Starting phenix.real_space_refine on Thu Mar 21 21:00:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jss_22459/03_2024/7jss_22459.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jss_22459/03_2024/7jss_22459.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/7jss_22459/03_2024/7jss_22459.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jss_22459/03_2024/7jss_22459.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jss_22459/03_2024/7jss_22459.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jss_22459/03_2024/7jss_22459.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= 0.013 sd= 1.099 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 4651 5.49 5 S 142 5.16 5 C 72716 2.51 5 N 27034 2.21 5 O 40347 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "b GLU 22": "OE1" <-> "OE2" Residue "b ASP 71": "OD1" <-> "OD2" Residue "b ASP 97": "OD1" <-> "OD2" Residue "b ASP 167": "OD1" <-> "OD2" Residue "b TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 13": "NH1" <-> "NH2" Residue "c PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 33": "NH1" <-> "NH2" Residue "c ARG 59": "NH1" <-> "NH2" Residue "c GLU 64": "OE1" <-> "OE2" Residue "c ARG 77": "NH1" <-> "NH2" Residue "c GLU 81": "OE1" <-> "OE2" Residue "c ARG 83": "NH1" <-> "NH2" Residue "c GLU 99": "OE1" <-> "OE2" Residue "c ASP 108": "OD1" <-> "OD2" Residue "c ARG 169": "NH1" <-> "NH2" Residue "c ARG 184": "NH1" <-> "NH2" Residue "d GLU 2": "OE1" <-> "OE2" 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 ARG 162": "NH1" <-> "NH2" Residue "d ARG 170": "NH1" <-> "NH2" Residue "d ASP 191": "OD1" <-> "OD2" Residue "d GLU 197": "OE1" <-> "OE2" Residue "d GLU 198": "OE1" <-> "OE2" Residue "e GLU 10": "OE1" <-> "OE2" Residue "e TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ASP 50": "OD1" <-> "OD2" Residue "e ASP 55": "OD1" <-> "OD2" Residue "e ARG 70": "NH1" <-> "NH2" Residue "e ARG 79": "NH1" <-> "NH2" Residue "e ARG 91": "NH1" <-> "NH2" Residue "e ARG 101": "NH1" <-> "NH2" Residue "e ARG 109": "NH1" <-> "NH2" Residue "e ARG 111": "NH1" <-> "NH2" Residue "e ARG 114": "NH1" <-> "NH2" Residue "e ASP 122": "OD1" <-> "OD2" Residue "e ARG 132": "NH1" <-> "NH2" Residue "e GLU 139": "OE1" <-> "OE2" Residue "e ASP 143": "OD1" <-> "OD2" Residue "e ASP 162": "OD1" <-> "OD2" Residue "f ARG 2": "NH1" <-> "NH2" Residue "f GLU 31": "OE1" <-> "OE2" Residue "f ASP 113": "OD1" <-> "OD2" Residue "f GLU 129": "OE1" <-> "OE2" Residue "f ARG 152": "NH1" <-> "NH2" Residue "f ARG 162": "NH1" <-> "NH2" Residue "f GLU 166": "OE1" <-> "OE2" Residue "f ARG 169": "NH1" <-> "NH2" Residue "f GLU 172": "OE1" <-> "OE2" Residue "g ASP 7": "OD1" <-> "OD2" Residue "g GLU 53": "OE1" <-> "OE2" Residue "g GLU 70": "OE1" <-> "OE2" Residue "g PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 114": "OE1" <-> "OE2" Residue "g PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ARG 13": "NH1" <-> "NH2" Residue "j ASP 14": "OD1" <-> "OD2" Residue "j GLU 31": "OE1" <-> "OE2" Residue "j ARG 37": "NH1" <-> "NH2" Residue "j ASP 49": "OD1" <-> "OD2" Residue "j GLU 91": "OE1" <-> "OE2" Residue "j ARG 96": "NH1" <-> "NH2" Residue "j GLU 102": "OE1" <-> "OE2" Residue "j ARG 120": "NH1" <-> "NH2" Residue "j ASP 141": "OD1" <-> "OD2" 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 GLU 51": "OE1" <-> "OE2" Residue "l ARG 60": "NH1" <-> "NH2" Residue "l ARG 78": "NH1" <-> "NH2" Residue "l ARG 126": "NH1" <-> "NH2" Residue "l GLU 136": "OE1" <-> "OE2" Residue "l GLU 143": "OE1" <-> "OE2" 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 GLU 111": "OE1" <-> "OE2" Residue "m ARG 114": "NH1" <-> "NH2" Residue "m PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ARG 8": "NH1" <-> "NH2" Residue "n ARG 12": "NH1" <-> "NH2" Residue "n ARG 17": "NH1" <-> "NH2" Residue "n ARG 22": "NH1" <-> "NH2" Residue "n ARG 46": "NH1" <-> "NH2" Residue "n ARG 63": "NH1" <-> "NH2" Residue "n ARG 64": "NH1" <-> "NH2" Residue "n ARG 69": "NH1" <-> "NH2" Residue "n ARG 71": "NH1" <-> "NH2" Residue "n ARG 96": "NH1" <-> "NH2" Residue "n ARG 118": "NH1" <-> "NH2" Residue "o ASP 2": "OD1" <-> "OD2" Residue "o ARG 10": "NH1" <-> "NH2" Residue "o ARG 16": "NH1" <-> "NH2" Residue "o ARG 25": "NH1" <-> "NH2" Residue "o GLU 60": "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 GLU 8": "OE1" <-> "OE2" Residue "p PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ARG 20": "NH1" <-> "NH2" Residue "p GLU 33": "OE1" <-> "OE2" Residue "p ARG 38": "NH1" <-> "NH2" Residue "p GLU 43": "OE1" <-> "OE2" Residue "p ARG 61": "NH1" <-> "NH2" Residue "p ARG 88": "NH1" <-> "NH2" Residue "p ARG 100": "NH1" <-> "NH2" Residue "p ARG 108": "NH1" <-> "NH2" Residue "q ARG 2": "NH1" <-> "NH2" Residue "q ARG 5": "NH1" <-> "NH2" Residue "q ARG 12": "NH1" <-> "NH2" Residue "q ARG 32": "NH1" <-> "NH2" Residue "q ARG 47": "NH1" <-> "NH2" Residue "q PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ARG 69": "NH1" <-> "NH2" Residue "q ASP 101": "OD1" <-> "OD2" Residue "r ARG 21": "NH1" <-> "NH2" Residue "r ARG 68": "NH1" <-> "NH2" Residue "r ARG 78": "NH1" <-> "NH2" Residue "r ARG 79": "NH1" <-> "NH2" Residue "r ARG 84": "NH1" <-> "NH2" Residue "s GLU 2": "OE1" <-> "OE2" Residue "s ASP 22": "OD1" <-> "OD2" Residue "s GLU 59": "OE1" <-> "OE2" Residue "s ASP 65": "OD1" <-> "OD2" Residue "s ARG 84": "NH1" <-> "NH2" Residue "s ARG 88": "NH1" <-> "NH2" Residue "s ARG 95": "NH1" <-> "NH2" Residue "s ARG 110": "NH1" <-> "NH2" Residue "t GLU 4": "OE1" <-> "OE2" Residue "t PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t GLU 56": "OE1" <-> "OE2" Residue "t ARG 73": "NH1" <-> "NH2" Residue "u ARG 5": "NH1" <-> "NH2" Residue "u ARG 6": "NH1" <-> "NH2" Residue "u ASP 7": "OD1" <-> "OD2" Residue "u GLU 9": "OE1" <-> "OE2" Residue "u GLU 59": "OE1" <-> "OE2" Residue "u ARG 81": "NH1" <-> "NH2" Residue "u ARG 85": "NH1" <-> "NH2" Residue "u PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ARG 93": "NH1" <-> "NH2" Residue "v TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y GLU 8": "OE1" <-> "OE2" Residue "y ARG 29": "NH1" <-> "NH2" Residue "y ARG 47": "NH1" <-> "NH2" Residue "y ARG 52": "NH1" <-> "NH2" Residue "z ARG 10": "NH1" <-> "NH2" Residue "z ARG 29": "NH1" <-> "NH2" Residue "z GLU 36": "OE1" <-> "OE2" Residue "z ARG 44": "NH1" <-> "NH2" Residue "B ARG 9": "NH1" <-> "NH2" Residue "B ARG 15": "NH1" <-> "NH2" Residue "B ARG 39": "NH1" <-> "NH2" Residue "B TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 51": "NH1" <-> "NH2" Residue "C GLU 6": "OE1" <-> "OE2" 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 TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 51": "OE1" <-> "OE2" Residue "G GLU 55": "OE1" <-> "OE2" Residue "G ASP 87": "OD1" <-> "OD2" Residue "G PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 164": "OD1" <-> "OD2" Residue "G ASP 166": "OD1" <-> "OD2" Residue "G ASP 187": "OD1" <-> "OD2" Residue "G ASP 204": "OD1" <-> "OD2" Residue "G ARG 224": "NH1" <-> "NH2" Residue "H ASP 35": "OD1" <-> "OD2" Residue "H GLU 104": "OE1" <-> "OE2" Residue "H ARG 106": "NH1" <-> "NH2" Residue "H ARG 130": "NH1" <-> "NH2" Residue "H GLU 169": "OE1" <-> "OE2" Residue "H ASP 182": "OD1" <-> "OD2" Residue "I ASP 17": "OD1" <-> "OD2" Residue "I GLU 77": "OE1" <-> "OE2" Residue "I GLU 87": "OE1" <-> "OE2" Residue "I ASP 140": "OD1" <-> "OD2" Residue "I GLU 159": "OE1" <-> "OE2" Residue "I ASP 173": "OD1" <-> "OD2" Residue "I GLU 196": "OE1" <-> "OE2" Residue "I GLU 201": "OE1" <-> "OE2" Residue "J GLU 54": "OE1" <-> "OE2" Residue "J GLU 115": "OE1" <-> "OE2" Residue "J ASP 141": "OD1" <-> "OD2" Residue "J ARG 156": "NH1" <-> "NH2" Residue "K GLU 65": "OE1" <-> "OE2" Residue "L GLU 39": "OE1" <-> "OE2" Residue "L GLU 47": "OE1" <-> "OE2" Residue "L ASP 125": "OD1" <-> "OD2" Residue "L ASP 139": "OD1" <-> "OD2" Residue "M ASP 4": "OD1" <-> "OD2" Residue "M PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 96": "OE1" <-> "OE2" Residue "N PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 123": "NH1" <-> "NH2" Residue "O ASP 19": "OD1" <-> "OD2" Residue "O GLU 24": "OE1" <-> "OE2" Residue "O GLU 27": "OE1" <-> "OE2" Residue "O GLU 66": "OE1" <-> "OE2" Residue "O ASP 91": "OD1" <-> "OD2" Residue "Q ARG 55": "NH1" <-> "NH2" Residue "Q PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 10": "OD1" <-> "OD2" Residue "R GLU 40": "OE1" <-> "OE2" Residue "R ASP 57": "OD1" <-> "OD2" Residue "R ASP 81": "OD1" <-> "OD2" Residue "S ASP 17": "OD1" <-> "OD2" Residue "S PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 85": "OE1" <-> "OE2" Residue "S GLU 91": "OE1" <-> "OE2" Residue "T GLU 13": "OE1" <-> "OE2" Residue "U ARG 28": "NH1" <-> "NH2" Residue "U PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 77": "OE1" <-> "OE2" Residue "V PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 79": "OE1" <-> "OE2" Residue "W ARG 11": "NH1" <-> "NH2" Residue "W GLU 34": "OE1" <-> "OE2" Residue "Y TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 58": "OD1" <-> "OD2" Residue "Z GLU 9": "OE1" <-> "OE2" Residue "Z PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 38": "OE1" <-> "OE2" Residue "Z ARG 66": "NH1" <-> "NH2" Residue "8 GLU 16": "OE1" <-> "OE2" Residue "8 PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 ASP 42": "OD1" <-> "OD2" Residue "8 GLU 54": "OE1" <-> "OE2" Residue "8 ARG 78": "NH1" <-> "NH2" Residue "8 GLU 81": "OE1" <-> "OE2" Residue "8 ARG 117": "NH1" <-> "NH2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 144890 Number of models: 1 Model: "" Number of chains: 54 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: "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: "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: 62317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2903, 62317 Classifications: {'RNA': 2903} Modifications used: {'5*END': 1, 'rna2p_pur': 215, 'rna2p_pyr': 95, 'rna3p_pur': 1459, 'rna3p_pyr': 1134} Link IDs: {'rna2p': 310, 'rna3p': 2592} Chain: "2" Number of atoms: 2568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2568 Classifications: {'RNA': 120} Modifications used: {'5*END': 1, 'rna2p_pur': 4, 'rna2p_pyr': 2, 'rna3p_pur': 61, 'rna3p_pyr': 53} Link IDs: {'rna2p': 6, 'rna3p': 113} Chain: "5" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1640 Classifications: {'RNA': 77} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 4, 'rna3p_pur': 33, 'rna3p_pyr': 34} Link IDs: {'rna2p': 9, 'rna3p': 67} Chain: "4" Number of atoms: 353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 353 Classifications: {'RNA': 16} Modifications used: {'rna2p_pur': 3, 'rna3p_pur': 11, 'rna3p_pyr': 2} Link IDs: {'rna2p': 2, 'rna3p': 13} Chain: "8" Number of atoms: 1031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1031 Classifications: {'peptide': 132} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 127} Time building chain proxies: 56.74, per 1000 atoms: 0.39 Number of scatterers: 144890 At special positions: 0 Unit cell: (259.26, 260.13, 240.99, 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 142 16.00 P 4651 15.00 O 40347 8.00 N 27034 7.00 C 72716 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 61.85 Conformation dependent library (CDL) restraints added in 8.3 seconds 11302 Ramachandran restraints generated. 5651 Oldfield, 0 Emsley, 5651 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10570 Finding SS restraints... Secondary structure from input PDB file: 176 helices and 71 sheets defined 34.4% alpha, 17.0% beta 1359 base pairs and 2677 stacking pairs defined. Time for finding SS restraints: 54.10 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 132 through 134 No H-bonds generated for 'chain 'b' and resid 132 through 134' Processing helix chain 'b' and resid 196 through 202 removed outlier: 3.925A pdb=" N MET b 200 " --> pdb=" O ALA b 197 " (cutoff:3.500A) Processing helix chain 'b' and resid 206 through 212 removed outlier: 3.576A pdb=" N ALA b 210 " --> pdb=" O LYS b 206 " (cutoff:3.500A) Processing helix chain 'b' and resid 220 through 224 Processing helix chain 'c' and resid 39 through 44 Processing helix chain 'c' and resid 61 through 72 Processing helix chain 'c' and resid 97 through 102 removed outlier: 3.660A pdb=" N LEU c 100 " --> pdb=" O SER c 97 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA c 102 " --> pdb=" O GLU c 99 " (cutoff:3.500A) Processing helix chain 'c' and resid 120 through 125 Processing helix chain 'd' and resid 24 through 40 removed outlier: 3.528A pdb=" N VAL d 31 " --> pdb=" O LEU d 27 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL d 33 " --> pdb=" O HIS d 29 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG d 40 " --> pdb=" O ALA d 36 " (cutoff:3.500A) Processing helix chain 'd' and resid 97 through 115 removed outlier: 3.540A pdb=" N ARG d 114 " --> pdb=" O SER d 110 " (cutoff:3.500A) Processing helix chain 'd' and resid 130 through 140 removed outlier: 3.591A pdb=" N LEU d 134 " --> pdb=" O LYS d 130 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS d 139 " --> pdb=" O ALA d 135 " (cutoff:3.500A) Processing helix chain 'd' and resid 154 through 161 Processing helix chain 'd' and resid 176 through 183 removed outlier: 3.545A pdb=" N LEU d 180 " --> pdb=" O ASP d 176 " (cutoff:3.500A) Processing helix chain 'd' and resid 190 through 198 removed outlier: 3.719A pdb=" N GLU d 198 " --> pdb=" O LYS d 194 " (cutoff:3.500A) Processing helix chain 'e' and resid 2 through 19 removed outlier: 3.575A pdb=" N VAL e 11 " --> pdb=" O TYR e 7 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N VAL e 12 " --> pdb=" O LYS e 8 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS e 13 " --> pdb=" O ASP e 9 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N THR e 17 " --> pdb=" O LYS e 13 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU e 18 " --> pdb=" O LYS e 14 " (cutoff:3.500A) Processing helix chain 'e' and resid 23 through 27 Processing helix chain 'e' and resid 46 through 61 removed outlier: 4.067A pdb=" N ASP e 50 " --> pdb=" O LYS e 46 " (cutoff:3.500A) Processing helix chain 'e' and resid 93 through 104 Processing helix chain 'e' and resid 106 through 110 Processing helix chain 'e' and resid 161 through 171 removed outlier: 3.818A pdb=" N LEU e 168 " --> pdb=" O GLU e 164 " (cutoff:3.500A) Processing helix chain 'f' and resid 59 through 78 removed outlier: 3.502A pdb=" N ALA f 69 " --> pdb=" O GLY f 65 " (cutoff:3.500A) Processing helix chain 'f' and resid 136 through 150 removed outlier: 3.587A pdb=" N LEU f 147 " --> pdb=" O VAL f 143 " (cutoff:3.500A) Processing helix chain 'g' and resid 22 through 29 removed outlier: 3.554A pdb=" N PHE g 29 " --> pdb=" O TYR g 25 " (cutoff:3.500A) Processing helix