=" O VAL c 178 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N ASP c 176 " --> pdb=" O LYS c 190 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N VAL c 107 " --> pdb=" O SER c 174 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N THR c 112 " --> pdb=" O ASP c 200 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N ASP c 200 " --> pdb=" O THR c 112 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'c' and resid 79 through 83 removed outlier: 3.551A pdb=" N ILE c 48 " --> pdb=" O PHE c 82 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ALA c 47 " --> pdb=" O VAL c 37 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N VAL c 37 " --> pdb=" O ALA c 47 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N GLN c 49 " --> pdb=" O THR c 35 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'c' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'd' and resid 2 through 4 Processing sheet with id=AA9, first strand: chain 'd' and resid 118 through 119 removed outlier: 6.303A pdb=" N LEU d 147 " --> pdb=" O VAL d 187 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N VAL d 146 " --> pdb=" O ASP d 168 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N ARG d 170 " --> pdb=" O VAL d 146 " (cutoff:3.500A) removed outlier: 6.036A 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 68 removed outlier: 3.579A pdb=" N GLY e 85 " --> pdb=" O THR e 67 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU e 90 " --> pdb=" O ILE e 33 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS e 32 " --> pdb=" O THR e 156 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR e 154 " --> pdb=" O THR e 34 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASN e 36 " --> pdb=" O ASP e 152 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP e 152 " --> pdb=" O ASN e 36 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'f' and resid 8 through 9 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 82 through 87 removed outlier: 7.343A pdb=" N GLU f 129 " --> pdb=" O PRO f 125 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'f' and resid 97 through 98 removed outlier: 3.753A pdb=" N HIS f 114 " --> pdb=" O ILE f 102 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU f 104 " --> pdb=" O VAL f 112 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'g' and resid 18 through 20 Processing sheet with id=AB7, first strand: chain 'g' and resid 79 through 82 removed outlier: 3.618A pdb=" N SER g 82 " --> pdb=" O VAL g 147 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'g' and resid 115 through 116 Processing sheet with id=AB9, first strand: chain 'i' and resid 8 through 10 removed outlier: 3.687A pdb=" N VAL i 8 " --> pdb=" O ILE i 58 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LEU i 10 " --> pdb=" O VAL i 56 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N THR i 67 " --> pdb=" O THR i 59 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'i' and resid 98 through 99 removed outlier: 5.722A pdb=" N GLY i 98 " --> pdb=" O VAL i 138 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'j' and resid 122 through 124 removed outlier: 6.586A pdb=" N ILE j 54 " --> pdb=" O LYS j 123 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N TYR j 16 " --> pdb=" O ILE j 55 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N TRP j 15 " --> pdb=" O GLN j 138 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'j' and resid 73 through 77 Processing sheet with id=AC4, first strand: chain 'k' and resid 6 through 7 removed outlier: 3.865A pdb=" N THR k 6 " --> pdb=" O CYS k 21 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ALA k 16 " --> pdb=" O ALA k 46 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N ALA k 46 " --> pdb=" O ALA k 16 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ARG k 18 " --> pdb=" O LYS k 44 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LYS k 40 " --> pdb=" O ILE k 22 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N VAL k 24 " --> pdb=" O ILE k 38 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N ILE k 38 " --> pdb=" O VAL k 24 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU k 58 " --> pdb=" O ILE k 41 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ALA k 83 " --> pdb=" O VAL k 63 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ASN k 9 " --> pdb=" O CYS k 84 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N LEU k 86 " --> pdb=" O ASN k 9 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'k' and resid 69 through 70 removed outlier: 4.456A pdb=" N VAL k 76 " --> pdb=" O VAL p 72 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG k 78 " --> pdb=" O GLU p 70 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ALA p 48 " --> pdb=" O THR p 59 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ARG p 61 " --> pdb=" O VAL p 46 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N VAL p 46 " --> pdb=" O ARG p 61 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N ILE p 63 " --> pdb=" O GLY p 44 " (cutoff:3.500A) removed outlier: 8.547A pdb=" N GLY p 44 " --> pdb=" O ILE p 63 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N THR p 24 " --> pdb=" O VAL p 85 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N VAL p 85 " --> pdb=" O THR p 24 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N GLU p 26 " --> pdb=" O ILE p 83 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ILE p 83 " --> pdb=" O GLU p 26 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N LYS p 28 " --> pdb=" O ASP p 81 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'l' and resid 74 through 78 removed outlier: 7.089A pdb=" N ALA l 75 " --> pdb=" O LYS l 109 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N ILE l 111 " --> pdb=" O ALA l 75 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ILE l 77 " --> pdb=" O ILE l 111 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'l' and resid 89 through 90 Processing sheet with id=AC8, first strand: chain 'm' and resid 62 through 63 removed outlier: 3.714A pdb=" N ASP m 106 " --> pdb=" O LYS m 62 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LYS m 100 " --> pdb=" O ALA m 35 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LEU m 33 " --> pdb=" O LEU m 102 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N GLU m 104 " --> pdb=" O PHE m 31 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N PHE m 31 " --> pdb=" O GLU m 104 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'm' and resid 39 through 42 removed outlier: 3.559A pdb=" N TYR m 91 " --> pdb=" O ILE m 73 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'n' and resid 33 through 37 Processing sheet with id=AD2, first strand: chain 'o' and resid 47 through 50 removed outlier: 6.595A pdb=" N VAL o 39 " --> pdb=" O LEU o 48 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N ALA o 50 " --> pdb=" O ALA o 37 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N ALA o 37 " --> pdb=" O ALA o 50 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLN o 38 " --> pdb=" O VAL o 27 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'p' and resid 32 through 33 Processing sheet with id=AD4, first strand: chain 'r' and resid 11 through 15 removed outlier: 7.133A pdb=" N TYR r 2 " --> pdb=" O ILE r 41 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N ILE r 41 " --> pdb=" O TYR r 2 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N VAL r 4 " --> pdb=" O LEU r 39 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'r' and resid 19 through 22 removed outlier: 6.514A pdb=" N LYS r 97 " --> pdb=" O VAL r 63 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N VAL r 63 " --> pdb=" O LYS r 97 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N THR r 99 " --> pdb=" O ALA r 61 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N ALA r 61 " --> pdb=" O THR r 99 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N ILE r 101 " --> pdb=" O ILE r 59 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N ILE r 59 " --> pdb=" O ILE r 101 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'r' and resid 72 through 73 Processing sheet with id=AD7, first strand: chain 'r' and resid 76 through 78 removed outlier: 4.147A pdb=" N TYR r 83 " --> pdb=" O ARG r 78 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 's' and resid 2 through 4 removed outlier: 3.640A pdb=" N THR s 3 " --> pdb=" O VAL s 107 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ILE s 103 " --> pdb=" O ARG s 8 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N ARG s 8 " --> pdb=" O ILE s 103 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 's' and resid 2 through 4 removed outlier: 3.640A pdb=" N THR s 3 " --> pdb=" O VAL s 107 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N SER s 108 " --> pdb=" O VAL s 71 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N VAL s 71 " --> pdb=" O SER s 108 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 's' and resid 83 through 86 Processing sheet with id=AE2, first strand: chain 't' and resid 11 through 13 removed outlier: 3.748A pdb=" N ALA t 13 " --> pdb=" O LYS t 33 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 't' and resid 29 through 31 removed outlier: 3.840A pdb=" N TRP t 80 " --> pdb=" O VAL t 63 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL t 63 " --> pdb=" O TRP t 80 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'u' and resid 63 through 65 removed outlier: 7.135A pdb=" N LYS u 32 " --> pdb=" O VAL u 27 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N VAL u 27 " --> pdb=" O LYS u 32 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N ILE u 34 " --> pdb=" O LYS u 25 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'u' and resid 40 through 44 Processing sheet with id=AE6, first strand: chain 'u' and resid 82 through 86 Processing sheet with id=AE7, first strand: chain 'v' and resid 68 through 70 removed outlier: 3.760A pdb=" N LYS v 68 " --> pdb=" O VAL v 65 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE v 63 " --> pdb=" O ILE v 70 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N ASN v 5 " --> pdb=" O ASP v 43 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N ASP v 43 " --> pdb=" O ASN v 5 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N GLN v 87 " --> pdb=" O LYS v 25 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ILE v 89 " --> pdb=" O PRO v 27 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N VAL v 92 " --> pdb=" O ALA v 74 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N ALA v 74 " --> pdb=" O VAL v 92 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'w' and resid 18 through 19 removed outlier: 6.553A pdb=" N ILE w 32 " --> pdb=" O ALA w 57 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ALA w 57 " --> pdb=" O ILE w 32 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'w' and resid 41 through 43 Processing sheet with id=AF1, first strand: chain 'x' and resid 12 through 15 Processing sheet with id=AF2, first strand: chain 'x' and resid 32 through 39 removed outlier: 3.521A pdb=" N ARG x 44 " --> pdb=" O VAL x 39 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'z' and resid 34 through 37 Processing sheet with id=AF4, first strand: chain 'C' and resid 22 through 24 removed outlier: 3.690A pdb=" N GLU C 6 " --> pdb=" O LYS C 24 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS C 9 " --> pdb=" O ALA C 51 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 37 through 39 removed outlier: 3.826A pdb=" N ASP C 39 " --> pdb=" O GLN C 44 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN C 44 " --> pdb=" O ASP C 39 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 14 through 15 removed outlier: 3.522A pdb=" N ALA E 47 " --> pdb=" O HIS E 23 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'F' and resid 15 through 17 Processing sheet with id=AF8, first strand: chain 'G' and resid 17 through 18 removed outlier: 3.833A pdb=" N HIS G 17 " --> pdb=" O HIS G 38 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'G' and resid 66 through 69 removed outlier: 6.290A pdb=" N LEU G 67 " --> pdb=" O PHE G 161 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF9 Processing sheet with id=AG1, first strand: chain 'G' and resid 183 through 186 Processing sheet with id=AG2, first strand: chain 'H' and resid 19 through 20 removed outlier: 3.749A pdb=" N ARG H 53 " --> pdb=" O HIS H 68 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N HIS H 68 " --> pdb=" O ARG H 53 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASN H 101 " --> pdb=" O VAL H 65 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE H 67 " --> pdb=" O ASN H 101 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'H' and resid 163 through 170 removed outlier: 3.546A pdb=" N GLY H 154 " --> pdb=" O ARG H 163 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL H 152 " --> pdb=" O GLU H 165 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N TYR H 167 " --> pdb=" O VAL H 150 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL H 150 " --> pdb=" O TYR H 167 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ASP H 180 " --> pdb=" O LYS H 203 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'I' and resid 122 through 124 removed outlier: 3.647A pdb=" N ASP I 140 " --> pdb=" O PHE I 181 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'J' and resid 13 through 21 removed outlier: 5.223A pdb=" N LEU J 14 " --> pdb=" O VAL J 37 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N VAL J 37 " --> pdb=" O LEU J 14 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA J 16 " --> pdb=" O LEU J 35 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA J 52 " --> pdb=" O PHE J 32 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'J' and resid 85 through 88 removed outlier: 3.978A pdb=" N VAL J 93 " --> pdb=" O GLY J 86 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N PHE J 94 " --> pdb=" O LYS J 125 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS J 125 " --> pdb=" O PHE J 94 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLN J 96 " --> pdb=" O LEU J 123 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU J 123 " --> pdb=" O GLN J 96 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'K' and resid 2 through 4 removed outlier: 3.684A pdb=" N LYS K 35 " --> pdb=" O GLU K 65 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'K' and resid 60 through 61 removed outlier: 3.813A pdb=" N VAL K 60 " --> pdb=" O PHE K 8 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N PHE K 8 " --> pdb=" O VAL K 60 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N VAL K 7 " --> pdb=" O SER K 87 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N SER K 87 " --> pdb=" O VAL K 7 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'K' and resid 44 through 45 Processing sheet with id=AH1, first strand: chain 'M' and resid 23 through 27 removed outlier: 3.986A pdb=" N THR M 61 " --> pdb=" O ASP M 47 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N ASP M 47 " --> pdb=" O THR M 61 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'M' and resid 74 through 76 Processing sheet with id=AH3, first strand: chain 'M' and resid 74 through 76 removed outlier: 3.707A pdb=" N GLU M 123 " --> pdb=" O SER M 104 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N VAL M 102 " --> pdb=" O ILE M 125 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N TYR M 127 " --> pdb=" O ILE M 100 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N ILE M 100 " --> pdb=" O TYR M 127 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL M 103 " --> pdb=" O MET M 110 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'N' and resid 5 through 9 removed outlier: 3.549A pdb=" N ARG N 17 " --> pdb=" O THR N 65 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR N 63 " --> pdb=" O PHE N 19 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS N 21 " --> pdb=" O ASP N 61 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N VAL N 28 " --> pdb=" O ILE N 64 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N VAL N 66 " --> pdb=" O VAL N 28 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'O' and resid 45 through 48 removed outlier: 3.940A pdb=" N ARG O 45 " --> pdb=" O THR O 69 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR O 69 " --> pdb=" O ARG O 45 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE O 67 " --> pdb=" O GLU O 47 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'O' and resid 45 through 48 removed outlier: 3.940A pdb=" N ARG O 45 " --> pdb=" O THR O 69 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR O 69 " --> pdb=" O ARG O 45 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE O 67 " --> pdb=" O GLU O 47 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'O' and resid 51 through 52 Processing sheet with id=AH8, first strand: chain 'P' and resid 40 through 44 removed outlier: 6.859A pdb=" N ILE P 33 " --> pdb=" O LEU P 41 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N TRP P 43 " --> pdb=" O VAL P 31 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N VAL P 31 " --> pdb=" O TRP P 43 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLY P 18 " --> pdb=" O ASN P 80 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU P 82 " --> pdb=" O GLY P 18 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR P 107 " --> pdb=" O LEU P 81 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N VAL P 83 " --> pdb=" O THR P 107 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N ILE P 109 " --> pdb=" O VAL P 83 " (cutoff:3.500A) removed outlier: 8.339A pdb=" N VAL P 85 " --> pdb=" O ILE P 109 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N ASP P 111 " --> pdb=" O VAL P 85 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'Q' and resid 28 through 31 removed outlier: 3.795A pdb=" N LYS Q 29 " --> pdb=" O ILE Q 81 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'Q' and resid 34 through 39 removed outlier: 5.006A pdb=" N ARG Q 35 " --> pdb=" O ARG Q 53 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARG Q 53 " --> pdb=" O ARG Q 35 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG Q 49 " --> pdb=" O THR Q 39 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'U' and resid 32 through 35 removed outlier: 6.779A pdb=" N PHE U 32 " --> pdb=" O ASP U 23 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N ASP U 23 " --> pdb=" O PHE U 32 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VAL U 2 " --> pdb=" O THR U 66 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'U' and resid 8 through 11 removed outlier: 3.533A pdb=" N ARG U 14 " --> pdb=" O ALA U 11 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'V' and resid 10 through 13 removed outlier: 3.793A pdb=" N ARG V 10 " --> pdb=" O ALA V 23 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N VAL V 21 " --> pdb=" O VAL V 12 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL V 22 " --> pdb=" O LEU V 43 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'V' and resid 59 through 62 removed outlier: 6.694A pdb=" N GLU V 59 " --> pdb=" O VAL V 75 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'X' and resid 31 through 32 Processing sheet with id=AI7, first strand: chain '8' and resid 5 through 7 removed outlier: 3.898A pdb=" N SER 8 5 " --> pdb=" O VAL 9 8 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL 9 8 " --> pdb=" O SER 8 5 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N HIS 8 7 " --> pdb=" O ARG 9 6 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ARG 9 6 " --> pdb=" O HIS 8 7 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI7 Processing sheet with id=AI8, first strand: chain '8' and resid 18 through 19 1408 hydrogen bonds defined for protein. 3921 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3160 hydrogen bonds 5226 hydrogen bond angles 0 basepair planarities 1280 basepair parallelities 2790 stacking parallelities Total time for adding SS restraints: 232.78 Time building geometry restraints manager: 61.48 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: 30968 1.34 - 1.46: 63090 1.46 - 1.58: 57594 1.58 - 1.70: 9295 1.70 - 1.82: 282 Bond restraints: 161229 Sorted by residual: bond pdb=" C VAL J 55 " pdb=" N PRO J 56 " ideal model delta sigma weight residual 1.337 1.404 -0.067 1.24e-02 6.50e+03 2.88e+01 bond pdb=" C1' C 5 75 " pdb=" N1 C 5 75 " ideal model delta sigma weight residual 1.470 1.524 -0.054 1.50e-02 4.44e+03 1.31e+01 bond pdb=" O5' G 12251 " pdb=" C5' G 12251 " ideal model delta sigma weight residual 1.420 1.471 -0.051 1.50e-02 4.44e+03 1.16e+01 bond pdb=" C3' C 5 74 " pdb=" O3' C 5 74 " ideal model delta sigma weight residual 1.417 1.465 -0.048 1.50e-02 4.44e+03 1.04e+01 bond pdb=" C5' C 5 75 " pdb=" C4' C 5 75 " ideal model delta sigma weight residual 1.509 1.557 -0.048 1.50e-02 4.44e+03 1.01e+01 ... (remaining 161224 not shown) Histogram of bond angle deviations from ideal: 95.41 - 103.22: 10428 103.22 - 111.04: 87976 111.04 - 118.85: 60124 118.85 - 126.66: 68814 126.66 - 134.47: 13378 Bond angle restraints: 240720 Sorted by residual: angle pdb=" N ASP K 82 " pdb=" CA ASP K 82 " pdb=" C ASP K 82 " ideal model delta sigma weight residual 111.28 122.50 -11.22 1.09e+00 8.42e-01 1.06e+02 angle pdb=" N ALA S 21 " pdb=" CA ALA S 21 " pdb=" C ALA S 21 " ideal model delta sigma weight residual 114.56 101.87 12.69 1.27e+00 6.20e-01 9.98e+01 angle pdb=" N THR R 107 " pdb=" CA THR R 107 " pdb=" C THR R 107 " ideal model delta sigma weight residual 112.45 99.15 13.30 1.39e+00 5.18e-01 9.16e+01 angle pdb=" N ARG 9 44 " pdb=" CA ARG 9 44 " pdb=" C ARG 9 44 " ideal model delta sigma weight residual 111.36 121.30 -9.94 1.09e+00 8.42e-01 8.31e+01 angle pdb=" C LEU 9 48 " pdb=" N PRO 9 49 " pdb=" CA PRO 9 49 " ideal model delta sigma weight residual 119.84 131.04 -11.20 1.25e+00 6.40e-01 8.03e+01 ... (remaining 240715 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 92376 35.95 - 71.90: 9655 71.90 - 107.86: 1214 107.86 - 143.81: 10 143.81 - 179.76: 15 Dihedral angle restraints: 103270 sinusoidal: 85449 harmonic: 17821 Sorted by residual: dihedral pdb=" C4' A 11913 " pdb=" C3' A 11913 " pdb=" C2' A 11913 " pdb=" C1' A 11913 " ideal model delta sinusoidal sigma weight residual 36.34 -38.35 74.69 1 3.10e+00 1.04e-01 7.35e+02 dihedral pdb=" O4' A 11913 " pdb=" C4' A 11913 " pdb=" C3' A 11913 " pdb=" C2' A 11913 " ideal model delta sinusoidal sigma weight residual -35.15 25.56 -60.71 1 4.00e+00 6.25e-02 3.06e+02 dihedral pdb=" C5' G 12251 " pdb=" C4' G 12251 " pdb=" C3' G 12251 " pdb=" O3' G 12251 " ideal model delta sinusoidal sigma weight residual 82.00 -10.85 92.85 1 8.00e+00 1.56e-02 1.57e+02 ... (remaining 103267 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.728: 30722 0.728 - 1.456: 1 1.456 - 2.184: 0 2.184 - 2.912: 0 2.912 - 3.640: 1 Chirality restraints: 30724 Sorted by residual: chirality pdb=" C3' G 12251 " pdb=" C4' G 12251 " pdb=" O3' G 12251 " pdb=" C2' G 12251 " both_signs ideal model delta sigma weight residual False -2.48 1.16 -3.64 2.00e-01 2.50e+01 3.31e+02 chirality pdb=" C4' C 5 75 " pdb=" C5' C 5 75 " pdb=" O4' C 5 75 " pdb=" C3' C 5 75 " both_signs ideal model delta sigma weight residual False -2.50 -1.77 -0.73 2.00e-01 2.50e+01 1.34e+01 chirality pdb=" P A 4 5 " pdb=" OP1 A 4 5 " pdb=" OP2 A 4 5 " pdb=" O5' A 4 5 " both_signs ideal model delta sigma weight residual True 2.41 -3.00 -0.59 2.00e-01 2.50e+01 8.60e+00 ... (remaining 30721 not shown) Planarity restraints: 13231 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A 12432 " 0.185 2.00e-02 2.50e+03 8.07e-02 1.79e+02 pdb=" N9 A 12432 " -0.009 2.00e-02 2.50e+03 pdb=" C8 A 12432 " -0.079 2.00e-02 2.50e+03 pdb=" N7 A 12432 " -0.071 2.00e-02 2.50e+03 pdb=" C5 A 12432 " -0.031 2.00e-02 2.50e+03 pdb=" C6 A 12432 " 0.032 2.00e-02 2.50e+03 pdb=" N6 A 12432 " 0.114 2.00e-02 2.50e+03 pdb=" N1 A 12432 " 0.025 2.00e-02 2.50e+03 pdb=" C2 A 12432 " -0.026 2.00e-02 2.50e+03 pdb=" N3 A 12432 " -0.078 2.00e-02 2.50e+03 pdb=" C4 A 12432 " -0.061 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U 11818 " -0.089 2.00e-02 2.50e+03 4.98e-02 5.57e+01 pdb=" N1 U 11818 " 0.003 2.00e-02 2.50e+03 pdb=" C2 U 11818 " 0.018 2.00e-02 2.50e+03 pdb=" O2 U 11818 " 0.031 2.00e-02 2.50e+03 pdb=" N3 U 11818 " 0.018 2.00e-02 2.50e+03 pdb=" C4 U 11818 " 0.019 2.00e-02 2.50e+03 pdb=" O4 U 11818 " -0.091 2.00e-02 2.50e+03 pdb=" C5 U 11818 " 0.049 2.00e-02 2.50e+03 pdb=" C6 U 11818 " 0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U 12431 " 0.089 2.00e-02 2.50e+03 4.71e-02 4.99e+01 pdb=" N1 U 12431 " -0.008 2.00e-02 2.50e+03 pdb=" C2 U 12431 " -0.021 2.00e-02 2.50e+03 pdb=" O2 U 12431 " -0.028 2.00e-02 2.50e+03 pdb=" N3 U 12431 " -0.015 2.00e-02 2.50e+03 pdb=" C4 U 12431 " -0.011 2.00e-02 2.50e+03 pdb=" O4 U 12431 " 0.082 2.00e-02 2.50e+03 pdb=" C5 U 12431 " -0.042 2.00e-02 2.50e+03 pdb=" C6 U 12431 " -0.044 2.00e-02 2.50e+03 ... (remaining 13228 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 2910 2.64 - 3.21: 121562 3.21 - 3.77: 280141 3.77 - 4.34: 388091 4.34 - 4.90: 526531 Nonbonded interactions: 1319235 Sorted by model distance: nonbonded pdb=" N3 A 12432 " pdb=" O5' C 5 75 " model vdw 2.077 3.120 nonbonded pdb=" O ALA g 63 " pdb=" OD1 ASN g 66 " model vdw 2.102 3.040 nonbonded pdb=" NH2 ARG L 94 " pdb=" O2' A 3 938 " model vdw 2.224 2.520 nonbonded pdb=" O ALA o 105 " pdb=" OD1 ASP o 108 " model vdw 2.235 3.040 nonbonded pdb=" OG SER z 11 " pdb=" OP2 G 1 989 " model vdw 2.243 2.440 ... (remaining 1319230 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.140 Extract box with map and model: 14.890 Check model and map are aligned: 1.570 Set scattering table: 1.010 Process input model: 497.470 Find NCS groups from input model: 2.780 Set up NCS constraints: 0.320 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 523.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 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 0.067 161229 Z= 0.382 Angle : 0.991 17.768 240720 Z= 0.656 Chirality : 0.084 3.640 30724 Planarity : 0.006 0.096 13231 Dihedral : 22.102 179.760 91766 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 1.74 % Allowed : 12.86 % Favored : 85.40 % Rotamer: Outliers : 1.24 % Allowed : 8.60 % Favored : 90.16 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.28 (0.08), residues: 6142 helix: -4.18 (0.07), residues: 1664 sheet: -2.81 (0.15), residues: 855 loop : -3.48 (0.08), residues: 3623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.007 TRP c 80 HIS 0.008 0.001 HIS J 82 PHE 0.028 0.005 PHE n 102 TYR 0.057 0.006 TYR L 43 ARG 0.012 0.001 ARG J 156 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12284 Ramachandran restraints generated. 6142 Oldfield, 0 Emsley, 6142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12284 Ramachandran restraints generated. 6142 Oldfield, 0 Emsley, 6142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1851 residues out of total 5093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 1788 time to evaluate : 6.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 99 GLU cc_start: 0.8281 (tm-30) cc_final: 0.7774 (tm-30) REVERT: b 152 GLN cc_start: 0.8302 (mp10) cc_final: 0.8041 (mm-40) REVERT: b 206 LYS cc_start: 0.8419 (pttt) cc_final: 0.8013 (pttp) REVERT: c 28 GLU cc_start: 0.9049 (tm-30) cc_final: 0.8810 (tp30) REVERT: c 36 GLN cc_start: 0.8406 (tt0) cc_final: 0.8166 (tp40) REVERT: c 45 TYR cc_start: 0.8041 (p90) cc_final: 0.7807 (p90) REVERT: c 64 GLU cc_start: 0.9026 (mm-30) cc_final: 0.8619 (mm-30) REVERT: c 68 PHE cc_start: 0.8808 (m-80) cc_final: 0.8503 (m-80) REVERT: c 74 GLU cc_start: 0.8308 (pm20) cc_final: 0.7756 (mp0) REVERT: c 131 ASP cc_start: 0.8672 (p0) cc_final: 0.8388 (p0) REVERT: c 169 ARG cc_start: 0.8219 (ttt180) cc_final: 0.7699 (ptt180) REVERT: c 173 GLN cc_start: 0.8157 (pt0) cc_final: 0.7906 (tm-30) REVERT: c 185 ASN cc_start: 0.9086 (m-40) cc_final: 0.8528 (m110) REVERT: d 23 PHE cc_start: 0.7565 (t80) cc_final: 0.6849 (t80) REVERT: d 25 GLU cc_start: 0.8178 (tt0) cc_final: 0.7623 (mp0) REVERT: d 100 MET cc_start: 0.9139 (mtp) cc_final: 0.8789 (mtp) REVERT: d 122 GLU cc_start: 0.8331 (tm-30) cc_final: 0.8044 (tm-30) REVERT: d 146 VAL cc_start: 0.9441 (p) cc_final: 0.9209 (m) REVERT: d 166 LYS cc_start: 0.8849 (mmtm) cc_final: 0.8583 (mmmt) REVERT: d 184 ASP cc_start: 0.8906 (t70) cc_final: 0.8129 (t70) REVERT: d 188 MET cc_start: 0.9239 (mmt) cc_final: 0.8695 (mmp) REVERT: e 97 GLU cc_start: 0.8187 (tp30) cc_final: 0.7922 (tm-30) REVERT: e 109 ARG cc_start: 0.9086 (tpm170) cc_final: 0.8721 (tpm170) REVERT: e 126 ASN cc_start: 0.7919 (m110) cc_final: 0.7584 (m-40) REVERT: e 136 ILE cc_start: 0.8678 (pt) cc_final: 0.8344 (pt) REVERT: e 137 PHE cc_start: 0.7705 (m-80) cc_final: 0.7344 (m-80) REVERT: f 82 PHE cc_start: 0.7496 (m-80) cc_final: 0.7014 (m-10) REVERT: f 88 LEU cc_start: 0.8810 (tp) cc_final: 0.8595 (tp) REVERT: f 132 LEU cc_start: 0.8893 (tp) cc_final: 0.8686 (tp) REVERT: f 137 LYS cc_start: 0.8646 (tmtt) cc_final: 0.8349 (tppt) REVERT: f 138 GLN cc_start: 0.8110 (tm-30) cc_final: 0.7797 (mt0) REVERT: g 17 ASP cc_start: 0.8519 (t0) cc_final: 0.7997 (p0) REVERT: g 18 GLN cc_start: 0.8843 (mp10) cc_final: 0.8213 (mp10) REVERT: g 28 ASN cc_start: 0.8853 (m-40) cc_final: 0.7697 (m-40) REVERT: g 46 PHE cc_start: 0.8519 (m-10) cc_final: 0.8137 (m-10) REVERT: g 55 GLU cc_start: 0.8720 (mt-10) cc_final: 0.8370 (mt-10) REVERT: g 87 GLU cc_start: 0.7944 (tp30) cc_final: 0.7626 (pm20) REVERT: g 129 GLU cc_start: 0.5722 (mt-10) cc_final: 0.5498 (mp0) REVERT: g 133 GLN cc_start: 0.8774 (tt0) cc_final: 0.8300 (tp-100) REVERT: h 52 MET cc_start: 0.8411 (tmm) cc_final: 0.8177 (tpp) REVERT: h 59 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7790 (mp) REVERT: h 86 MET cc_start: 0.3238 (mmm) cc_final: 0.1885 (tpp) REVERT: h 116 GLU cc_start: 0.8783 (mm-30) cc_final: 0.8342 (mm-30) REVERT: i 41 PHE cc_start: 0.8566 (t80) cc_final: 0.8188 (t80) REVERT: i 116 MET cc_start: -0.2474 (ttt) cc_final: -0.2982 (tpt) REVERT: j 43 GLU cc_start: 0.8516 (pt0) cc_final: 0.8155 (pm20) REVERT: j 44 TYR cc_start: 0.8874 (t80) cc_final: 0.8460 (t80) REVERT: j 54 ILE cc_start: 0.9393 (mt) cc_final: 0.9190 (mm) REVERT: j 67 ASN cc_start: 0.8130 (m-40) cc_final: 0.7697 (t0) REVERT: j 141 ASP cc_start: 0.8602 (t0) cc_final: 0.8205 (t0) REVERT: l 38 GLN cc_start: 0.8863 (tt0) cc_final: 0.8587 (tt0) REVERT: l 73 ILE cc_start: 0.8515 (pt) cc_final: 0.8268 (mp) REVERT: l 81 ASP cc_start: 0.8376 (p0) cc_final: 0.8150 (p0) REVERT: l 104 GLN cc_start: 0.8485 (mt0) cc_final: 0.8176 (mt0) REVERT: m 57 VAL cc_start: 0.8658 (m) cc_final: 0.7786 (p) REVERT: n 33 ILE cc_start: 0.8415 (tt) cc_final: 0.8109 (tp) REVERT: n 38 LEU cc_start: 0.9455 (tp) cc_final: 0.9156 (tp) REVERT: n 62 ASN cc_start: 0.8014 (m-40) cc_final: 0.7803 (m-40) REVERT: n 94 TYR cc_start: 0.8065 (m-80) cc_final: 0.7487 (m-80) REVERT: n 112 TYR cc_start: 0.8282 (m-80) cc_final: 0.7940 (m-80) REVERT: o 12 THR cc_start: 0.8691 (p) cc_final: 0.8390 (p) REVERT: o 34 HIS cc_start: 0.8014 (m90) cc_final: 0.7651 (m90) REVERT: o 43 ASN cc_start: 0.8424 (p0) cc_final: 0.8152 (p0) REVERT: o 55 GLU cc_start: 0.8022 (mt-10) cc_final: 0.7820 (mt-10) REVERT: o 80 GLU cc_start: 0.9170 (tp30) cc_final: 0.8961 (tp30) REVERT: o 87 ILE cc_start: 0.7909 (mm) cc_final: 0.7646 (tp) REVERT: o 98 GLN cc_start: 0.7684 (tt0) cc_final: 0.7274 (tt0) REVERT: o 104 GLN cc_start: 0.9592 (tt0) cc_final: 0.8996 (tp40) REVERT: p 6 GLN cc_start: 0.8246 (pt0) cc_final: 0.8044 (pt0) REVERT: p 37 LYS cc_start: 0.8530 (mttm) cc_final: 0.8311 (mptt) REVERT: p 93 LYS cc_start: 0.8675 (tppt) cc_final: 0.8346 (tppt) REVERT: q 21 LYS cc_start: 0.8465 (mmtt) cc_final: 0.7892 (ttmm) REVERT: q 24 TYR cc_start: 0.7186 (t80) cc_final: 0.6547 (t80) REVERT: q 54 ARG cc_start: 0.8904 (mtm180) cc_final: 0.8381 (mtm-85) REVERT: q 91 ARG cc_start: 0.8644 (mpt-90) cc_final: 0.7872 (mtt90) REVERT: q 93 ILE cc_start: 0.8474 (mm) cc_final: 0.8146 (mm) REVERT: q 97 ILE cc_start: 0.9211 (mt) cc_final: 0.8956 (mm) REVERT: q 110 GLU cc_start: 0.8845 (mm-30) cc_final: 0.8292 (mm-30) REVERT: r 11 GLN cc_start: 0.7694 (mt0) cc_final: 0.7221 (mt0) REVERT: r 13 ARG cc_start: 0.8837 (ttp80) cc_final: 0.8619 (ptm-80) REVERT: r 16 GLU cc_start: 0.8433 (tt0) cc_final: 0.8105 (tt0) REVERT: r 76 LYS cc_start: 0.9190 (mtmm) cc_final: 0.8722 (mppt) REVERT: r 85 LYS cc_start: 