chain 'g' and resid 40 through 48 Processing helix chain 'g' and resid 54 through 71 removed outlier: 3.543A pdb=" N LEU g 62 " --> pdb=" O LEU g 58 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LYS g 71 " --> pdb=" O ALA g 67 " (cutoff:3.500A) Processing helix chain 'g' and resid 95 through 105 removed outlier: 3.701A pdb=" N ALA g 102 " --> pdb=" O ASP g 98 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA g 105 " --> pdb=" O ASP g 101 " (cutoff:3.500A) Processing helix chain 'j' and resid 24 through 38 removed outlier: 3.877A pdb=" N GLU j 31 " --> pdb=" O ARG j 27 " (cutoff:3.500A) Processing helix chain 'j' and resid 59 through 62 removed outlier: 3.767A pdb=" N VAL j 62 " --> pdb=" O ALA j 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 59 through 62' Processing helix chain 'j' and resid 67 through 72 Processing helix chain 'j' and resid 88 through 96 Processing helix chain 'j' and resid 96 through 107 removed outlier: 3.957A pdb=" N VAL j 100 " --> pdb=" O ARG j 96 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ILE j 101 " --> pdb=" O PRO j 97 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU j 102 " --> pdb=" O GLU j 98 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY j 107 " --> pdb=" O ILE j 103 " (cutoff:3.500A) Processing helix chain 'j' and resid 112 through 120 removed outlier: 3.540A pdb=" N ARG j 120 " --> pdb=" O ARG j 116 " (cutoff:3.500A) Processing helix chain 'k' and resid 112 through 119 Processing helix chain 'l' and resid 29 through 33 removed outlier: 4.153A pdb=" N GLY l 32 " --> pdb=" O LYS l 29 " (cutoff:3.500A) Processing helix chain 'l' and resid 37 through 41 removed outlier: 3.719A pdb=" N ARG l 41 " --> pdb=" O GLN l 38 " (cutoff:3.500A) Processing helix chain 'l' and resid 56 through 61 Processing helix chain 'l' and resid 68 through 73 removed outlier: 3.773A pdb=" N ALA l 72 " --> pdb=" O SER l 68 " (cutoff:3.500A) Processing helix chain 'l' and resid 80 through 83 removed outlier: 3.876A pdb=" N ALA l 83 " --> pdb=" O SER l 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 80 through 83' Processing helix chain 'l' and resid 128 through 138 Processing helix chain 'm' and resid 43 through 58 removed outlier: 3.566A pdb=" N ARG m 55 " --> pdb=" O ARG m 51 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ALA m 56 " --> pdb=" O ALA m 52 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL m 57 " --> pdb=" O MET m 53 " (cutoff:3.500A) Processing helix chain 'm' and resid 109 through 124 removed outlier: 3.590A pdb=" N LYS m 118 " --> pdb=" O ARG m 114 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA m 122 " --> pdb=" O LYS m 118 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LYS m 123 " --> pdb=" O LEU m 119 " (cutoff:3.500A) Processing helix chain 'n' and resid 13 through 32 Processing helix chain 'n' and resid 37 through 56 removed outlier: 3.635A pdb=" N ARG n 45 " --> pdb=" O ALA n 41 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ARG n 46 " --> pdb=" O LYS n 42 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N VAL n 47 " --> pdb=" O GLU n 43 " (cutoff:3.500A) removed outlier: 3.577A 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: 3.620A pdb=" N ARG o 10 " --> pdb=" O ALA o 6 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ARG o 13 " --> pdb=" O ARG o 9 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ALA o 14 " --> pdb=" O ARG o 10 " (cutoff:3.500A) removed outlier: 3.634A 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 Processing helix chain 'o' and resid 101 through 114 removed outlier: 3.602A pdb=" N ASP o 108 " --> pdb=" O GLN o 104 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA o 109 " --> pdb=" O ALA o 105 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA o 110 " --> pdb=" O LEU o 106 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLY o 114 " --> pdb=" O ALA o 110 " (cutoff:3.500A) Processing helix chain 'p' and resid 2 through 9 Processing helix chain 'p' and resid 52 through 55 Processing helix chain 'p' and resid 96 through 101 removed outlier: 3.563A pdb=" N GLU p 101 " --> pdb=" O TYR p 98 " (cutoff:3.500A) Processing helix chain 'p' and resid 103 through 108 Processing helix chain 'q' and resid 6 through 20 removed outlier: 3.599A pdb=" N LYS q 18 " --> pdb=" O LYS q 14 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLN q 19 " --> pdb=" O LYS q 15 " (cutoff:3.500A) Processing helix chain 'q' and resid 24 through 29 Processing helix chain 'q' and resid 30 through 71 removed outlier: 3.959A pdb=" N GLN q 36 " --> pdb=" O ARG q 32 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ARG q 50 " --> pdb=" O TYR q 46 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LYS q 53 " --> pdb=" O ARG q 49 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG q 57 " --> pdb=" O LYS q 53 " (cutoff:3.500A) Processing helix chain 'q' and resid 74 through 85 Processing helix chain 'q' and resid 90 through 101 removed outlier: 3.815A pdb=" N ASP q 96 " --> pdb=" O LYS q 92 " (cutoff:3.500A) Processing helix chain 'q' and resid 101 through 117 Processing helix chain 's' and resid 13 through 24 removed outlier: 3.898A pdb=" N VAL s 17 " --> pdb=" O SER s 13 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG s 18 " --> pdb=" O ALA s 14 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU s 19 " --> pdb=" O GLN s 15 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL s 20 " --> pdb=" O LYS s 16 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU s 23 " --> pdb=" O LEU s 19 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE s 24 " --> pdb=" O VAL s 20 " (cutoff:3.500A) Processing helix chain 's' and resid 28 through 37 Processing helix chain 's' and resid 41 through 61 removed outlier: 3.615A pdb=" N VAL s 50 " --> pdb=" O LEU s 46 " (cutoff:3.500A) Processing helix chain 't' and resid 2 through 8 Processing helix chain 't' and resid 17 through 28 Processing helix chain 't' and resid 39 through 51 removed outlier: 3.576A pdb=" N GLN t 48 " --> pdb=" O LYS t 44 " (cutoff:3.500A) Processing helix chain 'v' and resid 13 through 22 Processing helix chain 'v' and resid 44 through 51 Processing helix chain 'v' and resid 53 through 58 Processing helix chain 'x' and resid 52 through 61 Processing helix chain 'x' and resid 62 through 73 Processing helix chain 'y' and resid 9 through 23 Processing helix chain 'y' and resid 23 through 34 removed outlier: 3.565A pdb=" N ASN y 27 " --> pdb=" O ARG y 23 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG y 29 " --> pdb=" O GLN y 25 " (cutoff:3.500A) Processing helix chain 'y' and resid 40 through 60 removed outlier: 3.531A pdb=" N LYS y 44 " --> pdb=" O SER y 40 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG y 47 " --> pdb=" O LEU y 43 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG y 48 " --> pdb=" O LYS y 44 " (cutoff:3.500A) Processing helix chain 'z' and resid 16 through 27 Processing helix chain 'z' and resid 40 through 50 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 24 removed outlier: 4.502A pdb=" N THR D 24 " --> pdb=" O ALA D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 24 through 38 removed outlier: 3.577A pdb=" N LEU D 31 " --> pdb=" O GLY D 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 11 removed outlier: 3.678A pdb=" N ALA E 10 " --> pdb=" O VAL E 6 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 43 Processing helix chain 'E' and resid 50 through 61 removed outlier: 4.134A pdb=" N GLY E 55 " --> pdb=" O LYS E 51 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N LEU E 56 " --> pdb=" O GLY E 52 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL E 57 " --> pdb=" O ASP E 53 " (cutoff:3.500A) Processing helix chain 'F' and resid 18 through 22 removed outlier: 3.609A pdb=" N GLY F 21 " --> pdb=" O LYS F 18 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL F 22 " --> pdb=" O ARG F 19 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 18 through 22' Processing helix chain 'G' and resid 5 through 10 removed outlier: 3.740A pdb=" N LYS G 10 " --> pdb=" O ARG G 6 " (cutoff:3.500A) Processing helix chain 'G' and resid 23 through 27 removed outlier: 3.549A pdb=" N LYS G 27 " --> pdb=" O PRO G 24 " (cutoff:3.500A) Processing helix chain 'G' and resid 33 through 37 removed outlier: 3.557A pdb=" N LYS G 36 " --> pdb=" O ALA G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 41 through 61 removed outlier: 3.829A pdb=" N THR G 45 " --> pdb=" O ASN G 41 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL G 46 " --> pdb=" O LEU G 42 " (cutoff:3.500A) Proline residue: G 47 - end of helix Processing helix chain 'G' and resid 75 through 87 removed outlier: 3.556A pdb=" N LYS G 80 " --> pdb=" O SER G 76 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N SER G 85 " --> pdb=" O ASP G 81 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N CYS G 86 " --> pdb=" O ALA G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 120 removed outlier: 3.539A pdb=" N VAL G 106 " --> pdb=" O ASN G 102 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N GLN G 108 " --> pdb=" O LYS G 104 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N SER G 109 " --> pdb=" O THR G 105 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR G 118 " --> pdb=" O LYS G 114 " (cutoff:3.500A) Processing helix chain 'G' and resid 129 through 147 removed outlier: 3.523A pdb=" N LEU G 140 " --> pdb=" O ARG G 136 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS G 142 " --> pdb=" O ARG G 138 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 178 Processing helix chain 'G' and resid 205 through 223 removed outlier: 3.665A pdb=" N ALA G 218 " --> pdb=" O GLY G 214 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR G 219 " --> pdb=" O ALA G 215 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG G 221 " --> pdb=" O ALA G 217 " (cutoff:3.500A) Processing helix chain 'H' and resid 7 through 11 removed outlier: 3.521A pdb=" N LEU H 11 " --> pdb=" O GLY H 8 " (cutoff:3.500A) Processing helix chain 'H' and resid 24 through 46 removed outlier: 4.576A pdb=" N ALA H 29 " --> pdb=" O THR H 25 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N ASP H 30 " --> pdb=" O LYS H 26 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS H 44 " --> pdb=" O GLN H 40 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU H 45 " --> pdb=" O TYR H 41 " (cutoff:3.500A) Processing helix chain 'H' and resid 71 through 77 Processing helix chain 'H' and resid 80 through 95 removed outlier: 3.583A pdb=" N LEU H 86 " --> pdb=" O ASP H 82 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASP H 92 " --> pdb=" O LYS H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 107 through 110 Processing helix chain 'H' and resid 111 through 124 removed outlier: 3.521A pdb=" N GLN H 122 " --> pdb=" O SER H 118 " (cutoff:3.500A) Processing helix chain 'H' and resid 128 through 144 removed outlier: 3.778A pdb=" N ALA H 132 " --> pdb=" O MET H 128 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA H 136 " --> pdb=" O ALA H 132 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N VAL H 137 " --> pdb=" O MET H 133 " (cutoff:3.500A) Processing helix chain 'H' and resid 155 through 159 removed outlier: 3.948A pdb=" N ALA H 159 " --> pdb=" O LEU H 156 " (cutoff:3.500A) Processing helix chain 'I' and resid 6 through 15 removed outlier: 3.570A pdb=" N GLU I 14 " --> pdb=" O LEU I 10 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 65 removed outlier: 3.808A pdb=" N TYR I 64 " --> pdb=" O VAL I 60 " (cutoff:3.500A) Processing helix chain 'I' and resid 67 through 80 Processing helix chain 'I' and resid 84 through 94 removed outlier: 3.854A pdb=" N LEU I 90 " --> pdb=" O GLY I 86 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU I 94 " --> pdb=" O LEU I 90 " (cutoff:3.500A) Processing helix chain 'I' and resid 96 through 105 Processing helix chain 'I' and resid 109 through 119 removed outlier: 3.554A pdb=" N LEU I 116 " --> pdb=" O GLU I 112 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N HIS I 119 " --> pdb=" O GLN I 115 " (cutoff:3.500A) Processing helix chain 'I' and resid 152 through 162 removed outlier: 3.615A pdb=" N ALA I 156 " --> pdb=" O SER I 152 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLU I 162 " --> pdb=" O LEU I 158 " (cutoff:3.500A) Processing helix chain 'I' and resid 195 through 203 removed outlier: 3.596A pdb=" N ILE I 199 " --> pdb=" O ASN I 195 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR I 203 " --> pdb=" O ILE I 199 " (cutoff:3.500A) Processing helix chain 'J' and resid 54 through 68 removed outlier: 3.525A pdb=" N MET J 63 " --> pdb=" O ILE J 59 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N GLU J 64 " --> pdb=" O GLN J 60 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N LYS J 65 " --> pdb=" O LYS J 61 " (cutoff:3.500A) Processing helix chain 'J' and resid 109 through 116 removed outlier: 3.503A pdb=" N VAL J 116 " --> pdb=" O ALA J 112 " (cutoff:3.500A) Processing helix chain 'J' and resid 131 through 145 removed outlier: 3.687A pdb=" N ASP J 141 " --> pdb=" O ARG J 137 " (cutoff:3.500A) Processing helix chain 'J' and resid 148 through 156 removed outlier: 4.291A pdb=" N ALA J 154 " --> pdb=" O GLU J 150 " (cutoff:3.500A) Processing helix chain 'J' and resid 159 through 165 removed outlier: 3.580A pdb=" N ILE J 163 " --> pdb=" O SER J 159 " (cutoff:3.500A) Processing helix chain 'K' and resid 12 through 16 removed outlier: 3.755A pdb=" N GLU K 16 " --> pdb=" O ASP K 13 " (cutoff:3.500A) Processing helix chain 'K' and resid 17 through 32 removed outlier: 3.643A pdb=" N MET K 21 " --> pdb=" O GLN K 17 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR K 30 " --> pdb=" O THR K 26 " (cutoff:3.500A) Processing helix chain 'K' and resid 69 through 80 removed outlier: 3.710A pdb=" N GLU K 73 " --> pdb=" O GLU K 69 " (cutoff:3.500A) Processing helix chain 'L' and resid 19 through 28 removed outlier: 3.692A pdb=" N ASN L 27 " --> pdb=" O ALA L 23 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE L 28 " --> pdb=" O LYS L 24 " (cutoff:3.500A) Processing helix chain 'L' and resid 34 through 48 Processing helix chain 'L' and resid 48 through 53 Processing helix chain 'L' and resid 56 through 66 removed outlier: 4.335A pdb=" N ALA L 64 " --> pdb=" O ALA L 60 " (cutoff:3.500A) Processing helix chain 'L' and resid 67 through 69 No H-bonds generated for 'chain 'L' and resid 67 through 69' Processing helix chain 'L' and resid 91 through 109 removed outlier: 3.651A pdb=" N ASN L 96 " --> pdb=" O PRO L 92 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N ALA L 97 " --> pdb=" O VAL L 93 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TRP L 102 " --> pdb=" O LEU L 98 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLU L 105 " --> pdb=" O ARG L 101 " (cutoff:3.500A) Processing helix chain 'L' and resid 114 through 128 removed outlier: 3.715A pdb=" N GLU L 122 " --> pdb=" O ARG L 118 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU L 128 " --> pdb=" O SER L 124 " (cutoff:3.500A) Processing helix chain 'L' and resid 131 through 147 removed outlier: 3.533A pdb=" N ALA L 146 " --> pdb=" O ARG L 142 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 19 removed outlier: 3.517A pdb=" N ASP M 8 " --> pdb=" O ASP M 4 " (cutoff:3.500A) Processing helix chain 'M' and resid 29 through 43 removed outlier: 3.606A pdb=" N VAL M 38 " --> pdb=" O ALA M 34 " (cutoff:3.500A) Processing helix chain 'M' and resid 93 through 97 Processing helix chain 'M' and resid 112 through 118 removed outlier: 4.115A pdb=" N GLN M 117 " --> pdb=" O ARG M 113 " (cutoff:3.500A) Processing helix chain 'N' and resid 10 through 14 removed outlier: 4.127A pdb=" N SER N 13 " --> pdb=" O ARG N 10 " (cutoff:3.500A) Processing helix chain 'N' and resid 33 through 38 Processing helix chain 'N' and resid 48 through 53 Processing helix chain 'N' and resid 70 through 85 removed outlier: 3.545A pdb=" N ARG N 79 " --> pdb=" O ALA N 75 " (cutoff:3.500A) removed outlier: 3.501A 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 34 removed outlier: 3.571A pdb=" N ILE O 25 " --> pdb=" O ALA O 21 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU O 27 " --> pdb=" O ALA O 23 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR O 32 " --> pdb=" O THR O 28 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA O 34 " --> pdb=" O LYS O 30 " (cutoff:3.500A) Processing helix chain 'P' and resid 45 through 49 removed outlier: 3.615A pdb=" N SER P 49 " --> pdb=" O ALA P 46 " (cutoff:3.500A) Processing helix chain 'P' and resid 52 through 57 removed outlier: 4.156A pdb=" N ARG P 55 " --> pdb=" O ARG P 52 " (cutoff:3.500A) Processing helix chain 'P' and resid 58 through 71 removed outlier: 3.606A pdb=" N ASP P 71 " --> pdb=" O GLU P 67 " (cutoff:3.500A) Processing helix chain 'P' and resid 91 through 101 removed outlier: 4.069A pdb=" N THR P 95 " --> pdb=" O GLY P 91 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE P 96 " --> pdb=" O ARG P 92 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ARG P 97 " --> pdb=" O GLU P 93 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN P 100 " --> pdb=" O ILE P 96 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 9 removed outlier: 3.581A pdb=" N LEU Q 6 " --> pdb=" O THR Q 2 " (cutoff:3.500A) Processing helix chain 'R' and resid 13 through 20 Processing helix chain 'R' and resid 25 through 35 removed outlier: 3.600A pdb=" N ALA R 31 " --> pdb=" O THR R 27 " (cutoff:3.500A) Processing helix chain 'R' and resid 48 through 60 removed outlier: 3.904A pdb=" N ASP R 53 " --> pdb=" O GLU R 49 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N THR R 54 " --> pdb=" O GLY R 50 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASP R 57 " --> pdb=" O ASP R 53 " (cutoff:3.500A) Processing helix chain 'R' and resid 64 through 80 Processing helix chain 'R' and resid 84 through 93 removed outlier: 3.557A pdb=" N HIS R 90 " --> pdb=" O ARG R 86 " (cutoff:3.500A) Processing helix chain 'S' and resid 2 through 17 Processing helix chain 'S' and resid 37 through 46 removed outlier: 3.938A pdb=" N VAL S 44 " --> pdb=" O ARG S 40 " (cutoff:3.500A) Processing helix chain 'S' and resid 47 through 50 removed outlier: 3.814A 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 Processing helix chain 'S' and resid 79 through 90 removed outlier: 3.549A pdb=" N ARG S 84 " --> pdb=" O ARG S 80 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLU S 85 " --> pdb=" O ILE S 81 " (cutoff:3.500A) Processing helix chain 'T' and resid 3 through 15 Processing helix chain 'T' and resid 23 through 44 removed outlier: 3.950A pdb=" N GLY T 40 " --> pdb=" O ASN T 36 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N HIS T 41 " --> pdb=" O HIS T 37 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU T 44 " --> pdb=" O GLY T 40 " (cutoff:3.500A) Processing helix chain 'T' and resid 48 through 73 removed outlier: 3.799A pdb=" N TYR T 68 " --> pdb=" O LYS T 64 " (cutoff:3.500A) Processing helix chain 'T' and resid 73 through 82 Processing helix chain 'U' and resid 53 through 62 Processing helix chain 'U' and resid 68 through 78 Processing helix chain 'W' and resid 24 through 29 Processing helix chain 'W' and resid 30 through 32 No H-bonds generated for 'chain 'W' and resid 30 through 32' Processing helix chain 'W' and resid 40 through 45 removed outlier: 3.566A pdb=" N THR W 44 " --> pdb=" O PRO W 40 " (cutoff:3.500A) Processing helix chain 'W' and resid 47 through 64 removed outlier: 3.511A pdb=" N GLN W 53 " --> pdb=" O LYS W 49 " (cutoff:3.500A) Processing helix chain 'X' and resid 11 through 23 Processing helix chain 'X' and resid 40 through 44 Processing helix chain 'X' and resid 69 through 74 Processing helix chain 'Y' and resid 4 through 6 No H-bonds generated for 'chain 'Y' and resid 4 through 6' Processing helix chain 'Y' and resid 7 through 41 removed outlier: 3.953A pdb=" N ILE Y 11 " --> pdb=" O LYS Y 7 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA Y 37 " --> pdb=" O LYS Y 33 " (cutoff:3.500A) Processing helix chain 'Y' and resid 42 through 62 removed outlier: 3.592A pdb=" N MET Y 53 " --> pdb=" O ALA Y 49 " (cutoff:3.500A) Proline residue: Y 55 - end of helix removed outlier: 3.576A pdb=" N ARG Y 59 " --> pdb=" O PRO Y 55 " (cutoff:3.500A) Processing helix chain 'Y' and resid 67 through 85 removed outlier: 3.572A pdb=" N LYS Y 75 " --> pdb=" O ALA Y 71 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU Y 78 " --> pdb=" O HIS Y 74 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR Y 79 " --> pdb=" O LYS Y 75 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 21 removed outlier: 4.179A pdb=" N ARG Z 20 " --> pdb=" O ARG Z 16 " (cutoff:3.500A) Processing helix chain 'Z' and resid 25 through 33 removed outlier: 3.842A pdb=" N GLU Z 30 " --> pdb=" O GLY Z 26 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ARG Z 33 " --> pdb=" O ALA Z 29 " (cutoff:3.500A) Processing helix chain 'Z' and resid 38 through 59 removed outlier: 4.023A pdb=" N THR Z 42 " --> pdb=" O GLU Z 38 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER Z 50 " --> pdb=" O ARG Z 46 " (cutoff:3.500A) Processing helix chain '8' and resid 27 through 32 Processing helix chain '8' and resid 49 through 55 removed outlier: 3.822A pdb=" N ARG 8 55 " --> pdb=" O TYR 8 51 " (cutoff:3.500A) Processing helix chain '8' and resid 79 through 90 removed outlier: 3.594A pdb=" N ASN 8 83 " --> pdb=" O SER 8 79 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA 8 89 " --> pdb=" O GLU 8 85 " (cutoff:3.500A) Processing helix chain '8' and resid 91 through 98 Processing helix chain '8' and resid 112 through 128 removed outlier: 4.635A pdb=" N ARG 8 118 " --> pdb=" O SER 8 114 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU 8 119 " --> pdb=" O LYS 8 115 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA 8 120 " --> pdb=" O GLU 8 116 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLN 8 124 " --> pdb=" O ALA 8 120 " (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 35 Processing sheet with id=AA3, first strand: chain 'b' and resid 100 through 104 removed outlier: 7.179A pdb=" N ILE b 90 " --> pdb=" O LEU b 80 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N LEU b 80 " --> pdb=" O ILE b 90 " (cutoff:3.500A) removed outlier: 7.129A 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: 7.312A pdb=" N ARG b 188 " --> pdb=" O VAL b 143 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N VAL b 143 " --> pdb=" O ARG b 188 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N ILE b 163 " --> pdb=" O ARG b 174 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ARG b 174 " --> pdb=" O ILE b 163 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA b 165 " --> pdb=" O THR b 172 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N MET b 180 " --> pdb=" O VAL b 267 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'c' and resid 4 through 15 removed outlier: 5.697A pdb=" N LYS c 8 " --> pdb=" O GLU c 28 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N GLU c 28 " --> pdb=" O LYS c 8 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLY c 10 " --> pdb=" O VAL c 26 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE c 27 " --> pdb=" O LEU c 187 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N LYS c 190 " --> pdb=" O VAL c 177 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL c 177 " --> pdb=" O LYS c 190 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N THR c 171 " --> pdb=" O GLY c 111 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N GLY c 111 " --> pdb=" O THR c 171 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N GLN c 173 " --> pdb=" O VAL c 109 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N VAL c 109 " --> pdb=" O GLN c 173 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N THR c 112 " --> pdb=" O ASP c 200 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N ASP c 200 " --> pdb=" O THR c 112 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'c' and resid 80 through 83 removed outlier: 6.366A pdb=" N ALA c 47 " --> pdb=" O VAL c 37 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N VAL c 37 " --> pdb=" O ALA c 47 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N GLN c 49 " --> pdb=" O THR c 35 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'c' and resid 117 through 119 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 121 Processing sheet with id=AB1, first strand: chain 'd' and resid 148 through 150 removed outlier: 6.016A pdb=" N ILE d 148 " --> pdb=" O ARG d 170 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'e' and resid 89 through 90 removed outlier: 3.521A pdb=" N LEU e 90 " --> pdb=" O ILE e 33 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS e 32 " --> pdb=" O THR e 156 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'e' and resid 65 through 68 removed outlier: 3.563A pdb=" N GLY e 85 " --> pdb=" O THR e 67 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'f' and resid 8 through 9 Processing sheet with id=AB5, first strand: chain 'f' and resid 17 through 19 Processing sheet with id=AB6, first strand: chain 'f' and resid 120 through 126 removed outlier: 7.150A pdb=" N GLU f 129 " --> pdb=" O PRO f 125 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'f' and resid 94 through 98 removed outlier: 3.535A pdb=" N ARG f 94 " --> pdb=" O SER f 105 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'g' and resid 17 through 20 removed outlier: 4.536A pdb=" N ASP g 17 " --> pdb=" O LEU g 5 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'g' and resid 77 through 80 removed outlier: 3.511A pdb=" N VAL g 78 " --> pdb=" O ILE g 143 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASN g 145 " --> pdb=" O VAL g 78 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'j' and resid 122 through 125 removed outlier: 6.548A pdb=" N ILE j 54 " --> pdb=" O LYS j 123 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N TYR j 125 " --> pdb=" O ILE j 54 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N VAL j 56 " --> pdb=" O TYR j 125 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N TYR j 16 " --> pdb=" O ILE j 55 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N LEU j 57 " --> pdb=" O TYR j 16 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N VAL j 18 " --> pdb=" O LEU j 57 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N TRP j 15 " --> pdb=" O GLN j 138 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'j' and resid 76 through 77 Processing sheet with id=AC3, first strand: chain 'k' and resid 7 through 10 removed outlier: 6.265A pdb=" N ARG k 17 " --> pdb=" O VAL k 10 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ALA k 16 " --> pdb=" O ALA k 46 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N ALA k 46 " --> pdb=" O ALA k 16 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N ARG k 18 " --> pdb=" O LYS k 44 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LYS k 40 " --> pdb=" O ILE k 22 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N VAL k 24 " --> pdb=" O ILE k 38 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N ILE k 38 " --> pdb=" O VAL k 24 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ALA k 83 " --> pdb=" O VAL k 63 " (cutoff:3.500A) removed outlier: 8.512A pdb=" N CYS k 84 " --> pdb=" O MET k 7 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ASN k 9 " --> pdb=" O CYS k 84 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N LEU k 86 " --> pdb=" O ASN k 9 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'k' and resid 69 through 70 removed outlier: 4.298A pdb=" N VAL k 76 " --> pdb=" O VAL p 72 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA p 48 " --> pdb=" O THR p 59 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ARG p 61 " --> pdb=" O VAL p 46 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N VAL p 46 " --> pdb=" O ARG p 61 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'l' and resid 74 through 78 Processing sheet with id=AC6, first strand: chain 'l' and resid 122 through 123 removed outlier: 5.184A pdb=" N VAL l 122 " --> pdb=" O GLU l 143 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'm' and resid 62 through 65 removed outlier: 6.479A pdb=" N LEU m 33 " --> pdb=" O LEU m 102 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N GLU m 104 " --> pdb=" O PHE m 31 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N PHE m 31 " --> pdb=" O GLU m 104 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'm' and resid 39 through 42 removed outlier: 3.589A pdb=" N ASN m 88 " --> pdb=" O GLU m 75 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ILE m 73 " --> pdb=" O GLU m 90 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'n' and resid 33 through 34 removed outlier: 6.680A pdb=" N MET n 110 " --> pdb=" O CYS n 100 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'o' and resid 47 through 52 removed outlier: 4.463A pdb=" N VAL o 49 " --> pdb=" O VAL o 39 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N HIS o 34 " --> pdb=" O THR o 31 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG o 25 " --> pdb=" O ILE o 40 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'p' and resid 36 through 40 removed outlier: 3.664A pdb=" N LYS p 36 " --> pdb=" O GLU p 33 