0.8530 (ttmt) cc_final: 0.8042 (ttmt) REVERT: r 86 GLN cc_start: 0.8556 (mt0) cc_final: 0.8352 (mt0) REVERT: s 2 GLU cc_start: 0.7442 (mt-10) cc_final: 0.7173 (mt-10) REVERT: s 38 TYR cc_start: 0.8940 (m-80) cc_final: 0.8709 (m-80) REVERT: s 88 ARG cc_start: 0.8041 (mmm-85) cc_final: 0.7813 (mmm-85) REVERT: t 1 MET cc_start: -0.0453 (mtt) cc_final: -0.0755 (mtt) REVERT: t 18 GLU cc_start: 0.8440 (pt0) cc_final: 0.7907 (pp20) REVERT: t 25 GLU cc_start: 0.8849 (pt0) cc_final: 0.8625 (pt0) REVERT: u 94 PHE cc_start: 0.8572 (p90) cc_final: 0.7896 (p90) REVERT: v 18 ARG cc_start: 0.9014 (mtt90) cc_final: 0.8737 (mtm-85) REVERT: v 45 ASP cc_start: 0.9023 (p0) cc_final: 0.8809 (p0) REVERT: v 46 LYS cc_start: 0.8594 (mmtp) cc_final: 0.7979 (mmtt) REVERT: v 50 MET cc_start: 0.8456 (mmm) cc_final: 0.8245 (mmm) REVERT: v 51 GLN cc_start: 0.8842 (pp30) cc_final: 0.8631 (pp30) REVERT: v 88 HIS cc_start: 0.8153 (t-90) cc_final: 0.7600 (t-170) REVERT: w 8 ASN cc_start: 0.6456 (m-40) cc_final: 0.6218 (p0) REVERT: w 20 LYS cc_start: 0.8457 (mmtt) cc_final: 0.8085 (mmtt) REVERT: w 74 LYS cc_start: 0.9011 (mttm) cc_final: 0.8184 (mtmt) REVERT: x 9 LYS cc_start: 0.7594 (mttm) cc_final: 0.7124 (mttm) REVERT: x 16 ASN cc_start: 0.9331 (t0) cc_final: 0.9076 (m-40) REVERT: y 5 GLU cc_start: 0.8721 (tt0) cc_final: 0.8325 (tp30) REVERT: y 6 LEU cc_start: 0.7868 (tt) cc_final: 0.7623 (tt) REVERT: y 13 GLU cc_start: 0.8195 (pt0) cc_final: 0.7595 (pt0) REVERT: y 23 ARG cc_start: 0.8020 (mmt180) cc_final: 0.7353 (mmm160) REVERT: y 45 GLN cc_start: 0.8779 (pt0) cc_final: 0.8515 (pp30) REVERT: y 48 ARG cc_start: 0.9248 (mmt90) cc_final: 0.8769 (mmt90) REVERT: z 2 LYS cc_start: 0.8167 (ptmm) cc_final: 0.7544 (tttt) REVERT: z 24 LEU cc_start: 0.8746 (tp) cc_final: 0.8420 (tp) REVERT: z 30 ARG cc_start: 0.6635 (pmt170) cc_final: 0.5840 (pmt170) REVERT: z 33 HIS cc_start: 0.8491 (t-170) cc_final: 0.8247 (t-170) REVERT: z 52 PHE cc_start: 0.8577 (p90) cc_final: 0.8352 (p90) REVERT: B 9 ARG cc_start: 0.8513 (mtt90) cc_final: 0.6316 (mtp180) REVERT: B 12 ARG cc_start: 0.7830 (mtm110) cc_final: 0.7000 (mtm180) REVERT: B 48 TYR cc_start: 0.8704 (t80) cc_final: 0.8475 (t80) REVERT: C 28 THR cc_start: 0.8373 (p) cc_final: 0.7522 (p) REVERT: E 39 ARG cc_start: 0.8795 (ttt180) cc_final: 0.8413 (ttt180) REVERT: F 4 ARG cc_start: 0.7928 (ptp-170) cc_final: 0.7542 (ptp-170) REVERT: F 18 LYS cc_start: 0.8225 (tttm) cc_final: 0.7930 (tptm) REVERT: F 19 ARG cc_start: 0.8362 (ttm170) cc_final: 0.7959 (tpp80) REVERT: G 26 MET cc_start: 0.7530 (mmm) cc_final: 0.6604 (tmm) REVERT: G 37 VAL cc_start: 0.8511 (OUTLIER) cc_final: 0.8308 (t) REVERT: G 183 PHE cc_start: 0.6336 (OUTLIER) cc_final: 0.5839 (m-10) REVERT: G 197 PHE cc_start: 0.8125 (m-80) cc_final: 0.7586 (m-80) REVERT: I 46 ARG cc_start: 0.8467 (mpp-170) cc_final: 0.8165 (ttp80) REVERT: I 74 TYR cc_start: 0.8475 (m-10) cc_final: 0.8180 (m-80) REVERT: I 76 LYS cc_start: 0.9375 (pttm) cc_final: 0.9121 (pttt) REVERT: I 77 GLU cc_start: 0.9403 (mm-30) cc_final: 0.8911 (mm-30) REVERT: I 88 ASN cc_start: 0.8709 (m110) cc_final: 0.8327 (m-40) REVERT: I 92 LEU cc_start: 0.8291 (mt) cc_final: 0.6979 (mt) REVERT: I 151 GLN cc_start: 0.8865 (mm110) cc_final: 0.8565 (mm110) REVERT: I 184 LYS cc_start: 0.9257 (tptt) cc_final: 0.8948 (tptt) REVERT: J 29 ILE cc_start: 0.6764 (tt) cc_final: 0.6485 (mm) REVERT: J 110 MET cc_start: 0.7297 (tpt) cc_final: 0.6966 (tpp) REVERT: J 137 ARG cc_start: 0.7592 (ttm-80) cc_final: 0.6989 (mtm180) REVERT: K 4 TYR cc_start: 0.6456 (m-80) cc_final: 0.6129 (m-80) REVERT: K 6 ILE cc_start: 0.7910 (OUTLIER) cc_final: 0.7618 (mm) REVERT: K 71 ILE cc_start: 0.8759 (mm) cc_final: 0.8520 (mm) REVERT: K 90 MET cc_start: 0.3704 (mtm) cc_final: 0.3362 (mtt) REVERT: L 29 LEU cc_start: 0.6571 (tt) cc_final: 0.5745 (mt) REVERT: L 30 MET cc_start: 0.5710 (tmm) cc_final: 0.4640 (tmm) REVERT: L 142 ARG cc_start: 0.6549 (ttp80) cc_final: 0.6177 (tpt-90) REVERT: M 32 LYS cc_start: 0.8805 (mptt) cc_final: 0.8569 (mmtt) REVERT: M 84 ILE cc_start: 0.8333 (mt) cc_final: 0.7933 (mm) REVERT: M 93 LYS cc_start: 0.7495 (mppt) cc_final: 0.7054 (mppt) REVERT: P 127 ARG cc_start: 0.6282 (OUTLIER) cc_final: 0.5580 (mtm110) REVERT: Q 11 ARG cc_start: 0.6534 (mmt180) cc_final: 0.5721 (mpt180) REVERT: Q 107 LYS cc_start: 0.6298 (tttp) cc_final: 0.5810 (mmtm) REVERT: Q 116 TYR cc_start: 0.7574 (m-80) cc_final: 0.7125 (m-80) REVERT: R 68 LEU cc_start: 0.8497 (mt) cc_final: 0.8283 (mt) REVERT: R 70 ARG cc_start: 0.7797 (mtm180) cc_final: 0.7056 (tmt-80) REVERT: R 74 MET cc_start: 0.2697 (tmm) cc_final: 0.1610 (tmm) REVERT: T 27 GLN cc_start: 0.8382 (mp10) cc_final: 0.8153 (mp10) REVERT: T 63 ARG cc_start: 0.8470 (mmt180) cc_final: 0.7686 (tpt170) REVERT: T 64 LYS cc_start: 0.8828 (mmtm) cc_final: 0.8494 (tmtt) REVERT: T 88 ARG cc_start: 0.5540 (mpp-170) cc_final: 0.2803 (mpt90) REVERT: U 3 THR cc_start: 0.7410 (p) cc_final: 0.7160 (p) REVERT: U 16 PHE cc_start: 0.5952 (t80) cc_final: 0.5499 (t80) REVERT: U 39 PHE cc_start: 0.7026 (t80) cc_final: 0.6192 (t80) REVERT: V 10 ARG cc_start: 0.7914 (ttp80) cc_final: 0.7705 (tpp80) REVERT: V 33 TYR cc_start: 0.6099 (m-80) cc_final: 0.5606 (m-10) REVERT: V 62 GLU cc_start: 0.5414 (tt0) cc_final: 0.4647 (tt0) REVERT: V 72 TRP cc_start: 0.6237 (m100) cc_final: 0.5895 (m100) REVERT: X 36 ARG cc_start: 0.7503 (ptt-90) cc_final: 0.7110 (ptp-170) REVERT: Y 17 ARG cc_start: 0.7424 (tmt170) cc_final: 0.7145 (tmt170) REVERT: Y 23 ARG cc_start: 0.8859 (mmm-85) cc_final: 0.8656 (mmm-85) REVERT: Y 27 MET cc_start: 0.9219 (tpt) cc_final: 0.8958 (tpp) REVERT: Y 38 ILE cc_start: 0.9597 (tp) cc_final: 0.9335 (tp) REVERT: Z 39 LYS cc_start: 0.7940 (mmmt) cc_final: 0.7555 (mmtt) REVERT: Z 43 GLU cc_start: 0.7627 (pp20) cc_final: 0.7326 (tm-30) REVERT: a 216 THR cc_start: 0.4103 (t) cc_final: 0.3288 (p) REVERT: 8 16 GLU cc_start: 0.7649 (mp0) cc_final: 0.6894 (mp0) REVERT: 8 21 ARG cc_start: 0.4465 (mtt180) cc_final: 0.3190 (mpt180) REVERT: 8 41 PHE cc_start: 0.8893 (t80) cc_final: 0.8046 (t80) REVERT: 8 97 GLU cc_start: 0.8531 (tt0) cc_final: 0.8100 (tp30) REVERT: 9 18 THR cc_start: 0.6207 (t) cc_final: 0.5969 (p) REVERT: 9 38 HIS cc_start: 0.6760 (m-70) cc_final: 0.6506 (m90) outliers start: 63 outliers final: 18 residues processed: 1830 average time/residue: 1.5040 time to fit residues: 4666.8668 Evaluate side-chains 1347 residues out of total 5093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 1324 time to evaluate : 6.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 40 LEU Chi-restraints excluded: chain h residue 59 LEU Chi-restraints excluded: chain j residue 3 THR Chi-restraints excluded: chain j residue 142 ILE Chi-restraints excluded: chain m residue 136 MET Chi-restraints excluded: chain o residue 40 ILE Chi-restraints excluded: chain q residue 59 LEU Chi-restraints excluded: chain F residue 33 HIS Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 183 PHE Chi-restraints excluded: chain I residue 7 LYS Chi-restraints excluded: chain K residue 6 ILE Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain N residue 24 ASN Chi-restraints excluded: chain P residue 127 ARG Chi-restraints excluded: chain R residue 53 ASP Chi-restraints excluded: chain U residue 78 VAL Chi-restraints excluded: chain V residue 7 LEU Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain Z residue 37 TYR Chi-restraints excluded: chain a residue 5 THR Chi-restraints excluded: chain a residue 55 SER Chi-restraints excluded: chain 8 residue 107 PRO Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1065 random chunks: chunk 899 optimal weight: 10.0000 chunk 807 optimal weight: 10.0000 chunk 447 optimal weight: 20.0000 chunk 275 optimal weight: 50.0000 chunk 544 optimal weight: 10.0000 chunk 431 optimal weight: 5.9990 chunk 834 optimal weight: 10.0000 chunk 323 optimal weight: 10.0000 chunk 507 optimal weight: 20.0000 chunk 621 optimal weight: 30.0000 chunk 967 optimal weight: 20.0000 overall best weight: 9.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 36 ASN b 57 HIS ** b 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 199 HIS b 225 ASN ** c 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 67 HIS ** d 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 41 GLN ** d 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 195 GLN e 4 HIS e 22 ASN e 51 ASN e 126 ASN f 37 ASN f 100 ASN f 127 GLN g 28 ASN g 133 GLN h 122 GLN i 11 GLN ** i 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 5 GLN k 29 HIS k 89 ASN l 54 GLN ** m 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 18 GLN n 62 ASN n 107 ASN ** p 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 114 ASN q 19 GLN r 82 HIS r 89 HIS s 9 HIS s 61 ASN u 73 ASN v 44 HIS ** v 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 53 HIS ** y 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 36 GLN y 58 ASN z 48 ASN B 3 GLN B 41 HIS ** D 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 41 ASN G 92 ASN ** G 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 176 ASN ** H 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 138 GLN ** I 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 99 ASN ** J 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 8 GLN L 129 ASN M 3 GLN ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 GLN N 49 GLN N 109 GLN P 117 HIS Q 4 ASN Q 111 GLN ** R 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 59 GLN ** T 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 9 HIS ** V 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 52 ASN X 55 GLN ** Y 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 67 HIS Y 74 HIS ** a 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 28 GLN ** 8 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 61 HIS ** 8 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 28 GLN ** 9 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 9 61 HIS Total number of N/Q/H flips: 63 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.3028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.100 161229 Z= 0.398 Angle : 0.849 15.737 240720 Z= 0.432 Chirality : 0.044 0.599 30724 Planarity : 0.007 0.105 13231 Dihedral : 23.158 179.970 79572 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 26.67 Ramachandran Plot: Outliers : 0.28 % Allowed : 10.57 % Favored : 89.16 % Rotamer: Outliers : 5.93 % Allowed : 18.54 % Favored : 75.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % Cis-general : 0.00 % Twisted Proline : 0.49 % 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: -4.24 (0.09), residues: 6142 helix: -2.54 (0.10), residues: 1768 sheet: -2.46 (0.16), residues: 882 loop : -3.17 (0.09), residues: 3492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.004 TRP m 64 HIS 0.015 0.002 HIS 9 7 PHE 0.028 0.003 PHE l 64 TYR 0.041 0.003 TYR M 85 ARG 0.017 0.001 ARG d 117 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12284 Ramachandran restraints generated. 6142 Oldfield, 0 Emsley, 6142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12284 Ramachandran restraints generated. 6142 Oldfield, 0 Emsley, 6142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1746 residues out of total 5093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 302 poor density : 1444 time to evaluate : 6.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 36 ASN cc_start: 0.8208 (OUTLIER) cc_final: 0.8004 (t0) REVERT: b 83 ASP cc_start: 0.8032 (t0) cc_final: 0.7663 (t0) REVERT: b 146 LYS cc_start: 0.7046 (tptt) cc_final: 0.6005 (tptt) REVERT: b 206 LYS cc_start: 0.8266 (pttt) cc_final: 0.8014 (pttp) REVERT: b 228 ASP cc_start: 0.8438 (OUTLIER) cc_final: 0.7871 (t70) REVERT: c 28 GLU cc_start: 0.9041 (tm-30) cc_final: 0.8810 (tp30) REVERT: c 36 GLN cc_start: 0.8301 (tt0) cc_final: 0.7986 (tp-100) REVERT: c 64 GLU cc_start: 0.9015 (mm-30) cc_final: 0.8520 (mm-30) REVERT: c 148 GLN cc_start: 0.8463 (mp10) cc_final: 0.8158 (mm-40) REVERT: c 185 ASN cc_start: 0.9035 (m-40) cc_final: 0.8536 (m110) REVERT: d 6 LYS cc_start: 0.8232 (ptmt) cc_final: 0.7668 (pttm) REVERT: d 23 PHE cc_start: 0.7704 (t80) cc_final: 0.7128 (p90) REVERT: d 122 GLU cc_start: 0.8341 (tm-30) cc_final: 0.8099 (tm-30) REVERT: d 146 VAL cc_start: 0.9409 (p) cc_final: 0.9202 (m) REVERT: d 168 ASP cc_start: 0.8132 (t0) cc_final: 0.7890 (t0) REVERT: d 183 PHE cc_start: 0.8584 (m-80) cc_final: 0.8359 (m-80) REVERT: d 184 ASP cc_start: 0.9023 (t70) cc_final: 0.8759 (t70) REVERT: d 188 MET cc_start: 0.9190 (mmt) cc_final: 0.8854 (mmt) REVERT: e 6 TYR cc_start: 0.9024 (t80) cc_final: 0.8692 (t80) REVERT: e 37 MET cc_start: 0.5181 (tpt) cc_final: 0.4954 (tpt) REVERT: e 78 ILE cc_start: 0.8957 (mt) cc_final: 0.8695 (mm) REVERT: e 97 GLU cc_start: 0.8235 (tp30) cc_final: 0.7980 (tm-30) REVERT: e 109 ARG cc_start: 0.9050 (tpm170) cc_final: 0.8297 (tpm170) REVERT: e 126 ASN cc_start: 0.8489 (m-40) cc_final: 0.8011 (m-40) REVERT: e 133 GLU cc_start: 0.6663 (tp30) cc_final: 0.6331 (tp30) REVERT: e 176 PHE cc_start: 0.7627 (m-80) cc_final: 0.7392 (m-80) REVERT: e 177 ARG cc_start: 0.7770 (ttt180) cc_final: 0.7318 (tpt170) REVERT: f 23 ILE cc_start: 0.8570 (mt) cc_final: 0.8133 (tp) REVERT: f 34 ARG cc_start: 0.7994 (mmm-85) cc_final: 0.7713 (mmm-85) REVERT: f 132 LEU cc_start: 0.9026 (tp) cc_final: 0.8735 (tt) REVERT: f 137 LYS cc_start: 0.8805 (tmtt) cc_final: 0.8506 (mmtt) REVERT: g 15 LEU cc_start: 0.8933 (tt) cc_final: 0.8708 (tp) REVERT: g 22 LYS cc_start: 0.8460 (mtmm) cc_final: 0.8101 (ptpt) REVERT: g 46 PHE cc_start: 0.8588 (m-10) cc_final: 0.8225 (m-10) REVERT: g 87 GLU cc_start: 0.8110 (tp30) cc_final: 0.7787 (pm20) REVERT: h 52 MET cc_start: 0.8672 (tmm) cc_final: 0.8469 (tpp) REVERT: h 86 MET cc_start: 0.3201 (mmm) cc_final: 0.2372 (tpp) REVERT: h 116 GLU cc_start: 0.8933 (mm-30) cc_final: 0.8443 (mm-30) REVERT: i 41 PHE cc_start: 0.8781 (t80) cc_final: 0.8389 (t80) REVERT: i 112 LYS cc_start: 0.5519 (pttp) cc_final: 0.5227 (pptt) REVERT: j 36 LEU cc_start: 0.9113 (OUTLIER) cc_final: 0.8601 (mm) REVERT: j 49 ASP cc_start: 0.7549 (OUTLIER) cc_final: 0.6589 (t70) REVERT: j 111 LYS cc_start: 0.8448 (mppt) cc_final: 0.8238 (mppt) REVERT: j 141 ASP cc_start: 0.8602 (t0) cc_final: 0.8220 (t0) REVERT: k 29 HIS cc_start: 0.8187 (t70) cc_final: 0.7785 (t-90) REVERT: k 41 ILE cc_start: 0.8746 (pt) cc_final: 0.8438 (mm) REVERT: k 66 LYS cc_start: 0.8481 (tttt) cc_final: 0.7900 (tttt) REVERT: l 39 LYS cc_start: 0.8968 (pttt) cc_final: 0.8384 (pttt) REVERT: l 76 GLU cc_start: 0.7790 (mt-10) cc_final: 0.7443 (mt-10) REVERT: n 20 MET cc_start: 0.8935 (OUTLIER) cc_final: 0.8290 (tpp) REVERT: n 62 ASN cc_start: 0.7932 (m110) cc_final: 0.7729 (m-40) REVERT: n 94 TYR cc_start: 0.7732 (m-80) cc_final: 0.7409 (m-80) REVERT: o 12 THR cc_start: 0.9431 (p) cc_final: 0.9177 (p) REVERT: o 15 ARG cc_start: 0.8174 (mtt90) cc_final: 0.7811 (mtt-85) REVERT: o 87 ILE cc_start: 0.7970 (mm) cc_final: 0.7573 (tp) REVERT: o 98 GLN cc_start: 0.7630 (tt0) cc_final: 0.7093 (tt0) REVERT: p 12 MET cc_start: 0.8184 (mtm) cc_final: 0.6800 (tmm) REVERT: p 37 LYS cc_start: 0.8535 (mttm) cc_final: 0.8207 (mptt) REVERT: p 50 ARG cc_start: 0.8496 (ttt180) cc_final: 0.7961 (ttt180) REVERT: p 74 GLN cc_start: 0.8402 (mp10) cc_final: 0.7495 (mp10) REVERT: p 86 LYS cc_start: 0.9225 (mmtp) cc_final: 0.8991 (mmpt) REVERT: p 93 LYS cc_start: 0.8758 (tppt) cc_final: 0.8387 (tppt) REVERT: p 100 ARG cc_start: 0.8026 (mtp180) cc_final: 0.7310 (tmt170) REVERT: q 2 ARG cc_start: 0.7688 (OUTLIER) cc_final: 0.7453 (ttm-80) REVERT: q 21 LYS cc_start: 0.8624 (mmtt) cc_final: 0.8331 (ttmm) REVERT: q 24 TYR cc_start: 0.7621 (t80) cc_final: 0.7213 (t80) REVERT: q 29 ARG cc_start: 0.8221 (ptp90) cc_final: 0.7933 (ptp90) REVERT: q 43 GLN cc_start: 0.8755 (tp40) cc_final: 0.8466 (tt0) REVERT: q 54 ARG cc_start: 0.8935 (mtm180) cc_final: 0.8528 (mtm-85) REVERT: q 56 PHE cc_start: 0.8818 (m-80) cc_final: 0.8544 (m-10) REVERT: q 88 GLU cc_start: 0.8384 (mp0) cc_final: 0.7970 (mp0) REVERT: q 110 GLU cc_start: 0.8822 (mm-30) cc_final: 0.8199 (mm-30) REVERT: r 10 LYS cc_start: 0.7241 (mtpp) cc_final: 0.6981 (mtpp) REVERT: r 16 GLU cc_start: 0.7935 (tt0) cc_final: 0.7733 (tt0) REVERT: r 24 LYS cc_start: 0.8100 (tptt) cc_final: 0.7816 (tptt) REVERT: r 52 PRO cc_start: 0.8385 (Cg_endo) cc_final: 0.7863 (Cg_exo) REVERT: r 81 LYS cc_start: 0.8616 (mmtm) cc_final: 0.7828 (mmtm) REVERT: s 38 TYR cc_start: 0.8896 (m-80) cc_final: 0.8529 (m-80) REVERT: t 1 MET cc_start: 0.0311 (mtt) cc_final: 0.0010 (mtt) REVERT: t 18 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.7778 (pp20) REVERT: t 25 GLU cc_start: 0.9056 (pt0) cc_final: 0.8715 (pt0) REVERT: t 32 LEU cc_start: 0.9653 (OUTLIER) cc_final: 0.9280 (pp) REVERT: u 53 GLN cc_start: 0.8770 (mm110) cc_final: 0.8564 (mm110) REVERT: u 100 GLU cc_start: 0.7909 (tm-30) cc_final: 0.7551 (tm-30) REVERT: v 1 MET cc_start: 0.8272 (tmm) cc_final: 0.8009 (ppp) REVERT: v 18 ARG cc_start: 0.9130 (mtt90) cc_final: 0.8901 (mtm-85) REVERT: v 46 LYS cc_start: 0.8643 (mmtp) cc_final: 0.7949 (mmtt) REVERT: v 50 MET cc_start: 0.8365 (mmm) cc_final: 0.8161 (mmm) REVERT: v 59 GLU cc_start: 0.8456 (mm-30) cc_final: 0.7557 (tp30) REVERT: x 16 ASN cc_start: 0.9385 (t0) cc_final: 0.9079 (m-40) REVERT: y 6 LEU cc_start: 0.7753 (tt) cc_final: 0.7489 (tt) REVERT: y 23 ARG cc_start: 0.8324 (mmt180) cc_final: 0.7959 (mmp-170) REVERT: y 30 MET cc_start: 0.8808 (mmm) cc_final: 0.8423 (mmm) REVERT: y 45 GLN cc_start: 0.8740 (pt0) cc_final: 0.8394 (pp30) REVERT: y 48 ARG cc_start: 0.9064 (mmt90) cc_final: 0.8758 (mmt90) REVERT: z 24 LEU cc_start: 0.9009 (tp) cc_final: 0.8679 (tp) REVERT: C 26 LYS cc_start: 0.8674 (mmtt) cc_final: 0.8124 (mmmm) REVERT: D 35 ARG cc_start: 0.9004 (mtt-85) cc_final: 0.8684 (mtt-85) REVERT: E 14 LYS cc_start: 0.8424 (mmmm) cc_final: 0.8203 (mmmt) REVERT: E 24 LYS cc_start: 0.8869 (tppp) cc_final: 0.8468 (tptp) REVERT: F 4 ARG cc_start: 0.8110 (ptp-170) cc_final: 0.7688 (ptp-170) REVERT: F 18 LYS cc_start: 0.8352 (tttm) cc_final: 0.8058 (tptm) REVERT: F 19 ARG cc_start: 0.8266 (ttm170) cc_final: 0.8037 (ttm110) REVERT: F 30 GLU cc_start: 0.8907 (mt-10) cc_final: 0.8689 (mp0) REVERT: G 26 MET cc_start: 0.7478 (mmm) cc_final: 0.6632 (tmm) REVERT: G 132 GLU cc_start: 0.8652 (tp30) cc_final: 0.8219 (tp30) REVERT: G 183 PHE cc_start: 0.6995 (OUTLIER) cc_final: 0.6615 (m-80) REVERT: G 197 PHE cc_start: 0.7796 (m-80) cc_final: 0.7321 (m-80) REVERT: H 5 HIS cc_start: 0.2515 (OUTLIER) cc_final: 0.2256 (m90) REVERT: I 88 ASN cc_start: 0.9113 (m110) cc_final: 0.8779 (m-40) REVERT: I 104 MET cc_start: 0.4026 (mmt) cc_final: 0.3606 (mmt) REVERT: I 151 GLN cc_start: 0.8784 (mm110) cc_final: 0.8392 (mm110) REVERT: I 154 VAL cc_start: 0.1427 (OUTLIER) cc_final: 0.0818 (p) REVERT: I 184 LYS cc_start: 0.9311 (tptt) cc_final: 0.9030 (tptt) REVERT: I 201 GLU cc_start: 0.9320 (mm-30) cc_final: 0.8553 (mm-30) REVERT: J 123 LEU cc_start: 0.5901 (OUTLIER) cc_final: 0.5593 (pp) REVERT: J 131 ASN cc_start: 0.7929 (t0) cc_final: 0.7710 (m-40) REVERT: K 4 TYR cc_start: 0.6726 (m-80) cc_final: 0.6398 (m-80) REVERT: K 71 ILE cc_start: 0.8783 (mm) cc_final: 0.8450 (mm) REVERT: K 88 MET cc_start: 0.4842 (ptm) cc_final: 0.4435 (tmm) REVERT: K 90 MET cc_start: 0.3803 (mtm) cc_final: 0.3060 (mtt) REVERT: L 95 ARG cc_start: 0.6926 (ttm170) cc_final: 0.6721 (mmt90) REVERT: L 100 MET cc_start: -0.0004 (mtt) cc_final: -0.0222 (mtt) REVERT: L 105 GLU cc_start: 0.5369 (pp20) cc_final: 0.5085 (pp20) REVERT: M 14 ARG cc_start: 0.8050 (OUTLIER) cc_final: 0.7674 (ptm160) REVERT: M 74 ILE cc_start: 0.8217 (tp) cc_final: 0.7405 (tp) REVERT: M 79 ARG cc_start: 0.9153 (ptt90) cc_final: 0.8769 (ptt90) REVERT: P 26 PHE cc_start: 0.7498 (OUTLIER) cc_final: 0.6953 (t80) REVERT: P 63 GLN cc_start: 0.5699 (OUTLIER) cc_final: 0.5367 (pp30) REVERT: Q 87 LYS cc_start: 0.8737 (tptp) cc_final: 0.7852 (tptm) REVERT: Q 107 LYS cc_start: 0.6643 (tttp) cc_final: 0.6065 (mmtm) REVERT: Q 116 TYR cc_start: 0.7513 (m-80) cc_final: 0.7011 (m-80) REVERT: R 68 LEU cc_start: 0.8545 (mt) cc_final: 0.8322 (mt) REVERT: R 74 MET cc_start: 0.3009 (tmm) cc_final: 0.1920 (mmt) REVERT: S 5 MET cc_start: -0.1203 (tmm) cc_final: -0.1669 (ppp) REVERT: T 27 GLN cc_start: 0.8042 (mp10) cc_final: 0.7799 (mp10) REVERT: T 44 GLU cc_start: 0.8709 (tp30) cc_final: 0.8400 (tp30) REVERT: T 46 LYS cc_start: 0.8103 (pttt) cc_final: 0.7710 (pttt) REVERT: T 57 ARG cc_start: 0.8464 (ttt-90) cc_final: 0.7542 (ttt-90) REVERT: T 64 LYS cc_start: 0.8842 (mmtm) cc_final: 0.8639 (tmtt) REVERT: T 88 ARG cc_start: 0.6218 (mpp-170) cc_final: 0.4772 (mtt180) REVERT: U 39 PHE cc_start: 0.7294 (t80) cc_final: 0.6849 (t80) REVERT: U 56 ARG cc_start: 0.7439 (mmm160) cc_final: 0.6856 (tpm170) REVERT: U 57 ILE cc_start: 0.4093 (OUTLIER) cc_final: 0.3887 (mp) REVERT: U 59 HIS cc_start: 0.9017 (t-90) cc_final: 0.8746 (t-90) REVERT: V 62 GLU cc_start: 0.5153 (tt0) cc_final: 0.4754 (tt0) REVERT: W 29 LYS cc_start: 0.7954 (mmtt) cc_final: 0.7555 (mmmt) REVERT: W 30 ASN cc_start: 0.8889 (m110) cc_final: 0.8664 (p0) REVERT: X 80 ARG cc_start: 0.3920 (ttm170) cc_final: 0.3572 (ttm170) REVERT: Y 17 ARG cc_start: 0.7786 (tmt170) cc_final: 0.7534 (tmt170) REVERT: Y 20 ASN cc_start: 0.8329 (m110) cc_final: 0.8057 (p0) REVERT: Y 54 GLN cc_start: 0.8328 (tt0) cc_final: 0.8004 (tp-100) REVERT: Y 68 LYS cc_start: 0.6511 (mttt) cc_final: 0.6296 (mttt) REVERT: a 216 THR cc_start: 0.4105 (t) cc_final: 0.3859 (p) REVERT: 8 16 GLU cc_start: 0.8113 (mp0) cc_final: 0.7513 (mp0) REVERT: 8 21 ARG cc_start: 0.4891 (mtt180) cc_final: 0.3467 (mpt180) REVERT: 8 41 PHE cc_start: 0.9038 (t80) cc_final: 0.7934 (t80) REVERT: 9 73 LYS cc_start: 0.6937 (ttpt) cc_final: 0.6467 (ttmm) outliers start: 302 outliers final: 198 residues processed: 1595 average time/residue: 1.3331 time to fit residues: 3614.1771 Evaluate side-chains 1466 residues out of total 5093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 214 poor density : 1252 time to evaluate : 6.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 3 VAL Chi-restraints excluded: chain b residue 8 THR Chi-restraints excluded: chain b residue 32 LEU Chi-restraints excluded: chain b residue 33 LEU Chi-restraints excluded: chain b residue 36 ASN Chi-restraints excluded: chain b residue 37 SER Chi-restraints excluded: chain b residue 48 ILE Chi-restraints excluded: chain b residue 128 THR Chi-restraints excluded: chain b residue 175 LEU Chi-restraints excluded: chain b residue 222 THR Chi-restraints excluded: chain b residue 228 ASP Chi-restraints excluded: chain b residue 239 PHE Chi-restraints excluded: chain b residue 266 ILE Chi-restraints excluded: chain c residue 100 LEU Chi-restraints excluded: chain c residue 121 THR Chi-restraints excluded: chain c residue 168 GLU Chi-restraints excluded: chain c residue 170 VAL Chi-restraints excluded: chain c residue 180 VAL Chi-restraints excluded: chain c residue 189 VAL Chi-restraints excluded: chain c residue 201 LEU Chi-restraints excluded: chain d residue 4 VAL Chi-restraints excluded: chain d residue 7 ASP Chi-restraints excluded: chain d residue 65 THR Chi-restraints excluded: chain d residue 92 HIS Chi-restraints excluded: chain d residue 169 VAL Chi-restraints excluded: chain d residue 193 VAL Chi-restraints excluded: chain e residue 4 HIS Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 56 LEU Chi-restraints excluded: chain e residue 112 ASP Chi-restraints excluded: chain e residue 148 VAL Chi-restraints excluded: chain e residue 153 ILE Chi-restraints excluded: chain e residue 157 THR Chi-restraints excluded: chain f residue 9 VAL Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 19 ASN Chi-restraints excluded: chain f residue 29 ASN Chi-restraints excluded: chain f residue 42 VAL Chi-restraints excluded: chain f residue 49 LEU Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 102 ILE Chi-restraints excluded: chain f residue 104 LEU Chi-restraints excluded: chain f residue 136 ASP Chi-restraints excluded: chain f residue 147 LEU Chi-restraints excluded: chain g residue 4 ILE Chi-restraints excluded: chain g residue 144 VAL Chi-restraints excluded: chain g residue 146 VAL Chi-restraints excluded: chain h residue 82 ILE Chi-restraints excluded: chain i residue 135 MET Chi-restraints excluded: chain j residue 3 THR Chi-restraints excluded: chain j residue 11 VAL Chi-restraints excluded: chain j residue 36 LEU Chi-restraints excluded: chain j residue 49 ASP Chi-restraints excluded: chain j residue 91 GLU Chi-restraints excluded: chain j residue 101 ILE Chi-restraints excluded: chain j residue 142 ILE Chi-restraints excluded: chain k residue 21 CYS Chi-restraints excluded: chain k residue 22 ILE Chi-restraints excluded: chain k residue 24 VAL Chi-restraints excluded: chain k residue 62 VAL Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 77 ILE Chi-restraints excluded: chain k residue 104 THR Chi-restraints excluded: chain l residue 47 ARG Chi-restraints excluded: chain l residue 67 THR Chi-restraints excluded: chain l residue 128 THR Chi-restraints excluded: chain m residue 2 LEU Chi-restraints excluded: chain m residue 20 LEU Chi-restraints excluded: chain m residue 28 PHE Chi-restraints excluded: chain m residue 42 THR Chi-restraints excluded: chain m residue 54 THR Chi-restraints excluded: chain m residue 106 ASP Chi-restraints excluded: chain m residue 128 THR Chi-restraints excluded: chain m residue 135 VAL Chi-restraints excluded: chain m residue 136 MET Chi-restraints excluded: chain n residue 9 GLN Chi-restraints excluded: chain n residue 18 GLN Chi-restraints excluded: chain n residue 20 MET Chi-restraints excluded: chain n residue 36 THR Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain o residue 35 ILE Chi-restraints excluded: chain o residue 47 VAL Chi-restraints excluded: chain o residue 53 THR Chi-restraints excluded: chain o residue 58 ILE Chi-restraints excluded: chain o residue 83 LEU Chi-restraints excluded: chain o residue 90 VAL Chi-restraints excluded: chain o residue 93 ASP Chi-restraints excluded: chain p residue 23 ASP Chi-restraints excluded: chain p residue 60 VAL Chi-restraints excluded: chain p residue 67 GLU Chi-restraints excluded: chain p residue 75 THR Chi-restraints excluded: chain q residue 2 ARG Chi-restraints excluded: chain q residue 19 GLN Chi-restraints excluded: chain q residue 33 VAL Chi-restraints excluded: chain q residue 59 LEU Chi-restraints excluded: chain q residue 61 ILE Chi-restraints excluded: chain r residue 15 SER Chi-restraints excluded: chain r residue 22 LEU Chi-restraints excluded: chain r residue 49 ILE Chi-restraints excluded: chain r residue 51 VAL Chi-restraints excluded: chain r residue 75 VAL Chi-restraints excluded: chain s residue 53 SER Chi-restraints excluded: chain s residue 76 VAL Chi-restraints excluded: chain s residue 96 ILE Chi-restraints excluded: chain s residue 100 THR Chi-restraints excluded: chain s residue 105 VAL Chi-restraints excluded: chain t residue 16 VAL Chi-restraints excluded: chain t residue 18 GLU Chi-restraints excluded: chain t residue 29 THR Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain t residue 34 VAL Chi-restraints excluded: chain t residue 86 THR Chi-restraints excluded: chain u residue 11 ILE Chi-restraints excluded: chain u residue 35 VAL Chi-restraints excluded: chain u residue 82 VAL Chi-restraints excluded: chain v residue 8 VAL Chi-restraints excluded: chain v residue 62 THR Chi-restraints excluded: chain v residue 63 ILE Chi-restraints excluded: chain v residue 64 VAL Chi-restraints excluded: chain v residue 77 VAL Chi-restraints excluded: chain v residue 92 VAL Chi-restraints excluded: chain w residue 19 VAL Chi-restraints excluded: chain w residue 27 VAL Chi-restraints excluded: chain w residue 34 VAL Chi-restraints excluded: chain x residue 13 THR Chi-restraints excluded: chain x residue 67 LEU Chi-restraints excluded: chain y residue 11 VAL Chi-restraints excluded: chain y residue 18 LEU Chi-restraints excluded: chain z residue 13 ILE Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain C residue 9 LYS Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 43 LEU Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain F residue 13 ASN Chi-restraints excluded: chain F residue 23 ILE Chi-restraints excluded: chain G residue 5 MET Chi-restraints excluded: chain G residue 14 HIS Chi-restraints excluded: chain G residue 15 PHE Chi-restraints excluded: chain G residue 128 LEU Chi-restraints excluded: chain G residue 183 PHE Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 190 SER Chi-restraints excluded: chain H residue 5 HIS Chi-restraints excluded: chain H residue 182 ASP Chi-restraints excluded: chain H residue 192 TYR Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain I residue 180 THR Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain K residue 76 THR Chi-restraints excluded: chain K residue 78 PHE Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 47 GLU Chi-restraints excluded: chain M residue 14 ARG Chi-restraints excluded: chain M residue 37 ASN Chi-restraints excluded: chain M residue 48 PHE Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain M residue 112 ASP Chi-restraints excluded: chain M residue 126 CYS Chi-restraints excluded: chain M residue 128 VAL Chi-restraints excluded: chain N residue 125 GLN Chi-restraints excluded: chain O residue 14 ASP Chi-restraints excluded: chain O residue 69 THR Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 26 PHE Chi-restraints excluded: chain P residue 35 ASP Chi-restraints excluded: chain P residue 63 GLN Chi-restraints excluded: chain P residue 85 VAL Chi-restraints excluded: chain P residue 108 ASN Chi-restraints excluded: chain P residue 118 ASN Chi-restraints excluded: chain P residue 124 LYS Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain T residue 4 THR Chi-restraints excluded: chain T residue 17 ASP Chi-restraints excluded: chain T residue 24 THR Chi-restraints excluded: chain T residue 28 VAL Chi-restraints excluded: chain T residue 30 LEU Chi-restraints excluded: chain T residue 77 TYR Chi-restraints excluded: chain U residue 32 PHE Chi-restraints excluded: chain U residue 57 ILE Chi-restraints excluded: chain U residue 78 VAL Chi-restraints excluded: chain V residue 6 THR Chi-restraints excluded: chain V residue 7 LEU Chi-restraints excluded: chain V residue 29 LYS Chi-restraints excluded: chain V residue 46 HIS Chi-restraints excluded: chain W residue 64 LEU Chi-restraints excluded: chain X residue 15 LEU Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain X residue 59 VAL Chi-restraints excluded: chain X residue 72 GLU Chi-restraints excluded: chain X residue 76 THR Chi-restraints excluded: chain Y residue 3 ILE Chi-restraints excluded: chain Y residue 19 HIS Chi-restraints excluded: chain Y residue 52 GLU Chi-restraints excluded: chain Z residue 5 VAL Chi-restraints excluded: chain a residue 5 THR Chi-restraints excluded: chain a residue 55 SER Chi-restraints excluded: chain 8 residue 35 THR Chi-restraints excluded: chain 9 residue 28 GLN Chi-restraints excluded: chain 9 residue 35 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1065 random chunks: chunk 537 optimal weight: 10.0000 chunk 300 optimal weight: 6.9990 chunk 804 optimal weight: 20.0000 chunk 658 optimal weight: 10.0000 chunk 266 optimal weight: 4.9990 chunk 968 optimal weight: 10.0000 chunk 1046 optimal weight: 30.0000 chunk 862 optimal weight: 10.0000 chunk 960 optimal weight: 10.0000 chunk 330 optimal weight: 7.9990 chunk 777 optimal weight: 10.0000 overall best weight: 7.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 130 GLN ** d 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 110 HIS ** g 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 133 GLN h 6 GLN ** i 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 106 GLN i 110 GLN ** j 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 5 GLN l 38 GLN ** m 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 15 GLN s 40 ASN ** v 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 22 ASN y 36 GLN ** D 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 30 HIS ** F 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 HIS ** H 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 73 ASN ** J 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 51 GLN M 75 GLN P 27 ASN Q 28 GLN ** Q 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 79 GLN ** V 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 53 GLN ** W 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 31 ASN ** 8 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.4213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 161229 Z= 0.341 Angle : 0.758 14.022 240720 Z= 0.387 Chirality : 0.041 0.430 30724 Planarity : 0.006 0.085 13231 Dihedral : 23.596 179.643 79544 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 27.43 Ramachandran Plot: Outliers : 0.21 % Allowed : 12.36 % Favored : 87.43 % Rotamer: Outliers : 6.97 % Allowed : 21.72 % Favored : 71.