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N THR p 24 " --> pdb=" O LYS p 86 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N SER p 82 " --> pdb=" O LYS p 28 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N TRP p 30 " --> pdb=" O VAL p 80 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N VAL p 80 " --> pdb=" O TRP p 30 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'r' and resid 11 through 14 removed outlier: 3.630A pdb=" N PHE r 5 " --> pdb=" O HIS r 12 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N TYR r 2 " --> pdb=" O ALA r 42 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'r' and resid 19 through 23 removed outlier: 3.943A pdb=" N GLU r 31 " --> pdb=" O VAL r 63 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'r' and resid 74 through 78 removed outlier: 3.982A pdb=" N TYR r 83 " --> pdb=" O ARG r 78 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 's' and resid 4 through 10 removed outlier: 5.532A pdb=" N SER s 101 " --> pdb=" O HIS s 9 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N HIS s 102 " --> pdb=" O GLU s 78 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N GLU s 78 " --> pdb=" O HIS s 102 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N THR s 104 " --> pdb=" O VAL s 76 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N VAL s 76 " --> pdb=" O THR s 104 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N VAL s 106 " --> pdb=" O ILE s 74 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N ILE s 74 " --> pdb=" O VAL s 106 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N SER s 108 " --> pdb=" O THR s 72 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N THR s 72 " --> pdb=" O SER s 108 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 't' and resid 11 through 14 removed outlier: 3.608A pdb=" N LYS t 81 " --> pdb=" O VAL t 34 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N TRP t 80 " --> pdb=" O VAL t 62 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N VAL t 62 " --> pdb=" O TRP t 80 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N LYS t 82 " --> pdb=" O THR t 60 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N THR t 60 " --> pdb=" O LYS t 82 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N TYR t 84 " --> pdb=" O VAL t 58 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N VAL t 58 " --> pdb=" O TYR t 84 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N THR t 86 " --> pdb=" O GLU t 56 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 't' and resid 67 through 70 Processing sheet with id=AD9, first strand: chain 'u' and resid 64 through 65 removed outlier: 6.842A pdb=" N LYS u 32 " --> pdb=" O VAL u 27 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N VAL u 27 " --> pdb=" O LYS u 32 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ILE u 34 " --> pdb=" O LYS u 25 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'u' and resid 40 through 44 Processing sheet with id=AE2, first strand: chain 'u' and resid 82 through 86 Processing sheet with id=AE3, first strand: chain 'v' and resid 3 through 5 removed outlier: 6.442A pdb=" N VAL v 72 " --> pdb=" O ARG v 93 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ARG v 93 " --> pdb=" O VAL v 72 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ALA v 74 " --> pdb=" O PHE v 91 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N PHE v 91 " --> pdb=" O ALA v 74 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ASP v 76 " --> pdb=" O ILE v 89 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N ILE v 89 " --> pdb=" O ASP v 76 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N GLN v 78 " --> pdb=" O GLN v 87 " (cutoff:3.500A) removed outlier: 9.076A pdb=" N LYS v 25 " --> pdb=" O GLN v 87 " (cutoff:3.500A) removed outlier: 10.283A pdb=" N ILE v 89 " --> pdb=" O LYS v 25 " (cutoff:3.500A) removed outlier: 8.593A pdb=" N PHE v 91 " --> pdb=" O PRO v 27 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ILE v 29 " --> pdb=" O PHE v 91 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ARG v 93 " --> pdb=" O ILE v 29 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N TYR v 31 " --> pdb=" O ARG v 93 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'w' and resid 18 through 19 removed outlier: 6.706A pdb=" N LEU w 55 " --> pdb=" O ILE w 33 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'w' and resid 26 through 27 removed outlier: 3.832A pdb=" N LYS w 68 " --> pdb=" O ARG w 73 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N ILE w 78 " --> pdb=" O GLY w 44 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'x' and resid 12 through 14 Processing sheet with id=AE7, first strand: chain 'x' and resid 32 through 39 Processing sheet with id=AE8, first strand: chain 'z' and resid 34 through 38 Processing sheet with id=AE9, first strand: chain 'B' and resid 27 through 29 Processing sheet with id=AF1, first strand: chain 'C' and resid 19 through 24 Processing sheet with id=AF2, first strand: chain 'E' and resid 14 through 15 Processing sheet with id=AF3, first strand: chain 'F' and resid 14 through 17 Processing sheet with id=AF4, first strand: chain 'G' and resid 89 through 91 removed outlier: 3.551A pdb=" N PHE G 89 " --> pdb=" O ILE G 66 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'G' and resid 185 through 186 Processing sheet with id=AF6, first strand: chain 'H' and resid 19 through 21 removed outlier: 3.571A pdb=" N ARG H 58 " --> pdb=" O THR H 20 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG H 53 " --> pdb=" O HIS H 68 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N ILE H 63 " --> pdb=" O GLN H 99 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N ASN H 101 " --> pdb=" O ILE H 63 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N VAL H 65 " --> pdb=" O ASN H 101 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 163 through 170 removed outlier: 3.579A pdb=" N GLY H 154 " --> pdb=" O ARG H 163 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ASP H 180 " --> pdb=" O LYS H 203 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'I' and resid 127 through 129 removed outlier: 4.677A pdb=" N ILE I 122 " --> pdb=" O VAL I 129 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'J' and resid 12 through 16 removed outlier: 6.914A pdb=" N LEU J 35 " --> pdb=" O ILE J 15 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'J' and resid 19 through 20 Processing sheet with id=AG2, first strand: chain 'J' and resid 84 through 85 removed outlier: 3.561A pdb=" N MET J 95 " --> pdb=" O VAL J 84 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'K' and resid 2 through 3 Processing sheet with id=AG4, first strand: chain 'K' and resid 58 through 61 removed outlier: 6.768A pdb=" N VAL K 7 " --> pdb=" O SER K 87 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N SER K 87 " --> pdb=" O VAL K 7 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'L' and resid 72 through 76 Processing sheet with id=AG6, first strand: chain 'M' and resid 23 through 27 Processing sheet with id=AG7, first strand: chain 'M' and resid 73 through 76 removed outlier: 6.856A pdb=" N VAL M 102 " --> pdb=" O ILE M 125 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N TYR M 127 " --> pdb=" O ILE M 100 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N ILE M 100 " --> pdb=" O TYR M 127 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'N' and resid 5 through 7 Processing sheet with id=AG9, first strand: chain 'O' and resid 45 through 52 removed outlier: 3.664A pdb=" N GLU O 47 " --> pdb=" O ILE O 67 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'O' and resid 45 through 52 removed outlier: 3.664A pdb=" N GLU O 47 " --> pdb=" O ILE O 67 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS S 96 " --> pdb=" O GLU O 66 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'P' and resid 40 through 44 removed outlier: 4.087A pdb=" N GLY P 42 " --> pdb=" O ILE P 33 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY P 18 " --> pdb=" O ASN P 80 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N LEU P 81 " --> pdb=" O ASN P 108 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N THR P 110 " --> pdb=" O LEU P 81 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N VAL P 83 " --> pdb=" O THR P 110 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N VAL P 112 " --> pdb=" O VAL P 83 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N VAL P 85 " --> pdb=" O VAL P 112 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'Q' and resid 29 through 31 removed outlier: 3.636A pdb=" N LYS Q 29 " --> pdb=" O ILE Q 81 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N TYR Q 94 " --> pdb=" O THR Q 63 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N LYS Q 50 " --> pdb=" O ILE Q 66 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ARG Q 35 " --> pdb=" O ARG Q 53 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'U' and resid 8 through 11 removed outlier: 3.504A pdb=" N ARG U 14 " --> pdb=" O ALA U 11 " (cutoff:3.500A) removed outlier: 8.355A pdb=" N PHE U 39 " --> pdb=" O PRO U 15 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N TYR U 17 " --> pdb=" O GLY U 37 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N GLY U 37 " --> pdb=" O TYR U 17 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N VAL U 19 " --> pdb=" O ARG U 35 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N ARG U 35 " --> pdb=" O VAL U 19 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VAL U 21 " --> pdb=" O ILE U 33 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'U' and resid 8 through 11 removed outlier: 3.504A pdb=" N ARG U 14 " --> pdb=" O ALA U 11 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA U 22 " --> pdb=" O THR U 3 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N VAL U 2 " --> pdb=" O THR U 66 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'V' and resid 6 through 13 removed outlier: 16.817A pdb=" N LEU V 7 " --> pdb=" O PHE V 27 " (cutoff:3.500A) removed outlier: 14.617A pdb=" N PHE V 27 " --> pdb=" O LEU V 7 " (cutoff:3.500A) removed outlier: 8.591A pdb=" N GLY V 9 " --> pdb=" O GLU V 25 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N GLU V 25 " --> pdb=" O GLY V 9 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N VAL V 11 " --> pdb=" O ALA V 23 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N ALA V 23 " --> pdb=" O VAL V 11 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER V 13 " --> pdb=" O VAL V 21 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL V 28 " --> pdb=" O ILE V 37 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TRP V 72 " --> pdb=" O HIS V 44 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N GLU V 59 " --> pdb=" O VAL V 75 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N VAL V 77 " --> pdb=" O VAL V 57 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N VAL V 57 " --> pdb=" O VAL V 77 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'X' and resid 31 through 32 Processing sheet with id=AH8, first strand: chain '8' and resid 15 through 20 1639 hydrogen bonds defined for protein. 4560 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3365 hydrogen bonds 5494 hydrogen bond angles 0 basepair planarities 1359 basepair parallelities 2677 stacking parallelities Total time for adding SS restraints: 257.87 Time building geometry restraints manager: 66.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 33273 1.35 - 1.47: 64139 1.47 - 1.60: 55073 1.60 - 1.72: 4740 1.72 - 1.85: 256 Bond restraints: 157481 Sorted by residual: bond pdb=" CA VAL G 46 " pdb=" CB VAL G 46 " ideal model delta sigma weight residual 1.539 1.569 -0.030 5.40e-03 3.43e+04 3.16e+01 bond pdb=" N GLY C 3 " pdb=" CA GLY C 3 " ideal model delta sigma weight residual 1.451 1.495 -0.044 1.60e-02 3.91e+03 7.68e+00 bond pdb=" CA THR G 2 " pdb=" CB THR G 2 " ideal model delta sigma weight residual 1.524 1.557 -0.033 1.22e-02 6.72e+03 7.25e+00 bond pdb=" P A 4 5 " pdb=" O5' A 4 5 " ideal model delta sigma weight residual 1.593 1.632 -0.039 1.50e-02 4.44e+03 6.89e+00 bond pdb=" N GLY H 1 " pdb=" CA GLY H 1 " ideal model delta sigma weight residual 1.451 1.493 -0.042 1.60e-02 3.91e+03 6.80e+00 ... (remaining 157476 not shown) Histogram of bond angle deviations from ideal: 97.71 - 104.98: 21628 104.98 - 112.25: 86919 112.25 - 119.52: 54857 119.52 - 126.79: 59795 126.79 - 134.06: 12494 Bond angle restraints: 235693 Sorted by residual: angle pdb=" N VAL J 122 " pdb=" CA VAL J 122 " pdb=" C VAL J 122 " ideal model delta sigma weight residual 109.34 126.08 -16.74 2.08e+00 2.31e-01 6.47e+01 angle pdb=" N GLY R 25 " pdb=" CA GLY R 25 " pdb=" C GLY R 25 " ideal model delta sigma weight residual 112.79 122.32 -9.53 1.20e+00 6.94e-01 6.31e+01 angle pdb=" N ARG P 68 " pdb=" CA ARG P 68 " pdb=" C ARG P 68 " ideal model delta sigma weight residual 113.20 103.80 9.40 1.21e+00 6.83e-01 6.03e+01 angle pdb=" N GLY M 67 " pdb=" CA GLY M 67 " pdb=" C GLY M 67 " ideal model delta sigma weight residual 115.30 104.54 10.76 1.39e+00 5.18e-01 5.99e+01 angle pdb=" N GLN G 18 " pdb=" CA GLN G 18 " pdb=" C GLN G 18 " ideal model delta sigma weight residual 107.98 121.55 -13.57 1.88e+00 2.83e-01 5.21e+01 ... (remaining 235688 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.40: 89773 35.40 - 70.79: 9871 70.79 - 106.19: 1250 106.19 - 141.59: 15 141.59 - 176.99: 16 Dihedral angle restraints: 100925 sinusoidal: 84544 harmonic: 16381 Sorted by residual: dihedral pdb=" C5' U 11130 " pdb=" C4' U 11130 " pdb=" C3' U 11130 " pdb=" O3' U 11130 " ideal model delta sinusoidal sigma weight residual 147.00 78.36 68.64 1 8.00e+00 1.56e-02 9.54e+01 dihedral pdb=" C4' U 11130 " pdb=" C3' U 11130 " pdb=" C2' U 11130 " pdb=" C1' U 11130 " ideal model delta sinusoidal sigma weight residual -35.00 32.91 -67.91 1 8.00e+00 1.56e-02 9.36e+01 dihedral pdb=" O4' U 12552 " pdb=" C1' U 12552 " pdb=" N1 U 12552 " pdb=" C2 U 12552 " ideal model delta sinusoidal sigma weight residual 200.00 40.02 159.98 1 1.50e+01 4.44e-03 8.28e+01 ... (remaining 100922 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.121: 26823 0.121 - 0.241: 3195 0.241 - 0.362: 103 0.362 - 0.482: 6 0.482 - 0.603: 1 Chirality restraints: 30128 Sorted by residual: 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 -3.01 -0.60 2.00e-01 2.50e+01 9.08e+00 chirality pdb=" C3' U 11130 " pdb=" C4' U 11130 " pdb=" O3' U 11130 " pdb=" C2' U 11130 " both_signs ideal model delta sigma weight residual False -2.74 -2.30 -0.45 2.00e-01 2.50e+01 4.97e+00 chirality pdb=" CA VAL J 122 " pdb=" N VAL J 122 " pdb=" C VAL J 122 " pdb=" CB VAL J 122 " both_signs ideal model delta sigma weight residual False 2.44 2.04 0.40 2.00e-01 2.50e+01 4.05e+00 ... (remaining 30125 not shown) Planarity restraints: 12572 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G 12061 " 0.109 2.00e-02 2.50e+03 4.52e-02 6.13e+01 pdb=" N9 G 12061 " -0.008 2.00e-02 2.50e+03 pdb=" C8 G 12061 " -0.049 2.00e-02 2.50e+03 pdb=" N7 G 12061 " -0.043 2.00e-02 2.50e+03 pdb=" C5 G 12061 " -0.021 2.00e-02 2.50e+03 pdb=" C6 G 12061 " 0.021 2.00e-02 2.50e+03 pdb=" O6 G 12061 " 0.066 2.00e-02 2.50e+03 pdb=" N1 G 12061 " 0.020 2.00e-02 2.50e+03 pdb=" C2 G 12061 " -0.010 2.00e-02 2.50e+03 pdb=" N2 G 12061 " -0.024 2.00e-02 2.50e+03 pdb=" N3 G 12061 " -0.030 2.00e-02 2.50e+03 pdb=" C4 G 12061 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U 11818 " -0.088 2.00e-02 2.50e+03 4.86e-02 5.32e+01 pdb=" N1 U 11818 " 0.004 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 " 0.018 2.00e-02 2.50e+03 pdb=" O4 U 11818 " -0.088 2.00e-02 2.50e+03 pdb=" C5 U 11818 " 0.046 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' G 1 512 " 0.092 2.00e-02 2.50e+03 3.78e-02 4.28e+01 pdb=" N9 G 1 512 " -0.007 2.00e-02 2.50e+03 pdb=" C8 G 1 512 " -0.041 2.00e-02 2.50e+03 pdb=" N7 G 1 512 " -0.034 2.00e-02 2.50e+03 pdb=" C5 G 1 512 " -0.015 2.00e-02 2.50e+03 pdb=" C6 G 1 512 " 0.019 2.00e-02 2.50e+03 pdb=" O6 G 1 512 " 0.051 2.00e-02 2.50e+03 pdb=" N1 G 1 512 " 0.020 2.00e-02 2.50e+03 pdb=" C2 G 1 512 " -0.009 2.00e-02 2.50e+03 pdb=" N2 G 1 512 " -0.019 2.00e-02 2.50e+03 pdb=" N3 G 1 512 " -0.030 2.00e-02 2.50e+03 pdb=" C4 G 1 512 " -0.027 2.00e-02 2.50e+03 ... (remaining 12569 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 11663 2.72 - 3.26: 133407 3.26 - 3.81: 292638 3.81 - 4.35: 379975 4.35 - 4.90: 495837 Nonbonded interactions: 1313520 Sorted by model distance: nonbonded pdb=" O HIS G 14 " pdb=" O PHE G 15 " model vdw 2.171 3.040 nonbonded pdb=" O GLN G 18 " pdb=" N ARG G 20 " model vdw 2.240 2.520 nonbonded pdb=" OE1 GLN F 37 " pdb=" O2' G 11124 " model vdw 2.247 2.440 nonbonded pdb=" O LYS T 64 " pdb=" OD1 ASP T 67 " model vdw 2.250 3.040 nonbonded pdb=" NH2 ARG H 171 " pdb=" OP1 G 31106 " model vdw 2.288 2.520 ... (remaining 1313515 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: 4.670 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: 0.160 Extract box with map and model: 22.410 Check model and map are aligned: 1.630 Set scattering table: 1.060 Process input model: 539.040 Find NCS groups from input model: 3.350 Set up NCS constraints: 0.410 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:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 575.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 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 : 0.007 0.060 157481 Z= 0.412 Angle : 0.926 16.736 235693 Z= 0.619 Chirality : 0.079 0.603 30128 Planarity : 0.007 0.062 12572 Dihedral : 22.220 176.987 90355 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 15.39 Ramachandran Plot: Outliers : 1.49 % Allowed : 12.37 % Favored : 86.14 % Rotamer: Outliers : 0.60 % Allowed : 6.32 % Favored : 93.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.45 (0.09), residues: 5651 helix: -2.98 (0.09), residues: 1634 sheet: -2.90 (0.15), residues: 909 loop : -3.00 (0.09), residues: 3108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.006 TRP m 92 HIS 0.002 0.000 HIS T 37 PHE 0.029 0.005 PHE H 22 TYR 0.048 0.007 TYR f 57 ARG 0.007 0.001 ARG q 5 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11302 Ramachandran restraints generated. 5651 Oldfield, 0 Emsley, 5651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11302 Ramachandran restraints generated. 5651 Oldfield, 0 Emsley, 5651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1546 residues out of total 4697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 1518 time to evaluate : 6.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 116 GLN cc_start: 0.8091 (pt0) cc_final: 0.7580 (pt0) REVERT: b 152 GLN cc_start: 0.8243 (mm110) cc_final: 0.7934 (mm110) REVERT: b 224 MET cc_start: 0.8282 (mtm) cc_final: 0.8017 (mtm) REVERT: b 250 GLN cc_start: 0.8388 (tm-30) cc_final: 0.8085 (tm-30) REVERT: b 259 ASN cc_start: 0.7545 (t0) cc_final: 0.7313 (t0) REVERT: b 268 ARG cc_start: 0.6878 (mmt-90) cc_final: 0.6481 (ttm110) REVERT: c 30 GLU cc_start: 0.8019 (tt0) cc_final: 0.7505 (tt0) REVERT: c 128 ARG cc_start: 0.7914 (mtt90) cc_final: 0.7462 (mtp85) REVERT: c 165 MET cc_start: 0.8111 (ttp) cc_final: 0.7829 (ttp) REVERT: d 35 TYR cc_start: 0.8733 (t80) cc_final: 0.8405 (t80) REVERT: d 116 ASP cc_start: 0.8924 (m-30) cc_final: 0.8711 (t0) REVERT: d 119 ILE cc_start: 0.8325 (mm) cc_final: 0.7804 (pt) REVERT: d 143 LEU cc_start: 0.8303 (mt) cc_final: 0.7978 (mt) REVERT: d 152 GLU cc_start: 0.6983 (tm-30) cc_final: 0.6579 (tm-30) REVERT: d 163 ASN cc_start: 0.6398 (OUTLIER) cc_final: 0.6015 (m-40) REVERT: e 21 TYR cc_start: 0.6135 (m-80) cc_final: 0.5600 (m-80) REVERT: e 25 MET cc_start: 0.6317 (mmt) cc_final: 0.5794 (mmm) REVERT: e 34 THR cc_start: 0.5549 (m) cc_final: 0.5030 (m) REVERT: e 86 CYS cc_start: 0.7977 (m) cc_final: 0.7608 (m) REVERT: e 89 THR cc_start: 0.7797 (p) cc_final: 0.7019 (p) REVERT: e 96 TRP cc_start: 0.6040 (m100) cc_final: 0.5831 (m100) REVERT: e 122 ASP cc_start: 0.3315 (t0) cc_final: 0.2517 (m-30) REVERT: e 142 TYR cc_start: 0.5989 (t80) cc_final: 0.5693 (t80) REVERT: e 172 PHE cc_start: 0.6831 (m-80) cc_final: 0.6321 (m-80) REVERT: f 94 ARG cc_start: 0.6218 (mmt-90) cc_final: 0.5925 (tpp80) REVERT: g 48 GLU cc_start: 0.7248 (mm-30) cc_final: 0.6492 (pp20) REVERT: g 55 GLU cc_start: 0.6451 (mm-30) cc_final: 0.6226 (mt-10) REVERT: g 122 LEU cc_start: 0.5306 (mp) cc_final: 0.4968 (tt) REVERT: j 31 GLU cc_start: 0.8152 (tp30) cc_final: 0.7948 (tp30) REVERT: j 60 ASP cc_start: 0.8024 (p0) cc_final: 0.7757 (p0) REVERT: j 108 MET cc_start: 0.8684 (mmp) cc_final: 0.8478 (mmm) REVERT: k 1 MET cc_start: 0.7834 (ttp) cc_final: 0.7625 (ttp) REVERT: k 17 ARG cc_start: 0.8352 (tpp-160) cc_final: 0.8148 (tpp80) REVERT: k 32 TYR cc_start: 0.8314 (m-80) cc_final: 0.8048 (m-10) REVERT: k 37 ASP cc_start: 0.7430 (m-30) cc_final: 0.7131 (m-30) REVERT: k 51 LYS cc_start: 0.8901 (mttm) cc_final: 0.8100 (mtmt) REVERT: k 56 ASP cc_start: 0.7206 (m-30) cc_final: 0.6831 (m-30) REVERT: k 67 LYS cc_start: 0.8730 (tppt) cc_final: 0.8188 (tppt) REVERT: k 88 ASN cc_start: 0.7904 (t0) cc_final: 0.7464 (t0) REVERT: k 121 GLU cc_start: 0.7812 (mp0) cc_final: 0.7421 (mp0) REVERT: l 54 GLN cc_start: 0.7646 (tt0) cc_final: 0.7330 (tt0) REVERT: l 104 GLN cc_start: 0.8199 (mm-40) cc_final: 0.7965 (mm110) REVERT: l 106 GLU cc_start: 0.8214 (mm-30) cc_final: 0.7995 (mm-30) REVERT: l 111 ILE cc_start: 0.8289 (mm) cc_final: 0.7718 (mm) REVERT: m 1 MET cc_start: 0.7084 (mmp) cc_final: 0.6661 (mmp) REVERT: m 22 GLN cc_start: 0.8032 (mm-40) cc_final: 0.7420 (mm-40) REVERT: m 44 ARG cc_start: 0.8780 (mtt180) cc_final: 0.8355 (mmt180) REVERT: m 70 ASP cc_start: 0.8659 (p0) cc_final: 0.8301 (p0) REVERT: m 90 GLU cc_start: 0.7623 (mm-30) cc_final: 0.7362 (mm-30) REVERT: m 104 GLU cc_start: 0.7181 (mt-10) cc_final: 0.6168 (mt-10) REVERT: n 4 ARG cc_start: 0.8025 (mmt180) cc_final: 0.7667 (mmm-85) REVERT: n 20 MET cc_start: 0.8588 (tmm) cc_final: 0.7985 (tpp) REVERT: n 49 GLU cc_start: 0.8317 (mt-10) cc_final: 0.7924 (mt-10) REVERT: n 73 ASN cc_start: 0.8440 (m-40) cc_final: 0.8197 (m-40) REVERT: n 106 ASP cc_start: 0.8679 (p0) cc_final: 0.8140 (p0) REVERT: n 110 MET cc_start: 0.8436 (mmm) cc_final: 0.8152 (mmm) REVERT: o 90 VAL cc_start: 0.8191 (p) cc_final: 0.7642 (m) REVERT: o 92 PHE cc_start: 0.8483 (t80) cc_final: 0.8261 (t80) REVERT: o 97 PHE cc_start: 0.8324 (m-80) cc_final: 0.7734 (m-80) REVERT: o 104 GLN cc_start: 0.8894 (tt0) cc_final: 0.8688 (tm-30) REVERT: o 108 ASP cc_start: 0.8741 (m-30) cc_final: 0.8073 (m-30) REVERT: o 116 GLN cc_start: 0.8323 (mm-40) cc_final: 0.8057 (mp10) REVERT: p 8 GLU cc_start: 0.8078 (pp20) cc_final: 0.7439 (pp20) REVERT: p 12 MET cc_start: 0.7979 (ptp) cc_final: 0.7738 (mtp) REVERT: q 12 ARG cc_start: 0.8697 (mmm160) cc_final: 0.8213 (tpp80) REVERT: q 23 TYR cc_start: 0.7215 (m-80) cc_final: 0.6719 (m-80) REVERT: q 24 TYR cc_start: 0.8472 (t80) cc_final: 0.8127 (t80) REVERT: q 28 SER cc_start: 0.6940 (p) cc_final: 0.6661 (p) REVERT: q 96 ASP cc_start: 0.8685 (t0) cc_final: 0.8070 (t0) REVERT: q 100 PHE cc_start: 0.8524 (m-80) cc_final: 0.8183 (m-10) REVERT: q 110 GLU cc_start: 0.8926 (mm-30) cc_final: 0.8714 (mt-10) REVERT: r 27 ILE cc_start: 0.8191 (mm) cc_final: 0.7742 (tp) REVERT: r 39 LEU cc_start: 0.7657 (mp) cc_final: 0.7349 (mt) REVERT: s 1 MET cc_start: 0.6697 (mmt) cc_final: 0.6072 (ttt) REVERT: s 9 HIS cc_start: 0.8336 (m-70) cc_final: 0.8023 (m-70) REVERT: s 40 ASN cc_start: 0.8973 (p0) cc_final: 0.8387 (p0) REVERT: s 57 ASN cc_start: 0.8740 (m110) cc_final: 0.8450 (m110) REVERT: s 62 ASP cc_start: 0.6583 (m-30) cc_final: 0.5164 (m-30) REVERT: s 67 ASP cc_start: 0.8359 (m-30) cc_final: 0.8141 (m-30) REVERT: s 77 ASP cc_start: 0.8333 (m-30) cc_final: 0.7844 (m-30) REVERT: s 82 MET cc_start: 0.7786 (mpp) cc_final: 0.7404 (mpp) REVERT: t 1 MET cc_start: 0.4622 (mpp) cc_final: 0.3073 (ptm) REVERT: t 5 GLU cc_start: 0.9067 (tm-30) cc_final: 0.8862 (tm-30) REVERT: t 91 GLN cc_start: 0.4555 (pp30) cc_final: 0.4271 (pp30) REVERT: u 8 ASP cc_start: 0.7785 (t70) cc_final: 0.7368 (m-30) REVERT: u 9 GLU cc_start: 0.8452 (pm20) cc_final: 0.8165 (tp30) REVERT: u 36 GLU cc_start: 0.8615 (tp30) cc_final: 0.7904 (tp30) REVERT: v 11 GLU cc_start: 0.9034 (tt0) cc_final: 0.8045 (pm20) REVERT: v 12 GLN cc_start: 0.7758 (pt0) cc_final: 0.7290 (pt0) REVERT: v 35 GLU cc_start: 0.8067 (mt-10) cc_final: 0.7521 (mp0) REVERT: v 41 GLU cc_start: 0.8581 (tm-30) cc_final: 0.8031 (tm-30) REVERT: w 16 ARG cc_start: 0.8476 (mpt180) cc_final: 0.7767 (mmt180) REVERT: w 40 LYS cc_start: 0.8022 (mmmm) cc_final: 0.7760 (mtmt) REVERT: w 51 ARG cc_start: 0.7562 (ptm-80) cc_final: 0.6616 (ptm160) REVERT: w 62 LYS cc_start: 0.8194 (mtpt) cc_final: 0.7854 (mtpp) REVERT: x 24 THR cc_start: 0.8259 (t) cc_final: 0.7934 (p) REVERT: x 48 LEU cc_start: 0.7945 (mt) cc_final: 0.7724 (mp) REVERT: x 70 LEU cc_start: 0.9105 (mm) cc_final: 0.8768 (tp) REVERT: x 75 GLU cc_start: 0.7961 (mm-30) cc_final: 0.7238 (mm-30) REVERT: y 2 LYS cc_start: 0.6927 (pttt) cc_final: 0.6532 (pttp) REVERT: y 8 GLU cc_start: 0.8245 (mm-30) cc_final: 0.7784 (mm-30) REVERT: y 49 ASP cc_start: 0.8693 (m-30) cc_final: 0.8161 (m-30) REVERT: y 52 ARG cc_start: 0.7886 (mtt180) cc_final: 0.7645 (mtt-85) REVERT: z 37 ARG cc_start: 0.7712 (mmt-90) cc_final: 0.7388 (mmt90) REVERT: z 38 GLU cc_start: 0.9087 (pt0) cc_final: 0.8440 (mp0) REVERT: B 45 ASP cc_start: 0.8692 (t0) cc_final: 0.8369 (t70) REVERT: B 47 TYR cc_start: 0.8562 (m-80) cc_final: 0.8197 (m-10) REVERT: B 51 ARG cc_start: 0.8159 (ttp80) cc_final: 0.7798 (ttp-170) REVERT: B 56 LYS cc_start: 0.7292 (tttt) cc_final: 0.7078 (mmtp) REVERT: C 24 LYS cc_start: 0.7370 (ttpp) cc_final: 0.6793 (ttpp) REVERT: C 33 LEU cc_start: 0.7996 (mt) cc_final: 0.7355 (tp) REVERT: C 34 GLU cc_start: 0.7981 (pt0) cc_final: 0.7683 (pt0) REVERT: C 39 ASP cc_start: 0.7743 (t70) cc_final: 0.7309 (t0) REVERT: D 2 LYS cc_start: 0.8145 (ttpt) cc_final: 0.7673 (ttpt) REVERT: D 22 MET cc_start: 0.9242 (mmm) cc_final: 0.8474 (mpp) REVERT: E 48 MET cc_start: 0.7648 (mmm) cc_final: 0.7444 (mmm) REVERT: F 19 ARG cc_start: 0.6438 (ttm110) cc_final: 0.5573 (ttm-80) REVERT: F 32 LYS cc_start: 0.7017 (mtmt) cc_final: 0.6676 (mttt) REVERT: G 73 ARG cc_start: 0.7019 (tpt170) cc_final: 0.6636 (ttt180) REVERT: G 168 GLU cc_start: 0.8076 (mm-30) cc_final: 0.7411 (mp0) REVERT: H 2 GLN cc_start: 0.8134 (pm20) cc_final: 0.7386 (pt0) REVERT: H 17 TRP cc_start: 0.7184 (m-90) cc_final: 0.6737 (m-10) REVERT: H 41 TYR cc_start: 0.7745 (t80) cc_final: 0.7540 (t80) REVERT: H 68 HIS cc_start: 0.7532 (m90) cc_final: 0.7284 (m-70) REVERT: H 74 ILE cc_start: 0.6314 (pt) cc_final: 0.5521 (pt) REVERT: H 107 LYS cc_start: 0.8445 (mptt) cc_final: 0.7832 (mtmt) REVERT: H 125 ARG cc_start: 0.7412 (mtm110) cc_final: 0.5487 (ttm-80) REVERT: H 126 ARG cc_start: 0.5548 (mtt90) cc_final: 0.5175 (mtm180) REVERT: H 138 GLN cc_start: 0.8675 (mp10) cc_final: 0.8288 (mp10) REVERT: H 151 GLU cc_start: 0.6754 (tp30) cc_final: 0.6084 (tm-30) REVERT: H 184 ASN cc_start: 0.6504 (t0) cc_final: 0.6281 (t0) REVERT: H 202 PHE cc_start: 0.7408 (t80) cc_final: 0.6997 (t80) REVERT: I 89 LEU cc_start: 0.8787 (mt) cc_final: 0.8533 (mt) REVERT: I 90 LEU cc_start: 0.7596 (mt) cc_final: 0.7122 (tp) REVERT: I 102 TYR cc_start: 0.7894 (t80) cc_final: 0.7604 (t80) REVERT: I 189 ASP cc_start: 0.8202 (t0) cc_final: 0.7616 (p0) REVERT: I 195 ASN cc_start: 0.7298 (t0) cc_final: 0.6794 (t0) REVERT: I 198 LEU cc_start: 0.7276 (mt) cc_final: 0.7073 (mt) REVERT: I 205 LYS cc_start: 0.6171 (ptmt) cc_final: 0.5914 (ptpp) REVERT: J 25 LYS cc_start: 0.7610 (tmmt) cc_final: 0.7122 (tttt) REVERT: J 79 THR cc_start: 0.8508 (t) cc_final: 0.8039 (m) REVERT: J 81 GLN cc_start: 0.8187 (tp-100) cc_final: 0.6833 (mm110) REVERT: J 87 VAL cc_start: 0.7966 (p) cc_final: 0.7757 (m) REVERT: J 100 GLU cc_start: 0.8439 (mm-30) cc_final: 0.8039 (tp30) REVERT: J 111 ARG cc_start: 0.7404 (ptm-80) cc_final: 0.7158 (ptm160) REVERT: K 1 MET cc_start: 0.5498 (mtm) cc_final: 0.4722 (mtm) REVERT: K 9 MET cc_start: 0.6640 (tpp) cc_final: 0.5952 (tpp) REVERT: K 55 HIS cc_start: 0.8003 (p-80) cc_final: 0.7122 (p-80) REVERT: K 88 MET cc_start: 0.5709 (mmm) cc_final: 0.5181 (mmm) REVERT: K 90 MET cc_start: 0.6648 (ttm) cc_final: 0.6284 (ttm) REVERT: L 24 LYS cc_start: 0.8803 (mmmt) cc_final: 0.8573 (mttt) REVERT: L 32 ASP cc_start: 0.6608 (m-30) cc_final: 0.6396 (m-30) REVERT: L 105 GLU cc_start: 0.7504 (pp20) cc_final: 0.7282 (pp20) REVERT: M 4 ASP cc_start: 0.7307 (t0) cc_final: 0.7102 (t0) REVERT: M 26 MET cc_start: 0.5913 (ptp) cc_final: 0.5345 (mpp) REVERT: M 27 PRO cc_start: 0.5561 (Cg_exo) cc_final: 0.5227 (Cg_endo) REVERT: M 46 GLU cc_start: 0.8327 (mt-10) cc_final: 0.8052 (mp0) REVERT: M 58 LEU cc_start: 0.7434 (tp) cc_final: 0.6587 (tp) REVERT: M 62 LEU cc_start: 0.6889 (mt) cc_final: 0.6518 (mp) REVERT: M 79 ARG cc_start: 0.7998 (mtm110) cc_final: 0.7748 (mtm-85) REVERT: M 89 ASP cc_start: 0.7852 (p0) cc_final: 0.7440 (m-30) REVERT: M 90 GLU cc_start: 0.8066 (mm-30) cc_final: 0.7840 (tp30) REVERT: N 27 ILE cc_start: 0.7622 (mp) cc_final: 0.6702 (mm) REVERT: N 34 LEU cc_start: 0.7649 (mp) cc_final: 0.7096 (tp) REVERT: N 113 LYS cc_start: 0.7744 (ttmt) cc_final: 0.7487 (tttm) REVERT: N 119 LYS cc_start: 0.7010 (pttm) cc_final: 0.6578 (pttm) REVERT: O 13 PHE cc_start: 0.5030 (m-80) cc_final: 0.4792 (m-80) REVERT: O 14 ASP cc_start: 0.8053 (t70) cc_final: 0.7722 (t0) REVERT: O 54 SER cc_start: 0.7910 (t) cc_final: 0.7630 (t) REVERT: O 66 GLU cc_start: 0.6900 (tm-30) cc_final: 0.6622 (tm-30) REVERT: O 67 ILE cc_start: 0.7141 (mm) cc_final: 0.6935 (mt) REVERT: P 26 PHE cc_start: 0.8672 (m-10) cc_final: 0.8257 (m-80) REVERT: P 126 ARG cc_start: 0.6515 (tpp-160) cc_final: 0.6306 (tpp-160) REVERT: Q 9 LYS cc_start: 0.8526 (tppt) cc_final: 0.8253 (ttmt) REVERT: R 71 GLU cc_start: 0.8780 (mt-10) cc_final: 0.8334 (mt-10) REVERT: R 77 LYS cc_start: 0.8525 (mttp) cc_final: 0.8118 (tptt) REVERT: R 79 LEU cc_start: 0.6884 (mp) cc_final: 0.6579 (mt) REVERT: R 101 THR cc_start: 0.7163 (p) cc_final: 0.6638 (p) REVERT: S 76 PHE cc_start: 0.7026 (m-80) cc_final: 0.6675 (m-80) REVERT: S 88 MET cc_start: 0.8226 (mmp) cc_final: 0.7947 (mmm) REVERT: T 44 GLU cc_start: 0.9142 (pt0) cc_final: 0.8886 (mp0) REVERT: T 48 ASP cc_start: 0.7610 (OUTLIER) cc_final: 0.7374 (m-30) REVERT: U 33 ILE cc_start: 0.7298 (mp) cc_final: 0.6844 (mm) REVERT: U 40 ASN cc_start: 0.8446 (t0) cc_final: 0.7984 (t0) REVERT: U 51 ARG cc_start: 0.8078 (ttm170) cc_final: 0.7796 (tpp-160) REVERT: X 43 MET cc_start: 0.4260 (mmp) cc_final: 0.4046 (mtm) REVERT: Y 22 SER cc_start: 0.8250 (p) cc_final: 0.7980 (m) REVERT: Y 81 GLN cc_start: 0.8689 (tt0) cc_final: 0.8346 (tp-100) REVERT: Z 18 PHE cc_start: 0.8455 (t80) cc_final: 0.8178 (t80) REVERT: 8 84 ARG cc_start: 0.8272 (mmm160) cc_final: 0.7554 (ttp-170) REVERT: 8 131 MET cc_start: 0.6437 (ptp) cc_final: 0.6158 (ptp) outliers start: 28 outliers final: 7 residues processed: 1539 average time/residue: 1.3483 time to fit residues: 3512.6536 Evaluate side-chains 1059 residues out of total 4697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 1050 time to evaluate : 6.