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % Cis-general : 0.00 % Twisted Proline : 0.49 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.71 (0.09), residues: 6142 helix: -1.86 (0.11), residues: 1756 sheet: -2.22 (0.16), residues: 870 loop : -2.95 (0.09), residues: 3516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP V 72 HIS 0.015 0.002 HIS j 40 PHE 0.031 0.003 PHE g 29 TYR 0.036 0.002 TYR J 127 ARG 0.012 0.001 ARG n 17 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12284 Ramachandran restraints generated. 6142 Oldfield, 0 Emsley, 6142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12284 Ramachandran restraints generated. 6142 Oldfield, 0 Emsley, 6142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1712 residues out of total 5093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 355 poor density : 1357 time to evaluate : 6.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 103 ILE cc_start: 0.9217 (pt) cc_final: 0.8995 (mp) REVERT: b 228 ASP cc_start: 0.8487 (OUTLIER) cc_final: 0.8038 (t70) REVERT: c 28 GLU cc_start: 0.8907 (tm-30) cc_final: 0.8671 (tp30) REVERT: c 36 GLN cc_start: 0.8249 (tt0) cc_final: 0.7999 (tp-100) REVERT: c 64 GLU cc_start: 0.8884 (mm-30) cc_final: 0.8539 (mm-30) REVERT: c 148 GLN cc_start: 0.8554 (mp10) cc_final: 0.8201 (mm-40) REVERT: c 185 ASN cc_start: 0.8965 (m-40) cc_final: 0.8580 (m110) REVERT: d 6 LYS cc_start: 0.8268 (ptmt) cc_final: 0.7757 (pttm) REVERT: d 9 GLN cc_start: 0.8610 (tm-30) cc_final: 0.8344 (tm-30) REVERT: d 23 PHE cc_start: 0.7662 (t80) cc_final: 0.7162 (p90) REVERT: d 119 ILE cc_start: 0.8416 (mm) cc_final: 0.7444 (tt) REVERT: d 120 VAL cc_start: 0.8843 (OUTLIER) cc_final: 0.8621 (p) REVERT: d 122 GLU cc_start: 0.8276 (tm-30) cc_final: 0.8042 (tm-30) REVERT: d 149 ILE cc_start: 0.7931 (OUTLIER) cc_final: 0.7354 (tp) REVERT: d 183 PHE cc_start: 0.8508 (m-80) cc_final: 0.8243 (m-80) REVERT: d 188 MET cc_start: 0.9091 (mmt) cc_final: 0.8784 (mmt) REVERT: e 6 TYR cc_start: 0.9012 (t80) cc_final: 0.8554 (t80) REVERT: e 97 GLU cc_start: 0.8139 (tp30) cc_final: 0.7743 (tp30) REVERT: e 99 PHE cc_start: 0.9361 (t80) cc_final: 0.8908 (t80) REVERT: e 102 LEU cc_start: 0.9115 (mt) cc_final: 0.8864 (pp) REVERT: e 109 ARG cc_start: 0.8966 (tpm170) cc_final: 0.8484 (tpm170) REVERT: e 139 GLU cc_start: 0.7352 (mp0) cc_final: 0.7041 (pm20) REVERT: e 166 ARG cc_start: 0.9018 (OUTLIER) cc_final: 0.8676 (tmm-80) REVERT: e 176 PHE cc_start: 0.7811 (m-80) cc_final: 0.7376 (m-80) REVERT: e 177 ARG cc_start: 0.7725 (ttt180) cc_final: 0.7266 (tpt170) REVERT: f 82 PHE cc_start: 0.7661 (OUTLIER) cc_final: 0.7174 (m-10) REVERT: f 132 LEU cc_start: 0.9144 (tp) cc_final: 0.8909 (tp) REVERT: f 137 LYS cc_start: 0.8809 (tmtt) cc_final: 0.8485 (mmtt) REVERT: g 17 ASP cc_start: 0.8506 (t70) cc_final: 0.7438 (p0) REVERT: g 18 GLN cc_start: 0.8495 (mp10) cc_final: 0.8105 (pm20) REVERT: g 22 LYS cc_start: 0.8401 (mtmm) cc_final: 0.8123 (ptpt) REVERT: g 46 PHE cc_start: 0.8562 (m-10) cc_final: 0.8200 (m-10) REVERT: g 55 GLU cc_start: 0.9144 (mt-10) cc_final: 0.8782 (mt-10) REVERT: g 87 GLU cc_start: 0.8109 (tp30) cc_final: 0.7854 (pm20) REVERT: g 133 GLN cc_start: 0.8876 (tt0) cc_final: 0.8301 (tm-30) REVERT: g 137 GLU cc_start: 0.8636 (pp20) cc_final: 0.8109 (pm20) REVERT: h 51 TYR cc_start: 0.4806 (OUTLIER) cc_final: 0.4601 (m-80) REVERT: h 86 MET cc_start: 0.3309 (mmm) cc_final: 0.3015 (tpp) REVERT: h 116 GLU cc_start: 0.8894 (mm-30) cc_final: 0.8489 (mm-30) REVERT: i 41 PHE cc_start: 0.8820 (t80) cc_final: 0.8487 (t80) REVERT: i 112 LYS cc_start: 0.5596 (pttp) cc_final: 0.4432 (tttt) REVERT: j 36 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8561 (mm) REVERT: j 111 LYS cc_start: 0.8488 (OUTLIER) cc_final: 0.8276 (mppt) REVERT: j 141 ASP cc_start: 0.8683 (t0) cc_final: 0.8289 (t0) REVERT: k 1 MET cc_start: 0.7743 (mtm) cc_final: 0.7498 (pmm) REVERT: k 5 GLN cc_start: 0.9063 (mm-40) cc_final: 0.8772 (mm-40) REVERT: k 29 HIS cc_start: 0.8299 (t70) cc_final: 0.7950 (t-90) REVERT: k 66 LYS cc_start: 0.8451 (tttt) cc_final: 0.7841 (tttt) REVERT: l 39 LYS cc_start: 0.8877 (pttt) cc_final: 0.8438 (pttt) REVERT: l 105 ILE cc_start: 0.8659 (mm) cc_final: 0.8436 (tp) REVERT: m 105 MET cc_start: 0.8886 (tpp) cc_final: 0.8623 (tpp) REVERT: n 103 ARG cc_start: 0.8109 (ttp-170) cc_final: 0.7864 (ttp80) REVERT: n 112 TYR cc_start: 0.8403 (m-80) cc_final: 0.8073 (m-80) REVERT: o 12 THR cc_start: 0.9510 (p) cc_final: 0.9259 (p) REVERT: o 87 ILE cc_start: 0.7715 (mm) cc_final: 0.7380 (tp) REVERT: o 98 GLN cc_start: 0.7801 (tt0) cc_final: 0.7333 (tt0) REVERT: p 5 LYS cc_start: 0.9195 (OUTLIER) cc_final: 0.8986 (ptpt) REVERT: p 37 LYS cc_start: 0.8483 (mttm) cc_final: 0.8183 (mptt) REVERT: p 50 ARG cc_start: 0.8545 (ttt180) cc_final: 0.8059 (ttt180) REVERT: p 74 GLN cc_start: 0.8330 (mp10) cc_final: 0.7628 (mp10) REVERT: p 93 LYS cc_start: 0.8759 (tppt) cc_final: 0.8349 (tppt) REVERT: q 21 LYS cc_start: 0.8592 (mmtt) cc_final: 0.8389 (mttp) REVERT: q 24 TYR cc_start: 0.7573 (t80) cc_final: 0.7202 (t80) REVERT: q 54 ARG cc_start: 0.8881 (mtm180) cc_final: 0.8351 (mtm-85) REVERT: q 88 GLU cc_start: 0.8510 (mp0) cc_final: 0.8105 (mp0) REVERT: q 106 THR cc_start: 0.9369 (p) cc_final: 0.9003 (p) REVERT: q 110 GLU cc_start: 0.8816 (mm-30) cc_final: 0.8159 (mm-30) REVERT: r 52 PRO cc_start: 0.8441 (Cg_endo) cc_final: 0.7810 (Cg_exo) REVERT: r 87 GLN cc_start: 0.5975 (tm-30) cc_final: 0.5568 (tm-30) REVERT: s 38 TYR cc_start: 0.8873 (m-80) cc_final: 0.8487 (m-80) REVERT: s 82 MET cc_start: 0.8254 (pmm) cc_final: 0.7873 (pmm) REVERT: t 1 MET cc_start: 0.0688 (mtt) cc_final: 0.0408 (mtt) REVERT: t 18 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7786 (pp20) REVERT: t 32 LEU cc_start: 0.9606 (OUTLIER) cc_final: 0.9217 (pp) REVERT: u 53 GLN cc_start: 0.8823 (mt0) cc_final: 0.8549 (mm110) REVERT: u 100 GLU cc_start: 0.8066 (tm-30) cc_final: 0.7623 (tm-30) REVERT: v 9 ARG cc_start: 0.7390 (mtp85) cc_final: 0.7187 (mtm180) REVERT: v 59 GLU cc_start: 0.8338 (mm-30) cc_final: 0.8069 (mm-30) REVERT: w 37 ARG cc_start: 0.8798 (tpp-160) cc_final: 0.8322 (tpm170) REVERT: w 62 LYS cc_start: 0.9105 (mtpt) cc_final: 0.8780 (mtpp) REVERT: x 16 ASN cc_start: 0.9211 (t0) cc_final: 0.8884 (m-40) REVERT: y 7 ARG cc_start: 0.9231 (ttp80) cc_final: 0.8759 (tmm160) REVERT: y 23 ARG cc_start: 0.8053 (mmt180) cc_final: 0.7658 (mmp-170) REVERT: y 45 GLN cc_start: 0.8705 (pt0) cc_final: 0.8261 (pp30) REVERT: y 56 LEU cc_start: 0.9029 (tp) cc_final: 0.8613 (tt) REVERT: z 24 LEU cc_start: 0.9055 (tp) cc_final: 0.8758 (tp) REVERT: C 26 LYS cc_start: 0.8775 (mmtt) cc_final: 0.8187 (mmmm) REVERT: D 28 ARG cc_start: 0.8749 (mtm-85) cc_final: 0.8271 (mtm-85) REVERT: D 29 GLN cc_start: 0.8916 (mm-40) cc_final: 0.8694 (mm-40) REVERT: D 35 ARG cc_start: 0.8987 (mtt-85) cc_final: 0.8574 (mtt-85) REVERT: D 37 LYS cc_start: 0.8444 (tptt) cc_final: 0.8207 (tptp) REVERT: E 22 LYS cc_start: 0.9077 (tptm) cc_final: 0.8739 (tppt) REVERT: E 39 ARG cc_start: 0.8581 (ttt180) cc_final: 0.8221 (ttt-90) REVERT: F 32 LYS cc_start: 0.8908 (OUTLIER) cc_final: 0.8617 (ptmt) REVERT: F 36 ARG cc_start: 0.7423 (ttt-90) cc_final: 0.7147 (mmm-85) REVERT: G 26 MET cc_start: 0.7478 (mmm) cc_final: 0.6514 (tmm) REVERT: G 38 HIS cc_start: 0.7540 (OUTLIER) cc_final: 0.6833 (m90) REVERT: G 95 TRP cc_start: 0.7911 (t-100) cc_final: 0.7582 (t-100) REVERT: G 139 GLU cc_start: 0.6347 (OUTLIER) cc_final: 0.5915 (pp20) REVERT: G 153 MET cc_start: 0.6153 (mmm) cc_final: 0.5899 (mmm) REVERT: G 183 PHE cc_start: 0.7049 (OUTLIER) cc_final: 0.6664 (m-80) REVERT: G 197 PHE cc_start: 0.7789 (m-80) cc_final: 0.7198 (m-80) REVERT: I 88 ASN cc_start: 0.9049 (m110) cc_final: 0.8719 (m-40) REVERT: I 104 MET cc_start: 0.4200 (mmt) cc_final: 0.3802 (mmt) REVERT: I 123 MET cc_start: 0.7280 (mmm) cc_final: 0.6920 (mmm) REVERT: I 128 VAL cc_start: 0.8253 (OUTLIER) cc_final: 0.7979 (p) REVERT: I 151 GLN cc_start: 0.8844 (mm110) cc_final: 0.8606 (mm110) REVERT: I 171 GLU cc_start: 0.5824 (OUTLIER) cc_final: 0.5560 (mp0) REVERT: I 184 LYS cc_start: 0.9315 (tptt) cc_final: 0.9029 (tptt) REVERT: I 187 ARG cc_start: 0.8852 (tpt90) cc_final: 0.8344 (tpt-90) REVERT: I 201 GLU cc_start: 0.9257 (mm-30) cc_final: 0.8311 (mm-30) REVERT: J 151 MET cc_start: 0.7624 (mtt) cc_final: 0.7374 (ptp) REVERT: K 44 ARG cc_start: 0.8081 (mtt180) cc_final: 0.7786 (mtt-85) REVERT: L 29 LEU cc_start: 0.6602 (tt) cc_final: 0.5324 (mt) REVERT: M 65 PHE cc_start: 0.8747 (t80) cc_final: 0.8412 (t80) REVERT: M 74 ILE cc_start: 0.8141 (tp) cc_final: 0.7832 (tp) REVERT: M 79 ARG cc_start: 0.9113 (OUTLIER) cc_final: 0.8661 (ptt90) REVERT: M 87 ARG cc_start: 0.8866 (ptm-80) cc_final: 0.8620 (ptm-80) REVERT: N 20 ILE cc_start: 0.7162 (OUTLIER) cc_final: 0.6647 (mm) REVERT: N 56 MET cc_start: 0.4491 (mpp) cc_final: 0.4180 (mpp) REVERT: P 109 ILE cc_start: 0.6964 (mm) cc_final: 0.6632 (mm) REVERT: Q 4 ASN cc_start: 0.8061 (OUTLIER) cc_final: 0.7490 (t0) REVERT: Q 71 HIS cc_start: 0.7480 (OUTLIER) cc_final: 0.6899 (p-80) REVERT: Q 73 LEU cc_start: 0.6912 (pt) cc_final: 0.6241 (mp) REVERT: Q 87 LYS cc_start: 0.8652 (tptp) cc_final: 0.7811 (tptm) REVERT: Q 116 TYR cc_start: 0.7170 (m-80) cc_final: 0.6674 (m-80) REVERT: R 2 ARG cc_start: 0.6333 (tpp-160) cc_final: 0.5885 (mmm160) REVERT: R 74 MET cc_start: 0.3054 (tmm) cc_final: 0.2078 (mtt) REVERT: T 46 LYS cc_start: 0.8021 (pttt) cc_final: 0.7609 (pptt) REVERT: T 57 ARG cc_start: 0.8367 (ttt-90) cc_final: 0.7481 (ttt-90) REVERT: T 64 LYS cc_start: 0.8842 (mmtm) cc_final: 0.8487 (tppt) REVERT: T 88 ARG cc_start: 0.7908 (mpp-170) cc_final: 0.7536 (mtt90) REVERT: U 1 MET cc_start: 0.2298 (ttm) cc_final: 0.1838 (ttm) REVERT: U 34 GLU cc_start: 0.7692 (pp20) cc_final: 0.7371 (pm20) REVERT: U 39 PHE cc_start: 0.7106 (t80) cc_final: 0.6586 (t80) REVERT: U 56 ARG cc_start: 0.7458 (mmm160) cc_final: 0.6350 (tpm170) REVERT: U 57 ILE cc_start: 0.4113 (OUTLIER) cc_final: 0.3873 (mp) REVERT: V 62 GLU cc_start: 0.5174 (tt0) cc_final: 0.4349 (tt0) REVERT: Y 17 ARG cc_start: 0.7918 (tmt170) cc_final: 0.7648 (tmt170) REVERT: Y 26 MET cc_start: 0.8372 (mmm) cc_final: 0.8090 (mmm) REVERT: Z 54 ARG cc_start: 0.8302 (tpt90) cc_final: 0.7816 (tpm170) REVERT: a 216 THR cc_start: 0.4571 (t) cc_final: 0.4223 (p) REVERT: 8 16 GLU cc_start: 0.8040 (mp0) cc_final: 0.7566 (mp0) REVERT: 8 21 ARG cc_start: 0.5015 (mtt180) cc_final: 0.3327 (mpt180) REVERT: 8 105 ARG cc_start: 0.7584 (OUTLIER) cc_final: 0.7310 (ttp-170) REVERT: 9 73 LYS cc_start: 0.6918 (ttpt) cc_final: 0.6436 (ttmm) REVERT: 9 99 THR cc_start: 0.3903 (OUTLIER) cc_final: 0.3676 (t) outliers start: 355 outliers final: 229 residues processed: 1547 average time/residue: 1.3398 time to fit residues: 3538.9125 Evaluate side-chains 1462 residues out of total 5093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 253 poor density : 1209 time to evaluate : 6.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 3 VAL Chi-restraints excluded: chain b residue 8 THR Chi-restraints excluded: chain b residue 32 LEU Chi-restraints excluded: chain b residue 33 LEU Chi-restraints excluded: chain b residue 52 HIS Chi-restraints excluded: chain b residue 104 LEU Chi-restraints excluded: chain b residue 113 ASP Chi-restraints excluded: chain b residue 175 LEU Chi-restraints excluded: chain b residue 219 VAL Chi-restraints excluded: chain b residue 222 THR Chi-restraints excluded: chain b residue 228 ASP Chi-restraints excluded: chain b residue 239 PHE Chi-restraints excluded: chain c residue 12 THR Chi-restraints excluded: chain c residue 35 THR Chi-restraints excluded: chain c residue 40 LEU Chi-restraints excluded: chain c residue 73 VAL Chi-restraints excluded: chain c residue 121 THR Chi-restraints excluded: chain c residue 133 THR Chi-restraints excluded: chain c residue 160 LYS Chi-restraints excluded: chain c residue 168 GLU Chi-restraints excluded: chain c residue 170 VAL Chi-restraints excluded: chain c residue 171 THR Chi-restraints excluded: chain c residue 180 VAL Chi-restraints excluded: chain c residue 189 VAL Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 4 VAL Chi-restraints excluded: chain d residue 7 ASP Chi-restraints excluded: chain d residue 48 THR Chi-restraints excluded: chain d residue 90 GLN Chi-restraints excluded: chain d residue 120 VAL Chi-restraints excluded: chain d residue 149 ILE Chi-restraints excluded: chain d residue 169 VAL Chi-restraints excluded: chain d residue 193 VAL Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 27 VAL Chi-restraints excluded: chain e residue 112 ASP Chi-restraints excluded: chain e residue 157 THR Chi-restraints excluded: chain e residue 166 ARG Chi-restraints excluded: chain f residue 3 VAL Chi-restraints excluded: chain f residue 9 VAL Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 17 LYS Chi-restraints excluded: chain f residue 19 ASN Chi-restraints excluded: chain f residue 29 ASN Chi-restraints excluded: chain f residue 49 LEU Chi-restraints excluded: chain f residue 82 PHE Chi-restraints excluded: chain f residue 102 ILE Chi-restraints excluded: chain f residue 104 LEU Chi-restraints excluded: chain f residue 136 ASP Chi-restraints excluded: chain g residue 4 ILE Chi-restraints excluded: chain g residue 58 LEU Chi-restraints excluded: chain g residue 119 ASN Chi-restraints excluded: chain g residue 144 VAL Chi-restraints excluded: chain g residue 146 VAL Chi-restraints excluded: chain h residue 51 TYR Chi-restraints excluded: chain h residue 82 ILE Chi-restraints excluded: chain j residue 3 THR Chi-restraints excluded: chain j residue 11 VAL Chi-restraints excluded: chain j residue 18 VAL Chi-restraints excluded: chain j residue 36 LEU Chi-restraints excluded: chain j residue 57 LEU Chi-restraints excluded: chain j residue 64 VAL Chi-restraints excluded: chain j residue 73 VAL Chi-restraints excluded: chain j residue 111 LYS Chi-restraints excluded: chain j residue 142 ILE Chi-restraints excluded: chain k residue 21 CYS Chi-restraints excluded: chain k residue 22 ILE Chi-restraints excluded: chain k residue 24 VAL Chi-restraints excluded: chain k residue 62 VAL Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 77 ILE Chi-restraints excluded: chain k residue 104 THR Chi-restraints excluded: chain l residue 47 ARG Chi-restraints excluded: chain l residue 63 LYS Chi-restraints excluded: chain l residue 67 THR Chi-restraints excluded: chain l residue 128 THR Chi-restraints excluded: chain m residue 2 LEU Chi-restraints excluded: chain m residue 42 THR Chi-restraints excluded: chain m residue 54 THR Chi-restraints excluded: chain m residue 57 VAL Chi-restraints excluded: chain m residue 71 LYS Chi-restraints excluded: chain m residue 106 ASP Chi-restraints excluded: chain m residue 128 THR Chi-restraints excluded: chain n residue 9 GLN Chi-restraints excluded: chain n residue 36 THR Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain n residue 113 ILE Chi-restraints excluded: chain o residue 34 HIS 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 83 LEU Chi-restraints excluded: chain o residue 90 VAL Chi-restraints excluded: chain o residue 93 ASP Chi-restraints excluded: chain p residue 5 LYS Chi-restraints excluded: chain p residue 23 ASP Chi-restraints excluded: chain p residue 43 GLU Chi-restraints excluded: chain p residue 60 VAL Chi-restraints excluded: chain p residue 75 THR Chi-restraints excluded: chain p residue 80 VAL Chi-restraints excluded: chain q residue 33 VAL Chi-restraints excluded: chain q residue 59 LEU Chi-restraints excluded: chain q residue 61 ILE Chi-restraints excluded: chain q residue 73 ILE Chi-restraints excluded: chain r residue 15 SER Chi-restraints excluded: chain r residue 22 LEU Chi-restraints excluded: chain r residue 38 VAL Chi-restraints excluded: chain r residue 39 LEU Chi-restraints excluded: chain r residue 40 MET Chi-restraints excluded: chain r residue 49 ILE Chi-restraints excluded: chain r residue 51 VAL Chi-restraints excluded: chain r residue 75 VAL Chi-restraints excluded: chain r residue 79 ARG Chi-restraints excluded: chain s residue 29 VAL Chi-restraints excluded: chain s residue 52 GLU Chi-restraints excluded: chain s residue 66 ILE Chi-restraints excluded: chain s residue 76 VAL Chi-restraints excluded: chain s residue 96 ILE Chi-restraints excluded: chain s residue 100 THR Chi-restraints excluded: chain t residue 9 LYS Chi-restraints excluded: chain t residue 16 VAL Chi-restraints excluded: chain t residue 18 GLU Chi-restraints excluded: chain t residue 29 THR Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain t residue 62 VAL Chi-restraints excluded: chain t residue 86 THR Chi-restraints excluded: chain u residue 11 ILE Chi-restraints excluded: chain u residue 35 VAL Chi-restraints excluded: chain v residue 2 PHE Chi-restraints excluded: chain v residue 8 VAL Chi-restraints excluded: chain v residue 56 PHE Chi-restraints excluded: chain v residue 62 THR Chi-restraints excluded: chain v residue 63 ILE Chi-restraints excluded: chain v residue 64 VAL Chi-restraints excluded: chain v residue 90 ASP Chi-restraints excluded: chain v residue 92 VAL Chi-restraints excluded: chain w residue 19 VAL Chi-restraints excluded: chain w residue 34 VAL Chi-restraints excluded: chain x residue 13 THR Chi-restraints excluded: chain x residue 22 ASN Chi-restraints excluded: chain x residue 59 ASP Chi-restraints excluded: chain x residue 67 LEU Chi-restraints excluded: chain y residue 11 VAL Chi-restraints excluded: chain y residue 46 VAL Chi-restraints excluded: chain y residue 49 ASP Chi-restraints excluded: chain z residue 13 ILE Chi-restraints excluded: chain z residue 40 THR Chi-restraints excluded: chain z residue 51 SER Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain C residue 9 LYS Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 43 LEU Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 23 ILE Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 32 LYS Chi-restraints excluded: chain F residue 34 LYS Chi-restraints excluded: chain G residue 5 MET Chi-restraints excluded: chain G residue 15 PHE Chi-restraints excluded: chain G residue 38 HIS Chi-restraints excluded: chain G residue 128 LEU Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain G residue 183 PHE Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 190 SER Chi-restraints excluded: chain G residue 210 THR Chi-restraints excluded: chain H residue 182 ASP Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 64 TYR Chi-restraints excluded: chain I residue 99 ASN Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 171 GLU Chi-restraints excluded: chain J residue 19 ARG Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 45 VAL Chi-restraints excluded: chain J residue 79 THR Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 121 ASN Chi-restraints excluded: chain K residue 64 VAL Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain K residue 78 PHE Chi-restraints excluded: chain K residue 84 VAL Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain L residue 6 ILE Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain L residue 147 ASN Chi-restraints excluded: chain M residue 37 ASN Chi-restraints excluded: chain M residue 48 PHE Chi-restraints excluded: chain M residue 79 ARG Chi-restraints excluded: chain M residue 90 GLU Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain M residue 126 CYS Chi-restraints excluded: chain M residue 128 VAL Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 125 GLN Chi-restraints excluded: chain P residue 15 VAL Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain P residue 35 ASP Chi-restraints excluded: chain P residue 85 VAL Chi-restraints excluded: chain P residue 118 ASN Chi-restraints excluded: chain Q residue 4 ASN Chi-restraints excluded: chain Q residue 28 GLN Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 71 HIS Chi-restraints excluded: chain Q residue 86 VAL Chi-restraints excluded: chain R residue 53 ASP Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain S residue 49 THR Chi-restraints excluded: chain S residue 61 ASN Chi-restraints excluded: chain T residue 17 ASP Chi-restraints excluded: chain T residue 24 THR Chi-restraints excluded: chain T residue 28 VAL Chi-restraints excluded: chain T residue 30 LEU Chi-restraints excluded: chain T residue 78 THR Chi-restraints excluded: chain U residue 32 PHE Chi-restraints excluded: chain U residue 57 ILE Chi-restraints excluded: chain U residue 69 ASP Chi-restraints excluded: chain U residue 78 VAL Chi-restraints excluded: chain V residue 7 LEU Chi-restraints excluded: chain V residue 46 HIS Chi-restraints excluded: chain V residue 75 VAL Chi-restraints excluded: chain W residue 64 LEU Chi-restraints excluded: chain X residue 15 LEU Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain X residue 59 VAL Chi-restraints excluded: chain X residue 70 LEU Chi-restraints excluded: chain X residue 76 THR Chi-restraints excluded: chain Y residue 3 ILE Chi-restraints excluded: chain Y residue 19 HIS Chi-restraints excluded: chain Y residue 31 ILE Chi-restraints excluded: chain Y residue 65 LEU Chi-restraints excluded: chain Z residue 5 VAL Chi-restraints excluded: chain Z residue 12 ASP Chi-restraints excluded: chain Z residue 52 VAL Chi-restraints excluded: chain a residue 5 THR Chi-restraints excluded: chain a residue 55 SER Chi-restraints excluded: chain a residue 58 ASN Chi-restraints excluded: chain 8 residue 35 THR Chi-restraints excluded: chain 8 residue 105 ARG Chi-restraints excluded: chain 9 residue 18 THR Chi-restraints excluded: chain 9 residue 20 ILE Chi-restraints excluded: chain 9 residue 99 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1065 random chunks: chunk 957 optimal weight: 10.0000 chunk 728 optimal weight: 10.0000 chunk 502 optimal weight: 10.0000 chunk 107 optimal weight: 6.9990 chunk 462 optimal weight: 7.9990 chunk 650 optimal weight: 20.0000 chunk 972 optimal weight: 10.0000 chunk 1029 optimal weight: 20.0000 chunk 508 optimal weight: 2.9990 chunk 921 optimal weight: 20.0000 chunk 277 optimal weight: 2.9990 overall best weight: 6.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 62 GLN ** d 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 33 GLN g 145 ASN ** i 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 54 GLN ** m 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 62 ASN ** p 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 19 GLN ** r 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 15 GLN u 65 GLN ** u 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 22 ASN ** D 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 HIS ** H 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 GLN P 63 GLN ** P 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 7 ASN ** R 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 44 HIS ** W 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 28 GLN 9 29 HIS 9 31 ASN ** 9 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.4619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 161229 Z= 0.276 Angle : 0.690 14.203 240720 Z= 0.354 Chirality : 0.039 0.360 30724 Planarity : 0.005 0.077 13231 Dihedral : 23.641 179.425 79541 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 26.16 Ramachandran Plot: Outliers : 0.18 % Allowed : 11.04 % Favored : 88.78 % Rotamer: Outliers : 7.17 % Allowed : 23.44 % Favored : 69.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % Cis-general : 0.00 % Twisted Proline : 0.49 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.45 (0.10), residues: 6142 helix: -1.55 (0.11), residues: 1792 sheet: -2.15 (0.16), residues: 898 loop : -2.83 (0.09), residues: 3452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP V 72 HIS 0.028 0.002 HIS G 38 PHE 0.024 0.002 PHE l 64 TYR 0.035 0.002 TYR J 127 ARG 0.014 0.001 ARG S 23 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12284 Ramachandran restraints generated. 6142 Oldfield, 0 Emsley, 6142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12284 Ramachandran restraints generated. 6142 Oldfield, 0 Emsley, 6142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1674 residues out of total 5093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 365 poor density : 1309 time to evaluate : 5.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 36 ASN cc_start: 0.8273 (t0) cc_final: 0.7985 (t0) REVERT: b 206 LYS cc_start: 0.8073 (pttp) cc_final: 0.7677 (pttp) REVERT: c 28 GLU cc_start: 0.8875 (tm-30) cc_final: 0.8631 (tp30) REVERT: c 36 GLN cc_start: 0.8271 (tt0) cc_final: 0.7977 (tp40) REVERT: c 64 GLU cc_start: 0.8882 (mm-30) cc_final: 0.8530 (mm-30) REVERT: c 131 ASP cc_start: 0.8589 (p0) cc_final: 0.8345 (p0) REVERT: c 148 GLN cc_start: 0.8605 (mp10) cc_final: 0.8295 (mp10) REVERT: c 185 ASN cc_start: 0.8873 (m-40) cc_final: 0.8490 (m110) REVERT: d 9 GLN cc_start: 0.8533 (tm-30) cc_final: 0.8259 (tm-30) REVERT: d 122 GLU cc_start: 0.8284 (tm-30) cc_final: 0.8061 (tm-30) REVERT: d 146 VAL cc_start: 0.9354 (p) cc_final: 0.9106 (m) REVERT: d 183 PHE cc_start: 0.8533 (m-80) cc_final: 0.8286 (m-80) REVERT: d 188 MET cc_start: 0.9100 (mmt) cc_final: 0.8807 (mmt) REVERT: e 6 TYR cc_start: 0.9026 (t80) cc_final: 0.8452 (t80) REVERT: e 80 GLN cc_start: 0.8600 (OUTLIER) cc_final: 0.8326 (tm-30) REVERT: e 97 GLU cc_start: 0.8136 (tp30) cc_final: 0.7837 (tm-30) REVERT: e 99 PHE cc_start: 0.9345 (t80) cc_final: 0.9052 (t80) REVERT: e 109 ARG cc_start: 0.8991 (OUTLIER) cc_final: 0.8322 (tpp-160) REVERT: e 137 PHE cc_start: 0.7885 (m-80) cc_final: 0.7665 (m-80) REVERT: e 163 GLU cc_start: 0.7106 (OUTLIER) cc_final: 0.6492 (mm-30) REVERT: e 166 ARG cc_start: 0.8984 (OUTLIER) cc_final: 0.8555 (tmm-80) REVERT: e 176 PHE cc_start: 0.7689 (m-80) cc_final: 0.7396 (m-80) REVERT: e 177 ARG cc_start: 0.7826 (ttt180) cc_final: 0.7165 (tpt170) REVERT: f 82 PHE cc_start: 0.7611 (OUTLIER) cc_final: 0.7203 (m-10) REVERT: f 137 LYS cc_start: 0.8808 (OUTLIER) cc_final: 0.8485 (mmtt) REVERT: g 17 ASP cc_start: 0.8493 (t70) cc_final: 0.7864 (p0) REVERT: g 18 GLN cc_start: 0.8420 (mp10) cc_final: 0.8204 (pm20) REVERT: g 22 LYS cc_start: 0.8338 (mtmm) cc_final: 0.8055 (ptpp) REVERT: g 46 PHE cc_start: 0.8552 (m-10) cc_final: 0.8237 (m-10) REVERT: g 55 GLU cc_start: 0.9137 (mt-10) cc_final: 0.8749 (mt-10) REVERT: g 87 GLU cc_start: 0.8116 (tp30) cc_final: 0.7878 (pm20) REVERT: h 52 MET cc_start: 0.8239 (tmm) cc_final: 0.7935 (tpp) REVERT: h 86 MET cc_start: 0.3253 (mmm) cc_final: 0.2856 (tpp) REVERT: h 116 GLU cc_start: 0.8878 (mm-30) cc_final: 0.8435 (mm-30) REVERT: i 41 PHE cc_start: 0.8755 (t80) cc_final: 0.8363 (t80) REVERT: i 112 LYS cc_start: 0.5465 (pttp) cc_final: 0.4385 (tttt) REVERT: j 36 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8780 (mm) REVERT: j 68 LYS cc_start: 0.8456 (mtpt) cc_final: 0.8117 (mtpt) REVERT: j 86 GLN cc_start: 0.8287 (pp30) cc_final: 0.7805 (pp30) REVERT: j 118 MET cc_start: 0.9070 (mmt) cc_final: 0.8675 (mmt) REVERT: k 29 HIS cc_start: 0.8328 (t70) cc_final: 0.7970 (t-90) REVERT: k 66 LYS cc_start: 0.8434 (tttt) cc_final: 0.7821 (tttt) REVERT: l 38 GLN cc_start: 0.9203 (tt0) cc_final: 0.8653 (tt0) REVERT: l 39 LYS cc_start: 0.8858 (pttt) cc_final: 0.8444 (pttt) REVERT: l 105 ILE cc_start: 0.8748 (mm) cc_final: 0.8478 (tp) REVERT: l 128 THR cc_start: 0.9148 (OUTLIER) cc_final: 0.8707 (t) REVERT: n 103 ARG cc_start: 0.8184 (ttp-170) cc_final: 0.7850 (ttp80) REVERT: n 112 TYR cc_start: 0.8359 (m-80) cc_final: 0.7840 (m-80) REVERT: o 12 THR cc_start: 0.9427 (p) cc_final: 0.9169 (p) REVERT: o 55 GLU cc_start: 0.8474 (mt-10) cc_final: 0.7516 (mm-30) REVERT: o 87 ILE cc_start: 0.7640 (mm) cc_final: 0.7420 (tp) REVERT: o 97 PHE cc_start: 0.7469 (OUTLIER) cc_final: 0.6683 (t80) REVERT: p 12 MET cc_start: 0.8092 (mtm) cc_final: 0.6660 (tmm) REVERT: p 37 LYS cc_start: 0.8469 (mttm) cc_final: 0.8158 (mptt) REVERT: p 50 ARG cc_start: 0.8488 (ttt-90) cc_final: 0.7979 (ttt-90) REVERT: p 74 GLN cc_start: 0.8331 (mp10) cc_final: 0.7624 (mp10) REVERT: p 93 LYS cc_start: 0.8736 (tppt) cc_final: 0.8320 (tppt) REVERT: q 21 LYS cc_start: 0.8616 (mmtt) cc_final: 0.8269 (ttmm) REVERT: q 24 TYR cc_start: 0.7550 (t80) cc_final: 0.7193 (t80) REVERT: q 54 ARG cc_start: 0.8912 (mtm180) cc_final: 0.8260 (mtt90) REVERT: q 88 GLU cc_start: 0.8535 (mp0) cc_final: 0.8289 (mp0) REVERT: q 106 THR cc_start: 0.9348 (p) cc_final: 0.8977 (p) REVERT: q 110 GLU cc_start: 0.8861 (mm-30) cc_final: 0.8188 (mm-30) REVERT: r 52 PRO cc_start: 0.8602 (Cg_endo) cc_final: 0.8235 (Cg_exo) REVERT: r 79 ARG cc_start: 0.7657 (ptt90) cc_final: 0.7431 (ptt180) REVERT: r 85 LYS cc_start: 0.8808 (ttmt) cc_final: 0.8577 (ttmt) REVERT: r 87 GLN cc_start: 0.5918 (tm-30) cc_final: 0.5452 (tm-30) REVERT: r 97 LYS cc_start: 0.8631 (tptp) cc_final: 0.8158 (tptp) REVERT: s 38 TYR cc_start: 0.8864 (m-80) cc_final: 0.8463 (m-80) REVERT: t 1 MET cc_start: -0.0604 (mtt) cc_final: -0.0980 (mtt) REVERT: t 8 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8507 (mt) REVERT: t 18 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7850 (pp20) REVERT: t 24 MET cc_start: 0.9214 (tpp) cc_final: 0.8923 (tpp) REVERT: t 74 ILE cc_start: 0.6777 (OUTLIER) cc_final: 0.6415 (mm) REVERT: u 53 GLN cc_start: 0.8842 (mt0) cc_final: 0.8540 (mm110) REVERT: v 2 PHE cc_start: 0.7837 (m-10) cc_final: 0.6815 (m-10) REVERT: v 51 GLN cc_start: 0.9096 (OUTLIER) cc_final: 0.8834 (tm-30) REVERT: v 59 GLU cc_start: 0.8279 (mm-30) cc_final: 0.8002 (mm-30) REVERT: x 15 ASN cc_start: 0.8710 (t0) cc_final: 0.8432 (t0) REVERT: x 16 ASN cc_start: 0.9174 (t0) cc_final: 0.8881 (m-40) REVERT: x 58 ILE cc_start: 0.9364 (mm) cc_final: 0.9135 (mm) REVERT: x 59 ASP cc_start: 0.8505 (OUTLIER) cc_final: 0.8270 (p0) REVERT: x 69 GLU cc_start: 0.8732 (mt-10) cc_final: 0.8459 (pt0) REVERT: y 23 ARG cc_start: 0.7945 (mmt180) cc_final: 0.7483 (mmp-170) REVERT: y 45 GLN cc_start: 0.8654 (pt0) cc_final: 0.8236 (pp30) REVERT: y 48 ARG cc_start: 0.9060 (mtt-85) cc_final: 0.8605 (mmt-90) REVERT: z 24 LEU cc_start: 0.9130 (tp) cc_final: 0.8851 (tp) REVERT: C 19 PHE cc_start: 0.8567 (p90) cc_final: 0.8366 (p90) REVERT: C 24 LYS cc_start: 0.8562 (tttm) cc_final: 0.8196 (tmtt) REVERT: D 28 ARG cc_start: 0.8755 (mtm-85) cc_final: 0.8173 (mtm-85) REVERT: D 35 ARG cc_start: 0.8978 (mtt-85) cc_final: 0.8564 (mtt-85) REVERT: D 37 LYS cc_start: 0.8504 (tptt) cc_final: 0.8277 (tptp) REVERT: F 4 ARG cc_start: 0.7919 (ptp-170) cc_final: 0.7648 (ptp-170) REVERT: G 26 MET cc_start: 0.7424 (tmm) cc_final: 0.6470 (tmm) REVERT: G 38 HIS cc_start: 0.7643 (OUTLIER) cc_final: 0.7133 (m90) REVERT: G 95 TRP cc_start: 0.7906 (t-100) cc_final: 0.7571 (t-100) REVERT: G 153 MET cc_start: 0.6147 (mmm) cc_final: 0.5871 (mmm) REVERT: G 183 PHE cc_start: 0.7114 (OUTLIER) cc_final: 0.6741 (m-80) REVERT: I 74 TYR cc_start: 0.8723 (m-10) cc_final: 0.8150 (m-80) REVERT: I 88 ASN cc_start: 0.9014 (m110) cc_final: 0.8690 (m-40) REVERT: I 92 LEU cc_start: 0.8383 (mt) cc_final: 0.7347 (mt) REVERT: I 123 MET cc_start: 0.7362 (mmm) cc_final: 0.7056 (mmm) REVERT: I 127 ARG cc_start: 0.8882 (mtt180) cc_final: 0.8408 (ttt180) REVERT: I 128 VAL cc_start: 0.8238 (OUTLIER) cc_final: 0.7919 (p) REVERT: I 151 GLN cc_start: 0.8838 (mm110) cc_final: 0.8583 (mm110) REVERT: I 171 GLU cc_start: 0.5777 (OUTLIER) cc_final: 0.5540 (mp0) REVERT: I 184 LYS cc_start: 0.9305 (tptt) cc_final: 0.9024 (tptt) REVERT: I 201 GLU cc_start: 0.9201 (mm-30) cc_final: 0.8324 (mm-30) REVERT: J 151 MET cc_start: 0.7603 (mtt) cc_final: 0.7357 (ptp) REVERT: L 29 LEU cc_start: 0.6019 (tt) cc_final: 0.4910 (mt) REVERT: L 30 MET cc_start: 0.5887 (pmm) cc_final: 0.5342 (pmm) REVERT: M 79 ARG cc_start: 0.9142 (ptt90) cc_final: 0.8665 (ptt90) REVERT: M 87 ARG cc_start: 0.8899 (ptm-80) cc_final: 0.8591 (ptm-80) REVERT: P 43 TRP cc_start: 0.6810 (p-90) cc_final: 0.5913 (p-90) REVERT: Q 4 ASN cc_start: 0.8052 (OUTLIER) cc_final: 0.7419 (t0) REVERT: Q 71 HIS cc_start: 0.7497 (OUTLIER) cc_final: 0.6963 (p-80) REVERT: Q 73 LEU cc_start: 0.7056 (pt) cc_final: 0.6421 (mp) REVERT: Q 79 ILE cc_start: 0.6723 (OUTLIER) cc_final: 0.6030 (tp) REVERT: Q 87 LYS cc_start: 0.8528 (tptp) cc_final: 0.7363 (tptm) REVERT: Q 116 TYR cc_start: 0.7302 (m-80) cc_final: 0.6741 (m-80) REVERT: R 2 ARG cc_start: 0.6346 (tpp-160) cc_final: 0.5923 (mmm160) REVERT: R 74 MET cc_start: 0.3029 (tmm) cc_final: 0.2172 (mtt) REVERT: T 27 GLN cc_start: 0.8135 (mp10) cc_final: 0.7932 (mp10) REVERT: T 44 GLU cc_start: 0.8567 (tp30) cc_final: 0.8246 (tp30) REVERT: T 46 LYS cc_start: 0.8140 (pttt) cc_final: 0.7702 (pptt) REVERT: T 57 ARG cc_start: 0.8295 (ttt-90) cc_final: 0.7168 (ttt-90) REVERT: T 58 MET cc_start: 0.8906 (mtm) cc_final: 0.8075 (mmm) REVERT: T 61 GLN cc_start: 0.9279 (tp40) cc_final: 0.9056 (tp-100) REVERT: T 64 LYS cc_start: 0.8851 (mmtm) cc_final: 0.8491 (tppt) REVERT: U 38 PHE cc_start: 0.8220 (p90) cc_final: 0.8008 (p90) REVERT: U 56 ARG cc_start: 0.7471 (mmm160) cc_final: 0.7198 (mmm-85) REVERT: V 62 GLU cc_start: 0.5370 (tt0) cc_final: 0.4492 (tt0) REVERT: W 58 ILE cc_start: 0.6621 (mt) cc_final: 0.6265 (mt) REVERT: Y 17 ARG cc_start: 0.8145 (tmt170) cc_final: 0.7825 (tmt170) REVERT: Y 18 LYS cc_start: 0.9114 (mmtt) cc_final: 0.8679 (tptt) REVERT: Y 23 ARG cc_start: 0.9010 (mmm-85) cc_final: 0.8740 (mmm-85) REVERT: Z 37 TYR cc_start: 0.2954 (OUTLIER) cc_final: 0.2726 (t80) REVERT: Z 38 GLU cc_start: 0.7286 (tt0) cc_final: 0.6730 (tt0) REVERT: a 170 ILE cc_start: 0.4858 (mm) cc_final: 0.4478 (tp) REVERT: a 216 THR cc_start: 0.4823 (t) cc_final: 0.4371 (p) REVERT: 8 16 GLU cc_start: 0.7720 (mp0) cc_final: 0.7410 (mp0) REVERT: 8 21 ARG cc_start: 0.5148 (mtt180) cc_final: 0.3450 (mpt180) REVERT: 8 41 PHE cc_start: 0.8877 (t80) cc_final: 0.7762 (t80) REVERT: 8 105 ARG cc_start: 0.7563 (OUTLIER) cc_final: 0.7306 (ttp-170) outliers start: 365 outliers final: 240 residues processed: 1515 average time/residue: 1.3086 time to fit residues: 3396.7236 Evaluate side-chains 1472 residues out of total 5093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 263 poor density : 1209 time to evaluate : 6.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 2 VAL Chi-restraints excluded: chain b residue 3 VAL Chi-restraints excluded: chain b residue 8 THR Chi-restraints excluded: chain b residue 32 LEU Chi-restraints excluded: chain b residue 33 LEU Chi-restraints excluded: chain b residue 104 LEU Chi-restraints excluded: chain b residue 128 THR Chi-restraints excluded: chain b residue 175 LEU Chi-restraints excluded: chain b residue 222 THR Chi-restraints excluded: chain b residue 239 PHE Chi-restraints excluded: chain b residue 259 ASN Chi-restraints excluded: chain c residue 12 THR Chi-restraints excluded: chain c residue 24 VAL Chi-restraints excluded: chain c residue 27 ILE Chi-restraints excluded: chain c residue 35 THR Chi-restraints excluded: chain c residue 40 LEU Chi-restraints excluded: chain c residue 73 VAL Chi-restraints excluded: chain c residue 79 LEU Chi-restraints excluded: chain c residue 100 LEU Chi-restraints excluded: chain c residue 133 THR Chi-restraints excluded: chain c residue 160 LYS Chi-restraints excluded: chain c residue 170 VAL Chi-restraints excluded: chain c residue 171 THR Chi-restraints excluded: chain c residue 180 VAL Chi-restraints excluded: chain c residue 189 VAL Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 4 VAL Chi-restraints excluded: chain d residue 7 ASP Chi-restraints excluded: chain d residue 48 THR Chi-restraints excluded: chain d residue 65 THR Chi-restraints excluded: chain d residue 169 VAL Chi-restraints excluded: chain d residue 193 VAL Chi-restraints excluded: chain e residue 4 HIS Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 27 VAL Chi-restraints excluded: chain e residue 50 ASP Chi-restraints excluded: chain e residue 80 GLN Chi-restraints excluded: chain e residue 109 ARG Chi-restraints excluded: chain e residue 112 ASP Chi-restraints excluded: chain e residue 140 ILE Chi-restraints excluded: chain e residue 148 VAL Chi-restraints excluded: chain e residue 153 ILE Chi-restraints excluded: chain e residue 154 THR Chi-restraints excluded: chain e residue 163 GLU Chi-restraints excluded: chain e residue 166 ARG Chi-restraints excluded: chain e residue 168 LEU Chi-restraints excluded: chain f residue 9 VAL Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 19 ASN Chi-restraints excluded: chain f residue 29 ASN Chi-restraints excluded: chain f residue 49 LEU Chi-restraints excluded: chain f residue 70 LEU Chi-restraints excluded: chain f residue 82 PHE Chi-restraints excluded: chain f residue 88 LEU Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 102 ILE Chi-restraints excluded: chain f residue 104 LEU Chi-restraints excluded: chain f residue 136 ASP Chi-restraints excluded: chain f residue 137 LYS Chi-restraints excluded: chain f residue 152 ARG Chi-restraints excluded: chain g residue 4 ILE Chi-restraints excluded: chain g residue 119 ASN Chi-restraints excluded: chain g residue 134 VAL Chi-restraints excluded: chain g residue 144 VAL Chi-restraints excluded: chain h residue 82 ILE Chi-restraints excluded: chain j residue 3 THR Chi-restraints excluded: chain j residue 11 VAL Chi-restraints excluded: chain j residue 36 LEU Chi-restraints excluded: chain j residue 44 TYR Chi-restraints excluded: chain j residue 142 ILE Chi-restraints excluded: chain k residue 21 CYS Chi-restraints excluded: chain k residue 22 ILE Chi-restraints excluded: chain k residue 24 VAL Chi-restraints excluded: chain k residue 62 VAL Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 77 ILE Chi-restraints excluded: chain k residue 103 VAL Chi-restraints excluded: chain k residue 104 THR Chi-restraints excluded: chain k residue 110 GLU Chi-restraints excluded: chain l residue 47 ARG Chi-restraints excluded: chain l residue 55 MET Chi-restraints excluded: chain l residue 63 LYS Chi-restraints excluded: chain l residue 67 THR Chi-restraints excluded: chain l residue 74 THR Chi-restraints excluded: chain l residue 107 PHE Chi-restraints excluded: chain l residue 128 THR Chi-restraints excluded: chain m residue 2 LEU Chi-restraints excluded: chain m residue 20 LEU Chi-restraints excluded: chain m residue 42 THR Chi-restraints excluded: chain m residue 106 ASP Chi-restraints excluded: chain m residue 128 THR Chi-restraints excluded: chain m residue 135 VAL Chi-restraints excluded: chain n residue 9 GLN Chi-restraints excluded: chain n residue 36 THR Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain n residue 74 GLU Chi-restraints excluded: chain o residue 5 SER Chi-restraints excluded: chain o residue 34 HIS Chi-restraints excluded: chain o residue 35 ILE Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain o residue 47 VAL Chi-restraints excluded: chain o residue 53 THR Chi-restraints excluded: chain o residue 83 LEU Chi-restraints excluded: chain o residue 90 VAL Chi-restraints excluded: chain o residue 93 ASP Chi-restraints excluded: chain o residue 97 PHE Chi-restraints excluded: chain p residue 23 ASP Chi-restraints excluded: chain p residue 43 GLU Chi-restraints excluded: chain p residue 60 VAL Chi-restraints excluded: chain p residue 75 THR Chi-restraints excluded: chain p residue 80 VAL Chi-restraints excluded: chain q residue 59 LEU Chi-restraints excluded: chain q residue 61 ILE Chi-restraints excluded: chain r residue 15 SER Chi-restraints excluded: chain r residue 19 THR Chi-restraints excluded: chain r residue 38 VAL Chi-restraints excluded: chain r residue 49 ILE Chi-restraints excluded: chain r residue 51 VAL Chi-restraints excluded: chain r residue 58 VAL Chi-restraints excluded: chain r residue 75 VAL Chi-restraints excluded: chain s residue 66 ILE Chi-restraints excluded: chain s residue 70 LYS Chi-restraints excluded: chain s residue 76 VAL Chi-restraints excluded: chain s residue 94 ASP Chi-restraints excluded: chain s residue 96 ILE Chi-restraints excluded: chain s residue 100 THR Chi-restraints excluded: chain t residue 8 LEU Chi-restraints excluded: chain t residue 16 VAL Chi-restraints excluded: chain t residue 18 GLU Chi-restraints excluded: chain t residue 29 THR Chi-restraints excluded: chain t residue 62 VAL Chi-restraints excluded: chain t residue 74 ILE Chi-restraints excluded: chain t residue 86 THR Chi-restraints excluded: chain u residue 10 VAL Chi-restraints excluded: chain u residue 11 ILE Chi-restraints excluded: chain u residue 35 VAL Chi-restraints excluded: chain u residue 81 ARG Chi-restraints excluded: chain v residue 8 VAL Chi-restraints excluded: chain v residue 51 GLN Chi-restraints excluded: chain v residue 56 PHE Chi-restraints excluded: chain v residue 62 THR Chi-restraints excluded: chain v residue 63 ILE Chi-restraints excluded: chain v residue 64 VAL Chi-restraints excluded: chain v residue 66 ASP Chi-restraints excluded: chain v residue 77 VAL Chi-restraints excluded: chain v residue 90 ASP Chi-restraints excluded: chain v residue 92 VAL Chi-restraints excluded: chain w residue 19 VAL Chi-restraints excluded: chain w residue 34 VAL Chi-restraints excluded: chain x residue 59 ASP Chi-restraints excluded: chain x residue 66 VAL Chi-restraints excluded: chain x residue 67 LEU Chi-restraints excluded: chain y residue 11 VAL Chi-restraints excluded: chain y residue 46 VAL Chi-restraints excluded: chain y residue 49 ASP Chi-restraints excluded: chain z residue 13 ILE Chi-restraints excluded: chain z residue 26 LEU Chi-restraints excluded: chain z residue 33 HIS Chi-restraints excluded: chain z residue 40 THR Chi-restraints excluded: chain z residue 51 SER Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain C residue 9 LYS Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain D residue 3 ARG Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 43 LEU Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 23 ILE Chi-restraints excluded: chain G residue 5 MET Chi-restraints excluded: chain G residue 14 HIS Chi-restraints excluded: chain G residue 15 PHE Chi-restraints excluded: chain G residue 38 HIS Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 128 LEU Chi-restraints excluded: chain G residue 183 PHE Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 190 SER Chi-restraints excluded: chain G residue 210 THR Chi-restraints excluded: chain H residue 182 ASP Chi-restraints excluded: chain I residue 64 TYR Chi-restraints excluded: chain I residue 99 ASN Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 141 VAL Chi-restraints excluded: chain I residue 171 GLU Chi-restraints excluded: chain J residue 19 ARG Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 79 THR Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 64 VAL Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain K residue 76 THR Chi-restraints excluded: chain K residue 78 PHE Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain L residue 6 ILE Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 47 GLU Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain M residue 26 MET Chi-restraints excluded: chain M residue 37 ASN Chi-restraints excluded: chain M residue 48 PHE Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain M residue 61 THR Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain M residue 126 CYS Chi-restraints excluded: chain M residue 128 VAL Chi-restraints excluded: chain N residue 24 ASN Chi-restraints excluded: chain O residue 69 THR Chi-restraints excluded: chain P residue 15 VAL Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 35 ASP Chi-restraints excluded: chain P residue 85 VAL Chi-restraints excluded: chain P residue 118 ASN Chi-restraints excluded: chain Q residue 4 ASN Chi-restraints excluded: chain Q residue 28 GLN Chi-restraints excluded: chain Q residue 71 HIS Chi-restraints excluded: chain Q residue 79 ILE Chi-restraints excluded: chain Q residue 86 VAL Chi-restraints excluded: chain R residue 53 ASP Chi-restraints excluded: chain S residue 23 ARG Chi-restraints excluded: chain S residue 49 THR Chi-restraints excluded: chain T residue 7 THR Chi-restraints excluded: chain T residue 17 ASP Chi-restraints excluded: chain T residue 24 THR Chi-restraints excluded: chain T residue 28 VAL Chi-restraints excluded: chain T residue 30 LEU Chi-restraints excluded: chain T residue 68 TYR Chi-restraints excluded: chain T residue 78 THR Chi-restraints excluded: chain U residue 69 ASP Chi-restraints excluded: chain V residue 29 LYS Chi-restraints excluded: chain V residue 46 HIS Chi-restraints excluded: chain W residue 22 TYR Chi-restraints excluded: chain W residue 64 LEU Chi-restraints excluded: chain X residue 15 LEU Chi-restraints excluded: chain X residue 43 MET Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain X residue 59 VAL Chi-restraints excluded: chain X residue 70 LEU Chi-restraints excluded: chain X residue 72 GLU Chi-restraints excluded: chain X residue 76 THR Chi-restraints excluded: chain Y residue 3 ILE Chi-restraints excluded: chain Y residue 19 HIS Chi-restraints excluded: chain Z residue 5 VAL Chi-restraints excluded: chain Z residue 12 ASP Chi-restraints excluded: chain Z residue 37 TYR Chi-restraints excluded: chain Z residue 52 VAL Chi-restraints excluded: chain a residue 5 THR Chi-restraints excluded: chain a residue 172 HIS Chi-restraints excluded: chain 8 residue 35 THR Chi-restraints excluded: chain 8 residue 100 THR Chi-restraints excluded: chain 8 residue 105 ARG Chi-restraints excluded: chain 9 residue 18 THR Chi-restraints excluded: chain 9 residue 20 ILE Chi-restraints excluded: chain 9 residue 35 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1065 random chunks: chunk 857 optimal weight: 10.0000 chunk 584 optimal weight: 20.0000 chunk 14 optimal weight: 10.0000 chunk 766 optimal weight: 20.0000 chunk 424 optimal weight: 0.0670 chunk 878 optimal weight: 10.0000 chunk 711 optimal weight: 40.0000 chunk 1 optimal weight: 7.9990 chunk 525 optimal weight: 8.9990 chunk 923 optimal weight: 10.0000 chunk 259 optimal weight: 9.9990 overall best weight: 7.4128 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 49 GLN ** d 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 19 ASN i 29 GLN ** i 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 104 GLN ** m 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 13 ASN n 62 ASN ** p 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 19 GLN ** r 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 15 GLN ** v 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 42 HIS ** x 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 58 ASN ** D 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 102 ASN G 176 ASN ** I 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 53 GLN ** J 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 49 GLN P 108 ASN Q 28 GLN ** Q 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 13 HIS S 42 ASN ** T 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 69 ASN Y 74 HIS ** a 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 172 HIS ** 8 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.5287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 161229 Z= 0.322 Angle : 0.737 13.526 240720 Z= 0.375 Chirality : 0.040 0.343 30724 Planarity : 0.006 0.082 13231 Dihedral : 23.881 179.945 79537 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 30.18 Ramachandran Plot: Outliers : 0.18 % Allowed : 12.86 % Favored : 86.96 % Rotamer: Outliers : 7.97 % Allowed : 24.72 % Favored : 67.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.31 (0.10), residues: 6142 helix: -1.47 (0.11), residues: 1788 sheet: -2.03 (0.16), residues: 881 loop : -2.73 (0.10), residues: 3473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP V 72 HIS 0.021 0.002 HIS G 38 PHE 0.037 0.003 PHE V 36 TYR 0.026 0.002 TYR J 127 ARG 0.012 0.001 ARG r 80 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12284 Ramachandran restraints generated. 6142 Oldfield, 0 Emsley, 6142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12284 Ramachandran restraints generated. 6142 Oldfield, 0 Emsley, 6142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1672 residues out of total 5093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 406 poor density : 1266 time to evaluate : 6.388 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: b 36 ASN cc_start: 0.8028 (t0) cc_final: 0.7761 (t0) REVERT: b 145 MET cc_start: 0.7941 (mtt) cc_final: 0.7636 (mtt) REVERT: c 28 GLU cc_start: 0.8948 (tm-30) cc_final: 0.8689 (tp30) REVERT: c 36 GLN cc_start: 0.8316 (tt0) cc_final: 0.8009 (tp40) REVERT: c 64 GLU cc_start: 0.8851 (mm-30) cc_final: 0.8522 (mm-30) REVERT: c 131 ASP cc_start: 0.8738 (p0) cc_final: 0.8443 (p0) REVERT: c 148 GLN cc_start: 0.8747 (mp10) cc_final: 0.8337 (mp10) REVERT: c 185 ASN cc_start: 0.8978 (m-40) cc_final: 0.8644 (m110) REVERT: d 6 LYS cc_start: 0.8237 (ptmt) cc_final: 0.7699 (pttm) REVERT: d 9 GLN cc_start: 0.8687 (tm-30) cc_final: 0.8472 (tm-30) REVERT: d 122 GLU cc_start: 0.8289 (tm-30) cc_final: 0.8082 (tm-30) REVERT: d 183 PHE cc_start: 0.8503 (m-80) cc_final: 0.8240 (m-80) REVERT: d 188 MET cc_start: 0.9066 (mmt) cc_final: 0.8816 (mmt) REVERT: e 6 TYR cc_start: 0.9153 (t80) cc_final: 0.8504 (t80) REVERT: e 97 GLU cc_start: 0.8366 (tp30) cc_final: 0.7828 (tp30) REVERT: e 133 GLU cc_start: 0.6784 (OUTLIER) cc_final: 0.5656 (tp30) REVERT: e 152 ASP cc_start: 0.7353 (OUTLIER) cc_final: 0.6970 (p0) REVERT: e 163 GLU cc_start: 0.6988 (OUTLIER) cc_final: 0.6433 (mm-30) REVERT: e 166 ARG cc_start: 0.8980 (OUTLIER) cc_final: 0.8582 (tmm-80) REVERT: e 177 ARG cc_start: 0.7934 (ttt180) cc_final: 0.7444 (tpt170) REVERT: f 82 PHE cc_start: 0.7579 (OUTLIER) cc_final: 0.7144 (m-10) REVERT: f 137 LYS cc_start: 0.8902 (OUTLIER) cc_final: 0.8531 (mmtt) REVERT: g 17 ASP cc_start: 0.8474 (t70) cc_final: 0.8273 (t0) REVERT: g 18 GLN cc_start: 0.8434 (OUTLIER) cc_final: 0.7768 (mp10) REVERT: g 46 PHE cc_start: 0.8526 (m-10) cc_final: 0.8251 (m-10) REVERT: g 55 GLU cc_start: 0.9151 (mt-10) cc_final: 0.8752 (mt-10) REVERT: g 87 GLU cc_start: 0.8123 (tp30) cc_final: 0.7678 (mm-30) REVERT: g 133 GLN cc_start: 0.8913 (tt0) cc_final: 0.8431 (tm-30) REVERT: h 52 MET cc_start: 0.8301 (tmm) cc_final: 0.8007 (tpp) REVERT: h 86 MET cc_start: 0.3444 (mmm) cc_final: 0.3043 (tpp) REVERT: h 116 GLU cc_start: 0.8934 (mm-30) cc_final: 0.8560 (mm-30) REVERT: i 41 PHE cc_start: 0.8815 (t80) cc_final: 0.8409 (t80) REVERT: i 112 LYS cc_start: 0.5608 (pttp) cc_final: 0.4336 (tttt) REVERT: j 7 LYS cc_start: 0.8786 (OUTLIER) cc_final: 0.8017 (mtmm) REVERT: j 118 MET cc_start: 0.9111 (mmt) cc_final: 0.8751 (mmm) REVERT: j 119 PHE cc_start: 0.9145 (t80) cc_final: 0.8832 (t80) REVERT: k 29 HIS cc_start: 0.8351 (t70) cc_final: 0.8012 (t-90) REVERT: k 66 LYS cc_start: 0.8489 (tttt) cc_final: 0.7855 (tttt) REVERT: k 116 ILE cc_start: 0.8282 (OUTLIER) cc_final: 0.7582 (tp) REVERT: l 39 LYS cc_start: 0.8914 (pttt) cc_final: 0.8489 (pttt) REVERT: l 82 LEU cc_start: 0.9614 (OUTLIER) cc_final: 0.9362 (mt) REVERT: l 128 THR cc_start: 0.9138 (OUTLIER) cc_final: 0.8750 (t) REVERT: m 64 TRP cc_start: 0.6498 (m-90) cc_final: 0.5821 (m-90) REVERT: n 20 MET cc_start: 0.9099 (OUTLIER) cc_final: 0.8895 (tpp) REVERT: n 103 ARG cc_start: 0.8168 (ttp-170) cc_final: 0.7951 (ttm170) REVERT: o 12 THR cc_start: 0.9457 (p) cc_final: 0.9216 (p) REVERT: o 55 GLU cc_start: 0.8522 (mt-10) cc_final: 0.7525 (mm-30) REVERT: p 12 MET cc_start: 0.8081 (mtm) cc_final: 0.6697 (tmm) REVERT: p 37 LYS cc_start: 0.8432 (mttm) cc_final: 0.8118 (mptt) REVERT: p 50 ARG cc_start: 0.8538 (ttt-90) cc_final: 0.7972 (ttt-90) REVERT: p 74 GLN cc_start: 0.8424 (mp10) cc_final: 0.7628 (mp10) REVERT: p 93 LYS cc_start: 0.8728 (tppt) cc_final: 0.8309 (tppt) REVERT: q 21 LYS cc_start: 0.8646 (mmtt) cc_final: 0.8280 (ttmm) REVERT: q 24 TYR cc_start: 0.7602 (t80) cc_final: 0.7198 (t80) REVERT: q 54 ARG cc_start: 0.8932 (mtm180) cc_final: 0.8601 (mtm-85) REVERT: q 88 GLU cc_start: 0.8567 (mp0) cc_final: 0.8203 (mp0) REVERT: q 106 THR cc_start: 0.9366 (p) cc_final: 0.8993 (p) REVERT: q 110 GLU cc_start: 0.8904 (mm-30) cc_final: 0.8249 (mm-30) REVERT: r 46 GLU cc_start: 0.8762 (mp0) cc_final: 0.7797 (tp30) REVERT: r 52 PRO cc_start: 0.8534 (Cg_endo) cc_final: 0.7847 (Cg_exo) REVERT: r 79 ARG cc_start: 0.7950 (ptt90) cc_final: 0.7600 (ptt180) REVERT: r 87 GLN cc_start: 0.6011 (tm-30) cc_final: 0.5411 (tm-30) REVERT: s 38 TYR cc_start: 0.8854 (m-80) cc_final: 0.8393 (m-80) REVERT: s 82 MET cc_start: 0.8208 (pmm) cc_final: 0.7856 (pmm) REVERT: t 18 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7828 (pp20) REVERT: t 24 MET cc_start: 0.9239 (tpp) cc_final: 0.8869 (tpp) REVERT: t 25 GLU cc_start: 0.9069 (OUTLIER) cc_final: 0.8735 (pt0) REVERT: t 74 ILE cc_start: 0.6582 (OUTLIER) cc_final: 0.6260 (mm) REVERT: v 31 TYR cc_start: 0.8397 (p90) cc_final: 0.8067 (p90) REVERT: v 50 MET cc_start: 0.8651 (mmt) cc_final: 0.8322 (tpp) REVERT: v 61 LEU cc_start: 0.8295 (OUTLIER) cc_final: 0.7942 (mm) REVERT: w 62 LYS cc_start: 0.9214 (mtpt) cc_final: 0.8891 (mtpp) REVERT: x 15 ASN cc_start: 0.8829 (t0) cc_final: 0.8612 (t0) REVERT: x 16 ASN cc_start: 0.9140 (t0) cc_final: 0.8856 (m-40) REVERT: y 6 LEU cc_start: 0.7375 (OUTLIER) cc_final: 0.7122 (tt) REVERT: y 45 GLN cc_start: 0.8694 (pt0) cc_final: 0.8198 (pp30) REVERT: y 48 ARG cc_start: 0.8966 (mtt-85) cc_final: 0.8617 (mmt90) REVERT: z 24 LEU cc_start: 0.9015 (tp) cc_final: 0.8788 (tp) REVERT: B 27 LEU cc_start: 0.8880 (tp) cc_final: 0.7745 (tt) REVERT: B 36 LYS cc_start: 0.9393 (OUTLIER) cc_final: 0.9145 (mmmm) REVERT: C 19 PHE cc_start: 0.8566 (p90) cc_final: 0.8349 (p90) REVERT: D 2 LYS cc_start: 0.8523 (ttpt) cc_final: 0.8301 (ttpt) REVERT: D 28 ARG cc_start: 0.8673 (mtm-85) cc_final: 0.8465 (mtm-85) REVERT: D 35 ARG cc_start: 0.8939 (mtt-85) cc_final: 0.8448 (mtt-85) REVERT: E 24 LYS cc_start: 0.8819 (tppp) cc_final: 0.8467 (tptp) REVERT: E 61 LEU cc_start: 0.8673 (pp) cc_final: 0.8400 (pp) REVERT: F 4 ARG cc_start: 0.7929 (ptp-170) cc_final: 0.7578 (ptp-170) REVERT: G 26 MET cc_start: 0.7536 (tmm) cc_final: 0.6621 (tmm) REVERT: G 38 HIS cc_start: 0.7539 (OUTLIER) cc_final: 0.6867 (t70) REVERT: G 153 MET cc_start: 0.6032 (mmm) cc_final: 0.5692 (mmm) REVERT: G 183 PHE cc_start: 0.7039 (OUTLIER) cc_final: 0.6759 (m-80) REVERT: I 74 TYR cc_start: 0.8804 (m-10) cc_final: 0.8258 (m-80) REVERT: I 88 ASN cc_start: 0.8957 (m110) cc_final: 0.8646 (m-40) REVERT: I 92 LEU cc_start: 0.8279 (mt) cc_final: 0.7399 (mt) REVERT: I 104 MET cc_start: 0.4031 (mmt) cc_final: 0.3779 (tpp) REVERT: I 123 MET cc_start: 0.7421 (mmm) cc_final: 0.7063 (mmm) REVERT: I 127 ARG cc_start: 0.8784 (mtt180) cc_final: 0.8396 (ttt180) REVERT: I 151 GLN cc_start: 0.8890 (mm110) cc_final: 0.8589 (mm110) REVERT: I 171 GLU cc_start: 0.5466 (OUTLIER) cc_final: 0.5124 (mp0) REVERT: I 184 LYS cc_start: 0.9313 (tptt) cc_final: 0.8999 (tptt) REVERT: I 187 ARG cc_start: 0.9012 (tpt90) cc_final: 0.8521 (tpt-90) REVERT: I 201 GLU cc_start: 0.9091 (mm-30) cc_final: 0.8199 (mm-30) REVERT: J 19 ARG cc_start: 0.4598 (OUTLIER) cc_final: 0.3713 (ppt90) REVERT: J 131 ASN cc_start: 0.8313 (m-40) cc_final: 0.7998 (m110) REVERT: K 44 ARG cc_start: 0.8198 (OUTLIER) cc_final: 0.7924 (mtt-85) REVERT: M 79 ARG cc_start: 0.9140 (OUTLIER) cc_final: 0.8747 (ptt90) REVERT: M 95 MET cc_start: 0.6955 (tpt) cc_final: 0.6692 (tpt) REVERT: N 20 ILE cc_start: 0.7060 (OUTLIER) cc_final: 0.6672 (mm) REVERT: N 56 MET cc_start: 0.4502 (mpp) cc_final: 0.4265 (mpp) REVERT: O 15 HIS cc_start: 0.2355 (OUTLIER) cc_final: 0.1917 (p90) REVERT: P 43 TRP cc_start: 0.7184 (p-90) cc_final: 0.6490 (p-90) REVERT: Q 4 ASN cc_start: 0.8006 (OUTLIER) cc_final: 0.7408 (t0) REVERT: Q 73 LEU cc_start: 0.7140 (pt) cc_final: 0.6541 (mt) REVERT: Q 87 LYS cc_start: 0.8514 (tptp) cc_final: 0.7263 (tptm) REVERT: Q 116 TYR cc_start: 0.7132 (m-80) cc_final: 0.6602 (m-80) REVERT: R 2 ARG cc_start: 0.6378 (tpp-160) cc_final: 0.5893 (mmm160) REVERT: R 74 MET cc_start: 0.3138 (tmm) cc_final: 0.2467 (mtt) REVERT: T 27 GLN cc_start: 0.8178 (mp10) cc_final: 0.7970 (mp10) REVERT: T 44 GLU cc_start: 0.8601 (tp30) cc_final: 0.8274 (tp30) REVERT: T 46 LYS cc_start: 0.8084 (pttt) cc_final: 0.7618 (pptt) REVERT: T 57 ARG cc_start: 0.8255 (ttt-90) cc_final: 0.6922 (ttt-90) REVERT: T 58 MET cc_start: 0.8884 (mtm) cc_final: 0.8069 (mmm) REVERT: T 61 GLN cc_start: 0.9259 (tp40) cc_final: 0.9036 (tp-100) REVERT: T 64 LYS cc_start: 0.8809 (mmtm) cc_final: 0.8493 (tppt) REVERT: U 34 GLU cc_start: 0.8557 (pm20) cc_final: 0.7751 (pm20) REVERT: U 35 ARG cc_start: 0.7849 (ttp80) cc_final: 0.7587 (ttp80) REVERT: U 38 PHE cc_start: 0.8193 (p90) cc_final: 0.7860 (p90) REVERT: V 62 GLU cc_start: 0.5446 (tt0) cc_final: 0.4626 (tt0) REVERT: V 79 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.7066 (mp0) REVERT: W 58 ILE cc_start: 0.6551 (mt) cc_final: 0.6213 (mt) REVERT: Y 18 LYS cc_start: 0.9082 (mmtt) cc_final: 0.8821 (tptt) REVERT: Y 20 ASN cc_start: 0.8511 (OUTLIER) cc_final: 0.8059 (p0) REVERT: Y 52 GLU cc_start: 0.8280 (mm-30) cc_final: 0.7928 (mp0) REVERT: Z 15 LEU cc_start: 0.2601 (OUTLIER) cc_final: 0.2390 (pp) REVERT: Z 23 GLU cc_start: 0.3868 (OUTLIER) cc_final: 0.3393 (mt-10) REVERT: Z 37 TYR cc_start: 0.3316 (OUTLIER) cc_final: 0.2950 (t80) REVERT: a 53 ARG cc_start: -0.0298 (OUTLIER) cc_final: -0.2272 (mmp-170) REVERT: 8 16 GLU cc_start: 0.7723 (mp0) cc_final: 0.7483 (mp0) REVERT: 8 64 ILE cc_start: 0.6770 (OUTLIER) cc_final: 0.6426 (mp) REVERT: 8 105 ARG cc_start: 0.7578 (OUTLIER) cc_final: 0.7309 (ttp-170) outliers start: 406 outliers final: 283 residues processed: 1513 average time/residue: 1.3163 time to fit residues: 3438.2644 Evaluate side-chains 1504 residues out of total 5093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 318 poor density : 1186 time to evaluate : 6.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 3 VAL Chi-restraints excluded: chain b residue 8 THR Chi-restraints excluded: chain b residue 32 LEU Chi-restraints excluded: chain b residue 33 LEU Chi-restraints excluded: chain b residue 104 LEU Chi-restraints excluded: chain b residue 113 ASP Chi-restraints excluded: chain b residue 128 THR Chi-restraints excluded: chain b residue 175 LEU Chi-restraints excluded: chain b residue 219 VAL Chi-restraints excluded: chain b residue 222 THR Chi-restraints excluded: chain b residue 224 MET Chi-restraints excluded: chain b residue 227 VAL Chi-restraints excluded: chain b residue 239 PHE Chi-restraints excluded: chain b residue 249 VAL Chi-restraints excluded: chain c residue 12 THR Chi-restraints excluded: chain c residue 27 ILE Chi-restraints excluded: chain c residue 35 THR Chi-restraints excluded: chain c residue 40 LEU Chi-restraints excluded: chain c residue 73 VAL Chi-restraints excluded: chain c residue 79 LEU Chi-restraints excluded: chain c residue 100 LEU Chi-restraints excluded: chain c residue 108 ASP Chi-restraints excluded: chain c residue 121 THR Chi-restraints excluded: chain c residue 160 LYS Chi-restraints excluded: chain c residue 170 VAL Chi-restraints excluded: chain c residue 171 THR Chi-restraints excluded: chain c residue 180 VAL Chi-restraints excluded: chain c residue 189 VAL Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 4 VAL Chi-restraints excluded: chain d residue 7 ASP Chi-restraints excluded: chain d residue 48 THR Chi-restraints excluded: chain d residue 65 THR Chi-restraints excluded: chain d residue 80 SER Chi-restraints excluded: chain d residue 133 LEU Chi-restraints excluded: chain d residue 169 VAL Chi-restraints excluded: chain d residue 193 VAL Chi-restraints excluded: chain e residue 4 HIS Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 27 VAL Chi-restraints excluded: chain e residue 50 ASP Chi-restraints excluded: chain e residue 80 GLN Chi-restraints excluded: chain e residue 102 LEU Chi-restraints excluded: chain e residue 112 ASP Chi-restraints excluded: chain e residue 133 GLU Chi-restraints excluded: chain e residue 148 VAL Chi-restraints excluded: chain e residue 152 ASP Chi-restraints excluded: chain e residue 153 ILE Chi-restraints excluded: chain e residue 154 THR Chi-restraints excluded: chain e residue 157 THR Chi-restraints excluded: chain e residue 163 GLU Chi-restraints excluded: chain e residue 166 ARG Chi-restraints excluded: chain e residue 168 LEU Chi-restraints excluded: chain f residue 9 VAL Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 17 LYS Chi-restraints excluded: chain f residue 18 ILE Chi-restraints excluded: chain f residue 19 ASN Chi-restraints excluded: chain f residue 29 ASN Chi-restraints excluded: chain f residue 70 LEU Chi-restraints excluded: chain f residue 82 PHE Chi-restraints excluded: chain f residue 88 LEU Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 102 ILE Chi-restraints excluded: chain f residue 104 LEU Chi-restraints excluded: chain f residue 106 LEU Chi-restraints excluded: chain f residue 136 ASP Chi-restraints excluded: chain f residue 137 LYS Chi-restraints excluded: chain g residue 4 ILE Chi-restraints excluded: chain g residue 18 GLN Chi-restraints excluded: chain g residue 119 ASN Chi-restraints excluded: chain g residue 134 VAL Chi-restraints excluded: chain g residue 143 ILE Chi-restraints excluded: chain h residue 74 ASP Chi-restraints excluded: chain h residue 82 ILE Chi-restraints excluded: chain j residue 3 THR Chi-restraints excluded: chain j residue 7 LYS Chi-restraints excluded: chain j residue 11 VAL Chi-restraints excluded: chain j residue 44 TYR Chi-restraints excluded: chain j residue 49 ASP Chi-restraints excluded: chain j residue 57 LEU Chi-restraints excluded: chain j residue 73 VAL Chi-restraints excluded: chain j residue 100 VAL Chi-restraints excluded: chain k residue 21 CYS Chi-restraints excluded: chain k residue 22 ILE Chi-restraints excluded: chain k residue 24 VAL Chi-restraints excluded: chain k residue 62 VAL Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 77 ILE Chi-restraints excluded: chain k residue 103 VAL Chi-restraints excluded: chain k residue 104 THR Chi-restraints excluded: chain k residue 110 GLU Chi-restraints excluded: chain k residue 116 ILE Chi-restraints excluded: chain l residue 47 ARG Chi-restraints excluded: chain l residue 55 MET Chi-restraints excluded: chain l residue 67 THR Chi-restraints excluded: chain l residue 74 THR Chi-restraints excluded: chain l residue 82 LEU Chi-restraints excluded: chain l residue 94 THR Chi-restraints excluded: chain l residue 107 PHE Chi-restraints excluded: chain l residue 128 THR Chi-restraints excluded: chain m residue 2 LEU Chi-restraints excluded: chain m residue 20 LEU Chi-restraints excluded: chain m residue 31 PHE Chi-restraints excluded: chain m residue 42 THR Chi-restraints excluded: chain m residue 106 ASP Chi-restraints excluded: chain m residue 124 LEU Chi-restraints excluded: chain m residue 128 THR Chi-restraints excluded: chain m residue 135 VAL Chi-restraints excluded: chain n residue 9 GLN Chi-restraints excluded: chain n residue 20 MET Chi-restraints excluded: chain n residue 36 THR Chi-restraints excluded: chain n residue 47 VAL Chi-restraints excluded: chain n residue 52 ILE Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain n residue 95 THR Chi-restraints excluded: chain n residue 110 MET Chi-restraints excluded: chain o residue 34 HIS Chi-restraints excluded: chain o residue 35 ILE Chi-restraints excluded: chain o residue 47 VAL Chi-restraints excluded: chain o residue 53 THR Chi-restraints excluded: chain o residue 83 LEU Chi-restraints excluded: chain o residue 90 VAL Chi-restraints excluded: chain o residue 93 ASP Chi-restraints excluded: chain p residue 23 ASP Chi-restraints excluded: chain p residue 43 GLU Chi-restraints excluded: chain p residue 60 VAL Chi-restraints excluded: chain p residue 75 THR Chi-restraints excluded: chain p residue 80 VAL Chi-restraints excluded: chain q residue 33 VAL Chi-restraints excluded: chain q residue 59 LEU Chi-restraints excluded: chain q residue 61 ILE Chi-restraints excluded: chain r residue 15 SER Chi-restraints excluded: chain r residue 19 THR Chi-restraints