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 163 ASN Chi-restraints excluded: chain f residue 132 LEU Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain z residue 23 LEU Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain O residue 57 VAL Chi-restraints excluded: chain T residue 48 ASP Chi-restraints excluded: chain W residue 30 ASN Chi-restraints excluded: chain 8 residue 35 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1016 random chunks: chunk 857 optimal weight: 10.0000 chunk 770 optimal weight: 10.0000 chunk 427 optimal weight: 30.0000 chunk 263 optimal weight: 9.9990 chunk 519 optimal weight: 40.0000 chunk 411 optimal weight: 30.0000 chunk 796 optimal weight: 20.0000 chunk 308 optimal weight: 20.0000 chunk 484 optimal weight: 8.9990 chunk 592 optimal weight: 20.0000 chunk 922 optimal weight: 20.0000 overall best weight: 11.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 59 GLN b 85 ASN b 89 ASN b 142 ASN ** c 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 49 GLN d 9 GLN ** d 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 22 ASN e 26 GLN ** f 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 80 HIS k 9 ASN k 93 GLN ** l 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 99 ASN l 104 GLN ** n 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 62 ASN ** n 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 55 HIS p 114 ASN q 36 GLN q 71 ASN ** s 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 57 ASN t 15 HIS t 59 ASN u 68 ASN v 5 ASN ** v 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 75 GLN ** v 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 88 HIS w 42 HIS w 46 ASN w 53 HIS ** x 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 20 ASN z 33 HIS z 48 ASN ** B 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 41 HIS E 42 HIS ** G 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 HIS G 50 ASN G 88 GLN ** G 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 119 GLN H 99 GLN ** H 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 189 HIS ** I 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 39 GLN I 40 HIS ** I 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 130 ASN ** J 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 81 GLN ** J 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 52 ASN K 68 GLN K 81 ASN ** L 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 121 ASN L 129 ASN ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 GLN ** N 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 74 GLN ** O 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 108 ASN ** P 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 118 ASN Q 19 ASN S 61 ASN T 36 ASN U 18 GLN U 29 ASN V 30 HIS Y 2 ASN Y 83 ASN 8 61 HIS Total number of N/Q/H flips: 61 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.123 157481 Z= 0.427 Angle : 0.844 11.435 235693 Z= 0.427 Chirality : 0.044 0.342 30128 Planarity : 0.007 0.080 12572 Dihedral : 23.181 179.027 79044 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 24.62 Ramachandran Plot: Outliers : 0.19 % Allowed : 10.33 % Favored : 89.47 % Rotamer: Outliers : 5.34 % Allowed : 15.18 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % 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: -3.30 (0.10), residues: 5651 helix: -1.48 (0.11), residues: 1743 sheet: -2.38 (0.15), residues: 922 loop : -2.60 (0.10), residues: 2986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP G 22 HIS 0.012 0.002 HIS B 18 PHE 0.047 0.003 PHE e 99 TYR 0.019 0.003 TYR r 2 ARG 0.010 0.001 ARG o 9 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11302 Ramachandran restraints generated. 5651 Oldfield, 0 Emsley, 5651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11302 Ramachandran restraints generated. 5651 Oldfield, 0 Emsley, 5651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1366 residues out of total 4697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 251 poor density : 1115 time to evaluate : 6.496 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: b 113 ASP cc_start: 0.7316 (t70) cc_final: 0.6945 (t70) REVERT: b 116 GLN cc_start: 0.8283 (pt0) cc_final: 0.7952 (pt0) REVERT: b 152 GLN cc_start: 0.7930 (mm110) cc_final: 0.7165 (mt0) REVERT: b 250 GLN cc_start: 0.8186 (tm-30) cc_final: 0.7767 (tm-30) REVERT: c 94 GLN cc_start: 0.7474 (tm-30) cc_final: 0.7262 (tm-30) REVERT: c 128 ARG cc_start: 0.8103 (mtt90) cc_final: 0.7617 (mmm160) REVERT: c 131 ASP cc_start: 0.7981 (p0) cc_final: 0.7758 (p0) REVERT: c 165 MET cc_start: 0.7081 (ttp) cc_final: 0.6858 (ttp) REVERT: d 19 PHE cc_start: 0.8474 (m-10) cc_final: 0.8182 (m-10) REVERT: d 90 GLN cc_start: 0.8615 (pm20) cc_final: 0.7953 (pm20) REVERT: d 100 MET cc_start: 0.8316 (mtm) cc_final: 0.7905 (mtp) REVERT: d 163 ASN cc_start: 0.6250 (OUTLIER) cc_final: 0.5640 (m-40) REVERT: e 21 TYR cc_start: 0.4866 (m-80) cc_final: 0.4590 (m-10) REVERT: e 46 LYS cc_start: 0.5039 (mmtm) cc_final: 0.4613 (mmtm) REVERT: e 86 CYS cc_start: 0.8182 (m) cc_final: 0.7884 (m) REVERT: e 89 THR cc_start: 0.7649 (p) cc_final: 0.7311 (p) REVERT: e 172 PHE cc_start: 0.6817 (m-80) cc_final: 0.6468 (m-80) REVERT: g 1 MET cc_start: 0.5385 (mmm) cc_final: 0.4587 (mmp) REVERT: g 48 GLU cc_start: 0.7304 (mm-30) cc_final: 0.6537 (pp20) REVERT: g 60 GLU cc_start: 0.6300 (mm-30) cc_final: 0.6089 (mp0) REVERT: g 122 LEU cc_start: 0.5216 (mp) cc_final: 0.5006 (tt) REVERT: j 108 MET cc_start: 0.8719 (mmp) cc_final: 0.7996 (mmm) REVERT: j 125 TYR cc_start: 0.8073 (m-10) cc_final: 0.7676 (m-10) REVERT: k 4 GLU cc_start: 0.9116 (mp0) cc_final: 0.8874 (mp0) REVERT: k 7 MET cc_start: 0.8900 (mmt) cc_final: 0.8432 (mmp) REVERT: k 17 ARG cc_start: 0.7881 (tpp-160) cc_final: 0.7088 (mmm-85) REVERT: k 37 ASP cc_start: 0.7844 (m-30) cc_final: 0.7545 (m-30) REVERT: k 45 GLU cc_start: 0.7847 (mm-30) cc_final: 0.7350 (tm-30) REVERT: k 51 LYS cc_start: 0.8937 (mttm) cc_final: 0.8109 (mtmt) REVERT: k 67 LYS cc_start: 0.9149 (tppt) cc_final: 0.8762 (mmmm) REVERT: k 87 LEU cc_start: 0.9155 (mt) cc_final: 0.8944 (mp) REVERT: k 88 ASN cc_start: 0.8587 (t0) cc_final: 0.7928 (t0) REVERT: l 54 GLN cc_start: 0.7793 (tt0) cc_final: 0.7567 (tt0) REVERT: l 104 GLN cc_start: 0.8533 (mm110) cc_final: 0.8209 (mm110) REVERT: l 106 GLU cc_start: 0.8161 (mm-30) cc_final: 0.7871 (mm-30) REVERT: l 111 ILE cc_start: 0.8341 (mm) cc_final: 0.7802 (mm) REVERT: m 1 MET cc_start: 0.7233 (mmp) cc_final: 0.6858 (mmm) REVERT: m 22 GLN cc_start: 0.8386 (mm-40) cc_final: 0.7890 (mm-40) REVERT: m 44 ARG cc_start: 0.8795 (mtt180) cc_final: 0.8378 (mmt180) REVERT: m 70 ASP cc_start: 0.8683 (p0) cc_final: 0.8412 (p0) REVERT: m 90 GLU cc_start: 0.7875 (mm-30) cc_final: 0.7635 (mm-30) REVERT: n 4 ARG cc_start: 0.8468 (mmt180) cc_final: 0.8122 (mmm-85) REVERT: n 43 GLU cc_start: 0.8687 (mm-30) cc_final: 0.8291 (tp30) REVERT: n 49 GLU cc_start: 0.8764 (mt-10) cc_final: 0.8222 (mt-10) REVERT: n 106 ASP cc_start: 0.8323 (p0) cc_final: 0.7979 (p0) REVERT: o 97 PHE cc_start: 0.8199 (m-80) cc_final: 0.7643 (m-80) REVERT: o 104 GLN cc_start: 0.8978 (tt0) cc_final: 0.8669 (tp40) REVERT: o 108 ASP cc_start: 0.8810 (m-30) cc_final: 0.8263 (m-30) REVERT: p 43 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7628 (tp30) REVERT: p 70 GLU cc_start: 0.6399 (mp0) cc_final: 0.6057 (mp0) REVERT: q 12 ARG cc_start: 0.8602 (mmm160) cc_final: 0.8079 (ttm-80) REVERT: q 24 TYR cc_start: 0.8368 (t80) cc_final: 0.7683 (t80) REVERT: r 23 GLU cc_start: 0.7805 (pp20) cc_final: 0.7569 (pp20) REVERT: r 79 ARG cc_start: 0.8785 (ptp90) cc_final: 0.8346 (ttp80) REVERT: r 98 ILE cc_start: 0.8862 (OUTLIER) cc_final: 0.8633 (tt) REVERT: s 9 HIS cc_start: 0.8014 (m-70) cc_final: 0.7810 (m-70) REVERT: s 40 ASN cc_start: 0.9070 (p0) cc_final: 0.8753 (p0) REVERT: s 57 ASN cc_start: 0.8970 (m-40) cc_final: 0.8652 (m-40) REVERT: s 82 MET cc_start: 0.7373 (mpp) cc_final: 0.7099 (mpp) REVERT: t 1 MET cc_start: 0.4714 (mpp) cc_final: 0.2701 (ttp) REVERT: u 8 ASP cc_start: 0.7823 (t0) cc_final: 0.7357 (m-30) REVERT: u 9 GLU cc_start: 0.8485 (pm20) cc_final: 0.8192 (tp30) REVERT: u 65 GLN cc_start: 0.8297 (mt0) cc_final: 0.7897 (mt0) REVERT: u 68 ASN cc_start: 0.8153 (m110) cc_final: 0.7433 (m-40) REVERT: v 1 MET cc_start: 0.8556 (tmm) cc_final: 0.8207 (ppp) REVERT: v 11 GLU cc_start: 0.9037 (tt0) cc_final: 0.8076 (pm20) REVERT: v 12 GLN cc_start: 0.7716 (pt0) cc_final: 0.7331 (pt0) REVERT: v 29 ILE cc_start: 0.8740 (tp) cc_final: 0.8514 (tp) REVERT: v 35 GLU cc_start: 0.8031 (mt-10) cc_final: 0.7497 (mp0) REVERT: v 41 GLU cc_start: 0.8414 (tm-30) cc_final: 0.8188 (tm-30) REVERT: w 16 ARG cc_start: 0.8682 (mpt180) cc_final: 0.8059 (mmm160) REVERT: w 40 LYS cc_start: 0.8112 (mmmm) cc_final: 0.7855 (mtmt) REVERT: w 51 ARG cc_start: 0.7467 (ptm-80) cc_final: 0.6433 (ptm160) REVERT: x 22 ASN cc_start: 0.8341 (m110) cc_final: 0.8115 (m-40) REVERT: x 33 HIS cc_start: 0.5366 (m-70) cc_final: 0.5110 (m-70) REVERT: x 36 ARG cc_start: 0.7785 (ptt-90) cc_final: 0.6690 (ptm160) REVERT: x 70 LEU cc_start: 0.9215 (mm) cc_final: 0.8875 (tp) REVERT: x 75 GLU cc_start: 0.8091 (mm-30) cc_final: 0.7326 (mp0) REVERT: y 2 LYS cc_start: 0.6991 (pttt) cc_final: 0.6594 (pttp) REVERT: y 39 GLN cc_start: 0.8904 (mt0) cc_final: 0.8525 (mt0) REVERT: y 49 ASP cc_start: 0.8568 (m-30) cc_final: 0.8074 (m-30) REVERT: z 18 LYS cc_start: 0.8340 (mmtt) cc_final: 0.8098 (mmtt) REVERT: z 36 GLU cc_start: 0.7017 (mm-30) cc_final: 0.6614 (mm-30) REVERT: z 37 ARG cc_start: 0.7676 (mmt-90) cc_final: 0.6899 (mmt-90) REVERT: z 38 GLU cc_start: 0.9162 (pt0) cc_final: 0.8564 (mp0) REVERT: B 45 ASP cc_start: 0.8717 (t0) cc_final: 0.8264 (t0) REVERT: B 47 TYR cc_start: 0.8589 (m-80) cc_final: 0.8106 (m-80) REVERT: B 51 ARG cc_start: 0.8205 (ttp80) cc_final: 0.7882 (ttp-170) REVERT: C 24 LYS cc_start: 0.7293 (ttpp) cc_final: 0.6671 (ttpp) REVERT: C 33 LEU cc_start: 0.7819 (mt) cc_final: 0.7416 (mp) REVERT: C 50 GLU cc_start: 0.8042 (pt0) cc_final: 0.7828 (pm20) REVERT: D 22 MET cc_start: 0.9238 (mmm) cc_final: 0.8911 (mmm) REVERT: E 21 PHE cc_start: 0.8364 (m-80) cc_final: 0.7539 (m-80) REVERT: E 48 MET cc_start: 0.7550 (mmm) cc_final: 0.7171 (mmm) REVERT: G 73 ARG cc_start: 0.7210 (tpt170) cc_final: 0.6782 (ttt180) REVERT: G 95 TRP cc_start: 0.6185 (t-100) cc_final: 0.5605 (t-100) REVERT: H 2 GLN cc_start: 0.7879 (pm20) cc_final: 0.7630 (pm20) REVERT: H 17 TRP cc_start: 0.7706 (m-90) cc_final: 0.7343 (m-10) REVERT: H 68 HIS cc_start: 0.7467 (m90) cc_final: 0.7244 (m-70) REVERT: H 107 LYS cc_start: 0.8448 (mptt) cc_final: 0.7779 (mtmt) REVERT: H 125 ARG cc_start: 0.7645 (mtm110) cc_final: 0.6959 (mtt-85) REVERT: H 126 ARG cc_start: 0.6052 (mtt90) cc_final: 0.5773 (ptt180) REVERT: H 151 GLU cc_start: 0.6813 (tp30) cc_final: 0.6548 (tm-30) REVERT: H 184 ASN cc_start: 0.6516 (t0) cc_final: 0.5896 (t0) REVERT: H 202 PHE cc_start: 0.7267 (t80) cc_final: 0.6721 (t80) REVERT: I 89 LEU cc_start: 0.8773 (mt) cc_final: 0.8549 (mt) REVERT: I 90 LEU cc_start: 0.7787 (mt) cc_final: 0.7153 (tp) REVERT: I 102 TYR cc_start: 0.7685 (t80) cc_final: 0.7474 (t80) REVERT: I 163 GLN cc_start: 0.7213 (tm-30) cc_final: 0.6997 (pp30) REVERT: I 189 ASP cc_start: 0.8154 (t0) cc_final: 0.7448 (p0) REVERT: I 195 ASN cc_start: 0.7362 (t0) cc_final: 0.7052 (t0) REVERT: J 13 LYS cc_start: 0.7307 (ptpt) cc_final: 0.6999 (ptpt) REVERT: J 25 LYS cc_start: 0.7949 (tmmt) cc_final: 0.7353 (tptt) REVERT: J 81 GLN cc_start: 0.8185 (tp40) cc_final: 0.6907 (mm110) REVERT: J 94 PHE cc_start: 0.7979 (t80) cc_final: 0.7755 (t80) REVERT: J 100 GLU cc_start: 0.8374 (mm-30) cc_final: 0.7819 (tp30) REVERT: J 111 ARG cc_start: 0.7112 (ptm-80) cc_final: 0.6889 (ptm160) REVERT: J 115 GLU cc_start: 0.7945 (mt-10) cc_final: 0.7689 (mt-10) REVERT: J 127 TYR cc_start: 0.8233 (m-80) cc_final: 0.8013 (m-10) REVERT: K 9 MET cc_start: 0.6639 (tpp) cc_final: 0.6187 (tpp) REVERT: K 90 MET cc_start: 0.6672 (ttm) cc_final: 0.6190 (ttp) REVERT: K 91 ARG cc_start: 0.6007 (tpm170) cc_final: 0.5626 (mmm160) REVERT: L 8 GLN cc_start: 0.7201 (pt0) cc_final: 0.6929 (mp10) REVERT: L 24 LYS cc_start: 0.8735 (mmmt) cc_final: 0.8289 (mtpt) REVERT: L 32 ASP cc_start: 0.6801 (m-30) cc_final: 0.6523 (m-30) REVERT: L 105 GLU cc_start: 0.7660 (pp20) cc_final: 0.7424 (pp20) REVERT: M 4 ASP cc_start: 0.7430 (t0) cc_final: 0.6985 (t0) REVERT: M 79 ARG cc_start: 0.8029 (mtm110) cc_final: 0.7739 (mtm-85) REVERT: M 110 MET cc_start: 0.6398 (ptp) cc_final: 0.5635 (pmm) REVERT: N 49 GLN cc_start: 0.7304 (mp10) cc_final: 0.7063 (mp10) REVERT: N 53 LEU cc_start: 0.5662 (tt) cc_final: 0.5277 (mm) REVERT: N 113 LYS cc_start: 0.7931 (ttmt) cc_final: 0.7722 (tttm) REVERT: O 53 ILE cc_start: 0.6437 (tt) cc_final: 0.6010 (pt) REVERT: O 54 SER cc_start: 0.6811 (t) cc_final: 0.6201 (t) REVERT: P 14 GLN cc_start: 0.8590 (pp30) cc_final: 0.8260 (pp30) REVERT: P 26 PHE cc_start: 0.8821 (m-10) cc_final: 0.8421 (m-80) REVERT: P 84 MET cc_start: 0.7977 (ttp) cc_final: 0.7180 (ttt) REVERT: P 85 VAL cc_start: 0.9123 (OUTLIER) cc_final: 0.8900 (p) REVERT: R 101 THR cc_start: 0.7055 (p) cc_final: 0.6810 (p) REVERT: S 6 LYS cc_start: 0.5937 (ttmt) cc_final: 0.5649 (ttmt) REVERT: S 59 GLN cc_start: 0.5193 (mm110) cc_final: 0.4945 (mm-40) REVERT: U 31 ARG cc_start: 0.7351 (tmm-80) cc_final: 0.6877 (tmm-80) REVERT: U 40 ASN cc_start: 0.8547 (t0) cc_final: 0.8120 (t0) REVERT: U 48 GLU cc_start: 0.6165 (mt-10) cc_final: 0.5699 (tt0) REVERT: U 51 ARG cc_start: 0.7964 (ttm170) cc_final: 0.7489 (tmm-80) REVERT: U 53 ASP cc_start: 0.8124 (m-30) cc_final: 0.7664 (p0) REVERT: W 34 GLU cc_start: 0.8094 (mp0) cc_final: 0.7892 (mp0) REVERT: X 43 MET cc_start: 0.4457 (mmp) cc_final: 0.4256 (mtm) REVERT: Y 22 SER cc_start: 0.8217 (p) cc_final: 0.7860 (m) REVERT: Y 23 ARG cc_start: 0.8567 (mmm-85) cc_final: 0.8031 (mmt90) REVERT: Y 81 GLN cc_start: 0.8508 (tt0) cc_final: 0.8227 (tp40) REVERT: 8 84 ARG cc_start: 0.8305 (mmm160) cc_final: 0.7579 (ttp-170) REVERT: 8 131 MET cc_start: 0.6709 (ptp) cc_final: 0.6455 (ptp) outliers start: 251 outliers final: 183 residues processed: 1265 average time/residue: 1.2397 time to fit residues: 2733.2415 Evaluate side-chains 1168 residues out of total 4697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 981 time to evaluate : 6.