excluded: chain r residue 22 LEU Chi-restraints excluded: chain r residue 26 ASP Chi-restraints excluded: chain r residue 38 VAL Chi-restraints excluded: chain r residue 39 LEU Chi-restraints excluded: chain r residue 49 ILE Chi-restraints excluded: chain r residue 51 VAL Chi-restraints excluded: chain r residue 58 VAL Chi-restraints excluded: chain r residue 75 VAL Chi-restraints excluded: chain s residue 20 VAL Chi-restraints excluded: chain s residue 25 ARG Chi-restraints excluded: chain s residue 52 GLU Chi-restraints excluded: chain s residue 53 SER Chi-restraints excluded: chain s residue 66 ILE Chi-restraints excluded: chain s residue 70 LYS Chi-restraints excluded: chain s residue 76 VAL Chi-restraints excluded: chain s residue 96 ILE Chi-restraints excluded: chain s residue 100 THR Chi-restraints excluded: chain s residue 105 VAL Chi-restraints excluded: chain t residue 16 VAL Chi-restraints excluded: chain t residue 18 GLU Chi-restraints excluded: chain t residue 25 GLU Chi-restraints excluded: chain t residue 29 THR Chi-restraints excluded: chain t residue 62 VAL Chi-restraints excluded: chain t residue 74 ILE Chi-restraints excluded: chain t residue 86 THR Chi-restraints excluded: chain u residue 10 VAL Chi-restraints excluded: chain u residue 11 ILE Chi-restraints excluded: chain u residue 26 ASN Chi-restraints excluded: chain u residue 35 VAL Chi-restraints excluded: chain u residue 81 ARG Chi-restraints excluded: chain u residue 86 PHE Chi-restraints excluded: chain v residue 8 VAL Chi-restraints excluded: chain v residue 45 ASP Chi-restraints excluded: chain v residue 56 PHE Chi-restraints excluded: chain v residue 61 LEU Chi-restraints excluded: chain v residue 63 ILE Chi-restraints excluded: chain v residue 64 VAL Chi-restraints excluded: chain v residue 66 ASP Chi-restraints excluded: chain v residue 90 ASP Chi-restraints excluded: chain w residue 19 VAL Chi-restraints excluded: chain w residue 27 VAL Chi-restraints excluded: chain w residue 34 VAL Chi-restraints excluded: chain x residue 12 VAL Chi-restraints excluded: chain x residue 13 THR Chi-restraints excluded: chain x residue 67 LEU Chi-restraints excluded: chain y residue 6 LEU Chi-restraints excluded: chain y residue 18 LEU Chi-restraints excluded: chain y residue 46 VAL Chi-restraints excluded: chain y residue 49 ASP Chi-restraints excluded: chain z residue 13 ILE Chi-restraints excluded: chain z residue 26 LEU Chi-restraints excluded: chain z residue 33 HIS Chi-restraints excluded: chain z residue 40 THR Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 36 LYS Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain C residue 9 LYS Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain D residue 3 ARG Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 43 LEU Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 23 ILE Chi-restraints excluded: chain F residue 33 HIS Chi-restraints excluded: chain G residue 4 SER Chi-restraints excluded: chain G residue 5 MET Chi-restraints excluded: chain G residue 14 HIS Chi-restraints excluded: chain G residue 15 PHE Chi-restraints excluded: chain G residue 38 HIS Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 128 LEU Chi-restraints excluded: chain G residue 166 ASP Chi-restraints excluded: chain G residue 183 PHE Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 190 SER Chi-restraints excluded: chain G residue 210 THR Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 194 VAL Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 64 TYR Chi-restraints excluded: chain I residue 99 ASN Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 141 VAL Chi-restraints excluded: chain I residue 171 GLU Chi-restraints excluded: chain J residue 15 ILE Chi-restraints excluded: chain J residue 19 ARG Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 79 THR Chi-restraints excluded: chain J residue 121 ASN Chi-restraints excluded: chain K residue 8 PHE Chi-restraints excluded: chain K residue 44 ARG Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 64 VAL Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain K residue 78 PHE Chi-restraints excluded: chain K residue 84 VAL Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain L residue 6 ILE Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 47 GLU Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain L residue 147 ASN Chi-restraints excluded: chain M residue 33 VAL Chi-restraints excluded: chain M residue 37 ASN Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain M residue 79 ARG Chi-restraints excluded: chain M residue 90 GLU Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain M residue 112 ASP Chi-restraints excluded: chain M residue 128 VAL Chi-restraints excluded: chain N residue 10 ARG Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 24 ASN Chi-restraints excluded: chain N residue 125 GLN Chi-restraints excluded: chain O residue 15 HIS Chi-restraints excluded: chain O residue 69 THR Chi-restraints excluded: chain P residue 15 VAL Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain P residue 35 ASP Chi-restraints excluded: chain P residue 85 VAL Chi-restraints excluded: chain P residue 107 THR Chi-restraints excluded: chain P residue 118 ASN Chi-restraints excluded: chain Q residue 4 ASN Chi-restraints excluded: chain Q residue 28 GLN Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 86 VAL Chi-restraints excluded: chain R residue 53 ASP Chi-restraints excluded: chain R residue 67 ASP Chi-restraints excluded: chain S residue 23 ARG Chi-restraints excluded: chain S residue 49 THR Chi-restraints excluded: chain S residue 61 ASN Chi-restraints excluded: chain T residue 17 ASP Chi-restraints excluded: chain T residue 24 THR Chi-restraints excluded: chain T residue 28 VAL Chi-restraints excluded: chain T residue 30 LEU Chi-restraints excluded: chain T residue 56 LEU Chi-restraints excluded: chain T residue 68 TYR Chi-restraints excluded: chain U residue 69 ASP Chi-restraints excluded: chain U residue 77 GLU Chi-restraints excluded: chain V residue 29 LYS Chi-restraints excluded: chain V residue 46 HIS Chi-restraints excluded: chain V residue 69 THR Chi-restraints excluded: chain V residue 79 GLU Chi-restraints excluded: chain W residue 22 TYR Chi-restraints excluded: chain W residue 34 GLU Chi-restraints excluded: chain W residue 64 LEU Chi-restraints excluded: chain X residue 15 LEU Chi-restraints excluded: chain X residue 39 ILE Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain X residue 59 VAL Chi-restraints excluded: chain X residue 70 LEU Chi-restraints excluded: chain X residue 72 GLU Chi-restraints excluded: chain X residue 76 THR Chi-restraints excluded: chain Y residue 19 HIS Chi-restraints excluded: chain Y residue 20 ASN Chi-restraints excluded: chain Y residue 31 ILE Chi-restraints excluded: chain Y residue 69 ASN Chi-restraints excluded: chain Z residue 5 VAL Chi-restraints excluded: chain Z residue 12 ASP Chi-restraints excluded: chain Z residue 15 LEU Chi-restraints excluded: chain Z residue 23 GLU Chi-restraints excluded: chain Z residue 37 TYR Chi-restraints excluded: chain Z residue 52 VAL Chi-restraints excluded: chain a residue 5 THR Chi-restraints excluded: chain a residue 18 THR Chi-restraints excluded: chain a residue 53 ARG Chi-restraints excluded: chain a residue 172 HIS Chi-restraints excluded: chain 8 residue 35 THR Chi-restraints excluded: chain 8 residue 64 ILE Chi-restraints excluded: chain 8 residue 100 THR Chi-restraints excluded: chain 8 residue 105 ARG Chi-restraints excluded: chain 9 residue 18 THR Chi-restraints excluded: chain 9 residue 20 ILE Chi-restraints excluded: chain 9 residue 35 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1065 random chunks: chunk 346 optimal weight: 0.0770 chunk 927 optimal weight: 10.0000 chunk 203 optimal weight: 4.9990 chunk 604 optimal weight: 20.0000 chunk 254 optimal weight: 3.9990 chunk 1030 optimal weight: 10.0000 chunk 855 optimal weight: 10.0000 chunk 477 optimal weight: 50.0000 chunk 85 optimal weight: 5.9990 chunk 340 optimal weight: 10.0000 chunk 540 optimal weight: 0.0970 overall best weight: 3.0342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 90 GLN ** d 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 22 ASN h 122 GLN i 29 GLN i 42 ASN l 38 GLN l 104 GLN ** m 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 3 HIS n 9 GLN ** n 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 19 GLN ** r 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 15 GLN u 98 ASN ** v 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 58 ASN ** D 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 13 ASN G 38 HIS ** I 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 75 GLN N 49 GLN ** P 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 95 HIS S 34 ASN ** T 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 50 HIS ** U 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 47 GLN ** Y 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 47 ASN ** a 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 172 HIS ** 9 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.5275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 161229 Z= 0.174 Angle : 0.613 14.108 240720 Z= 0.313 Chirality : 0.035 0.294 30724 Planarity : 0.005 0.068 13231 Dihedral : 23.714 179.869 79535 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 21.73 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.26 % Favored : 90.61 % Rotamer: Outliers : 5.69 % Allowed : 27.78 % Favored : 66.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % 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: -2.95 (0.10), residues: 6142 helix: -1.10 (0.12), residues: 1778 sheet: -1.82 (0.17), residues: 865 loop : -2.54 (0.10), residues: 3499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP G 95 HIS 0.045 0.001 HIS a 172 PHE 0.034 0.002 PHE V 36 TYR 0.028 0.002 TYR p 98 ARG 0.013 0.001 ARG e 101 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12284 Ramachandran restraints generated. 6142 Oldfield, 0 Emsley, 6142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12284 Ramachandran restraints generated. 6142 Oldfield, 0 Emsley, 6142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1607 residues out of total 5093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 290 poor density : 1317 time to evaluate : 8.803 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: c 28 GLU cc_start: 0.8904 (tm-30) cc_final: 0.8674 (tp30) REVERT: c 36 GLN cc_start: 0.8180 (tt0) cc_final: 0.7927 (tp-100) REVERT: c 64 GLU cc_start: 0.8808 (mm-30) cc_final: 0.8460 (mm-30) REVERT: c 80 TRP cc_start: 0.8535 (m-90) cc_final: 0.7861 (m-90) REVERT: c 148 GLN cc_start: 0.8697 (mp10) cc_final: 0.8426 (mp10) REVERT: c 185 ASN cc_start: 0.8806 (m-40) cc_final: 0.8529 (m110) REVERT: d 6 LYS cc_start: 0.8237 (ptmt) cc_final: 0.7675 (pttm) REVERT: d 9 GLN cc_start: 0.8628 (tm-30) cc_final: 0.8265 (tm-30) REVERT: d 122 GLU cc_start: 0.8315 (tm-30) cc_final: 0.8066 (pp20) REVERT: d 146 VAL cc_start: 0.9382 (p) cc_final: 0.9134 (m) REVERT: d 183 PHE cc_start: 0.8322 (m-80) cc_final: 0.8072 (m-80) REVERT: d 188 MET cc_start: 0.9084 (mmt) cc_final: 0.8796 (mmt) REVERT: e 3 LEU cc_start: 0.9174 (mp) cc_final: 0.8721 (tt) REVERT: e 6 TYR cc_start: 0.9132 (t80) cc_final: 0.8438 (t80) REVERT: e 80 GLN cc_start: 0.8392 (OUTLIER) cc_final: 0.8094 (tm-30) REVERT: e 97 GLU cc_start: 0.8148 (tp30) cc_final: 0.7555 (tp30) REVERT: e 109 ARG cc_start: 0.8857 (tpp-160) cc_final: 0.8314 (tpp-160) REVERT: e 133 GLU cc_start: 0.6715 (tp30) cc_final: 0.6279 (tp30) REVERT: e 134 GLN cc_start: 0.8255 (pm20) cc_final: 0.7073 (pm20) REVERT: e 177 ARG cc_start: 0.7641 (ttt180) cc_final: 0.7119 (tpt170) REVERT: f 82 PHE cc_start: 0.7564 (m-10) cc_final: 0.7123 (m-10) REVERT: f 137 LYS cc_start: 0.8820 (OUTLIER) cc_final: 0.8522 (mmtt) REVERT: g 17 ASP cc_start: 0.8318 (t70) cc_final: 0.7273 (p0) REVERT: g 18 GLN cc_start: 0.8302 (OUTLIER) cc_final: 0.7884 (pm20) REVERT: g 46 PHE cc_start: 0.8488 (m-10) cc_final: 0.8128 (m-10) REVERT: g 87 GLU cc_start: 0.8111 (tp30) cc_final: 0.7658 (mm-30) REVERT: g 145 ASN cc_start: 0.7814 (m-40) cc_final: 0.7525 (m110) REVERT: h 116 GLU cc_start: 0.8820 (mm-30) cc_final: 0.8441 (mm-30) REVERT: i 41 PHE cc_start: 0.8696 (t80) cc_final: 0.8317 (t80) REVERT: i 116 MET cc_start: -0.1996 (tpt) cc_final: -0.2985 (tpt) REVERT: j 68 LYS cc_start: 0.8479 (mtpt) cc_final: 0.8115 (mtpt) REVERT: j 118 MET cc_start: 0.9173 (mmt) cc_final: 0.8897 (mmt) REVERT: j 119 PHE cc_start: 0.9096 (t80) cc_final: 0.8767 (t80) REVERT: k 29 HIS cc_start: 0.8223 (t70) cc_final: 0.7853 (t-90) REVERT: k 66 LYS cc_start: 0.8277 (tttt) cc_final: 0.7608 (tttt) REVERT: l 38 GLN cc_start: 0.8905 (tt0) cc_final: 0.8359 (tp-100) REVERT: l 39 LYS cc_start: 0.8744 (pttt) cc_final: 0.8271 (ptpp) REVERT: l 48 ARG cc_start: 0.7321 (mtm-85) cc_final: 0.7014 (mtm-85) REVERT: m 127 LYS cc_start: 0.8572 (mmtt) cc_final: 0.8297 (mmtt) REVERT: n 46 ARG cc_start: 0.8517 (ttm110) cc_final: 0.8282 (ttm110) REVERT: o 12 THR cc_start: 0.9460 (p) cc_final: 0.9233 (p) REVERT: o 55 GLU cc_start: 0.8531 (mt-10) cc_final: 0.7599 (mm-30) REVERT: p 12 MET cc_start: 0.8035 (mtm) cc_final: 0.6809 (tmm) REVERT: p 37 LYS cc_start: 0.8464 (mttm) cc_final: 0.8210 (mptt) REVERT: p 50 ARG cc_start: 0.8390 (ttt-90) cc_final: 0.7739 (ttt-90) REVERT: p 74 GLN cc_start: 0.8304 (mp10) cc_final: 0.7672 (mp10) REVERT: p 93 LYS cc_start: 0.8649 (tppt) cc_final: 0.8305 (tppt) REVERT: q 21 LYS cc_start: 0.8576 (mmtt) cc_final: 0.8223 (ttmm) REVERT: q 24 TYR cc_start: 0.7554 (t80) cc_final: 0.7159 (t80) REVERT: q 54 ARG cc_start: 0.8885 (mtm180) cc_final: 0.8223 (mtm-85) REVERT: q 106 THR cc_start: 0.9348 (p) cc_final: 0.8929 (p) REVERT: q 110 GLU cc_start: 0.8913 (mm-30) cc_final: 0.8247 (mm-30) REVERT: r 40 MET cc_start: 0.7537 (tmm) cc_final: 0.7062 (tmm) REVERT: r 52 PRO cc_start: 0.8466 (Cg_endo) cc_final: 0.8191 (Cg_exo) REVERT: r 71 LYS cc_start: 0.8698 (mppt) cc_final: 0.8216 (ttpt) REVERT: r 79 ARG cc_start: 0.7795 (ptt90) cc_final: 0.7510 (ptt180) REVERT: r 87 GLN cc_start: 0.5836 (tm-30) cc_final: 0.5226 (tm-30) REVERT: s 38 TYR cc_start: 0.8823 (m-80) cc_final: 0.8393 (m-80) REVERT: s 82 MET cc_start: 0.8306 (pmm) cc_final: 0.7930 (pmm) REVERT: t 18 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7914 (pp20) REVERT: t 24 MET cc_start: 0.9116 (tpp) cc_final: 0.8695 (tpp) REVERT: t 59 ASN cc_start: 0.8941 (m110) cc_final: 0.8709 (m-40) REVERT: u 94 PHE cc_start: 0.8543 (p90) cc_final: 0.7827 (p90) REVERT: v 7 GLU cc_start: 0.6218 (mp0) cc_final: 0.5901 (mp0) REVERT: v 31 TYR cc_start: 0.8318 (p90) cc_final: 0.7982 (p90) REVERT: x 15 ASN cc_start: 0.8731 (t0) cc_final: 0.8471 (t0) REVERT: x 16 ASN cc_start: 0.9148 (t0) cc_final: 0.8830 (m-40) REVERT: y 6 LEU cc_start: 0.7663 (OUTLIER) cc_final: 0.7461 (tt) REVERT: y 45 GLN cc_start: 0.8760 (pt0) cc_final: 0.8234 (pp30) REVERT: y 48 ARG cc_start: 0.8932 (mtt-85) cc_final: 0.8652 (mmt90) REVERT: z 13 ILE cc_start: 0.7836 (OUTLIER) cc_final: 0.7514 (tp) REVERT: z 24 LEU cc_start: 0.8992 (tp) cc_final: 0.8750 (tp) REVERT: z 52 PHE cc_start: 0.8688 (p90) cc_final: 0.8356 (p90) REVERT: B 27 LEU cc_start: 0.8700 (tp) cc_final: 0.8345 (tt) REVERT: B 35 GLU cc_start: 0.8749 (mm-30) cc_final: 0.8446 (mm-30) REVERT: C 29 LYS cc_start: 0.8776 (tppt) cc_final: 0.8538 (tptp) REVERT: D 35 ARG cc_start: 0.8966 (mtt-85) cc_final: 0.8472 (mtt90) REVERT: E 24 LYS cc_start: 0.8791 (tppp) cc_final: 0.8490 (tptp) REVERT: E 29 ARG cc_start: 0.7939 (mmt180) cc_final: 0.7566 (mmt90) REVERT: E 39 ARG cc_start: 0.8694 (ttt180) cc_final: 0.8436 (ttt-90) REVERT: E 48 MET cc_start: 0.8279 (OUTLIER) cc_final: 0.7930 (mmt) REVERT: F 15 LYS cc_start: 0.7634 (mmtp) cc_final: 0.7328 (mmtt) REVERT: F 30 GLU cc_start: 0.8716 (mt-10) cc_final: 0.8461 (mt-10) REVERT: G 26 MET cc_start: 0.7413 (tmm) cc_final: 0.6922 (tmm) REVERT: G 95 TRP cc_start: 0.8129 (t-100) cc_final: 0.7750 (t-100) REVERT: G 153 MET cc_start: 0.5993 (mmm) cc_final: 0.5561 (mmm) REVERT: G 183 PHE cc_start: 0.6988 (OUTLIER) cc_final: 0.6722 (m-80) REVERT: I 74 TYR cc_start: 0.8747 (m-10) cc_final: 0.8247 (m-80) REVERT: I 88 ASN cc_start: 0.9056 (m110) cc_final: 0.8716 (m-40) REVERT: I 92 LEU cc_start: 0.8403 (mt) cc_final: 0.7504 (mt) REVERT: I 104 MET cc_start: 0.4299 (mmt) cc_final: 0.3884 (mmt) REVERT: I 123 MET cc_start: 0.7491 (mmm) cc_final: 0.7116 (mmm) REVERT: I 127 ARG cc_start: 0.8768 (mtt180) cc_final: 0.8347 (ttt180) REVERT: I 151 GLN cc_start: 0.8870 (mm110) cc_final: 0.8629 (mm110) REVERT: I 171 GLU cc_start: 0.5472 (OUTLIER) cc_final: 0.5220 (mp0) REVERT: I 184 LYS cc_start: 0.9221 (tptt) cc_final: 0.8890 (tptt) REVERT: I 201 GLU cc_start: 0.8997 (mm-30) cc_final: 0.8186 (mm-30) REVERT: J 19 ARG cc_start: 0.4125 (OUTLIER) cc_final: 0.3390 (ppt90) REVERT: J 70 MET cc_start: 0.4894 (tmm) cc_final: 0.4539 (tmm) REVERT: J 131 ASN cc_start: 0.8187 (m-40) cc_final: 0.7967 (m110) REVERT: J 151 MET cc_start: 0.8111 (ptp) cc_final: 0.7779 (pmm) REVERT: K 90 MET cc_start: 0.2528 (mmt) cc_final: 0.2033 (mmt) REVERT: M 2 MET cc_start: 0.8477 (tmm) cc_final: 0.8267 (tmm) REVERT: M 12 ARG cc_start: 0.8012 (mtt180) cc_final: 0.7571 (mtt-85) REVERT: M 79 ARG cc_start: 0.9104 (OUTLIER) cc_final: 0.8698 (ptt90) REVERT: M 87 ARG cc_start: 0.8594 (ptm-80) cc_final: 0.8371 (ptm-80) REVERT: N 20 ILE cc_start: 0.7060 (OUTLIER) cc_final: 0.6682 (mm) REVERT: N 56 MET cc_start: 0.4391 (mpp) cc_final: 0.4128 (mpp) REVERT: O 15 HIS cc_start: 0.2190 (OUTLIER) cc_final: 0.1786 (p90) REVERT: P 43 TRP cc_start: 0.7246 (p-90) cc_final: 0.6626 (p-90) REVERT: Q 71 HIS cc_start: 0.7252 (OUTLIER) cc_final: 0.6718 (p-80) REVERT: Q 73 LEU cc_start: 0.7145 (pt) cc_final: 0.6526 (mt) REVERT: Q 79 ILE cc_start: 0.6402 (OUTLIER) cc_final: 0.5552 (tp) REVERT: Q 116 TYR cc_start: 0.7088 (m-80) cc_final: 0.6626 (m-80) REVERT: R 2 ARG cc_start: 0.6250 (tpp-160) cc_final: 0.5868 (mmm160) REVERT: R 74 MET cc_start: 0.4028 (tmm) cc_final: 0.3347 (mtt) REVERT: T 46 LYS cc_start: 0.8112 (pttt) cc_final: 0.7703 (pptt) REVERT: T 57 ARG cc_start: 0.8212 (ttt-90) cc_final: 0.7071 (tpm170) REVERT: T 58 MET cc_start: 0.8802 (mtm) cc_final: 0.8121 (mmm) REVERT: T 61 GLN cc_start: 0.9230 (tp40) cc_final: 0.8944 (tp-100) REVERT: T 64 LYS cc_start: 0.8810 (mmtm) cc_final: 0.8441 (tppt) REVERT: U 34 GLU cc_start: 0.8564 (pm20) cc_final: 0.7836 (pm20) REVERT: U 38 PHE cc_start: 0.8231 (p90) cc_final: 0.7978 (p90) REVERT: V 62 GLU cc_start: 0.5553 (tt0) cc_final: 0.4644 (tt0) REVERT: V 79 GLU cc_start: 0.7434 (OUTLIER) cc_final: 0.6906 (mp0) REVERT: W 58 ILE cc_start: 0.6420 (mt) cc_final: 0.6021 (mt) REVERT: X 80 ARG cc_start: 0.3553 (ttm170) cc_final: 0.3277 (ttm170) REVERT: Y 23 ARG cc_start: 0.9039 (mmm-85) cc_final: 0.8754 (mmt180) REVERT: Y 27 MET cc_start: 0.9040 (tpp) cc_final: 0.8806 (mmt) REVERT: Y 30 PHE cc_start: 0.9196 (m-10) cc_final: 0.8753 (m-80) REVERT: Y 32 LYS cc_start: 0.8882 (mttp) cc_final: 0.8647 (mttm) REVERT: Y 53 MET cc_start: 0.9239 (ppp) cc_final: 0.8969 (ppp) REVERT: Z 37 TYR cc_start: 0.3370 (OUTLIER) cc_final: 0.2903 (t80) REVERT: Z 46 ARG cc_start: 0.8326 (ptp-170) cc_final: 0.8060 (mmp-170) REVERT: a 53 ARG cc_start: -0.0472 (OUTLIER) cc_final: -0.2256 (mmp-170) REVERT: a 170 ILE cc_start: 0.4053 (mm) cc_final: 0.3577 (tp) REVERT: 8 21 ARG cc_start: 0.4963 (mtt180) cc_final: 0.3216 (mpt180) REVERT: 8 41 PHE cc_start: 0.8786 (t80) cc_final: 0.7453 (t80) REVERT: 8 64 ILE cc_start: 0.6690 (OUTLIER) cc_final: 0.6326 (mp) REVERT: 8 131 MET cc_start: 0.3209 (mmt) cc_final: 0.2946 (mmt) outliers start: 290 outliers final: 203 residues processed: 1487 average time/residue: 1.3002 time to fit residues: 3324.5015 Evaluate side-chains 1449 residues out of total 5093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 222 poor density : 1227 time to evaluate : 6.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 2 VAL Chi-restraints excluded: chain b residue 32 LEU Chi-restraints excluded: chain b residue 33 LEU Chi-restraints excluded: chain b residue 53 ILE Chi-restraints excluded: chain b residue 128 THR Chi-restraints excluded: chain b residue 222 THR Chi-restraints excluded: chain b residue 259 ASN Chi-restraints excluded: chain c residue 12 THR Chi-restraints excluded: chain c residue 73 VAL Chi-restraints excluded: chain c residue 79 LEU Chi-restraints excluded: chain c residue 100 LEU Chi-restraints excluded: chain c residue 108 ASP Chi-restraints excluded: chain c residue 142 VAL Chi-restraints excluded: chain c residue 170 VAL Chi-restraints excluded: chain c residue 171 THR Chi-restraints excluded: chain c residue 180 VAL Chi-restraints excluded: chain c residue 189 VAL Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 4 VAL Chi-restraints excluded: chain d residue 48 THR Chi-restraints excluded: chain d residue 65 THR Chi-restraints excluded: chain d residue 80 SER Chi-restraints excluded: chain d residue 90 GLN Chi-restraints excluded: chain d residue 169 VAL Chi-restraints excluded: chain d residue 193 VAL Chi-restraints excluded: chain e residue 50 ASP Chi-restraints excluded: chain e residue 80 GLN Chi-restraints excluded: chain e residue 107 VAL Chi-restraints excluded: chain e residue 112 ASP Chi-restraints excluded: chain e residue 140 ILE Chi-restraints excluded: chain e residue 153 ILE Chi-restraints excluded: chain e residue 157 THR Chi-restraints excluded: chain e residue 168 LEU Chi-restraints excluded: chain f residue 9 VAL Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 29 ASN Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 104 LEU Chi-restraints excluded: chain f residue 136 ASP Chi-restraints excluded: chain f residue 137 LYS Chi-restraints excluded: chain g residue 18 GLN Chi-restraints excluded: chain g residue 134 VAL Chi-restraints excluded: chain g residue 144 VAL Chi-restraints excluded: chain h residue 82 ILE Chi-restraints excluded: chain h residue 122 GLN Chi-restraints excluded: chain i residue 115 ASP Chi-restraints excluded: chain j residue 3 THR Chi-restraints excluded: chain j residue 11 VAL Chi-restraints excluded: chain j residue 44 TYR Chi-restraints excluded: chain j residue 73 VAL Chi-restraints excluded: chain j residue 100 VAL Chi-restraints excluded: chain j residue 142 ILE Chi-restraints excluded: chain k residue 21 CYS Chi-restraints excluded: chain k residue 22 ILE Chi-restraints excluded: chain k residue 24 VAL Chi-restraints excluded: chain k residue 62 VAL Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 77 ILE Chi-restraints excluded: chain k residue 104 THR Chi-restraints excluded: chain k residue 110 GLU Chi-restraints excluded: chain l residue 55 MET Chi-restraints excluded: chain l residue 63 LYS Chi-restraints excluded: chain l residue 74 THR Chi-restraints excluded: chain l residue 94 THR Chi-restraints excluded: chain l residue 107 PHE Chi-restraints excluded: chain m residue 20 LEU Chi-restraints excluded: chain m residue 42 THR Chi-restraints excluded: chain m residue 135 VAL Chi-restraints excluded: chain n residue 54 LEU Chi-restraints excluded: chain n residue 95 THR Chi-restraints excluded: chain n residue 97 ILE 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 83 LEU Chi-restraints excluded: chain o residue 93 ASP Chi-restraints excluded: chain p residue 23 ASP Chi-restraints excluded: chain p residue 43 GLU Chi-restraints excluded: chain p residue 59 THR Chi-restraints excluded: chain p residue 60 VAL Chi-restraints excluded: chain p residue 80 VAL Chi-restraints excluded: chain q residue 59 LEU Chi-restraints excluded: chain q residue 61 ILE Chi-restraints excluded: chain r residue 15 SER Chi-restraints excluded: chain r residue 19 THR Chi-restraints excluded: chain r residue 38 VAL Chi-restraints excluded: chain r residue 49 ILE Chi-restraints excluded: chain r residue 51 VAL Chi-restraints excluded: chain r residue 58 VAL Chi-restraints excluded: chain r residue 75 VAL Chi-restraints excluded: chain s residue 25 ARG Chi-restraints excluded: chain s residue 52 GLU Chi-restraints excluded: chain s residue 70 LYS Chi-restraints excluded: chain s residue 76 VAL Chi-restraints excluded: chain s residue 96 ILE Chi-restraints excluded: chain s residue 100 THR Chi-restraints excluded: chain s residue 105 VAL Chi-restraints excluded: chain t residue 11 LEU Chi-restraints excluded: chain t residue 18 GLU Chi-restraints excluded: chain t residue 62 VAL Chi-restraints excluded: chain t residue 86 THR Chi-restraints excluded: chain u residue 8 ASP Chi-restraints excluded: chain u residue 10 VAL Chi-restraints excluded: chain u residue 11 ILE Chi-restraints excluded: chain u residue 35 VAL Chi-restraints excluded: chain u residue 81 ARG Chi-restraints excluded: chain v residue 8 VAL Chi-restraints excluded: chain v residue 56 PHE Chi-restraints excluded: chain v residue 63 ILE Chi-restraints excluded: chain v residue 64 VAL Chi-restraints excluded: chain v residue 66 ASP Chi-restraints excluded: chain v residue 77 VAL Chi-restraints excluded: chain v residue 90 ASP Chi-restraints excluded: chain w residue 19 VAL Chi-restraints excluded: chain w residue 34 VAL Chi-restraints excluded: chain x residue 66 VAL Chi-restraints excluded: chain x residue 67 LEU Chi-restraints excluded: chain y residue 6 LEU Chi-restraints excluded: chain y residue 49 ASP Chi-restraints excluded: chain z residue 13 ILE Chi-restraints excluded: chain z residue 40 THR Chi-restraints excluded: chain z residue 51 SER Chi-restraints excluded: chain B residue 11 LYS Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain E residue 43 LEU Chi-restraints excluded: chain E residue 48 MET Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain F residue 13 ASN Chi-restraints excluded: chain F residue 23 ILE Chi-restraints excluded: chain G residue 4 SER Chi-restraints excluded: chain G residue 15 PHE Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 128 LEU Chi-restraints excluded: chain G residue 183 PHE Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 182 ASP Chi-restraints excluded: chain H residue 194 VAL Chi-restraints excluded: chain I residue 64 TYR Chi-restraints excluded: chain I residue 99 ASN Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 141 VAL Chi-restraints excluded: chain I residue 171 GLU Chi-restraints excluded: chain J residue 19 ARG Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 79 THR Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 121 ASN Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 64 VAL Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain K residue 76 THR Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain L residue 6 ILE Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 47 GLU Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain M residue 33 VAL Chi-restraints excluded: chain M residue 37 ASN Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain M residue 79 ARG Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain M residue 128 VAL Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 24 ASN Chi-restraints excluded: chain O residue 15 HIS Chi-restraints excluded: chain O residue 69 THR Chi-restraints excluded: chain P residue 15 VAL Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain P residue 35 ASP Chi-restraints excluded: chain Q residue 7 VAL Chi-restraints excluded: chain Q residue 28 GLN Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 71 HIS Chi-restraints excluded: chain Q residue 79 ILE Chi-restraints excluded: chain Q residue 86 VAL Chi-restraints excluded: chain R residue 53 ASP Chi-restraints excluded: chain S residue 23 ARG Chi-restraints excluded: chain S residue 49 THR Chi-restraints excluded: chain T residue 17 ASP Chi-restraints excluded: chain T residue 24 THR Chi-restraints excluded: chain T residue 28 VAL Chi-restraints excluded: chain T residue 30 LEU Chi-restraints excluded: chain T residue 68 TYR Chi-restraints excluded: chain T residue 78 THR Chi-restraints excluded: chain U residue 69 ASP Chi-restraints excluded: chain U residue 77 GLU Chi-restraints excluded: chain V residue 29 LYS Chi-restraints excluded: chain V residue 46 HIS Chi-restraints excluded: chain V residue 75 VAL Chi-restraints excluded: chain V residue 79 GLU Chi-restraints excluded: chain W residue 22 TYR Chi-restraints excluded: chain W residue 30 ASN Chi-restraints excluded: chain W residue 64 LEU Chi-restraints excluded: chain X residue 15 LEU Chi-restraints excluded: chain X residue 39 ILE Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain X residue 59 VAL Chi-restraints excluded: chain X residue 72 GLU Chi-restraints excluded: chain Y residue 19 HIS Chi-restraints excluded: chain Z residue 12 ASP Chi-restraints excluded: chain Z residue 37 TYR Chi-restraints excluded: chain a residue 5 THR Chi-restraints excluded: chain a residue 18 THR Chi-restraints excluded: chain a residue 53 ARG Chi-restraints excluded: chain a residue 172 HIS Chi-restraints excluded: chain 8 residue 64 ILE Chi-restraints excluded: chain 8 residue 100 THR Chi-restraints excluded: chain 9 residue 18 THR Chi-restraints excluded: chain 9 residue 20 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1065 random chunks: chunk 993 optimal weight: 10.0000 chunk 116 optimal weight: 10.0000 chunk 587 optimal weight: 40.0000 chunk 752 optimal weight: 10.0000 chunk 583 optimal weight: 30.0000 chunk 867 optimal weight: 10.0000 chunk 575 optimal weight: 40.0000 chunk 1026 optimal weight: 20.0000 chunk 642 optimal weight: 20.0000 chunk 625 optimal weight: 40.0000 chunk 473 optimal weight: 0.1980 overall best weight: 8.0396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 90 GLN ** d 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 9 GLN ** n 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 19 GLN ** r 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 58 ASN ** D 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 HIS G 121 GLN ** I 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 49 GLN O 64 GLN ** P 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 28 GLN ** Q 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 60 GLN Y 69 ASN ** a 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 172 HIS ** 8 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.5779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 161229 Z= 0.337 Angle : 0.748 15.198 240720 Z= 0.378 Chirality : 0.040 0.318 30724 Planarity : 0.006 0.085 13231 Dihedral : 23.932 179.272 79535 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 31.52 Ramachandran Plot: Outliers : 0.16 % Allowed : 12.55 % Favored : 87.28 % Rotamer: Outliers : 6.95 % Allowed : 27.21 % Favored : 65.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % 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: -3.11 (0.10), residues: 6142 helix: -1.30 (0.12), residues: 1783 sheet: -1.88 (0.17), residues: 850 loop : -2.61 (0.10), residues: 3509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP d 78 HIS 0.012 0.002 HIS j 40 PHE 0.038 0.002 PHE V 36 TYR 0.026 0.002 TYR p 98 ARG 0.014 0.001 ARG M 14 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12284 Ramachandran restraints generated. 6142 Oldfield, 0 Emsley, 6142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12284 Ramachandran restraints generated. 6142 Oldfield, 0 Emsley, 6142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1544 residues out of total 5093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 354 poor density : 1190 time to evaluate : 6.302 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: c 28 GLU cc_start: 0.8945 (tm-30) cc_final: 0.8656 (tp30) REVERT: c 36 GLN cc_start: 0.8320 (tt0) cc_final: 0.8010 (tp40) REVERT: c 64 GLU cc_start: 0.8834 (mm-30) cc_final: 0.8494 (mm-30) REVERT: c 131 ASP cc_start: 0.8768 (p0) cc_final: 0.8540 (p0) REVERT: c 133 THR cc_start: 0.8714 (OUTLIER) cc_final: 0.8449 (t) REVERT: c 148 GLN cc_start: 0.8785 (mp10) cc_final: 0.8287 (mp-120) REVERT: c 185 ASN cc_start: 0.8909 (m-40) cc_final: 0.8614 (m110) REVERT: d 1 MET cc_start: 0.8450 (OUTLIER) cc_final: 0.7999 (mpp) REVERT: d 6 LYS cc_start: 0.8325 (ptmt) cc_final: 0.7764 (pttm) REVERT: d 9 GLN cc_start: 0.8659 (tm-30) cc_final: 0.8348 (tm-30) REVERT: d 78 TRP cc_start: 0.8443 (m-10) cc_final: 0.8136 (m-10) REVERT: d 122 GLU cc_start: 0.8310 (tm-30) cc_final: 0.8104 (tm-30) REVERT: d 166 LYS cc_start: 0.8881 (mmtm) cc_final: 0.8615 (mmmt) REVERT: d 188 MET cc_start: 0.9048 (mmt) cc_final: 0.8778 (mmt) REVERT: e 6 TYR cc_start: 0.9128 (t80) cc_final: 0.8473 (t80) REVERT: e 33 ILE cc_start: 0.9145 (OUTLIER) cc_final: 0.8895 (tp) REVERT: e 80 GLN cc_start: 0.8365 (OUTLIER) cc_final: 0.8060 (tm-30) REVERT: e 97 GLU cc_start: 0.8296 (tp30) cc_final: 0.7952 (tp30) REVERT: e 100 GLU cc_start: 0.7852 (tm-30) cc_final: 0.7600 (tm-30) REVERT: e 109 ARG cc_start: 0.8872 (tpp-160) cc_final: 0.8358 (tpp-160) REVERT: e 133 GLU cc_start: 0.7123 (tp30) cc_final: 0.6890 (tp30) REVERT: e 166 ARG cc_start: 0.9013 (OUTLIER) cc_final: 0.8675 (tmm-80) REVERT: e 177 ARG cc_start: 0.7375 (ttt180) cc_final: 0.7039 (tpt170) REVERT: f 82 PHE cc_start: 0.7586 (OUTLIER) cc_final: 0.7195 (m-10) REVERT: f 137 LYS cc_start: 0.8758 (OUTLIER) cc_final: 0.8465 (mmtt) REVERT: f 148 ARG cc_start: 0.8683 (ttp80) cc_final: 0.8343 (ttm-80) REVERT: g 18 GLN cc_start: 0.8265 (OUTLIER) cc_final: 0.8031 (pm20) REVERT: g 46 PHE cc_start: 0.8554 (m-10) cc_final: 0.8209 (m-10) REVERT: g 55 GLU cc_start: 0.9130 (mt-10) cc_final: 0.8794 (mt-10) REVERT: g 87 GLU cc_start: 0.8110 (tp30) cc_final: 0.7693 (mm-30) REVERT: g 139 PHE cc_start: 0.8614 (m-80) cc_final: 0.8395 (m-80) REVERT: h 52 MET cc_start: 0.6986 (tpp) cc_final: 0.5598 (mmm) REVERT: h 114 GLU cc_start: 0.8129 (tp30) cc_final: 0.7441 (tp30) REVERT: h 116 GLU cc_start: 0.8956 (mm-30) cc_final: 0.8335 (mm-30) REVERT: i 41 PHE cc_start: 0.8807 (t80) cc_final: 0.8397 (t80) REVERT: i 116 MET cc_start: -0.1644 (tpt) cc_final: -0.2596 (tpt) REVERT: j 7 LYS cc_start: 0.8762 (OUTLIER) cc_final: 0.7981 (mtmm) REVERT: j 68 LYS cc_start: 0.8567 (mtpt) cc_final: 0.8209 (mtpt) REVERT: j 86 GLN cc_start: 0.8385 (pm20) cc_final: 0.7975 (pp30) REVERT: j 118 MET cc_start: 0.9155 (mmt) cc_final: 0.8899 (mmt) REVERT: j 119 PHE cc_start: 0.9169 (t80) cc_final: 0.8869 (t80) REVERT: k 29 HIS cc_start: 0.8368 (t70) cc_final: 0.8058 (t-90) REVERT: k 66 LYS cc_start: 0.8379 (tttt) cc_final: 0.7801 (tttt) REVERT: k 116 ILE cc_start: 0.8239 (OUTLIER) cc_final: 0.7622 (tp) REVERT: l 38 GLN cc_start: 0.9149 (tt0) cc_final: 0.8646 (tt0) REVERT: l 39 LYS cc_start: 0.8929 (pttt) cc_final: 0.8513 (pttt) REVERT: l 107 PHE cc_start: 0.7708 (OUTLIER) cc_final: 0.7397 (t80) REVERT: l 128 THR cc_start: 0.9165 (OUTLIER) cc_final: 0.8762 (t) REVERT: m 115 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.8187 (tp30) REVERT: n 114 GLU cc_start: 0.8575 (tt0) cc_final: 0.8206 (tp30) REVERT: o 12 THR cc_start: 0.9466 (p) cc_final: 0.9233 (p) REVERT: o 55 GLU cc_start: 0.8473 (mt-10) cc_final: 0.7507 (mm-30) REVERT: o 104 GLN cc_start: 0.9637 (tt0) cc_final: 0.9311 (tt0) REVERT: p 12 MET cc_start: 0.8073 (mtm) cc_final: 0.6720 (tmm) REVERT: p 37 LYS cc_start: 0.8461 (mttm) cc_final: 0.8188 (mptt) REVERT: p 50 ARG cc_start: 0.8532 (ttt-90) cc_final: 0.7952 (ttt180) REVERT: p 74 GLN cc_start: 0.8532 (mp10) cc_final: 0.7709 (mp10) REVERT: p 93 LYS cc_start: 0.8750 (tppt) cc_final: 0.8370 (tppt) REVERT: q 24 TYR cc_start: 0.7615 (t80) cc_final: 0.7200 (t80) REVERT: q 54 ARG cc_start: 0.8952 (mtm180) cc_final: 0.8688 (mtm-85) REVERT: q 106 THR cc_start: 0.9359 (p) cc_final: 0.8997 (p) REVERT: q 110 GLU cc_start: 0.8894 (mm-30) cc_final: 0.8249 (mm-30) REVERT: r 46 GLU cc_start: 0.8727 (mp0) cc_final: 0.7729 (tp30) REVERT: r 85 LYS cc_start: 0.8783 (ttmt) cc_final: 0.8536 (ttmt) REVERT: s 25 ARG cc_start: 0.8592 (OUTLIER) cc_final: 0.7790 (mtm180) REVERT: s 38 TYR cc_start: 0.8832 (m-80) cc_final: 0.8381 (m-80) REVERT: s 82 MET cc_start: 0.8184 (pmm) cc_final: 0.7829 (pmm) REVERT: t 18 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.7853 (pp20) REVERT: t 24 MET cc_start: 0.9202 (tpp) cc_final: 0.8948 (tmm) REVERT: u 94 PHE cc_start: 0.8618 (p90) cc_final: 0.7828 (p90) REVERT: v 31 TYR cc_start: 0.8385 (p90) cc_final: 0.7994 (p90) REVERT: v 50 MET cc_start: 0.8423 (mmt) cc_final: 0.8074 (tpp) REVERT: v 61 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8102 (mm) REVERT: w 62 LYS cc_start: 0.9272 (mtpt) cc_final: 0.9004 (mtpp) REVERT: x 16 ASN cc_start: 0.9144 (t0) cc_final: 0.8858 (m-40) REVERT: x 43 LYS cc_start: 0.8900 (mmtp) cc_final: 0.8618 (pttp) REVERT: y 6 LEU cc_start: 0.7670 (OUTLIER) cc_final: 0.7442 (tt) REVERT: y 45 GLN cc_start: 0.8787 (pt0) cc_final: 0.8327 (pp30) REVERT: y 48 ARG cc_start: 0.9015 (mtt-85) cc_final: 0.8696 (mmt90) REVERT: z 18 LYS cc_start: 0.8491 (mmtt) cc_final: 0.8079 (mmtt) REVERT: B 27 LEU cc_start: 0.8937 (tp) cc_final: 0.8429 (tt) REVERT: B 36 LYS cc_start: 0.9408 (mmtp) cc_final: 0.9117 (mmmt) REVERT: C 29 LYS cc_start: 0.8852 (tppt) cc_final: 0.8607 (tptp) REVERT: D 35 ARG cc_start: 0.8935 (mtt-85) cc_final: 0.8463 (mtt-85) REVERT: E 24 LYS cc_start: 0.8789 (tppp) cc_final: 0.8423 (tptp) REVERT: E 48 MET cc_start: 0.8401 (OUTLIER) cc_final: 0.7961 (mpp) REVERT: F 15 LYS cc_start: 0.7718 (mmtp) cc_final: 0.7333 (mmtt) REVERT: G 26 MET cc_start: 0.7586 (tmm) cc_final: 0.6598 (tmm) REVERT: G 29 PHE cc_start: 0.6983 (m-80) cc_final: 0.6428 (m-10) REVERT: G 95 TRP cc_start: 0.8107 (t-100) cc_final: 0.7815 (t-100) REVERT: G 153 MET cc_start: 0.6080 (mmm) cc_final: 0.5688 (mmm) REVERT: G 183 PHE cc_start: 0.7083 (OUTLIER) cc_final: 0.6836 (m-80) REVERT: I 74 TYR cc_start: 0.8843 (m-10) cc_final: 0.8326 (m-10) REVERT: I 88 ASN cc_start: 0.8925 (m110) cc_final: 0.8605 (m-40) REVERT: I 92 LEU cc_start: 0.8505 (mt) cc_final: 0.7842 (mt) REVERT: I 104 MET cc_start: 0.4536 (mmt) cc_final: 0.4073 (mmt) REVERT: I 120 LYS cc_start: 0.6762 (mttm) cc_final: 0.6289 (ttpp) REVERT: I 123 MET cc_start: 0.7393 (mmm) cc_final: 0.7062 (mmm) REVERT: I 127 ARG cc_start: 0.8679 (mtt180) cc_final: 0.8277 (ttt180) REVERT: I 151 GLN cc_start: 0.8816 (mm110) cc_final: 0.8249 (mm110) REVERT: I 171 GLU cc_start: 0.5588 (OUTLIER) cc_final: 0.5307 (mp0) REVERT: I 184 LYS cc_start: 0.9272 (tptt) cc_final: 0.8966 (tptt) REVERT: I 201 GLU cc_start: 0.8993 (mm-30) cc_final: 0.8091 (mm-30) REVERT: J 70 MET cc_start: 0.5890 (tmm) cc_final: 0.5571 (tmm) REVERT: J 131 ASN cc_start: 0.8282 (m-40) cc_final: 0.7999 (m110) REVERT: J 151 MET cc_start: 0.8209 (ptp) cc_final: 0.7874 (pmm) REVERT: K 90 MET cc_start: 0.2920 (mmt) cc_final: 0.2206 (mmt) REVERT: M 75 GLN cc_start: 0.8680 (mm-40) cc_final: 0.7845 (mp10) REVERT: M 79 ARG cc_start: 0.9189 (OUTLIER) cc_final: 0.8655 (ptt90) REVERT: N 20 ILE cc_start: 0.6977 (OUTLIER) cc_final: 0.6573 (mm) REVERT: O 15 HIS cc_start: 0.2134 (OUTLIER) cc_final: 0.1658 (p90) REVERT: Q 4 ASN cc_start: 0.7966 (OUTLIER) cc_final: 0.7369 (t0) REVERT: Q 73 LEU cc_start: 0.7083 (pt) cc_final: 0.6391 (mt) REVERT: Q 87 LYS cc_start: 0.8506 (OUTLIER) cc_final: 0.7553 (tptm) REVERT: Q 116 TYR cc_start: 0.7075 (m-80) cc_final: 0.6596 (m-80) REVERT: R 2 ARG cc_start: 0.6259 (tpp-160) cc_final: 0.5731 (mmm160) REVERT: R 74 MET cc_start: 0.3871 (tmm) cc_final: 0.3241 (mtt) REVERT: T 9 LYS cc_start: 0.9332 (pttp) cc_final: 0.9096 (pttm) REVERT: T 44 GLU cc_start: 0.8637 (tp30) cc_final: 0.8369 (tp30) REVERT: T 46 LYS cc_start: 0.8079 (pttt) cc_final: 0.7639 (pptt) REVERT: T 57 ARG cc_start: 0.8223 (ttt-90) cc_final: 0.6893 (tpm170) REVERT: T 58 MET cc_start: 0.8894 (mtm) cc_final: 0.8140 (mmm) REVERT: T 61 GLN cc_start: 0.9244 (tp40) cc_final: 0.8983 (tp-100) REVERT: V 78 VAL cc_start: 0.8704 (OUTLIER) cc_final: 0.8501 (m) REVERT: V 79 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.6960 (mp0) REVERT: W 58 ILE cc_start: 0.6627 (mt) cc_final: 0.6310 (mt) REVERT: Y 23 ARG cc_start: 0.9094 (mmm-85) cc_final: 0.8739 (mmt180) REVERT: Y 26 MET cc_start: 0.8526 (mmt) cc_final: 0.8266 (mmt) REVERT: Y 53 MET cc_start: 0.9089 (ppp) cc_final: 0.8839 (ppp) REVERT: Z 37 TYR cc_start: 0.3448 (OUTLIER) cc_final: 0.2834 (t80) REVERT: Z 54 ARG cc_start: 0.7988 (tpm170) cc_final: 0.7733 (tpm170) REVERT: a 53 ARG cc_start: -0.0653 (OUTLIER) cc_final: -0.2372 (mmp-170) REVERT: 8 41 PHE cc_start: 0.8595 (t80) cc_final: 0.8267 (t80) REVERT: 8 64 ILE cc_start: 0.6731 (OUTLIER) cc_final: 0.6358 (mp) REVERT: 8 105 ARG cc_start: 0.7667 (OUTLIER) cc_final: 0.7417 (ttp-170) REVERT: 9 94 MET cc_start: 0.1981 (ttt) cc_final: 0.1230 (ttt) outliers start: 354 outliers final: 272 residues processed: 1396 average time/residue: 1.3094 time to fit residues: 3152.5770 Evaluate side-chains 1455 residues out of total 5093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 303 poor density : 1152 time to evaluate : 6.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 2 VAL Chi-restraints excluded: chain b residue 32 LEU Chi-restraints excluded: chain b residue 33 LEU Chi-restraints excluded: chain b residue 37 SER Chi-restraints excluded: chain b residue 53 ILE Chi-restraints excluded: chain b residue 104 LEU Chi-restraints excluded: chain b residue 113 ASP Chi-restraints excluded: chain b residue 128 THR Chi-restraints excluded: chain b residue 133 ASN Chi-restraints excluded: chain b residue 222 THR Chi-restraints excluded: chain b residue 239 PHE Chi-restraints excluded: chain b residue 249 VAL Chi-restraints excluded: chain c residue 12 THR Chi-restraints excluded: chain c residue 35 THR Chi-restraints excluded: chain c residue 40 LEU Chi-restraints excluded: chain c residue 60 VAL Chi-restraints excluded: chain c residue 73 VAL Chi-restraints excluded: chain c residue 79 LEU Chi-restraints excluded: chain c residue 100 LEU Chi-restraints excluded: chain c residue 108 ASP Chi-restraints excluded: chain c residue 121 THR Chi-restraints excluded: chain c residue 133 THR Chi-restraints excluded: chain c residue 142 VAL Chi-restraints excluded: chain c residue 160 LYS Chi-restraints excluded: chain c residue 168 GLU Chi-restraints excluded: chain c residue 170 VAL Chi-restraints excluded: chain c residue 171 THR Chi-restraints excluded: chain c residue 180 VAL Chi-restraints excluded: chain c residue 201 LEU Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 4 VAL Chi-restraints excluded: chain d residue 7 ASP Chi-restraints excluded: chain d residue 12 LEU Chi-restraints excluded: chain d residue 48 THR Chi-restraints excluded: chain d residue 65 THR Chi-restraints excluded: chain d residue 80 SER Chi-restraints excluded: chain d residue 96 VAL Chi-restraints excluded: chain d residue 169 VAL Chi-restraints excluded: chain d residue 193 VAL Chi-restraints excluded: chain e residue 4 HIS Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 27 VAL Chi-restraints excluded: chain e residue 33 ILE Chi-restraints excluded: chain e residue 50 ASP Chi-restraints excluded: chain e residue 80 GLN Chi-restraints excluded: chain e residue 107 VAL Chi-restraints excluded: chain e residue 112 ASP Chi-restraints excluded: chain e residue 153 ILE Chi-restraints excluded: chain e residue 157 THR Chi-restraints excluded: chain e residue 166 ARG Chi-restraints excluded: chain e residue 168 LEU Chi-restraints excluded: chain f residue 9 VAL Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 18 ILE Chi-restraints excluded: chain f residue 19 ASN Chi-restraints excluded: chain f residue 29 ASN Chi-restraints excluded: chain f residue 49 LEU Chi-restraints excluded: chain f residue 57 TYR Chi-restraints excluded: chain f residue 70 LEU Chi-restraints excluded: chain f residue 82 PHE Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 102 ILE Chi-restraints excluded: chain f residue 104 LEU Chi-restraints excluded: chain f residue 106 LEU Chi-restraints excluded: chain f residue 136 ASP Chi-restraints excluded: chain f residue 137 LYS Chi-restraints excluded: chain f residue 152 ARG Chi-restraints excluded: chain g residue 4 ILE Chi-restraints excluded: chain g residue 18 GLN Chi-restraints excluded: chain g residue 22 LYS Chi-restraints excluded: chain g residue 37 VAL Chi-restraints excluded: chain g residue 134 VAL Chi-restraints excluded: chain g residue 144 VAL Chi-restraints excluded: chain h residue 82 ILE Chi-restraints excluded: chain i residue 115 ASP Chi-restraints excluded: chain j residue 3 THR Chi-restraints excluded: chain j residue 7 LYS Chi-restraints excluded: chain j residue 11 VAL Chi-restraints excluded: chain j residue 44 TYR Chi-restraints excluded: chain j residue 49 ASP Chi-restraints excluded: chain j residue 57 LEU Chi-restraints excluded: chain j residue 73 VAL Chi-restraints excluded: chain j residue 100 VAL Chi-restraints excluded: chain k residue 22 ILE Chi-restraints excluded: chain k residue 24 VAL Chi-restraints excluded: chain k residue 62 VAL Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 77 ILE Chi-restraints excluded: chain k residue 103 VAL Chi-restraints excluded: chain k residue 104 THR Chi-restraints excluded: chain k residue 110 GLU Chi-restraints excluded: chain k residue 116 ILE Chi-restraints excluded: chain l residue 46 VAL Chi-restraints excluded: chain l residue 55 MET Chi-restraints excluded: chain l residue 63 LYS Chi-restraints excluded: chain l residue 74 THR Chi-restraints excluded: chain l residue 94 THR Chi-restraints excluded: chain l residue 101 ILE Chi-restraints excluded: chain l residue 107 PHE Chi-restraints excluded: chain l residue 128 THR Chi-restraints excluded: chain l residue 143 GLU Chi-restraints excluded: chain m residue 20 LEU Chi-restraints excluded: chain m residue 42 THR Chi-restraints excluded: chain m residue 54 THR Chi-restraints excluded: chain m residue 106 ASP Chi-restraints excluded: chain m residue 115 GLU Chi-restraints excluded: chain m residue 128 THR Chi-restraints excluded: chain m residue 135 VAL Chi-restraints excluded: chain n residue 18 GLN Chi-restraints excluded: chain n residue 47 VAL Chi-restraints excluded: chain n residue 52 ILE Chi-restraints excluded: chain n residue 54 LEU Chi-restraints excluded: chain n residue 97 ILE Chi-restraints excluded: chain o residue 34 HIS 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 83 LEU Chi-restraints excluded: chain o residue 90 VAL Chi-restraints excluded: chain o residue 93 ASP Chi-restraints excluded: chain p residue 23 ASP Chi-restraints excluded: chain p residue 43 GLU Chi-restraints excluded: chain p residue 59 THR Chi-restraints excluded: chain p residue 60 VAL Chi-restraints excluded: chain p residue 75 THR Chi-restraints excluded: chain p residue 80 VAL Chi-restraints excluded: chain q residue 39 ILE Chi-restraints excluded: chain q residue 59 LEU Chi-restraints excluded: chain q residue 61 ILE Chi-restraints excluded: chain q residue 93 ILE Chi-restraints excluded: chain r residue 15 SER Chi-restraints excluded: chain r residue 19 THR Chi-restraints excluded: chain r residue 38 VAL Chi-restraints excluded: chain r residue 49 ILE Chi-restraints excluded: chain r residue 58 VAL Chi-restraints excluded: chain r residue 75 VAL Chi-restraints excluded: chain s residue 20 VAL Chi-restraints excluded: chain s residue 24 ILE Chi-restraints excluded: chain s residue 25 ARG Chi-restraints excluded: chain s residue 52 GLU Chi-restraints excluded: chain s residue 66 ILE Chi-restraints excluded: chain s residue 70 LYS Chi-restraints excluded: chain s residue 96 ILE Chi-restraints excluded: chain s residue 100 THR Chi-restraints excluded: chain t residue 11 LEU Chi-restraints excluded: chain t residue 16 VAL Chi-restraints excluded: chain t residue 18 GLU Chi-restraints excluded: chain t residue 86 THR Chi-restraints excluded: chain u residue 8 ASP Chi-restraints excluded: chain u residue 10 VAL Chi-restraints excluded: chain u residue 11 ILE Chi-restraints excluded: chain u residue 35 VAL Chi-restraints excluded: chain u residue 81 ARG Chi-restraints excluded: chain u residue 86 PHE Chi-restraints excluded: chain u residue 102 ILE Chi-restraints excluded: chain v residue 8 VAL Chi-restraints excluded: chain v residue 56 PHE Chi-restraints excluded: chain v residue 61 LEU Chi-restraints excluded: chain v residue 63 ILE Chi-restraints excluded: chain v residue 64 VAL Chi-restraints excluded: chain v residue 66 ASP Chi-restraints excluded: chain v residue 77 VAL Chi-restraints excluded: chain v residue 90 ASP Chi-restraints excluded: chain w residue 19 VAL Chi-restraints excluded: chain w residue 34 VAL Chi-restraints excluded: chain x residue 22 ASN Chi-restraints excluded: chain x residue 67 LEU Chi-restraints excluded: chain y residue 6 LEU Chi-restraints excluded: chain y residue 7 ARG Chi-restraints excluded: chain y residue 49 ASP Chi-restraints excluded: chain z residue 13 ILE Chi-restraints excluded: chain z residue 33 HIS Chi-restraints excluded: chain z residue 40 THR Chi-restraints excluded: chain z residue 51 SER Chi-restraints excluded: chain z residue 53 MET Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain D residue 3 ARG Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 43 LEU Chi-restraints excluded: chain E residue 48 MET Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain F residue 13 ASN Chi-restraints excluded: chain F residue 23 ILE Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 33 HIS Chi-restraints excluded: chain G residue 4 SER Chi-restraints excluded: chain G residue 5 MET Chi-restraints excluded: chain G residue 14 HIS Chi-restraints excluded: chain G residue 15 PHE Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 128 LEU Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain G residue 183 PHE Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 190 SER Chi-restraints excluded: chain G residue 210 THR Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 182 ASP Chi-restraints excluded: chain H residue 192 TYR Chi-restraints excluded: chain H residue 194 VAL Chi-restraints excluded: chain I residue 64 TYR Chi-restraints excluded: chain I residue 99 ASN Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 141 VAL Chi-restraints excluded: chain I residue 171 GLU Chi-restraints excluded: chain J residue 15 ILE Chi-restraints excluded: chain J residue 19 ARG Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 121 ASN Chi-restraints excluded: chain K residue 8 PHE Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain K residue 78 PHE Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain L residue 6 ILE Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 47 GLU Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain L residue 147 ASN Chi-restraints excluded: chain M residue 37 ASN Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain M residue 79 ARG Chi-restraints excluded: chain M residue 90 GLU Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain M residue 128 VAL Chi-restraints excluded: chain N residue 10 ARG Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 24 ASN Chi-restraints excluded: chain N residue 74 GLN Chi-restraints excluded: chain N residue 125 GLN Chi-restraints excluded: chain O residue 15 HIS Chi-restraints excluded: chain O residue 69 THR Chi-restraints excluded: chain P residue 15 VAL Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain P residue 35 ASP Chi-restraints excluded: chain P residue 85 VAL Chi-restraints excluded: chain P residue 107 THR Chi-restraints excluded: chain Q residue 4 ASN Chi-restraints excluded: chain Q residue 7 VAL Chi-restraints excluded: chain Q residue 28 GLN Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 86 VAL Chi-restraints excluded: chain Q residue 87 LYS Chi-restraints excluded: chain R residue 53 ASP Chi-restraints excluded: chain S residue 23 ARG Chi-restraints excluded: chain S residue 49 THR Chi-restraints excluded: chain T residue 17 ASP Chi-restraints excluded: chain T residue 24 THR Chi-restraints excluded: chain T residue 28 VAL Chi-restraints excluded: chain T residue 30 LEU Chi-restraints excluded: chain T residue 68 TYR Chi-restraints excluded: chain T residue 78 THR Chi-restraints excluded: chain U residue 69 ASP Chi-restraints excluded: chain U residue 77 GLU Chi-restraints excluded: chain V residue 11 VAL Chi-restraints excluded: chain V residue 28 VAL Chi-restraints excluded: chain V residue 29 LYS Chi-restraints excluded: chain V residue 46 HIS Chi-restraints excluded: chain V residue 78 VAL Chi-restraints excluded: chain V residue 79 GLU Chi-restraints excluded: chain W residue 22 TYR Chi-restraints excluded: chain W residue 30 ASN Chi-restraints excluded: chain W residue 64 LEU Chi-restraints excluded: chain X residue 15 LEU Chi-restraints excluded: chain X residue 39 ILE Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain X residue 59 VAL Chi-restraints excluded: chain X residue 70 LEU Chi-restraints excluded: chain X residue 72 GLU Chi-restraints excluded: chain Y residue 19 HIS Chi-restraints excluded: chain Y residue 47 GLN Chi-restraints excluded: chain Z residue 12 ASP Chi-restraints excluded: chain Z residue 37 TYR Chi-restraints excluded: chain a residue 5 THR Chi-restraints excluded: chain a residue 8 MET Chi-restraints excluded: chain a residue 18 THR Chi-restraints excluded: chain a residue 53 ARG Chi-restraints excluded: chain a residue 172 HIS Chi-restraints excluded: chain 8 residue 56 LEU Chi-restraints excluded: chain 8 residue 64 ILE Chi-restraints excluded: chain 8 residue 100 THR Chi-restraints excluded: chain 8 residue 105 ARG Chi-restraints excluded: chain 9 residue 10 ILE Chi-restraints excluded: chain 9 residue 18 THR Chi-restraints excluded: chain 9 residue 20 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1065 random chunks: chunk 635 optimal weight: 20.0000 chunk 409 optimal weight: 20.0000 chunk 613 optimal weight: 10.0000 chunk 309 optimal weight: 7.9990 chunk 201 optimal weight: 10.0000 chunk 198 optimal weight: 5.9990 chunk 652 optimal weight: 10.0000 chunk 699 optimal weight: 40.0000 chunk 507 optimal weight: 6.9990 chunk 95 optimal weight: 20.0000 chunk 806 optimal weight: 10.0000 overall best weight: 8.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 9 GLN h 122 GLN ** i 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 19 GLN ** r 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 15 GLN s 40 ASN ** v 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 15 ASN D 26 ASN ** F 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 HIS ** G 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 67 ASN ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 172 HIS ** 8 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.6110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 161229 Z= 0.341 Angle : 0.752 13.738 240720 Z= 0.380 Chirality : 0.041 0.333 30724 Planarity : 0.006 0.097 13231 Dihedral : 24.067 179.921 79535 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 31.45 Ramachandran Plot: Outliers : 0.11 % Allowed : 12.34 % Favored : 87.54 % Rotamer: Outliers : 7.15 % Allowed : 27.59 % Favored : 65.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % 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: -3.20 (0.10), residues: 6142 helix: -1.40 (0.11), residues: 1792 sheet: -1.92 (0.17), residues: 867 loop : -2.66 (0.10), residues: 3483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.003 TRP m 64 HIS 0.039 0.002 HIS a 172 PHE 0.036 0.003 PHE V 36 TYR 0.029 0.002 TYR p 98 ARG 0.013 0.001 ARG G 94 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12284 Ramachandran restraints generated. 6142 Oldfield, 0 Emsley, 6142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12284 Ramachandran restraints generated. 6142 Oldfield, 0 Emsley, 6142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1564 residues out of total 5093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 364 poor density : 1200 time to evaluate : 6.363 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: c 28 GLU cc_start: 0.8952 (tm-30) cc_final: 0.8653 (tp30) REVERT: c 36 GLN cc_start: 0.8349 (tt0) cc_final: 0.8119 (tp-100) REVERT: c 64 GLU cc_start: 0.8833 (mm-30) cc_final: 0.8488 (mm-30) REVERT: c 131 ASP cc_start: 0.8678 (p0) cc_final: 0.8470 (p0) REVERT: c 133 THR cc_start: 0.8715 (OUTLIER) cc_final: 0.8442 (t) REVERT: c 148 GLN cc_start: 0.8859 (mp10) cc_final: 0.8427 (mp10) REVERT: c 185 ASN cc_start: 0.8941 (m-40) cc_final: 0.8719 (m-40) REVERT: d 1 MET cc_start: 0.8402 (OUTLIER) cc_final: 0.7855 (mpp) REVERT: d 6 LYS cc_start: 0.8308 (ptmt) cc_final: 0.7761 (pttm) REVERT: d 9 GLN cc_start: 0.8719 (tm-30) cc_final: 0.8427 (tm-30) REVERT: d 78 TRP cc_start: 0.8563 (m-10) cc_final: 0.8161 (m-10) REVERT: d 122 GLU cc_start: 0.8295 (tm-30) cc_final: 0.8092 (tm-30) REVERT: d 166 LYS cc_start: 0.8821 (mmtm) cc_final: 0.8617 (mmmt) REVERT: d 188 MET cc_start: 0.9030 (mmt) cc_final: 0.8749 (mmt) REVERT: e 6 TYR cc_start: 0.9172 (t80) cc_final: 0.8392 (t80) REVERT: e 33 ILE cc_start: 0.9192 (tp) cc_final: 0.8944 (tp) REVERT: e 80 GLN cc_start: 0.8375 (OUTLIER) cc_final: 0.8154 (tm-30) REVERT: e 97 GLU cc_start: 0.8451 (tp30) cc_final: 0.8015 (tp30) REVERT: e 100 GLU cc_start: 0.8108 (tm-30) cc_final: 0.7868 (tm-30) REVERT: e 109 ARG cc_start: 0.8809 (tpp-160) cc_final: 0.8206 (tpp-160) REVERT: e 166 ARG cc_start: 0.9069 (OUTLIER) cc_final: 0.8733 (tmm-80) REVERT: e 177 ARG cc_start: 0.7414 (ttt180) cc_final: 0.7080 (tpt170) REVERT: f 82 PHE cc_start: 0.7604 (m-10) cc_final: 0.7210 (m-10) REVERT: f 137 LYS cc_start: 0.8712 (OUTLIER) cc_final: 0.8356 (mmtt) REVERT: g 18 GLN cc_start: 0.8339 (OUTLIER) cc_final: 0.8073 (pm20) REVERT: g 55 GLU cc_start: 0.9128 (mt-10) cc_final: 0.8801 (mt-10) REVERT: g 87 GLU cc_start: 0.8099 (tp30) cc_final: 0.7697 (mm-30) REVERT: g 139 PHE cc_start: 0.8637 (m-80) cc_final: 0.8429 (m-80) REVERT: h 52 MET cc_start: 0.7433 (tpp) cc_final: 0.6098 (mmm) REVERT: h 116 GLU cc_start: 0.8952 (mm-30) cc_final: 0.8524 (mm-30) REVERT: i 41 PHE cc_start: 0.8801 (t80) cc_final: 0.8364 (t80) REVERT: i 116 MET cc_start: -0.1476 (tpt) cc_final: -0.2347 (tpt) REVERT: j 7 LYS cc_start: 0.8844 (OUTLIER) cc_final: 0.8125 (mtmm) REVERT: j 68 LYS cc_start: 0.8572 (mtpt) cc_final: 0.8230 (mtpt) REVERT: j 118 MET cc_start: 0.9161 (mmt) cc_final: 0.8905 (mmt) REVERT: j 119 PHE cc_start: 0.9149 (t80) cc_final: 0.8860 (t80) REVERT: k 29 HIS cc_start: 0.8403 (t70) cc_final: 0.8129 (t-90) REVERT: k 66 LYS cc_start: 0.8414 (tttt) cc_final: 0.7812 (tttt) REVERT: k 116 ILE cc_start: 0.8322 (OUTLIER) cc_final: 0.7821 (tp) REVERT: l 39 LYS cc_start: 0.8894 (pttt) cc_final: 0.8480 (pttt) REVERT: l 128 THR cc_start: 0.9177 (OUTLIER) cc_final: 0.8777 (t) REVERT: m 127 LYS cc_start: 0.8479 (mmtt) cc_final: 0.8163 (mmtt) REVERT: n 103 ARG cc_start: 0.8130 (ttm170) cc_final: 0.7917 (ttm170) REVERT: n 114 GLU cc_start: 0.8757 (tt0) cc_final: 0.8346 (tp30) REVERT: o 20 GLU cc_start: 0.8962 (tp30) cc_final: 0.8667 (tp30) REVERT: o 55 GLU cc_start: 0.8487 (mt-10) cc_final: 0.7458 (mm-30) REVERT: o 104 GLN cc_start: 0.9638 (tt0) cc_final: 0.9320 (tt0) REVERT: p 37 LYS cc_start: 0.8446 (mttm) cc_final: 0.8172 (mptt) REVERT: p 50 ARG cc_start: 0.8521 (ttt-90) cc_final: 0.7886 (ttt180) REVERT: p 74 GLN cc_start: 0.8504 (mp10) cc_final: 0.7739 (mp10) REVERT: p 93 LYS cc_start: 0.8736 (tppt) cc_final: 0.8357 (tppt) REVERT: q 24 TYR cc_start: 0.7611 (t80) cc_final: 0.7170 (t80) REVERT: q 35 PHE cc_start: 0.8921 (t80) cc_final: 0.8638 (t80) REVERT: q 54 ARG cc_start: 0.8968 (mtm180) cc_final: 0.8676 (mtm-85) REVERT: q 106 THR cc_start: 0.9356 (p) cc_final: 0.9030 (p) REVERT: q 110 GLU cc_start: 0.8925 (mm-30) cc_final: 0.8304 (mm-30) REVERT: r 85 LYS cc_start: 0.8784 (ttmt) cc_final: 0.8521 (ttmt) REVERT: s 25 ARG cc_start: 0.8583 (OUTLIER) cc_final: 0.7802 (mtm180) REVERT: s 38 TYR cc_start: 0.8854 (m-80) cc_final: 0.8446 (m-80) REVERT: s 82 MET cc_start: 0.8271 (pmm) cc_final: 0.7935 (pmm) REVERT: s 92 ARG cc_start: 0.7793 (OUTLIER) cc_final: 0.7208 (tmm160) REVERT: t 18 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7862 (pp20) REVERT: t 24 MET cc_start: 0.9315 (tpp) cc_final: 0.9024 (tpp) REVERT: t 74 ILE cc_start: 0.6792 (OUTLIER) cc_final: 0.6457 (mm) REVERT: u 94 PHE cc_start: 0.8632 (p90) cc_final: 0.8385 (p90) REVERT: v 50 MET cc_start: 0.8491 (mmt) cc_final: 0.8026 (tpp) REVERT: v 61 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8057 (mm) REVERT: w 62 LYS cc_start: 0.9236 (mtpt) cc_final: 0.8995 (mtpp) REVERT: x 16 ASN cc_start: 0.9060 (t0) cc_final: 0.8820 (m-40) REVERT: x 43 LYS cc_start: 0.8965 (mmtp) cc_final: 0.8561 (pttp) REVERT: x 55 MET cc_start: 0.8039 (ppp) cc_final: 0.7732 (ppp) REVERT: y 6 LEU cc_start: 0.7538 (OUTLIER) cc_final: 0.7314 (tt) REVERT: y 45 GLN cc_start: 0.8883 (pt0) cc_final: 0.8371 (pp30) REVERT: z 20 LYS cc_start: 0.9018 (mmtt) cc_final: 0.8446 (mmtp) REVERT: z 46 MET cc_start: 0.8298 (mtt) cc_final: 0.7715 (mtp) REVERT: B 27 LEU cc_start: 0.8949 (tp) cc_final: 0.7902 (tt) REVERT: B 36 LYS cc_start: 0.9431 (mmtp) cc_final: 0.9119 (mmmm) REVERT: C 26 LYS cc_start: 0.8837 (mmtt) cc_final: 0.8498 (mmmt) REVERT: C 48 TYR cc_start: 0.6531 (m-80) cc_final: 0.5686 (m-80) REVERT: D 35 ARG cc_start: 0.8946 (mtt-85) cc_final: 0.8397 (mtt90) REVERT: E 48 MET cc_start: 0.8422 (OUTLIER) cc_final: 0.7981 (mpp) REVERT: F 1 MET cc_start: 0.7008 (OUTLIER) cc_final: 0.6463 (tmm) REVERT: F 15 LYS cc_start: 0.7687 (mmtp) cc_final: 0.7372 (mmtt) REVERT: G 26 MET cc_start: 0.7628 (tmm) cc_final: 0.6608 (tmm) REVERT: G 29 PHE cc_start: 0.7194 (m-80) cc_final: 0.6679 (m-10) REVERT: G 139 GLU cc_start: 0.6611 (OUTLIER) cc_final: 0.6115 (pp20) REVERT: G 153 MET cc_start: 0.6060 (mmm) cc_final: 0.5689 (mmm) REVERT: G 183 PHE cc_start: 0.7107 (OUTLIER) cc_final: 0.6880 (m-80) REVERT: I 74 TYR cc_start: 0.8852 (m-10) cc_final: 0.8330 (m-80) REVERT: I 88 ASN cc_start: 0.8892 (m110) cc_final: 0.8559 (m-40) REVERT: I 92 LEU cc_start: 0.8518 (mt) cc_final: 0.7825 (mt) REVERT: I 120 LYS cc_start: 0.6782 (mttm) cc_final: 0.6338 (ttpp) REVERT: I 123 MET cc_start: 0.7244 (mmm) cc_final: 0.6851 (mmm) REVERT: I 127 ARG cc_start: 0.8606 (mtt180) cc_final: 0.8263 (ttt180) REVERT: I 151 GLN cc_start: 0.8797 (mm110) cc_final: 0.8536 (mm-40) REVERT: I 169 TRP cc_start: 0.8824 (p90) cc_final: 0.8545 (p90) REVERT: I 171 GLU cc_start: 0.5493 (OUTLIER) cc_final: 0.5205 (mp0) REVERT: I 177 MET cc_start: 0.5360 (tmm) cc_final: 0.5134 (tmm) REVERT: I 184 LYS cc_start: 0.9266 (tptt) cc_final: 0.8974 (tptt) REVERT: I 201 GLU cc_start: 0.8930 (mm-30) cc_final: 0.8012 (mm-30) REVERT: J 70 MET cc_start: 0.6143 (tmm) cc_final: 0.5849 (tmm) REVERT: J 131 ASN cc_start: 0.8292 (m-40) cc_final: 0.7994 (m-40) REVERT: J 151 MET cc_start: 0.8242 (ptp) cc_final: 0.7921 (pmm) REVERT: K 90 MET cc_start: 0.2996 (mmt) cc_final: 0.2293 (mmt) REVERT: M 14 ARG cc_start: 0.7838 (ttm110) cc_final: 0.7374 (ptm160) REVERT: M 75 GLN cc_start: 0.8683 (mm-40) cc_final: 0.7845 (mp10) REVERT: M 79 ARG cc_start: 0.9186 (OUTLIER) cc_final: 0.8660 (ptt90) REVERT: M 86 LYS cc_start: 0.8470 (mmmt) cc_final: 0.8269 (mmtm) REVERT: N 20 ILE cc_start: 0.6862 (OUTLIER) cc_final: 0.6459 (mm) REVERT: N 56 MET cc_start: 0.4520 (mpp) cc_final: 0.4294 (mpp) REVERT: N 125 GLN cc_start: 0.5022 (OUTLIER) cc_final: 0.4789 (mp10) REVERT: O 15 HIS cc_start: 0.2162 (OUTLIER) cc_final: 0.1634 (p90) REVERT: Q 4 ASN cc_start: 0.8053 (OUTLIER) cc_final: 0.7403 (t0) REVERT: Q 73 LEU cc_start: 0.7126 (pt) cc_final: 0.6429 (mt) REVERT: Q 87 LYS cc_start: 0.8455 (OUTLIER) cc_final: 0.7599 (tptm) REVERT: R 2 ARG cc_start: 0.6341 (tpp-160) cc_final: 0.5865 (mmm160) REVERT: R 70 ARG cc_start: 0.7657 (mtm180) cc_final: 0.6997 (tmt-80) REVERT: T 9 LYS cc_start: 0.9348 (pttp) cc_final: 0.9040 (ptpp) REVERT: T 44 GLU cc_start: 0.8637 (tp30) cc_final: 0.8409 (tp30) REVERT: T 46 LYS cc_start: 0.8084 (pttt) cc_final: 0.7685 (pptt) REVERT: T 57 ARG cc_start: 0.8178 (ttt-90) cc_final: 0.6956 (tpm170) REVERT: T 58 MET cc_start: 0.8891 (mtm) cc_final: 0.8134 (mmt) REVERT: T 64 LYS cc_start: 0.8761 (mmtm) cc_final: 0.8344 (tptp) REVERT: U 5 ARG cc_start: 0.7652 (ptp90) cc_final: 0.7396 (ptp90) REVERT: V 79 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.6970 (mp0) REVERT: W 34 GLU cc_start: 0.7640 (tp30) cc_final: 0.7011 (tm-30) REVERT: W 58 ILE cc_start: 0.6678 (mt) cc_final: 0.6360 (mt) REVERT: Y 23 ARG cc_start: 0.9151 (mmm-85) cc_final: 0.8801 (mmt180) REVERT: Y 26 MET cc_start: 0.8569 (mmt) cc_final: 0.8332 (mmt) REVERT: Y 52 GLU cc_start: 0.7668 (mp0) cc_final: 0.7384 (mp0) REVERT: Y 53 MET cc_start: 0.9086 (ppp) cc_final: 0.8759 (ppp) REVERT: Z 37 TYR cc_start: 0.3725 (OUTLIER) cc_final: 0.2986 (t80) REVERT: Z 46 ARG cc_start: 0.8463 (ptt180) cc_final: 0.8255 (mmp-170) REVERT: a 53 ARG cc_start: -0.0717 (OUTLIER) cc_final: -0.2377 (mmp-170) REVERT: 8 41 PHE cc_start: 0.8717 (t80) cc_final: 0.8413 (t80) REVERT: 8 64 ILE cc_start: 0.6696 (OUTLIER) cc_final: 0.6352 (mp) REVERT: 8 105 ARG cc_start: 0.7715 (OUTLIER) cc_final: 0.7435 (ttp-170) REVERT: 8 132 ARG cc_start: 0.6770 (ptp90) cc_final: 0.6548 (ptp90) outliers start: 364 outliers final: 282 residues processed: 1412 average time/residue: 1.3016 time to fit residues: 3171.8151 Evaluate side-chains 1472 residues out of total 5093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 313 poor density : 1159 time to evaluate : 6.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 2 VAL Chi-restraints excluded: chain b residue 8 THR Chi-restraints excluded: chain b residue 32 LEU Chi-restraints excluded: chain b residue 33 LEU Chi-restraints excluded: chain b residue 37 SER Chi-restraints excluded: chain b residue 52 HIS Chi-restraints excluded: chain b residue 53 ILE Chi-restraints excluded: chain b residue 85 ASN Chi-restraints excluded: chain b residue 104 LEU Chi-restraints excluded: chain b residue 113 ASP Chi-restraints excluded: chain b residue 128 THR Chi-restraints excluded: chain b residue 133 ASN Chi-restraints excluded: chain b residue 219 VAL Chi-restraints excluded: chain b residue 222 THR Chi-restraints excluded: chain c residue 12 THR Chi-restraints excluded: chain c residue 35 THR Chi-restraints excluded: chain c residue 40 LEU Chi-restraints excluded: chain c residue 60 VAL Chi-restraints excluded: chain c residue 73 VAL Chi-restraints excluded: chain c residue 79 LEU Chi-restraints excluded: chain c residue 100 LEU Chi-restraints excluded: chain c residue 108 ASP Chi-restraints excluded: chain c residue 121 THR Chi-restraints excluded: chain c residue 133 THR Chi-restraints excluded: chain c residue 142 VAL Chi-restraints excluded: chain c residue 160 LYS Chi-restraints excluded: chain c residue 168 GLU Chi-restraints excluded: chain c residue 170 VAL Chi-restraints excluded: chain c residue 171 THR Chi-restraints excluded: chain c residue 180 VAL Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 4 VAL Chi-restraints excluded: chain d residue 7 ASP Chi-restraints excluded: chain d residue 12 LEU Chi-restraints excluded: chain d residue 48 THR Chi-restraints excluded: chain d residue 65 THR Chi-restraints excluded: chain d residue 80 SER Chi-restraints excluded: chain d residue 169 VAL Chi-restraints excluded: chain d residue 193 VAL Chi-restraints excluded: chain e residue 4 HIS Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 27 VAL Chi-restraints excluded: chain e residue 50 ASP Chi-restraints excluded: chain e residue 59 ILE Chi-restraints excluded: chain e residue 80 GLN Chi-restraints excluded: chain e residue 107 VAL Chi-restraints excluded: chain e residue 112 ASP Chi-restraints excluded: chain e residue 140 ILE Chi-restraints excluded: chain e residue 153 ILE Chi-restraints excluded: chain e residue 157 THR Chi-restraints excluded: chain e residue 166 ARG Chi-restraints excluded: chain e residue 168 LEU Chi-restraints excluded: chain f residue 9 VAL Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 18 ILE Chi-restraints excluded: chain f residue 19 ASN Chi-restraints excluded: chain f residue 29 ASN Chi-restraints excluded: chain f residue 49 LEU Chi-restraints excluded: chain f residue 57 TYR Chi-restraints excluded: chain f residue 70 LEU Chi-restraints excluded: chain f residue 83 THR Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 102 ILE Chi-restraints excluded: chain f residue 104 LEU Chi-restraints excluded: chain f residue 106 LEU Chi-restraints excluded: chain f residue 136 ASP Chi-restraints excluded: chain f residue 137 LYS Chi-restraints excluded: chain g residue 4 ILE Chi-restraints excluded: chain g residue 18 GLN Chi-restraints excluded: chain g residue 37 VAL Chi-restraints excluded: chain g residue 119 ASN Chi-restraints excluded: chain g residue 134 VAL Chi-restraints excluded: chain g residue 144 VAL Chi-restraints excluded: chain h residue 82 ILE Chi-restraints excluded: chain h residue 122 GLN Chi-restraints excluded: chain i residue 115 ASP Chi-restraints excluded: chain j residue 3 THR Chi-restraints excluded: chain j residue 7 LYS Chi-restraints excluded: chain j residue 11 VAL Chi-restraints excluded: chain j residue 44 TYR Chi-restraints excluded: chain j residue 49 ASP Chi-restraints excluded: chain j residue 57 LEU Chi-restraints excluded: chain j residue 73 VAL Chi-restraints excluded: chain j residue 100 VAL Chi-restraints excluded: chain k residue 22 ILE Chi-restraints excluded: chain k residue 24 VAL Chi-restraints excluded: chain k residue 62 VAL Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 77 ILE Chi-restraints excluded: chain k residue 103 VAL Chi-restraints excluded: chain k residue 104 THR Chi-restraints excluded: chain k residue 110 GLU Chi-restraints excluded: chain k residue 116 ILE Chi-restraints excluded: chain l residue 46 VAL Chi-restraints excluded: chain l residue 55 MET Chi-restraints excluded: chain l residue 63 LYS Chi-restraints excluded: chain l residue 67 THR Chi-restraints excluded: chain l residue 74 THR Chi-restraints excluded: chain l residue 94 THR Chi-restraints excluded: chain l residue 107 PHE Chi-restraints excluded: chain l residue 128 THR Chi-restraints excluded: chain l residue 143 GLU Chi-restraints excluded: chain m residue 20 LEU Chi-restraints excluded: chain m residue 42 THR Chi-restraints excluded: chain m residue 54 THR Chi-restraints excluded: chain m residue 106 ASP Chi-restraints excluded: chain m residue 115 GLU Chi-restraints excluded: chain m residue 124 LEU Chi-restraints excluded: chain m residue 128 THR Chi-restraints excluded: chain m residue 132 THR Chi-restraints excluded: chain m residue 135 VAL Chi-restraints excluded: chain n residue 15 SER Chi-restraints excluded: chain n residue 18 GLN Chi-restraints excluded: chain n residue 52 ILE Chi-restraints excluded: chain n residue 54 LEU Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain n residue 97 ILE Chi-restraints excluded: chain o residue 34 HIS 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 83 LEU Chi-restraints excluded: chain o residue 90 VAL Chi-restraints excluded: chain o residue 93 ASP Chi-restraints excluded: chain p residue 23 ASP Chi-restraints excluded: chain p residue 43 GLU Chi-restraints excluded: chain p residue 59 THR Chi-restraints excluded: chain p residue 60 VAL Chi-restraints excluded: chain p residue 75 THR Chi-restraints excluded: chain p residue 80 VAL Chi-restraints excluded: chain q residue 33 VAL Chi-restraints excluded: chain q residue 59 LEU Chi-restraints excluded: chain q residue 61 ILE Chi-restraints excluded: chain q residue 93 ILE Chi-restraints excluded: chain r residue 15 SER Chi-restraints excluded: chain r residue 19 THR Chi-restraints excluded: chain r residue 26 ASP Chi-restraints excluded: chain r residue 38 VAL Chi-restraints excluded: chain r residue 49 ILE Chi-restraints excluded: chain r residue 51 VAL Chi-restraints excluded: chain r residue 58 VAL Chi-restraints excluded: chain r residue 75 VAL Chi-restraints excluded: chain s residue 20 VAL Chi-restraints excluded: chain s residue 25 ARG Chi-restraints excluded: chain s residue 52 GLU Chi-restraints excluded: chain s residue 53 SER Chi-restraints excluded: chain s residue 66 ILE Chi-restraints excluded: chain s residue 70 LYS Chi-restraints excluded: chain s residue 76 VAL Chi-restraints excluded: chain s residue 92 ARG Chi-restraints excluded: chain s residue 96 ILE Chi-restraints excluded: chain s residue 100 THR Chi-restraints excluded: chain t residue 11 LEU Chi-restraints excluded: chain t residue 16 VAL Chi-restraints excluded: chain t residue 18 GLU Chi-restraints excluded: chain t residue 74 ILE Chi-restraints excluded: chain t residue 86 THR Chi-restraints excluded: chain u residue 8 ASP Chi-restraints excluded: chain u residue 10 VAL Chi-restraints excluded: chain u residue 11 ILE Chi-restraints excluded: chain u residue 26 ASN Chi-restraints excluded: chain u residue 35 VAL Chi-restraints excluded: chain u residue 81 ARG Chi-restraints excluded: chain v residue 8 VAL Chi-restraints excluded: chain v residue 56 PHE Chi-restraints excluded: chain v residue 61 LEU Chi-restraints excluded: chain v residue 63 ILE Chi-restraints excluded: chain v residue 64 VAL Chi-restraints excluded: chain v residue 66 ASP Chi-restraints excluded: chain v residue 77 VAL Chi-restraints excluded: chain v residue 90 ASP Chi-restraints excluded: chain w residue 19 VAL Chi-restraints excluded: chain w residue 27 VAL Chi-restraints excluded: chain w residue 34 VAL Chi-restraints excluded: chain w residue 63 VAL Chi-restraints excluded: chain x residue 13 THR Chi-restraints excluded: chain x residue 22 ASN Chi-restraints excluded: chain x residue 67 LEU Chi-restraints excluded: chain x residue 77 TYR Chi-restraints excluded: chain y residue 6 LEU Chi-restraints excluded: chain y residue 7 ARG Chi-restraints excluded: chain y residue 46 VAL Chi-restraints excluded: chain y residue 49 ASP Chi-restraints excluded: chain z residue 13 ILE Chi-restraints excluded: chain z residue 26 LEU Chi-restraints excluded: chain z residue 33 HIS Chi-restraints excluded: chain z residue 40 THR Chi-restraints excluded: chain z residue 51 SER Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain D residue 3 ARG Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 43 LEU Chi-restraints excluded: chain E residue 48 MET Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 33 HIS Chi-restraints excluded: chain G residue 15 PHE Chi-restraints excluded: chain G residue 38 HIS Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 128 LEU Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain G residue 183 PHE Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 190 SER Chi-restraints excluded: chain G residue 210 THR Chi-restraints excluded: chain H residue 4 VAL Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 182 ASP Chi-restraints excluded: chain H residue 194 VAL Chi-restraints excluded: chain I residue 64 TYR Chi-restraints excluded: chain I residue 99 ASN Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 141 VAL Chi-restraints excluded: chain I residue 171 GLU Chi-restraints excluded: chain J residue 15 ILE Chi-restraints excluded: chain J residue 19 ARG Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 82 HIS Chi-restraints excluded: chain J residue 95 MET Chi-restraints excluded: chain J residue 121 ASN Chi-restraints excluded: chain K residue 8 PHE Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain K residue 76 THR Chi-restraints excluded: chain K residue 78 PHE Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain L residue 6 ILE Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 47 GLU Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain L residue 147 ASN Chi-restraints excluded: chain M residue 37 ASN Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain M residue 59 GLU Chi-restraints excluded: chain M residue 79 ARG Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain M residue 128 VAL Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 24 ASN Chi-restraints excluded: chain N residue 125 GLN Chi-restraints excluded: chain O residue 15 HIS Chi-restraints excluded: chain O residue 69 THR Chi-restraints excluded: chain P residue 15 VAL Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain P residue 35 ASP Chi-restraints excluded: chain P residue 85 VAL Chi-restraints excluded: chain P residue 118 ASN Chi-restraints excluded: chain Q residue 4 ASN Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 86 VAL Chi-restraints excluded: chain Q residue 87 LYS Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain R residue 53 ASP Chi-restraints excluded: chain R residue 67 ASP Chi-restraints excluded: chain S residue 23 ARG Chi-restraints excluded: chain S residue 49 THR Chi-restraints excluded: chain T residue 17 ASP Chi-restraints excluded: chain T residue 28 VAL Chi-restraints excluded: chain T residue 30 LEU Chi-restraints excluded: chain T residue 56 LEU Chi-restraints excluded: chain T residue 68 TYR Chi-restraints excluded: chain T residue 78 THR Chi-restraints excluded: chain U residue 69 ASP Chi-restraints excluded: chain U residue 77 GLU Chi-restraints excluded: chain U residue 78 VAL Chi-restraints excluded: chain V residue 11 VAL Chi-restraints excluded: chain V residue 18 LYS Chi-restraints excluded: chain V residue 28 VAL Chi-restraints excluded: chain V residue 29 LYS Chi-restraints excluded: chain V residue 46 HIS Chi-restraints excluded: chain V residue 79 GLU Chi-restraints excluded: chain W residue 22 TYR Chi-restraints excluded: chain W residue 30 ASN Chi-restraints excluded: chain W residue 64 LEU Chi-restraints excluded: chain X residue 15 LEU Chi-restraints excluded: chain X residue 39 ILE Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain X residue 59 VAL Chi-restraints excluded: chain X residue 70 LEU Chi-restraints excluded: chain X residue 72 GLU Chi-restraints excluded: chain X residue 76 THR Chi-restraints excluded: chain Y residue 19 HIS Chi-restraints excluded: chain Y residue 70 LYS Chi-restraints excluded: chain Z residue 12 ASP Chi-restraints excluded: chain Z residue 37 TYR Chi-restraints excluded: chain Z residue 52 VAL Chi-restraints excluded: chain a residue 5 THR Chi-restraints excluded: chain a residue 18 THR Chi-restraints excluded: chain a residue 53 ARG Chi-restraints excluded: chain a residue 172 HIS Chi-restraints excluded: chain 8 residue 56 LEU Chi-restraints excluded: chain 8 residue 64 ILE Chi-restraints excluded: chain 8 residue 100 THR Chi-restraints excluded: chain 8 residue 105 ARG Chi-restraints excluded: chain 9 residue 18 THR Chi-restraints excluded: chain 9 residue 20 ILE Chi-restraints excluded: chain 9 residue 35 THR Chi-restraints excluded: chain 9 residue 52 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1065 random chunks: chunk 933 optimal weight: 10.0000 chunk 983 optimal weight: 10.0000 chunk 897 optimal weight: 10.0000 chunk 956 optimal weight: 10.0000 chunk 575 optimal weight: 20.0000 chunk 416 optimal weight: 6.9990 chunk 751 optimal weight: 10.0000 chunk 293 optimal weight: 1.9990 chunk 864 optimal weight: 10.0000 chunk 904 optimal weight: 10.0000 chunk 953 optimal weight: 10.0000 overall best weight: 7.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 20 ASN ** e 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 80 GLN g 66 ASN g 145 ASN h 9 GLN ** i 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 93 GLN l 38 GLN ** l 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 19 GLN ** r 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 36 GLN ** F 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 50 ASN ** I 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 28 GLN ** Q 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 50 HIS U 18 GLN ** W 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.6430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 161229 Z= 0.329 Angle : 0.754 17.622 240720 Z= 0.381 Chirality : 0.041 0.341 30724 Planarity : 0.006 0.105 13231 Dihedral : 24.158 179.783 79535 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 32.27 Ramachandran Plot: Outliers : 0.16 % Allowed : 13.16 % Favored : 86.68 % Rotamer: Outliers : 6.72 % Allowed : 28.55 % Favored : 64.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.21 (0.10), residues: 6142 helix: -1.41 (0.11), residues: 1782 sheet: -1.96 (0.16), residues: 890 loop : -2.66 (0.10), residues: 3470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP m 64 HIS 0.069 0.002 HIS G 38 PHE 0.039 0.003 PHE V 36 TYR 0.030 0.002 TYR I 102 ARG 0.018 0.001 ARG h 125 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12284 Ramachandran restraints generated. 6142 Oldfield, 0 Emsley, 6142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12284 Ramachandran restraints generated. 6142 Oldfield, 0 Emsley, 6142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1544 residues out of total 5093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 342 poor density : 1202 time to evaluate : 6.350 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: c 28 GLU cc_start: 0.8910 (tm-30) cc_final: 0.8570 (tp30) REVERT: c 36 GLN cc_start: 0.8331 (tt0) cc_final: 0.8020 (tp40) REVERT: c 64 GLU cc_start: 0.8843 (mm-30) cc_final: 0.8503 (mm-30) REVERT: c 133 THR cc_start: 0.8677 (OUTLIER) cc_final: 0.8424 (t) REVERT: c 148 GLN cc_start: 0.8896 (mp10) cc_final: 0.8422 (mp10) REVERT: c 185 ASN cc_start: 0.8919 (m-40) cc_final: 0.8717 (m-40) REVERT: d 1 MET cc_start: 0.8356 (OUTLIER) cc_final: 0.7736 (mpp) REVERT: d 6 LYS cc_start: 0.8299 (ptmt) cc_final: 0.7763 (pttm) REVERT: d 9 GLN cc_start: 0.8691 (tm-30) cc_final: 0.8398 (tm-30) REVERT: e 6 TYR cc_start: 0.9194 (t80) cc_final: 0.8391 (t80) REVERT: e 33 ILE cc_start: 0.9189 (tp) cc_final: 0.8847 (tp) REVERT: e 80 GLN cc_start: 0.8276 (OUTLIER) cc_final: 0.8047 (tm-30) REVERT: e 97 GLU cc_start: 0.8381 (tp30) cc_final: 0.7931 (tp30) REVERT: e 100 GLU cc_start: 0.8051 (tm-30) cc_final: 0.7733 (tm-30) REVERT: e 109 ARG cc_start: 0.8814 (tpp-160) cc_final: 0.8244 (tpp-160) REVERT: e 166 ARG cc_start: 0.9049 (OUTLIER) cc_final: 0.8740 (tmm-80) REVERT: e 177 ARG cc_start: 0.7577 (ttt180) cc_final: 0.7145 (tpt170) REVERT: f 82 PHE cc_start: 0.7608 (m-10) cc_final: 0.7231 (m-10) REVERT: f 137 LYS cc_start: 0.8702 (OUTLIER) cc_final: 0.8350 (mmtt) REVERT: g 25 TYR cc_start: 0.7943 (t80) cc_final: 0.7418 (t80) REVERT: g 55 GLU cc_start: 0.9157 (mt-10) cc_final: 0.8807 (mt-10) REVERT: g 87 GLU cc_start: 0.8071 (tp30) cc_final: 0.7695 (mm-30) REVERT: h 52 MET cc_start: 0.7518 (tpp) cc_final: 0.6314 (mmm) REVERT: h 116 GLU cc_start: 0.8958 (mm-30) cc_final: 0.8515 (mm-30) REVERT: i 41 PHE cc_start: 0.8825 (t80) cc_final: 0.8363 (t80) REVERT: i 116 MET cc_start: -0.1773 (tpt) cc_final: -0.2600 (tpt) REVERT: j 7 LYS cc_start: 0.8871 (OUTLIER) cc_final: 0.8122 (mtmm) REVERT: j 49 ASP cc_start: 0.8264 (OUTLIER) cc_final: 0.7825 (t70) REVERT: j 68 LYS cc_start: 0.8564 (mtpt) cc_final: 0.8194 (mtpt) REVERT: j 118 MET cc_start: 0.9182 (mmt) cc_final: 0.8863 (mmt) REVERT: j 119 PHE cc_start: 0.9107 (t80) cc_final: 0.8810 (t80) REVERT: k 29 HIS cc_start: 0.8391 (t70) cc_final: 0.8160 (t-90) REVERT: k 66 LYS cc_start: 0.8461 (tttt) cc_final: 0.7838 (tttt) REVERT: k 116 ILE cc_start: 0.8330 (OUTLIER) cc_final: 0.8096 (tp) REVERT: l 38 GLN cc_start: 0.9140 (tt0) cc_final: 0.8754 (tt0) REVERT: l 39 LYS cc_start: 0.8876 (pttt) cc_final: 0.8406 (pttt) REVERT: l 82 LEU cc_start: 0.9632 (mt) cc_final: 0.9319 (mt) REVERT: l 128 THR cc_start: 0.9181 (OUTLIER) cc_final: 0.8783 (t) REVERT: m 127 LYS cc_start: 0.8493 (mmtt) cc_final: 0.8202 (mmtt) REVERT: n 115 LEU cc_start: 0.8923 (mt) cc_final: 0.8507 (mt) REVERT: o 20 GLU cc_start: 0.8951 (tp30) cc_final: 0.8679 (tp30) REVERT: o 104 GLN cc_start: 0.9620 (tt0) cc_final: 0.9351 (tt0) REVERT: p 37 LYS cc_start: 0.8375 (mttm) cc_final: 0.8097 (mptt) REVERT: p 50 ARG cc_start: 0.8477 (ttt-90) cc_final: 0.7953 (ttt-90) REVERT: p 74 GLN cc_start: 0.8514 (mp10) cc_final: 0.7762 (mp10) REVERT: p 93 LYS cc_start: 0.8719 (tppt) cc_final: 0.8393 (tppt) REVERT: q 24 TYR cc_start: 0.7552 (t80) cc_final: 0.7199 (t80) REVERT: q 35 PHE cc_start: 0.8865 (t80) cc_final: 0.8591 (t80) REVERT: q 54 ARG cc_start: 0.8962 (mtm180) cc_final: 0.8672 (mtm-85) REVERT: q 57 ARG cc_start: 0.8830 (tpt-90) cc_final: 0.8529 (tpt-90) REVERT: q 106 THR cc_start: 0.9363 (p) cc_final: 0.9092 (p) REVERT: q 110 GLU cc_start: 0.8976 (mm-30) cc_final: 0.8359 (mm-30) REVERT: r 46 GLU cc_start: 0.8724 (mp0) cc_final: 0.7855 (tp30) REVERT: r 85 LYS cc_start: 0.8844 (ttmt) cc_final: 0.8585 (ttmt) REVERT: s 25 ARG cc_start: 0.8560 (OUTLIER) cc_final: 0.7777 (mtm180) REVERT: s 38 TYR cc_start: 0.8844 (m-80) cc_final: 0.8429 (m-80) REVERT: s 82 MET cc_start: 0.8285 (pmm) cc_final: 0.7938 (pmm) REVERT: s 92 ARG cc_start: 0.7782 (OUTLIER) cc_final: 0.7189 (tmm160) REVERT: t 18 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7855 (pp20) REVERT: t 74 ILE cc_start: 0.6571 (OUTLIER) cc_final: 0.6202 (mm) REVERT: v 61 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8046 (mm) REVERT: w 62 LYS cc_start: 0.9161 (mtpt) cc_final: 0.8953 (mtpp) REVERT: x 16 ASN cc_start: 0.9087 (t0) cc_final: 0.8781 (m-40) REVERT: y 6 LEU cc_start: 0.7511 (OUTLIER) cc_final: 0.7254 (tt) REVERT: y 7 ARG cc_start: 0.8942 (OUTLIER) cc_final: 0.8627 (tmm160) REVERT: y 45 GLN cc_start: 0.8878 (pt0) cc_final: 0.8325 (pp30) REVERT: y 47 ARG cc_start: 0.9106 (ptp-110) cc_final: 0.8570 (ptp90) REVERT: z 18 LYS cc_start: 0.8366 (mmtt) cc_final: 0.8017 (mmmt) REVERT: z 20 LYS cc_start: 0.9009 (mmtt) cc_final: 0.8494 (mmtp) REVERT: z 46 MET cc_start: 0.8279 (mtt) cc_final: 0.7689 (mtp) REVERT: B 27 LEU cc_start: 0.8982 (tp) cc_final: 0.7954 (tt) REVERT: B 36 LYS cc_start: 0.9436 (mmtp) cc_final: 0.9114 (mmmm) REVERT: C 48 TYR cc_start: 0.6637 (m-80) cc_final: 0.5695 (m-80) REVERT: D 35 ARG cc_start: 0.8943 (mtt-85) cc_final: 0.8401 (mtt90) REVERT: E 24 LYS cc_start: 0.8800 (tppp) cc_final: 0.8377 (tptp) REVERT: E 48 MET cc_start: 0.8121 (OUTLIER) cc_final: 0.7664 (mpp) REVERT: F 1 MET cc_start: 0.7104 (OUTLIER) cc_final: 0.6891 (tmm) REVERT: F 15 LYS cc_start: 0.7580 (mmtp) cc_final: 0.7252 (mmtt) REVERT: G 26 MET cc_start: 0.7567 (tmm) cc_final: 0.6485 (tmm) REVERT: G 38 HIS cc_start: 0.7579 (OUTLIER) cc_final: 0.7326 (t-90) REVERT: G 139 GLU cc_start: 0.6860 (OUTLIER) cc_final: 0.6405 (pp20) REVERT: G 153 MET cc_start: 0.6038 (mmm) cc_final: 0.5707 (mmm) REVERT: G 166 ASP cc_start: 0.8801 (OUTLIER) cc_final: 0.8505 (m-30) REVERT: G 183 PHE cc_start: 0.7120 (OUTLIER) cc_final: 0.6841 (m-80) REVERT: I 74 TYR cc_start: 0.8865 (m-10) cc_final: 0.8363 (m-80) REVERT: I 88 ASN cc_start: 0.8864 (m110) cc_final: 0.8515 (m-40) REVERT: I 92 LEU cc_start: 0.8502 (mt) cc_final: 0.7833 (mt) REVERT: I 123 MET cc_start: 0.7257 (mmm) cc_final: 0.6854 (mmm) REVERT: I 127 ARG cc_start: 0.8680 (mtt180) cc_final: 0.8326 (ttt180) REVERT: I 151 GLN cc_start: 0.8820 (mm110) cc_final: 0.8575 (mm-40) REVERT: I 169 TRP cc_start: 0.8847 (p90) cc_final: 0.8645 (p-90) REVERT: I 171 GLU cc_start: 0.5216 (OUTLIER) cc_final: 0.4784 (mp0) REVERT: I 177 MET cc_start: 0.5436 (tmm) cc_final: 0.5213 (tmm) REVERT: I 184 LYS cc_start: 0.9266 (tptt) cc_final: 0.8956 (tptt) REVERT: I 187 ARG cc_start: 0.9084 (tpt90) cc_final: 0.8790 (tpt-90) REVERT: I 201 GLU cc_start: 0.8941 (mm-30) cc_final: 0.8056 (mm-30) REVERT: J 70 MET cc_start: 0.6215 (tmm) cc_final: 0.5983 (tmm) REVERT: J 110 MET cc_start: 0.8193 (tpp) cc_final: 0.7653 (tpp) REVERT: J 151 MET cc_start: 0.8350 (ptp) cc_final: 0.8035 (pmm) REVERT: K 90 MET cc_start: 0.3012 (mmt) cc_final: 0.2323 (mmt) REVERT: M 6 ILE cc_start: 0.7099 (OUTLIER) cc_final: 0.6765 (tt) REVERT: M 14 ARG cc_start: 0.7826 (ttm110) cc_final: 0.7429 (ptm160) REVERT: M 75 GLN cc_start: 0.8638 (mm-40) cc_final: 0.7831 (mp10) REVERT: M 79 ARG cc_start: 0.9182 (OUTLIER) cc_final: 0.8619 (ptt90) REVERT: M 86 LYS cc_start: 0.8511 (mmmt) cc_final: 0.8159 (mmmt) REVERT: N 20 ILE cc_start: 0.6495 (OUTLIER) cc_final: 0.6052 (mm) REVERT: N 56 MET cc_start: 0.4540 (mpp) cc_final: 0.4331 (mpp) REVERT: N 125 GLN cc_start: 0.4995 (OUTLIER) cc_final: 0.4676 (mp10) REVERT: O 15 HIS cc_start: 0.2132 (OUTLIER) cc_final: 0.1610 (p90) REVERT: Q 4 ASN cc_start: 0.8025 (OUTLIER) cc_final: 0.7384 (t0) REVERT: Q 87 LYS cc_start: 0.8416 (OUTLIER) cc_final: 0.7274 (tptt) REVERT: Q 116 TYR cc_start: 0.7721 (m-80) cc_final: 0.7209 (m-80) REVERT: R 2 ARG cc_start: 0.6420 (tpp-160) cc_final: 0.5930 (mmm160) REVERT: R 70 ARG cc_start: 0.7604 (mtm180) cc_final: 0.6934 (tmt-80) REVERT: T 9 LYS cc_start: 0.9353 (pttp) cc_final: 0.9027 (ptpp) REVERT: T 44 GLU cc_start: 0.8654 (tp30) cc_final: 0.8440 (tp30) REVERT: T 46 LYS cc_start: 0.8071 (pttt) cc_final: 0.7679 (pptt) REVERT: T 50 HIS cc_start: 0.7404 (m90) cc_final: 0.7168 (m-70) REVERT: T 57 ARG cc_start: 0.8076 (ttt-90) cc_final: 0.6867 (tpm170) REVERT: T 58 MET cc_start: 0.8900 (mtm) cc_final: 0.8177 (mmt) REVERT: T 83 ARG cc_start: 0.7452 (mtt180) cc_final: 0.6926 (mtt-85) REVERT: V 79 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.7149 (mp0) REVERT: W 34 GLU cc_start: 0.7289 (tp30) cc_final: 0.6701 (tm-30) REVERT: W 58 ILE cc_start: 0.6716 (mt) cc_final: 0.6396 (mt) REVERT: Y 23 ARG cc_start: 0.9157 (mmm-85) cc_final: 0.8790 (mmt180) REVERT: Y 52 GLU cc_start: 0.7646 (mp0) cc_final: 0.7320 (mp0) REVERT: Y 53 MET cc_start: 0.9097 (ppp) cc_final: 0.8783 (ppp) REVERT: Z 37 TYR cc_start: 0.3774 (OUTLIER) cc_final: 0.2916 (t80) REVERT: a 53 ARG cc_start: -0.0823 (OUTLIER) cc_final: -0.2343 (mmp-170) REVERT: 8 41 PHE cc_start: 0.8620 (t80) cc_final: 0.8357 (t80) REVERT: 8 64 ILE cc_start: 0.6657 (OUTLIER) cc_final: 0.6397 (mp) REVERT: 8 105 ARG cc_start: 0.7772 (OUTLIER) cc_final: 0.7488 (ttp-170) REVERT: 8 131 MET cc_start: 0.2611 (mmt) cc_final: 0.1309 (ppp) outliers start: 342 outliers final: 273 residues processed: 1398 average time/residue: 1.3030 time to fit residues: 3141.4199 Evaluate side-chains 1477 residues out of total 5093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 308 poor density : 1169 time to evaluate : 5.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 2 VAL Chi-restraints excluded: chain b residue 8 THR Chi-restraints excluded: chain b residue 32 LEU Chi-restraints excluded: chain b residue 33 LEU Chi-restraints excluded: chain b residue 37 SER Chi-restraints excluded: chain b residue 85 ASN Chi-restraints excluded: chain b residue 104 LEU Chi-restraints excluded: chain b residue 113 ASP Chi-restraints excluded: chain b residue 128 THR Chi-restraints excluded: chain b residue 133 ASN Chi-restraints excluded: chain b residue 219 VAL Chi-restraints excluded: chain b residue 222 THR Chi-restraints excluded: chain b residue 249 VAL Chi-restraints excluded: chain b residue 259 ASN Chi-restraints excluded: chain c residue 12 THR Chi-restraints excluded: chain c residue 35 THR Chi-restraints excluded: chain c residue 40 LEU Chi-restraints excluded: chain c residue 60 VAL Chi-restraints excluded: chain c residue 73 VAL Chi-restraints excluded: chain c residue 79 LEU Chi-restraints excluded: chain c residue 108 ASP Chi-restraints excluded: chain c residue 121 THR Chi-restraints excluded: chain c residue 133 THR Chi-restraints excluded: chain c residue 142 VAL Chi-restraints excluded: chain c residue 160 LYS Chi-restraints excluded: chain c residue 168 GLU Chi-restraints excluded: chain c residue 170 VAL Chi-restraints excluded: chain c residue 171 THR Chi-restraints excluded: chain c residue 180 VAL Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 4 VAL Chi-restraints excluded: chain d residue 7 ASP Chi-restraints excluded: chain d residue 48 THR Chi-restraints excluded: chain d residue 52 VAL Chi-restraints excluded: chain d residue 65 THR Chi-restraints excluded: chain d residue 80 SER Chi-restraints excluded: chain d residue 90 GLN Chi-restraints excluded: chain d residue 96 VAL Chi-restraints excluded: chain d residue 133 LEU Chi-restraints excluded: chain d residue 169 VAL Chi-restraints excluded: chain d residue 193 VAL Chi-restraints excluded: chain e residue 4 HIS Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 20 ASN Chi-restraints excluded: chain e residue 27 VAL Chi-restraints excluded: chain e residue 43 ILE Chi-restraints excluded: chain e residue 50 ASP Chi-restraints excluded: chain e residue 80 GLN Chi-restraints excluded: chain e residue 107 VAL Chi-restraints excluded: chain e residue 112 ASP Chi-restraints excluded: chain e residue 148 VAL Chi-restraints excluded: chain e residue 157 THR Chi-restraints excluded: chain e residue 166 ARG Chi-restraints excluded: chain e residue 168 LEU Chi-restraints excluded: chain f residue 9 VAL Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 18 ILE Chi-restraints excluded: chain f residue 19 ASN Chi-restraints excluded: chain f residue 29 ASN Chi-restraints excluded: chain f residue 49 LEU Chi-restraints excluded: chain f residue 57 TYR Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 102 ILE Chi-restraints excluded: chain f residue 104 LEU Chi-restraints excluded: chain f residue 106 LEU Chi-restraints excluded: chain f residue 136 ASP Chi-restraints excluded: chain f residue 137 LYS Chi-restraints excluded: chain g residue 134 VAL Chi-restraints excluded: chain h residue 82 ILE Chi-restraints excluded: chain i residue 115 ASP Chi-restraints excluded: chain j residue 3 THR Chi-restraints excluded: chain j residue 7 LYS Chi-restraints excluded: chain j residue 11 VAL Chi-restraints excluded: chain j residue 44 TYR Chi-restraints excluded: chain j residue 49 ASP Chi-restraints excluded: chain j residue 57 LEU Chi-restraints excluded: chain j residue 73 VAL Chi-restraints excluded: chain j residue 100 VAL Chi-restraints excluded: chain k residue 22 ILE Chi-restraints excluded: chain k residue 24 VAL Chi-restraints excluded: chain k residue 62 VAL Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 77 ILE Chi-restraints excluded: chain k residue 103 VAL Chi-restraints excluded: chain k residue 104 THR Chi-restraints excluded: chain k residue 110 GLU Chi-restraints excluded: chain k residue 116 ILE Chi-restraints excluded: chain l residue 46 VAL Chi-restraints excluded: chain l residue 55 MET Chi-restraints excluded: chain l residue 63 LYS Chi-restraints excluded: chain l residue 67 THR Chi-restraints excluded: chain l residue 74 THR Chi-restraints excluded: chain l residue 94 THR Chi-restraints excluded: chain l residue 107 PHE Chi-restraints excluded: chain l residue 128 THR Chi-restraints excluded: chain m residue 20 LEU Chi-restraints excluded: chain m residue 33 LEU Chi-restraints excluded: chain m residue 42 THR Chi-restraints excluded: chain m residue 115 GLU Chi-restraints excluded: chain m residue 124 LEU Chi-restraints excluded: chain m residue 128 THR Chi-restraints excluded: chain m residue 132 THR Chi-restraints excluded: chain m residue 135 VAL Chi-restraints excluded: chain n residue 15 SER Chi-restraints excluded: chain n residue 18 GLN Chi-restraints excluded: chain n residue 54 LEU Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain n residue 97 ILE Chi-restraints excluded: chain o residue 34 HIS Chi-restraints excluded: chain o residue 35 ILE Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain o residue 49 VAL Chi-restraints excluded: chain o residue 53 THR Chi-restraints excluded: chain o residue 83 LEU Chi-restraints excluded: chain o residue 90 VAL Chi-restraints excluded: chain o residue 93 ASP Chi-restraints excluded: chain p residue 23 ASP Chi-restraints excluded: chain p residue 43 GLU Chi-restraints excluded: chain p residue 59 THR Chi-restraints excluded: chain p residue 60 VAL Chi-restraints excluded: chain p residue 75 THR Chi-restraints excluded: chain p residue 80 VAL Chi-restraints excluded: chain q residue 19 GLN Chi-restraints excluded: chain q residue 33 VAL Chi-restraints excluded: chain q residue 59 LEU Chi-restraints excluded: chain q residue 61 ILE Chi-restraints excluded: chain q residue 93 ILE Chi-restraints excluded: chain r residue 15 SER Chi-restraints excluded: chain r residue 19 THR Chi-restraints excluded: chain r residue 26 ASP Chi-restraints excluded: chain r residue 38 VAL Chi-restraints excluded: chain r residue 49 ILE Chi-restraints excluded: chain r residue 58 VAL Chi-restraints excluded: chain r residue 75 VAL Chi-restraints excluded: chain s residue 20 VAL Chi-restraints excluded: chain s residue 25 ARG Chi-restraints excluded: chain s residue 52 GLU Chi-restraints excluded: chain s residue 53 SER Chi-restraints excluded: chain s residue 66 ILE Chi-restraints excluded: chain s residue 70 LYS Chi-restraints excluded: chain s residue 76 VAL Chi-restraints excluded: chain s residue 92 ARG Chi-restraints excluded: chain s residue 96 ILE Chi-restraints excluded: chain s residue 100 THR Chi-restraints excluded: chain t residue 11 LEU Chi-restraints excluded: chain t residue 16 VAL Chi-restraints excluded: chain t residue 18 GLU Chi-restraints excluded: chain t residue 74 ILE Chi-restraints excluded: chain t residue 86 THR Chi-restraints excluded: chain u residue 8 ASP Chi-restraints excluded: chain u residue 10 VAL Chi-restraints excluded: chain u residue 11 ILE Chi-restraints excluded: chain u residue 26 ASN Chi-restraints excluded: chain u residue 35 VAL Chi-restraints excluded: chain u residue 81 ARG Chi-restraints excluded: chain v residue 8 VAL Chi-restraints excluded: chain v residue 45 ASP Chi-restraints excluded: chain v residue 56 PHE Chi-restraints excluded: chain v residue 61 LEU Chi-restraints excluded: chain v residue 63 ILE Chi-restraints excluded: chain v residue 64 VAL Chi-restraints excluded: chain v residue 66 ASP Chi-restraints excluded: chain v residue 77 VAL Chi-restraints excluded: chain v residue 90 ASP Chi-restraints excluded: chain w residue 19 VAL Chi-restraints excluded: chain w residue 27 VAL Chi-restraints excluded: chain w residue 34 VAL Chi-restraints excluded: chain w residue 63 VAL Chi-restraints excluded: chain x residue 12 VAL Chi-restraints excluded: chain x residue 13 THR Chi-restraints excluded: chain x residue 22 ASN Chi-restraints excluded: chain x residue 67 LEU Chi-restraints excluded: chain x residue 77 TYR Chi-restraints excluded: chain y residue 6 LEU Chi-restraints excluded: chain y residue 7 ARG Chi-restraints excluded: chain y residue 46 VAL Chi-restraints excluded: chain y residue 49 ASP Chi-restraints excluded: chain z residue 26 LEU Chi-restraints excluded: chain z residue 33 HIS Chi-restraints excluded: chain z residue 40 THR Chi-restraints excluded: chain z residue 51 SER Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain D residue 3 ARG Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 43 LEU Chi-restraints excluded: chain E residue 48 MET Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 33 HIS Chi-restraints excluded: chain G residue 5 MET Chi-restraints excluded: chain G residue 15 PHE Chi-restraints excluded: chain G residue 38 HIS Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 128 LEU Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain G residue 166 ASP Chi-restraints excluded: chain G residue 183 PHE Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 190 SER Chi-restraints excluded: chain G residue 210 THR Chi-restraints excluded: chain H residue 4 VAL Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 182 ASP Chi-restraints excluded: chain H residue 194 VAL Chi-restraints excluded: chain I residue 64 TYR Chi-restraints excluded: chain I residue 99 ASN Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 141 VAL Chi-restraints excluded: chain I residue 171 GLU Chi-restraints excluded: chain J residue 15 ILE Chi-restraints excluded: chain J residue 19 ARG Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 82 HIS Chi-restraints excluded: chain J residue 121 ASN Chi-restraints excluded: chain K residue 8 PHE Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 78 PHE Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain L residue 6 ILE Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 47 GLU Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain L residue 147 ASN Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain M residue 48 PHE Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain M residue 79 ARG Chi-restraints excluded: chain M residue 90 GLU Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain M residue 128 VAL Chi-restraints excluded: chain N residue 10 ARG Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 24 ASN Chi-restraints excluded: chain N residue 74 GLN Chi-restraints excluded: chain N residue 125 GLN Chi-restraints excluded: chain O residue 15 HIS Chi-restraints excluded: chain O residue 69 THR Chi-restraints excluded: chain P residue 15 VAL Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain P residue 35 ASP Chi-restraints excluded: chain P residue 85 VAL Chi-restraints excluded: chain Q residue 4 ASN Chi-restraints excluded: chain Q residue 28 GLN Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 71 HIS Chi-restraints excluded: chain Q residue 86 VAL Chi-restraints excluded: chain Q residue 87 LYS Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain R residue 53 ASP Chi-restraints excluded: chain R residue 67 ASP Chi-restraints excluded: chain S residue 23 ARG Chi-restraints excluded: chain S residue 49 THR Chi-restraints excluded: chain T residue 17 ASP Chi-restraints excluded: chain T residue 30 LEU Chi-restraints excluded: chain T residue 56 LEU Chi-restraints excluded: chain T residue 68 TYR Chi-restraints excluded: chain T residue 78 THR Chi-restraints excluded: chain U residue 69 ASP Chi-restraints excluded: chain U residue 77 GLU Chi-restraints excluded: chain V residue 11 VAL Chi-restraints excluded: chain V residue 18 LYS Chi-restraints excluded: chain V residue 28 VAL Chi-restraints excluded: chain V residue 29 LYS Chi-restraints excluded: chain V residue 46 HIS Chi-restraints excluded: chain V residue 79 GLU Chi-restraints excluded: chain W residue 22 TYR Chi-restraints excluded: chain W residue 30 ASN Chi-restraints excluded: chain W residue 64 LEU Chi-restraints excluded: chain W residue 67 LEU Chi-restraints excluded: chain X residue 15 LEU Chi-restraints excluded: chain X residue 39 ILE Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain X residue 59 VAL Chi-restraints excluded: chain X residue 70 LEU Chi-restraints excluded: chain X residue 72 GLU Chi-restraints excluded: chain X residue 76 THR Chi-restraints excluded: chain Y residue 19 HIS Chi-restraints excluded: chain Y residue 70 LYS Chi-restraints excluded: chain Z residue 12 ASP Chi-restraints excluded: chain Z residue 37 TYR Chi-restraints excluded: chain Z residue 52 VAL Chi-restraints excluded: chain a residue 5 THR Chi-restraints excluded: chain a residue 18 THR Chi-restraints excluded: chain a residue 53 ARG Chi-restraints excluded: chain a residue 172 HIS Chi-restraints excluded: chain 8 residue 56 LEU Chi-restraints excluded: chain 8 residue 64 ILE Chi-restraints excluded: chain 8 residue 100 THR Chi-restraints excluded: chain 8 residue 105 ARG Chi-restraints excluded: chain 9 residue 18 THR Chi-restraints excluded: chain 9 residue 20 ILE Chi-restraints excluded: chain 9 residue 35 THR Chi-restraints excluded: chain 9 residue 52 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1065 random chunks: chunk 628 optimal weight: 30.0000 chunk 1011 optimal weight: 10.0000 chunk 617 optimal weight: 20.0000 chunk 479 optimal weight: 7.9990 chunk 703 optimal weight: 40.0000 chunk 1061 optimal weight: 20.0000 chunk 976 optimal weight: 10.0000 chunk 844 optimal weight: 20.0000 chunk 87 optimal weight: 8.9990 chunk 652 optimal weight: 20.0000 chunk 518 optimal weight: 10.0000 overall best weight: 9.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 19 ASN f 114 HIS h 9 GLN ** i 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 9 ASN ** l 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 19 GLN ** r 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 15 GLN ** x 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 36 GLN ** F 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 HIS ** G 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 28 GLN ** Q 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 172 HIS ** 8 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.6773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 161229 Z= 0.386 Angle : 0.818 14.104 240720 Z= 0.412 Chirality : 0.043 0.356 30724 Planarity : 0.006 0.099 13231 Dihedral : 24.338 179.244 79535 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 36.13 Ramachandran Plot: Outliers : 0.13 % Allowed : 13.29 % Favored : 86.58 % Rotamer: Outliers : 6.56 % Allowed : 29.16 % Favored : 64.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % 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: -3.34 (0.10), residues: 6142 helix: -1.54 (0.11), residues: 1774 sheet: -2.02 (0.16), residues: 870 loop : -2.73 (0.10), residues: 3498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.004 TRP m 64 HIS 0.031 0.002 HIS a 172 PHE 0.056 0.003 PHE M 44 TYR 0.029 0.003 TYR g 25 ARG 0.013 0.001 ARG o 10 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12284 Ramachandran restraints generated. 6142 Oldfield, 0 Emsley, 6142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12284 Ramachandran restraints generated. 6142 Oldfield, 0 Emsley, 6142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1496 residues out of total 5093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 334 poor density : 1162 time to evaluate : 6.337 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: c 28 GLU cc_start: 0.8926 (tm-30) cc_final: 0.8572 (tp30) REVERT: c 36 GLN cc_start: 0.8362 (tt0) cc_final: 0.8107 (tp-100) REVERT: c 64 GLU cc_start: 0.8854 (mm-30) cc_final: 0.8535 (mm-30) REVERT: c 148 GLN cc_start: 0.8973 (mp10) cc_final: 0.8485 (mp10) REVERT: d 1 MET cc_start: 0.8343 (OUTLIER) cc_final: 0.7681 (mpp) REVERT: d 9 GLN cc_start: 0.8731 (tm-30) cc_final: 0.8436 (tm-30) REVERT: d 188 MET cc_start: 0.8972 (mmt) cc_final: 0.8494 (mmp) REVERT: e 6 TYR cc_start: 0.9304 (t80) cc_final: 0.8462 (t80) REVERT: e 33 ILE cc_start: 0.9272 (tp) cc_final: 0.9052 (tp) REVERT: e 80 GLN cc_start: 0.8459 (OUTLIER) cc_final: 0.8100 (tp40) REVERT: e 94 ARG cc_start: 0.7964 (OUTLIER) cc_final: 0.7582 (ptt90) REVERT: e 97 GLU cc_start: 0.8388 (tp30) cc_final: 0.7880 (tp30) REVERT: e 100 GLU cc_start: 0.8127 (tm-30) cc_final: 0.7842 (tm-30) REVERT: e 109 ARG cc_start: 0.8856 (tpp-160) cc_final: 0.8282 (tpp-160) REVERT: e 113 PHE cc_start: 0.8292 (p90) cc_final: 0.7584 (p90) REVERT: e 166 ARG cc_start: 0.9044 (OUTLIER) cc_final: 0.8740 (tmm-80) REVERT: e 177 ARG cc_start: 0.7598 (ttt180) cc_final: 0.7211 (tpt170) REVERT: f 82 PHE cc_start: 0.7591 (m-10) cc_final: 0.7211 (m-10) REVERT: f 98 LYS cc_start: 0.8430 (mttp) cc_final: 0.8180 (tptp) REVERT: f 137 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.8274 (mmtt) REVERT: h 52 MET cc_start: 0.7733 (tpp) cc_final: 0.6554 (mmm) REVERT: h 116 GLU cc_start: 0.8879 (mm-30) cc_final: 0.8447 (mm-30) REVERT: i 41 PHE cc_start: 0.8785 (t80) cc_final: 0.8286 (t80) REVERT: i 116 MET cc_start: -0.1705 (tpt) cc_final: -0.2529 (tpt) REVERT: j 7 LYS cc_start: 0.8877 (OUTLIER) cc_final: 0.8163 (mtmm) REVERT: j 49 ASP cc_start: 0.8374 (OUTLIER) cc_final: 0.7884 (t70) REVERT: j 54 ILE cc_start: 0.9312 (mm) cc_final: 0.9062 (mm) REVERT: j 68 LYS cc_start: 0.8543 (mtpt) cc_final: 0.8219 (mtpt) REVERT: j 118 MET cc_start: 0.9207 (mmt) cc_final: 0.8872 (mmt) REVERT: j 119 PHE cc_start: 0.9171 (t80) cc_final: 0.8862 (t80) REVERT: k 66 LYS cc_start: 0.8435 (tttt) cc_final: 0.7832 (tttt) REVERT: k 112 PHE cc_start: 0.8495 (m-80) cc_final: 0.7973 (m-10) REVERT: l 39 LYS cc_start: 0.8938 (pttt) cc_final: 0.8526 (pttt) REVERT: l 82 LEU cc_start: 0.9641 (mt) cc_final: 0.9331 (mt) REVERT: l 128 THR cc_start: 0.9186 (OUTLIER) cc_final: 0.8810 (t) REVERT: m 127 LYS cc_start: 0.8501 (mmtt) cc_final: 0.8218 (mmtt) REVERT: o 20 GLU cc_start: 0.8971 (tp30) cc_final: 0.8724 (tp30) REVERT: o 104 GLN cc_start: 0.9625 (tt0) cc_final: 0.9317 (tt0) REVERT: p 37 LYS cc_start: 0.8398 (mttm) cc_final: 0.8108 (mptt) REVERT: p 50 ARG cc_start: 0.8522 (ttt-90) cc_final: 0.7983 (ttt-90) REVERT: p 67 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7468 (pt0) REVERT: p 74 GLN cc_start: 0.8523 (mp10) cc_final: 0.7805 (mp10) REVERT: p 93 LYS cc_start: 0.8736 (tppt) cc_final: 0.8417 (tppt) REVERT: q 21 LYS cc_start: 0.8727 (mmtt) cc_final: 0.8388 (ttmm) REVERT: q 24 TYR cc_start: 0.7632 (t80) cc_final: 0.7248 (t80) REVERT: q 35 PHE cc_start: 0.8910 (t80) cc_final: 0.8633 (t80) REVERT: q 54 ARG cc_start: 0.8965 (mtm180) cc_final: 0.8446 (mtm-85) REVERT: q 106 THR cc_start: 0.9366 (p) cc_final: 0.9114 (p) REVERT: q 110 GLU cc_start: 0.8999 (mm-30) cc_final: 0.8363 (mm-30) REVERT: r 46 GLU cc_start: 0.8740 (mp0) cc_final: 0.8292 (mp0) REVERT: r 85 LYS cc_start: 0.8817 (ttmt) cc_final: 0.8544 (ttmt) REVERT: s 25 ARG cc_start: 0.8566 (OUTLIER) cc_final: 0.7771 (mtm180) REVERT: s 38 TYR cc_start: 0.8864 (m-80) cc_final: 0.8472 (m-80) REVERT: s 82 MET cc_start: 0.8245 (pmm) cc_final: 0.7892 (pmm) REVERT: t 18 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7767 (pp20) REVERT: t 74 ILE cc_start: 0.6615 (OUTLIER) cc_final: 0.6204 (mm) REVERT: v 50 MET cc_start: 0.8560 (mmt) cc_final: 0.8065 (tpp) REVERT: v 61 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8110 (mm) REVERT: x 16 ASN cc_start: 0.9118 (t0) cc_final: 0.8845 (m-40) REVERT: y 6 LEU cc_start: 0.7544 (OUTLIER) cc_final: 0.7269 (tt) REVERT: y 45 GLN cc_start: 0.8908 (pt0) cc_final: 0.8324 (pp30) REVERT: z 18 LYS cc_start: 0.8365 (mmtt) cc_final: 0.8070 (mmtt) REVERT: z 29 ARG cc_start: 0.8448 (mmt90) cc_final: 0.8042 (mmt180) REVERT: z 46 MET cc_start: 0.8292 (mtt) cc_final: 0.7697 (mtp) REVERT: B 27 LEU cc_start: 0.9028 (tp) cc_final: 0.8004 (tt) REVERT: B 36 LYS cc_start: 0.9449 (mmtp) cc_final: 0.9122 (mmmm) REVERT: C 48 TYR cc_start: 0.6904 (m-80) cc_final: 0.5894 (m-80) REVERT: D 35 ARG cc_start: 0.8930 (mtt-85) cc_final: 0.8463 (mtt-85) REVERT: E 48 MET cc_start: 0.8367 (OUTLIER) cc_final: 0.7951 (mpp) REVERT: F 1 MET cc_start: 0.7146 (OUTLIER) cc_final: 0.6919 (tmm) REVERT: F 8 LYS cc_start: 0.8720 (pttt) cc_final: 0.8310 (pttp) REVERT: F 15 LYS cc_start: 0.7663 (mmtp) cc_final: 0.7345 (mmtt) REVERT: G 26 MET cc_start: 0.7677 (tmm) cc_final: 0.6586 (tmm) REVERT: G 29 PHE cc_start: 0.7429 (m-80) cc_final: 0.6787 (m-10) REVERT: G 48 MET cc_start: 0.9341 (mmp) cc_final: 0.8942 (mtm) REVERT: G 95 TRP cc_start: 0.8207 (t-100) cc_final: 0.7817 (t-100) REVERT: G 153 MET cc_start: 0.6143 (mmm) cc_final: 0.5841 (mmm) REVERT: G 166 ASP cc_start: 0.8837 (OUTLIER) cc_final: 0.8506 (m-30) REVERT: G 167 HIS cc_start: 0.8579 (OUTLIER) cc_final: 0.8139 (t-170) REVERT: G 183 PHE cc_start: 0.7233 (OUTLIER) cc_final: 0.6860 (m-80) REVERT: G 197 PHE cc_start: 0.7841 (m-80) cc_final: 0.7271 (m-80) REVERT: I 88 ASN cc_start: 0.8792 (m110) cc_final: 0.8361 (m-40) REVERT: I 123 MET cc_start: 0.7298 (mmm) cc_final: 0.6906 (mmm) REVERT: I 151 GLN cc_start: 0.8851 (mm110) cc_final: 0.8476 (mm110) REVERT: I 169 TRP cc_start: 0.8884 (p90) cc_final: 0.8580 (p90) REVERT: I 171 GLU cc_start: 0.5687 (OUTLIER) cc_final: 0.5382 (mp0) REVERT: I 184 LYS cc_start: 0.9288 (tptt) cc_final: 0.8997 (tptt) REVERT: I 187 ARG cc_start: 0.9053 (tpt90) cc_final: 0.8778 (tpt-90) REVERT: I 201 GLU cc_start: 0.8936 (mm-30) cc_final: 0.8046 (mm-30) REVERT: J 151 MET cc_start: 0.8428 (ptp) cc_final: 0.8109 (pmm) REVERT: K 90 MET cc_start: 0.2937 (mmt) cc_final: 0.2191 (mmt) REVERT: L 77 ARG cc_start: 0.7124 (tpt90) cc_final: 0.6666 (tpt-90) REVERT: M 12 ARG cc_start: 0.7940 (OUTLIER) cc_final: 0.7524 (mtt90) REVERT: M 41 GLU cc_start: 0.8719 (mm-30) cc_final: 0.8477 (mm-30) REVERT: M 75 GLN cc_start: 0.8673 (mm-40) cc_final: 0.7906 (mp10) REVERT: M 79 ARG cc_start: 0.9159 (OUTLIER) cc_final: 0.8483 (ptt90) REVERT: M 86 LYS cc_start: 0.8515 (mmmt) cc_final: 0.8159 (mmmt) REVERT: N 20 ILE cc_start: 0.6659 (OUTLIER) cc_final: 0.6243 (mm) REVERT: O 15 HIS cc_start: 0.2405 (OUTLIER) cc_final: 0.1817 (p90) REVERT: Q 87 LYS cc_start: 0.8461 (OUTLIER) cc_final: 0.7252 (tptm) REVERT: R 2 ARG cc_start: 0.6499 (tpp-160) cc_final: 0.5998 (mmm160) REVERT: R 70 ARG cc_start: 0.7628 (mtm180) cc_final: 0.6955 (tmt-80) REVERT: S 37 ASP cc_start: 0.8103 (p0) cc_final: 0.7858 (p0) REVERT: T 9 LYS cc_start: 0.9354 (pttp) cc_final: 0.9067 (ptpp) REVERT: T 46 LYS cc_start: 0.8065 (pttt) cc_final: 0.7811 (pttt) REVERT: T 57 ARG cc_start: 0.8119 (ttt-90) cc_final: 0.6909 (tpm170) REVERT: T 58 MET cc_start: 0.8914 (mtm) cc_final: 0.8161 (mmt) REVERT: T 71 ARG cc_start: 0.8876 (tmt170) cc_final: 0.8353 (ttt-90) REVERT: U 5 ARG cc_start: 0.7626 (ptp90) cc_final: 0.6936 (ttp80) REVERT: V 79 GLU cc_start: 0.7521 (OUTLIER) cc_final: 0.6961 (mp0) REVERT: W 34 GLU cc_start: 0.7094 (tp30) cc_final: 0.6890 (tp30) REVERT: W 58 ILE cc_start: 0.6531 (mt) cc_final: 0.6246 (mt) REVERT: Y 52 GLU cc_start: 0.7711 (mp0) cc_final: 0.7371 (mp0) REVERT: Y 53 MET cc_start: 0.9070 (ppp) cc_final: 0.8747 (ppp) REVERT: Z 37 TYR cc_start: 0.3889 (OUTLIER) cc_final: 0.2922 (t80) REVERT: a 53 ARG cc_start: -0.0862 (OUTLIER) cc_final: -0.2391 (mmp-170) REVERT: 8 41 PHE cc_start: 0.8635 (t80) cc_final: 0.8385 (t80) REVERT: 8 64 ILE cc_start: 0.6541 (OUTLIER) cc_final: 0.6302 (mp) REVERT: 8 105 ARG cc_start: 0.7745 (OUTLIER) cc_final: 0.7507 (ttp-170) REVERT: 8 131 MET cc_start: 0.2832 (mmt) cc_final: 0.1522 (ppp) REVERT: 9 18 THR cc_start: 0.6298 (OUTLIER) cc_final: 0.5919 (p) REVERT: 9 73 LYS cc_start: 0.6285 (ttpt) cc_final: 0.5777 (ttmm) outliers start: 334 outliers final: 277 residues processed: 1356 average time/residue: 1.2983 time to fit residues: 3034.4517 Evaluate side-chains 1443 residues out of total 5093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 308 poor density : 1135 time to evaluate : 6.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 2 VAL Chi-restraints excluded: chain b residue 8 THR Chi-restraints excluded: chain b residue 32 LEU Chi-restraints excluded: chain b residue 33 LEU Chi-restraints excluded: chain b residue 36 ASN Chi-restraints excluded: chain b residue 37 SER Chi-restraints excluded: chain b residue 85 ASN Chi-restraints excluded: chain b residue 104 LEU Chi-restraints excluded: chain b residue 113 ASP Chi-restraints excluded: chain b residue 115 ILE Chi-restraints excluded: chain b residue 128 THR Chi-restraints excluded: chain b residue 133 ASN Chi-restraints excluded: chain b residue 219 VAL Chi-restraints excluded: chain b residue 222 THR Chi-restraints excluded: chain b residue 249 VAL Chi-restraints excluded: chain c residue 35 THR Chi-restraints excluded: chain c residue 40 LEU Chi-restraints excluded: chain c residue 73 VAL Chi-restraints excluded: chain c residue 108 ASP Chi-restraints excluded: chain c residue 121 THR Chi-restraints excluded: chain c residue 142 VAL Chi-restraints excluded: chain c residue 160 LYS Chi-restraints excluded: chain c residue 168 GLU Chi-restraints excluded: chain c residue 170 VAL Chi-restraints excluded: chain c residue 171 THR Chi-restraints excluded: chain c residue 180 VAL Chi-restraints excluded: chain c residue 201 LEU Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 4 VAL Chi-restraints excluded: chain d residue 7 ASP Chi-restraints excluded: chain d residue 48 THR Chi-restraints excluded: chain d residue 52 VAL Chi-restraints excluded: chain d residue 65 THR Chi-restraints excluded: chain d residue 80 SER Chi-restraints excluded: chain d residue 90 GLN Chi-restraints excluded: chain d residue 96 VAL Chi-restraints excluded: chain d residue 169 VAL Chi-restraints excluded: chain d residue 193 VAL Chi-restraints excluded: chain e residue 4 HIS Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 27 VAL Chi-restraints excluded: chain e residue 43 ILE Chi-restraints excluded: chain e residue 50 ASP Chi-restraints excluded: chain e residue 78 ILE Chi-restraints excluded: chain e residue 80 GLN Chi-restraints excluded: chain e residue 94 ARG Chi-restraints excluded: chain e residue 107 VAL Chi-restraints excluded: chain e residue 112 ASP Chi-restraints excluded: chain e residue 148 VAL Chi-restraints excluded: chain e residue 157 THR Chi-restraints excluded: chain e residue 166 ARG Chi-restraints excluded: chain e residue 168 LEU Chi-restraints excluded: chain f residue 9 VAL Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 18 ILE Chi-restraints excluded: chain f residue 29 ASN Chi-restraints excluded: chain f residue 57 TYR Chi-restraints excluded: chain f residue 88 LEU Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 102 ILE Chi-restraints excluded: chain f residue 104 LEU Chi-restraints excluded: chain f residue 136 ASP Chi-restraints excluded: chain f residue 137 LYS Chi-restraints excluded: chain g residue 37 VAL Chi-restraints excluded: chain g residue 134 VAL Chi-restraints excluded: chain h residue 9 GLN Chi-restraints excluded: chain i residue 115 ASP Chi-restraints excluded: chain j residue 3 THR Chi-restraints excluded: chain j residue 7 LYS Chi-restraints excluded: chain j residue 11 VAL Chi-restraints excluded: chain j residue 44 TYR Chi-restraints excluded: chain j residue 49 ASP Chi-restraints excluded: chain j residue 57 LEU Chi-restraints excluded: chain j residue 73 VAL Chi-restraints excluded: chain j residue 100 VAL Chi-restraints excluded: chain k residue 22 ILE Chi-restraints excluded: chain k residue 24 VAL Chi-restraints excluded: chain k residue 62 VAL Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 77 ILE Chi-restraints excluded: chain k residue 103 VAL Chi-restraints excluded: chain k residue 104 THR Chi-restraints excluded: chain k residue 110 GLU Chi-restraints excluded: chain l residue 55 MET Chi-restraints excluded: chain l residue 63 LYS Chi-restraints excluded: chain l residue 67 THR Chi-restraints excluded: chain l residue 74 THR Chi-restraints excluded: chain l residue 94 THR Chi-restraints excluded: chain l residue 107 PHE Chi-restraints excluded: chain l residue 128 THR Chi-restraints excluded: chain m residue 20 LEU Chi-restraints excluded: chain m residue 33 LEU Chi-restraints excluded: chain m residue 42 THR Chi-restraints excluded: chain m residue 54 THR Chi-restraints excluded: chain m residue 115 GLU Chi-restraints excluded: chain m residue 124 LEU Chi-restraints excluded: chain m residue 128 THR Chi-restraints excluded: chain m residue 132 THR Chi-restraints excluded: chain m residue 135 VAL Chi-restraints excluded: chain n residue 15 SER Chi-restraints excluded: chain n residue 18 GLN Chi-restraints excluded: chain n residue 54 LEU Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain n residue 97 ILE Chi-restraints excluded: chain o residue 34 HIS Chi-restraints excluded: chain o residue 35 ILE Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain o residue 49 VAL Chi-restraints excluded: chain o residue 53 THR Chi-restraints excluded: chain o residue 83 LEU Chi-restraints excluded: chain o residue 90 VAL Chi-restraints excluded: chain o residue 93 ASP Chi-restraints excluded: chain p residue 23 ASP Chi-restraints excluded: chain p residue 43 GLU Chi-restraints excluded: chain p residue 59 THR Chi-restraints excluded: chain p residue 60 VAL Chi-restraints excluded: chain p residue 67 GLU Chi-restraints excluded: chain p residue 75 THR Chi-restraints excluded: chain p residue 80 VAL Chi-restraints excluded: chain q residue 33 VAL Chi-restraints excluded: chain q residue 59 LEU Chi-restraints excluded: chain q residue 61 ILE Chi-restraints excluded: chain q residue 93 ILE Chi-restraints excluded: chain r residue 4 VAL Chi-restraints excluded: chain r residue 10 LYS Chi-restraints excluded: chain r residue 15 SER Chi-restraints excluded: chain r residue 19 THR Chi-restraints excluded: chain r residue 26 ASP Chi-restraints excluded: chain r residue 38 VAL Chi-restraints excluded: chain r residue 49 ILE Chi-restraints excluded: chain r residue 58 VAL Chi-restraints excluded: chain r residue 75 VAL Chi-restraints excluded: chain s residue 20 VAL Chi-restraints excluded: chain s residue 25 ARG Chi-restraints excluded: chain s residue 52 GLU Chi-restraints excluded: chain s residue 53 SER Chi-restraints excluded: chain s residue 66 ILE Chi-restraints excluded: chain s residue 70 LYS Chi-restraints excluded: chain s residue 76 VAL Chi-restraints excluded: chain s residue 92 ARG Chi-restraints excluded: chain s residue 96 ILE Chi-restraints excluded: chain s residue 100 THR Chi-restraints excluded: chain t residue 11 LEU Chi-restraints excluded: chain t residue 16 VAL Chi-restraints excluded: chain t residue 18 GLU Chi-restraints excluded: chain t residue 74 ILE Chi-restraints excluded: chain t residue 86 THR Chi-restraints excluded: chain u residue 8 ASP Chi-restraints excluded: chain u residue 10 VAL Chi-restraints excluded: chain u residue 11 ILE Chi-restraints excluded: chain u residue 26 ASN Chi-restraints excluded: chain u residue 35 VAL Chi-restraints excluded: chain u residue 81 ARG Chi-restraints excluded: chain v residue 8 VAL Chi-restraints excluded: chain v residue 45 ASP Chi-restraints excluded: chain v residue 56 PHE Chi-restraints excluded: chain v residue 61 LEU Chi-restraints excluded: chain v residue 63 ILE Chi-restraints excluded: chain v residue 64 VAL Chi-restraints excluded: chain v residue 66 ASP Chi-restraints excluded: chain v residue 77 VAL Chi-restraints excluded: chain v residue 90 ASP Chi-restraints excluded: chain w residue 19 VAL Chi-restraints excluded: chain w residue 27 VAL Chi-restraints excluded: chain w residue 34 VAL Chi-restraints excluded: chain w residue 63 VAL Chi-restraints excluded: chain x residue 12 VAL Chi-restraints excluded: chain x residue 13 THR Chi-restraints excluded: chain x residue 22 ASN Chi-restraints excluded: chain x residue 67 LEU Chi-restraints excluded: chain x residue 77 TYR Chi-restraints excluded: chain y residue 6 LEU Chi-restraints excluded: chain y residue 7 ARG Chi-restraints excluded: chain y residue 49 ASP Chi-restraints excluded: chain z residue 13 ILE Chi-restraints excluded: chain z residue 26 LEU Chi-restraints excluded: chain z residue 33 HIS Chi-restraints excluded: chain z residue 40 THR Chi-restraints excluded: chain z residue 51 SER Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain D residue 3 ARG Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 43 LEU Chi-restraints excluded: chain E residue 48 MET Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 13 ASN Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 33 HIS Chi-restraints excluded: chain G residue 5 MET Chi-restraints excluded: chain G residue 15 PHE Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 128 LEU Chi-restraints excluded: chain G residue 166 ASP Chi-restraints excluded: chain G residue 167 HIS Chi-restraints excluded: chain G residue 183 PHE Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 190 SER Chi-restraints excluded: chain G residue 210 THR Chi-restraints excluded: chain H residue 4 VAL Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 182 ASP Chi-restraints excluded: chain H residue 194 VAL Chi-restraints excluded: chain I residue 64 TYR Chi-restraints excluded: chain I residue 99 ASN Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 141 VAL Chi-restraints excluded: chain I residue 171 GLU Chi-restraints excluded: chain J residue 15 ILE Chi-restraints excluded: chain J residue 19 ARG Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 82 HIS Chi-restraints excluded: chain J residue 121 ASN Chi-restraints excluded: chain K residue 8 PHE Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 76 THR Chi-restraints excluded: chain K residue 78 PHE Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain L residue 6 ILE Chi-restraints excluded: chain L residue 47 GLU Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain L residue 147 ASN Chi-restraints excluded: chain M residue 12 ARG Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain M residue 79 ARG Chi-restraints excluded: chain M residue 90 GLU Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain M residue 128 VAL Chi-restraints excluded: chain N residue 10 ARG Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 24 ASN Chi-restraints excluded: chain N residue 74 GLN Chi-restraints excluded: chain O residue 15 HIS Chi-restraints excluded: chain O residue 69 THR Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain P residue 35 ASP Chi-restraints excluded: chain P residue 85 VAL Chi-restraints excluded: chain P residue 118 ASN Chi-restraints excluded: chain Q residue 4 ASN Chi-restraints excluded: chain Q residue 28 GLN Chi-restraints excluded: chain Q residue 37 TYR Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 71 HIS Chi-restraints excluded: chain Q residue 86 VAL Chi-restraints excluded: chain Q residue 87 LYS Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain R residue 53 ASP Chi-restraints excluded: chain R residue 67 ASP Chi-restraints excluded: chain S residue 23 ARG Chi-restraints excluded: chain S residue 49 THR Chi-restraints excluded: chain T residue 17 ASP Chi-restraints excluded: chain T residue 30 LEU Chi-restraints excluded: chain T residue 56 LEU Chi-restraints excluded: chain T residue 68 TYR Chi-restraints excluded: chain T residue 78 THR Chi-restraints excluded: chain U residue 69 ASP Chi-restraints excluded: chain U residue 77 GLU Chi-restraints excluded: chain U residue 78 VAL Chi-restraints excluded: chain V residue 11 VAL Chi-restraints excluded: chain V residue 18 LYS Chi-restraints excluded: chain V residue 28 VAL Chi-restraints excluded: chain V residue 29 LYS Chi-restraints excluded: chain V residue 46 HIS Chi-restraints excluded: chain V residue 79 GLU Chi-restraints excluded: chain W residue 22 TYR Chi-restraints excluded: chain W residue 30 ASN Chi-restraints excluded: chain W residue 64 LEU Chi-restraints excluded: chain W residue 67 LEU Chi-restraints excluded: chain X residue 15 LEU Chi-restraints excluded: chain X residue 39 ILE Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain X residue 59 VAL Chi-restraints excluded: chain X residue 70 LEU Chi-restraints excluded: chain X residue 76 THR Chi-restraints excluded: chain Y residue 19 HIS Chi-restraints excluded: chain Y residue 70 LYS Chi-restraints excluded: chain Z residue 5 VAL Chi-restraints excluded: chain Z residue 12 ASP Chi-restraints excluded: chain Z residue 37 TYR Chi-restraints excluded: chain Z residue 52 VAL Chi-restraints excluded: chain a residue 5 THR Chi-restraints excluded: chain a residue 8 MET Chi-restraints excluded: chain a residue 53 ARG Chi-restraints excluded: chain 8 residue 56 LEU Chi-restraints excluded: chain 8 residue 64 ILE Chi-restraints excluded: chain 8 residue 100 THR Chi-restraints excluded: chain 8 residue 105 ARG Chi-restraints excluded: chain 9 residue 18 THR Chi-restraints excluded: chain 9 residue 20 ILE Chi-restraints excluded: chain 9 residue 35 THR Chi-restraints excluded: chain 9 residue 52 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1065 random chunks: chunk 671 optimal weight: 10.0000 chunk 900 optimal weight: 10.0000 chunk 258 optimal weight: 10.0000 chunk 779 optimal weight: 10.0000 chunk 124 optimal weight: 5.9990 chunk 234 optimal weight: 9.9990 chunk 846 optimal weight: 10.0000 chunk 354 optimal weight: 6.9990 chunk 868 optimal weight: 10.0000 chunk 107 optimal weight: 7.9990 chunk 155 optimal weight: 2.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 80 GLN ** g 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 19 GLN ** r 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 36 GLN ** F 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 28 GLN ** Q 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 50 HIS ** W 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 47 GLN ** Y 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.109775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.085972 restraints weight = 619237.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.088203 restraints weight = 209478.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.089212 restraints weight = 103485.604| |-----------------------------------------------------------------------------| r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.6795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 161229 Z= 0.294 Angle : 0.733 14.703 240720 Z= 0.371 Chirality : 0.040 0.349 30724 Planarity : 0.005 0.087 13231 Dihedral : 24.266 179.686 79535 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 30.77 Ramachandran Plot: Outliers : 0.11 % Allowed : 12.60 % Favored : 87.28 % Rotamer: Outliers : 6.30 % Allowed : 29.77 % Favored : 63.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.22 (0.10), residues: 6142 helix: -1.42 (0.12), residues: 1779 sheet: -1.94 (0.16), residues: 895 loop : -2.67 (0.10), residues: 3468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.003 TRP m 64 HIS 0.014 0.002 HIS N 80 PHE 0.037 0.002 PHE M 44 TYR 0.031 0.002 TYR p 98 ARG 0.012 0.001 ARG i 102 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 44757.35 seconds wall clock time: 781 minutes 52.48 seconds (46912.48 seconds total)