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 37 SER Chi-restraints excluded: chain b residue 39 SER Chi-restraints excluded: chain b residue 52 HIS Chi-restraints excluded: chain b residue 103 ILE Chi-restraints excluded: chain b residue 173 LEU Chi-restraints excluded: chain b residue 203 VAL Chi-restraints excluded: chain b residue 222 THR Chi-restraints excluded: chain b residue 238 ASN Chi-restraints excluded: chain b residue 256 THR Chi-restraints excluded: chain b residue 265 PHE Chi-restraints excluded: chain c residue 24 VAL Chi-restraints excluded: chain c residue 112 THR Chi-restraints excluded: chain c residue 137 SER Chi-restraints excluded: chain c residue 145 SER Chi-restraints excluded: chain c residue 177 VAL Chi-restraints excluded: chain c residue 189 VAL Chi-restraints excluded: chain c residue 199 SER Chi-restraints excluded: chain d residue 4 VAL Chi-restraints excluded: chain d residue 72 SER Chi-restraints excluded: chain d residue 112 LEU Chi-restraints excluded: chain d residue 113 VAL Chi-restraints excluded: chain d residue 116 ASP Chi-restraints excluded: chain d residue 163 ASN Chi-restraints excluded: chain e residue 11 VAL Chi-restraints excluded: chain e residue 102 LEU Chi-restraints excluded: chain e residue 134 GLN Chi-restraints excluded: chain e residue 157 THR Chi-restraints excluded: chain f residue 24 THR Chi-restraints excluded: chain f residue 42 VAL Chi-restraints excluded: chain f residue 48 THR Chi-restraints excluded: chain f residue 103 ASN Chi-restraints excluded: chain f residue 121 THR Chi-restraints excluded: chain f residue 126 THR Chi-restraints excluded: chain f residue 128 THR Chi-restraints excluded: chain f residue 130 ILE Chi-restraints excluded: chain f residue 132 LEU Chi-restraints excluded: chain g residue 4 ILE Chi-restraints excluded: chain g residue 17 ASP Chi-restraints excluded: chain g residue 18 GLN Chi-restraints excluded: chain j residue 49 ASP Chi-restraints excluded: chain j residue 73 VAL Chi-restraints excluded: chain k residue 22 ILE Chi-restraints excluded: chain k residue 28 SER Chi-restraints excluded: chain l residue 7 SER Chi-restraints excluded: chain l residue 23 ILE Chi-restraints excluded: chain l residue 46 VAL Chi-restraints excluded: chain l residue 85 VAL Chi-restraints excluded: chain m residue 7 THR Chi-restraints excluded: chain m residue 26 VAL Chi-restraints excluded: chain m residue 54 THR Chi-restraints excluded: chain m residue 135 VAL Chi-restraints excluded: chain n residue 13 ASN Chi-restraints excluded: chain n residue 29 VAL Chi-restraints excluded: chain n residue 33 ILE Chi-restraints excluded: chain n residue 36 THR Chi-restraints excluded: chain n residue 60 VAL Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 28 VAL Chi-restraints excluded: chain p residue 6 GLN Chi-restraints excluded: chain p residue 43 GLU Chi-restraints excluded: chain p residue 47 ILE Chi-restraints excluded: chain p residue 85 VAL Chi-restraints excluded: chain q residue 3 VAL Chi-restraints excluded: chain q residue 33 VAL Chi-restraints excluded: chain q residue 86 SER Chi-restraints excluded: chain q residue 103 VAL Chi-restraints excluded: chain q residue 108 LEU Chi-restraints excluded: chain r residue 11 GLN Chi-restraints excluded: chain r residue 37 GLU Chi-restraints excluded: chain r residue 54 VAL Chi-restraints excluded: chain r residue 63 VAL Chi-restraints excluded: chain r residue 75 VAL Chi-restraints excluded: chain r residue 98 ILE Chi-restraints excluded: chain s residue 35 ILE Chi-restraints excluded: chain s residue 45 VAL Chi-restraints excluded: chain s residue 46 LEU Chi-restraints excluded: chain s residue 55 ILE Chi-restraints excluded: chain t residue 8 LEU Chi-restraints excluded: chain t residue 10 VAL Chi-restraints excluded: chain t residue 55 VAL Chi-restraints excluded: chain t residue 63 VAL Chi-restraints excluded: chain u residue 11 ILE Chi-restraints excluded: chain u residue 51 LEU Chi-restraints excluded: chain v residue 5 ASN Chi-restraints excluded: chain v residue 8 VAL Chi-restraints excluded: chain v residue 24 ASN Chi-restraints excluded: chain v residue 45 ASP Chi-restraints excluded: chain v residue 48 MET Chi-restraints excluded: chain v residue 66 ASP Chi-restraints excluded: chain v residue 79 ARG Chi-restraints excluded: chain v residue 86 LEU Chi-restraints excluded: chain w residue 46 ASN Chi-restraints excluded: chain w residue 63 VAL Chi-restraints excluded: chain w residue 71 LYS Chi-restraints excluded: chain x residue 24 THR Chi-restraints excluded: chain x residue 39 VAL Chi-restraints excluded: chain x residue 46 VAL Chi-restraints excluded: chain x residue 47 THR Chi-restraints excluded: chain y residue 11 VAL Chi-restraints excluded: chain y residue 58 ASN Chi-restraints excluded: chain z residue 13 ILE Chi-restraints excluded: chain z residue 23 LEU Chi-restraints excluded: chain z residue 56 VAL Chi-restraints excluded: chain B residue 5 ASN Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 30 HIS Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 196 ASP Chi-restraints excluded: chain G residue 225 SER Chi-restraints excluded: chain H residue 50 SER Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain H residue 197 VAL Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain I residue 67 LEU Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 29 ILE Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 120 HIS Chi-restraints excluded: chain J residue 147 ASN Chi-restraints excluded: chain K residue 39 LEU Chi-restraints excluded: chain K residue 44 ARG Chi-restraints excluded: chain K residue 76 THR Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 76 SER Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 96 ASN Chi-restraints excluded: chain M residue 48 PHE Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 78 SER Chi-restraints excluded: chain M residue 102 VAL Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain M residue 128 VAL Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 71 ILE Chi-restraints excluded: chain N residue 87 MET Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain O residue 42 LEU Chi-restraints excluded: chain O residue 98 VAL Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain P residue 58 THR Chi-restraints excluded: chain P residue 69 CYS Chi-restraints excluded: chain P residue 85 VAL Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 112 VAL Chi-restraints excluded: chain P residue 115 ILE Chi-restraints excluded: chain Q residue 4 ASN Chi-restraints excluded: chain Q residue 23 LEU Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 56 LEU Chi-restraints excluded: chain Q residue 58 ASN Chi-restraints excluded: chain Q residue 78 VAL Chi-restraints excluded: chain R residue 21 ILE Chi-restraints excluded: chain R residue 22 TYR Chi-restraints excluded: chain S residue 26 LEU Chi-restraints excluded: chain S residue 73 LEU Chi-restraints excluded: chain T residue 67 ASP Chi-restraints excluded: chain U residue 66 THR Chi-restraints excluded: chain U residue 79 ASN Chi-restraints excluded: chain V residue 40 THR Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain W residue 30 ASN Chi-restraints excluded: chain W residue 70 THR Chi-restraints excluded: chain X residue 11 ASP Chi-restraints excluded: chain X residue 46 LEU Chi-restraints excluded: chain X residue 73 PHE Chi-restraints excluded: chain Y residue 2 ASN Chi-restraints excluded: chain Y residue 3 ILE Chi-restraints excluded: chain Y residue 11 ILE Chi-restraints excluded: chain Y residue 26 MET Chi-restraints excluded: chain Y residue 34 VAL Chi-restraints excluded: chain Y residue 69 ASN Chi-restraints excluded: chain 8 residue 35 THR Chi-restraints excluded: chain 8 residue 46 SER Chi-restraints excluded: chain 8 residue 71 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1016 random chunks: chunk 512 optimal weight: 20.0000 chunk 286 optimal weight: 3.9990 chunk 767 optimal weight: 10.0000 chunk 628 optimal weight: 10.0000 chunk 254 optimal weight: 10.0000 chunk 924 optimal weight: 20.0000 chunk 998 optimal weight: 20.0000 chunk 823 optimal weight: 10.0000 chunk 916 optimal weight: 10.0000 chunk 315 optimal weight: 9.9990 chunk 741 optimal weight: 20.0000 overall best weight: 8.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 32 ASN d 41 GLN ** d 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 195 GLN ** f 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 114 HIS ** f 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 66 ASN j 58 ASN k 93 GLN ** l 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 9 GLN ** n 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 44 HIS ** v 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 17 HIS ** G 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 53 GLN ** I 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 ASN ** M 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 118 ASN S 3 GLN T 36 ASN ** T 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.3390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 157481 Z= 0.317 Angle : 0.695 10.134 235693 Z= 0.358 Chirality : 0.039 0.374 30128 Planarity : 0.005 0.067 12572 Dihedral : 23.302 178.174 79039 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 20.84 Ramachandran Plot: Outliers : 0.16 % Allowed : 10.44 % Favored : 89.40 % Rotamer: Outliers : 6.43 % Allowed : 18.48 % Favored : 75.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.82 (0.10), residues: 5651 helix: -0.90 (0.11), residues: 1766 sheet: -2.21 (0.15), residues: 944 loop : -2.39 (0.11), residues: 2941 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP G 95 HIS 0.010 0.002 HIS T 45 PHE 0.021 0.002 PHE G 49 TYR 0.025 0.002 TYR I 74 ARG 0.008 0.001 ARG O 62 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11302 Ramachandran restraints generated. 5651 Oldfield, 0 Emsley, 5651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11302 Ramachandran restraints generated. 5651 Oldfield, 0 Emsley, 5651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1363 residues out of total 4697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 302 poor density : 1061 time to evaluate : 6.595 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: b 82 TYR cc_start: 0.8442 (t80) cc_final: 0.8150 (t80) REVERT: b 113 ASP cc_start: 0.7466 (t70) cc_final: 0.7100 (t70) REVERT: b 116 GLN cc_start: 0.8156 (pt0) cc_final: 0.7854 (pt0) REVERT: b 152 GLN cc_start: 0.8094 (mm110) cc_final: 0.7285 (mt0) REVERT: b 160 TYR cc_start: 0.8687 (p90) cc_final: 0.8477 (p90) REVERT: b 250 GLN cc_start: 0.8190 (tm-30) cc_final: 0.7704 (tm-30) REVERT: c 94 GLN cc_start: 0.7543 (tm-30) cc_final: 0.7239 (tm-30) REVERT: c 128 ARG cc_start: 0.8154 (mtt90) cc_final: 0.7609 (mtp85) REVERT: c 145 SER cc_start: 0.9249 (OUTLIER) cc_final: 0.8290 (m) REVERT: c 165 MET cc_start: 0.7079 (ttp) cc_final: 0.6844 (ttp) REVERT: d 19 PHE cc_start: 0.8456 (m-10) cc_final: 0.7915 (m-10) REVERT: d 163 ASN cc_start: 0.6192 (OUTLIER) cc_final: 0.5495 (m110) REVERT: d 195 GLN cc_start: 0.8400 (OUTLIER) cc_final: 0.8144 (tp40) REVERT: e 16 MET cc_start: 0.7522 (tmm) cc_final: 0.7288 (tmm) REVERT: e 89 THR cc_start: 0.7552 (p) cc_final: 0.7342 (p) REVERT: e 124 ARG cc_start: 0.8219 (mmt180) cc_final: 0.7287 (mmm160) REVERT: e 172 PHE cc_start: 0.7041 (m-80) cc_final: 0.6511 (m-80) REVERT: f 61 TRP cc_start: 0.7194 (OUTLIER) cc_final: 0.6740 (t-100) REVERT: g 1 MET cc_start: 0.4993 (mmm) cc_final: 0.4426 (mmm) REVERT: g 48 GLU cc_start: 0.7324 (mm-30) cc_final: 0.6560 (pp20) REVERT: g 60 GLU cc_start: 0.6500 (mm-30) cc_final: 0.6260 (mp0) REVERT: j 16 TYR cc_start: 0.8359 (m-80) cc_final: 0.7930 (m-80) REVERT: j 90 GLU cc_start: 0.9105 (tt0) cc_final: 0.8805 (tp30) REVERT: j 92 MET cc_start: 0.9007 (tpt) cc_final: 0.8785 (tpt) REVERT: j 96 ARG cc_start: 0.7930 (ttp80) cc_final: 0.7549 (ttp80) REVERT: j 108 MET cc_start: 0.8683 (mmp) cc_final: 0.7954 (mmm) REVERT: j 125 TYR cc_start: 0.8005 (m-10) cc_final: 0.7662 (m-10) REVERT: k 1 MET cc_start: 0.8455 (OUTLIER) cc_final: 0.7978 (ttp) REVERT: k 4 GLU cc_start: 0.9107 (mp0) cc_final: 0.8897 (mp0) REVERT: k 7 MET cc_start: 0.8915 (mmt) cc_final: 0.8544 (mmp) REVERT: k 17 ARG cc_start: 0.7892 (tpp-160) cc_final: 0.7050 (mmm-85) REVERT: k 32 TYR cc_start: 0.8497 (m-10) cc_final: 0.8041 (m-10) REVERT: k 45 GLU cc_start: 0.7823 (mm-30) cc_final: 0.7388 (tm-30) REVERT: k 51 LYS cc_start: 0.8881 (mttm) cc_final: 0.7997 (mtmt) REVERT: k 85 VAL cc_start: 0.7828 (OUTLIER) cc_final: 0.7395 (m) REVERT: k 88 ASN cc_start: 0.8546 (t0) cc_final: 0.8250 (t0) REVERT: l 58 TYR cc_start: 0.8565 (p90) cc_final: 0.8258 (p90) REVERT: l 104 GLN cc_start: 0.8616 (mm110) cc_final: 0.8245 (mm110) REVERT: l 106 GLU cc_start: 0.8232 (mm-30) cc_final: 0.7966 (mm-30) REVERT: l 111 ILE cc_start: 0.8207 (mm) cc_final: 0.7672 (mm) REVERT: m 1 MET cc_start: 0.7487 (mmp) cc_final: 0.6968 (mmp) REVERT: m 22 GLN cc_start: 0.8386 (mm-40) cc_final: 0.7949 (mm-40) REVERT: m 44 ARG cc_start: 0.8752 (mtt180) cc_final: 0.8335 (mmt180) REVERT: m 70 ASP cc_start: 0.8583 (p0) cc_final: 0.8354 (p0) REVERT: m 90 GLU cc_start: 0.7746 (mm-30) cc_final: 0.7463 (mm-30) REVERT: m 96 ILE cc_start: 0.8696 (mp) cc_final: 0.8488 (mp) REVERT: n 4 ARG cc_start: 0.8611 (mmt180) cc_final: 0.8220 (mmm-85) REVERT: n 24 MET cc_start: 0.8626 (tpp) cc_final: 0.8205 (mmt) REVERT: n 43 GLU cc_start: 0.8835 (mm-30) cc_final: 0.8465 (tp30) REVERT: n 106 ASP cc_start: 0.8384 (p0) cc_final: 0.8097 (p0) REVERT: o 62 LEU cc_start: 0.6144 (pp) cc_final: 0.5907 (pp) REVERT: o 97 PHE cc_start: 0.8060 (m-80) cc_final: 0.7464 (m-80) REVERT: o 104 GLN cc_start: 0.9012 (tt0) cc_final: 0.8704 (tm-30) REVERT: o 108 ASP cc_start: 0.8795 (m-30) cc_final: 0.7934 (m-30) REVERT: p 43 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7620 (tp30) REVERT: q 24 TYR cc_start: 0.8488 (t80) cc_final: 0.7763 (t80) REVERT: r 23 GLU cc_start: 0.7794 (pp20) cc_final: 0.7338 (pp20) REVERT: r 24 LYS cc_start: 0.8527 (tttt) cc_final: 0.8016 (ttmt) REVERT: r 79 ARG cc_start: 0.8731 (ptp90) cc_final: 0.8278 (ttp80) REVERT: r 98 ILE cc_start: 0.8824 (OUTLIER) cc_final: 0.8624 (tt) REVERT: s 9 HIS cc_start: 0.7983 (m-70) cc_final: 0.7763 (m-70) REVERT: s 40 ASN cc_start: 0.9047 (p0) cc_final: 0.8736 (p0) REVERT: s 57 ASN cc_start: 0.9093 (m-40) cc_final: 0.8726 (m-40) REVERT: s 59 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.8199 (tt0) REVERT: s 88 ARG cc_start: 0.7560 (mmm160) cc_final: 0.6773 (mmm-85) REVERT: s 100 THR cc_start: 0.8685 (m) cc_final: 0.8465 (m) REVERT: t 1 MET cc_start: 0.4963 (mpp) cc_final: 0.2885 (ttm) REVERT: t 48 GLN cc_start: 0.8493 (mt0) cc_final: 0.8276 (mt0) REVERT: u 8 ASP cc_start: 0.8010 (t0) cc_final: 0.7495 (m-30) REVERT: u 9 GLU cc_start: 0.8481 (pm20) cc_final: 0.8144 (tp30) REVERT: u 65 GLN cc_start: 0.8290 (mt0) cc_final: 0.7761 (mt0) REVERT: u 68 ASN cc_start: 0.7596 (m110) cc_final: 0.6736 (m-40) REVERT: v 1 MET cc_start: 0.8583 (OUTLIER) cc_final: 0.8302 (ppp) REVERT: v 11 GLU cc_start: 0.9041 (tt0) cc_final: 0.8106 (pm20) REVERT: v 12 GLN cc_start: 0.7728 (pt0) cc_final: 0.7312 (pt0) REVERT: w 13 GLU cc_start: 0.8835 (tp30) cc_final: 0.8579 (tp30) REVERT: w 40 LYS cc_start: 0.8124 (mmmm) cc_final: 0.7862 (mtmt) REVERT: w 51 ARG cc_start: 0.7374 (ptm-80) cc_final: 0.6476 (ptm160) REVERT: x 22 ASN cc_start: 0.8376 (m110) cc_final: 0.8016 (m-40) REVERT: x 33 HIS cc_start: 0.5482 (m-70) cc_final: 0.5246 (m-70) REVERT: x 36 ARG cc_start: 0.7902 (ptt-90) cc_final: 0.6727 (ptm160) REVERT: y 1 MET cc_start: 0.8160 (mmm) cc_final: 0.7788 (tpt) REVERT: y 2 LYS cc_start: 0.6970 (pttt) cc_final: 0.6610 (pttp) REVERT: y 8 GLU cc_start: 0.7626 (mm-30) cc_final: 0.7398 (mm-30) REVERT: y 49 ASP cc_start: 0.8589 (m-30) cc_final: 0.8044 (m-30) REVERT: z 10 ARG cc_start: 0.8532 (OUTLIER) cc_final: 0.7309 (mpp80) REVERT: z 36 GLU cc_start: 0.6778 (mm-30) cc_final: 0.6446 (mm-30) REVERT: z 37 ARG cc_start: 0.7734 (mmt-90) cc_final: 0.6841 (mmt-90) REVERT: z 38 GLU cc_start: 0.9239 (pt0) cc_final: 0.8590 (mp0) REVERT: B 21 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.7913 (tt) REVERT: B 45 ASP cc_start: 0.8749 (t0) cc_final: 0.8267 (t0) REVERT: B 47 TYR cc_start: 0.8542 (m-80) cc_final: 0.8091 (m-80) REVERT: C 24 LYS cc_start: 0.7334 (ttpp) cc_final: 0.6748 (ttpp) REVERT: C 47 ILE cc_start: 0.7323 (OUTLIER) cc_final: 0.6970 (tt) REVERT: C 49 LYS cc_start: 0.8145 (mmtp) cc_final: 0.7906 (mmtm) REVERT: D 18 PHE cc_start: 0.8476 (t80) cc_final: 0.8261 (t80) REVERT: D 22 MET cc_start: 0.9196 (mmm) cc_final: 0.8930 (tpp) REVERT: E 21 PHE cc_start: 0.8285 (m-80) cc_final: 0.7316 (m-80) REVERT: E 48 MET cc_start: 0.7408 (mmm) cc_final: 0.7049 (mmm) REVERT: F 19 ARG cc_start: 0.6983 (ttm110) cc_final: 0.6634 (ttm110) REVERT: G 26 MET cc_start: 0.7252 (tpp) cc_final: 0.6794 (ttm) REVERT: G 95 TRP cc_start: 0.5770 (t-100) cc_final: 0.5491 (t-100) REVERT: G 99 MET cc_start: 0.8579 (mtt) cc_final: 0.7835 (mtt) REVERT: H 2 GLN cc_start: 0.7832 (pm20) cc_final: 0.7545 (pm20) REVERT: H 17 TRP cc_start: 0.7710 (m-90) cc_final: 0.7307 (m-10) REVERT: H 107 LYS cc_start: 0.8393 (mptt) cc_final: 0.7765 (mtmt) REVERT: H 126 ARG cc_start: 0.6339 (mtt90) cc_final: 0.5890 (ptt180) REVERT: H 133 MET cc_start: 0.7832 (ttt) cc_final: 0.7403 (tmm) REVERT: H 138 GLN cc_start: 0.8319 (mp10) cc_final: 0.8038 (mp10) REVERT: H 151 GLU cc_start: 0.6854 (tp30) cc_final: 0.6648 (tm-30) REVERT: H 184 ASN cc_start: 0.6219 (t0) cc_final: 0.5591 (t0) REVERT: I 195 ASN cc_start: 0.7366 (t0) cc_final: 0.7124 (t0) REVERT: I 205 LYS cc_start: 0.6205 (ptmt) cc_final: 0.5688 (ptpp) REVERT: J 25 LYS cc_start: 0.8060 (tmmt) cc_final: 0.7534 (tptt) REVERT: J 70 MET cc_start: 0.7942 (OUTLIER) cc_final: 0.7037 (mmm) REVERT: J 81 GLN cc_start: 0.8343 (tp40) cc_final: 0.7331 (tt0) REVERT: J 87 VAL cc_start: 0.8156 (p) cc_final: 0.7882 (m) REVERT: J 100 GLU cc_start: 0.8448 (mm-30) cc_final: 0.7877 (tp30) REVERT: J 125 LYS cc_start: 0.6975 (tptp) cc_final: 0.6412 (tptp) REVERT: J 127 TYR cc_start: 0.8244 (m-80) cc_final: 0.8039 (m-10) REVERT: K 9 MET cc_start: 0.6596 (tpp) cc_final: 0.6127 (tpp) REVERT: K 90 MET cc_start: 0.6624 (ttm) cc_final: 0.6140 (ttp) REVERT: K 91 ARG cc_start: 0.5863 (tpm170) cc_final: 0.5611 (mmm160) REVERT: L 24 LYS cc_start: 0.8761 (mmmt) cc_final: 0.8298 (mttt) REVERT: L 32 ASP cc_start: 0.6805 (m-30) cc_final: 0.6459 (m-30) REVERT: L 83 THR cc_start: 0.6802 (OUTLIER) cc_final: 0.6577 (m) REVERT: M 4 ASP cc_start: 0.7293 (t0) cc_final: 0.6571 (t0) REVERT: M 79 ARG cc_start: 0.8037 (mtm110) cc_final: 0.7588 (mtm-85) REVERT: M 90 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7787 (tp30) REVERT: M 110 MET cc_start: 0.6132 (ptp) cc_final: 0.5379 (pmm) REVERT: N 49 GLN cc_start: 0.7340 (mp10) cc_final: 0.7014 (mp10) REVERT: N 53 LEU cc_start: 0.5606 (tt) cc_final: 0.5191 (mm) REVERT: O 13 PHE cc_start: 0.5632 (m-80) cc_final: 0.5414 (m-80) REVERT: O 52 LEU cc_start: 0.5840 (mt) cc_final: 0.5602 (mt) REVERT: O 53 ILE cc_start: 0.6402 (tt) cc_final: 0.5974 (pt) REVERT: O 54 SER cc_start: 0.6863 (t) cc_final: 0.6629 (t) REVERT: O 66 GLU cc_start: 0.8262 (pt0) cc_final: 0.7726 (tm-30) REVERT: P 14 GLN cc_start: 0.8557 (pp30) cc_final: 0.8259 (pp30) REVERT: P 26 PHE cc_start: 0.8661 (m-10) cc_final: 0.8326 (m-80) REVERT: R 71 GLU cc_start: 0.8775 (mt-10) cc_final: 0.8548 (mt-10) REVERT: R 88 LEU cc_start: 0.5825 (OUTLIER) cc_final: 0.5614 (mm) REVERT: S 99 SER cc_start: 0.3181 (t) cc_final: 0.2301 (m) REVERT: U 1 MET cc_start: 0.6329 (tpp) cc_final: 0.6096 (mmt) REVERT: U 31 ARG cc_start: 0.7656 (tmm-80) cc_final: 0.7114 (tmm-80) REVERT: U 40 ASN cc_start: 0.8619 (t0) cc_final: 0.8168 (t0) REVERT: U 48 GLU cc_start: 0.5943 (mt-10) cc_final: 0.5582 (tt0) REVERT: U 51 ARG cc_start: 0.8028 (ttm170) cc_final: 0.7522 (ttt-90) REVERT: U 53 ASP cc_start: 0.7991 (m-30) cc_final: 0.7679 (p0) REVERT: X 43 MET cc_start: 0.4583 (mmp) cc_final: 0.4336 (mtm) REVERT: Y 22 SER cc_start: 0.8208 (p) cc_final: 0.7941 (m) REVERT: Y 23 ARG cc_start: 0.8558 (mmm-85) cc_final: 0.8080 (mmt90) REVERT: Y 81 GLN cc_start: 0.8529 (tt0) cc_final: 0.8161 (tp40) REVERT: 8 84 ARG cc_start: 0.8253 (mmm160) cc_final: 0.7554 (ttp-170) REVERT: 8 131 MET cc_start: 0.6819 (ptp) cc_final: 0.6534 (ptp) outliers start: 302 outliers final: 198 residues processed: 1235 average time/residue: 1.2418 time to fit residues: 2682.2357 Evaluate side-chains 1184 residues out of total 4697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 215 poor density : 969 time to evaluate : 6.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 37 SER Chi-restraints excluded: chain b residue 39 SER Chi-restraints excluded: chain b residue 52 HIS Chi-restraints excluded: chain b residue 63 ILE Chi-restraints excluded: chain b residue 173 LEU Chi-restraints excluded: chain b residue 175 LEU Chi-restraints excluded: chain b residue 222 THR Chi-restraints excluded: chain b residue 238 ASN Chi-restraints excluded: chain b residue 256 THR Chi-restraints excluded: chain c residue 112 THR Chi-restraints excluded: chain c residue 145 SER Chi-restraints excluded: chain c residue 171 THR Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain c residue 177 VAL Chi-restraints excluded: chain c residue 207 VAL Chi-restraints excluded: chain d residue 4 VAL Chi-restraints excluded: chain d residue 72 SER Chi-restraints excluded: chain d residue 84 THR Chi-restraints excluded: chain d residue 112 LEU Chi-restraints excluded: chain d residue 113 VAL Chi-restraints excluded: chain d residue 163 ASN Chi-restraints excluded: chain d residue 195 GLN Chi-restraints excluded: chain e residue 20 ASN Chi-restraints excluded: chain e residue 30 VAL Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 84 ILE Chi-restraints excluded: chain f residue 24 THR Chi-restraints excluded: chain f residue 35 THR Chi-restraints excluded: chain f residue 61 TRP Chi-restraints excluded: chain f residue 103 ASN Chi-restraints excluded: chain f residue 121 THR Chi-restraints excluded: chain f residue 126 THR Chi-restraints excluded: chain f residue 128 THR Chi-restraints excluded: chain f residue 131 VAL Chi-restraints excluded: chain f residue 132 LEU Chi-restraints excluded: chain f residue 136 ASP Chi-restraints excluded: chain f residue 167 VAL Chi-restraints excluded: chain g residue 12 LEU Chi-restraints excluded: chain g residue 17 ASP Chi-restraints excluded: chain j residue 73 VAL Chi-restraints excluded: chain k residue 1 MET Chi-restraints excluded: chain k residue 28 SER Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 77 ILE Chi-restraints excluded: chain k residue 85 VAL Chi-restraints excluded: chain k residue 90 ASN Chi-restraints excluded: chain l residue 7 SER Chi-restraints excluded: chain l residue 23 ILE Chi-restraints excluded: chain l residue 46 VAL Chi-restraints excluded: chain l residue 57 LEU Chi-restraints excluded: chain l residue 61 LEU Chi-restraints excluded: chain l residue 101 ILE Chi-restraints excluded: chain l residue 116 VAL Chi-restraints excluded: chain m residue 54 THR Chi-restraints excluded: chain m residue 73 ILE Chi-restraints excluded: chain m residue 74 THR Chi-restraints excluded: chain m residue 135 VAL Chi-restraints excluded: chain n residue 13 ASN Chi-restraints excluded: chain n residue 14 SER Chi-restraints excluded: chain n residue 33 ILE Chi-restraints excluded: chain n residue 51 LEU Chi-restraints excluded: chain n residue 60 VAL Chi-restraints excluded: chain n residue 74 GLU Chi-restraints excluded: chain o residue 21 LEU Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 28 VAL Chi-restraints excluded: chain o residue 54 VAL Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain p residue 1 SER Chi-restraints excluded: chain p residue 15 ASP Chi-restraints excluded: chain p residue 26 GLU Chi-restraints excluded: chain p residue 29 VAL Chi-restraints excluded: chain p residue 43 GLU Chi-restraints excluded: chain p residue 47 ILE Chi-restraints excluded: chain p residue 85 VAL Chi-restraints excluded: chain q residue 3 VAL Chi-restraints excluded: chain q residue 17 LEU Chi-restraints excluded: chain q residue 33 VAL Chi-restraints excluded: chain q residue 38 VAL Chi-restraints excluded: chain q residue 86 SER Chi-restraints excluded: chain r residue 14 VAL Chi-restraints excluded: chain r residue 54 VAL Chi-restraints excluded: chain r residue 63 VAL Chi-restraints excluded: chain r residue 75 VAL Chi-restraints excluded: chain r residue 98 ILE Chi-restraints excluded: chain s residue 4 ILE Chi-restraints excluded: chain s residue 35 ILE Chi-restraints excluded: chain s residue 45 VAL Chi-restraints excluded: chain s residue 46 LEU Chi-restraints excluded: chain s residue 59 GLU Chi-restraints excluded: chain s residue 77 ASP Chi-restraints excluded: chain t residue 8 LEU Chi-restraints excluded: chain t residue 31 VAL Chi-restraints excluded: chain t residue 62 VAL Chi-restraints excluded: chain u residue 11 ILE Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain u residue 76 THR Chi-restraints excluded: chain v residue 1 MET Chi-restraints excluded: chain v residue 8 VAL Chi-restraints excluded: chain v residue 24 ASN Chi-restraints excluded: chain v residue 45 ASP Chi-restraints excluded: chain v residue 66 ASP Chi-restraints excluded: chain v residue 86 LEU Chi-restraints excluded: chain w residue 42 HIS Chi-restraints excluded: chain w residue 46 ASN Chi-restraints excluded: chain w residue 60 ASP Chi-restraints excluded: chain w residue 63 VAL Chi-restraints excluded: chain w residue 71 LYS Chi-restraints excluded: chain x residue 3 VAL Chi-restraints excluded: chain x residue 46 VAL Chi-restraints excluded: chain x residue 47 THR Chi-restraints excluded: chain y residue 11 VAL Chi-restraints excluded: chain y residue 58 ASN Chi-restraints excluded: chain z residue 10 ARG Chi-restraints excluded: chain z residue 13 ILE Chi-restraints excluded: chain z residue 56 VAL Chi-restraints excluded: chain B residue 5 ASN Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain C residue 4 ILE Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 30 HIS Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain G residue 146 SER Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 196 ASP Chi-restraints excluded: chain H residue 28 PHE Chi-restraints excluded: chain H residue 74 ILE Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 122 GLN Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain H residue 197 VAL Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain I residue 67 LEU Chi-restraints excluded: chain I residue 198 LEU Chi-restraints excluded: chain J residue 29 ILE Chi-restraints excluded: chain J residue 65 LYS Chi-restraints excluded: chain J residue 70 MET Chi-restraints excluded: chain J residue 95 MET Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 135 VAL Chi-restraints excluded: chain K residue 7 VAL Chi-restraints excluded: chain K residue 13 ASP Chi-restraints excluded: chain K residue 44 ARG Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 73 GLU Chi-restraints excluded: chain K residue 76 THR Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 76 SER Chi-restraints excluded: chain L residue 83 THR Chi-restraints excluded: chain L residue 119 LEU Chi-restraints excluded: chain M residue 42 GLU Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 78 SER Chi-restraints excluded: chain M residue 89 ASP Chi-restraints excluded: chain M residue 90 GLU Chi-restraints excluded: chain M residue 102 VAL Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain M residue 113 ARG Chi-restraints excluded: chain M residue 128 VAL Chi-restraints excluded: chain N residue 28 VAL Chi-restraints excluded: chain N residue 67 LYS Chi-restraints excluded: chain N residue 87 MET Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 117 LEU Chi-restraints excluded: chain O residue 42 LEU Chi-restraints excluded: chain O residue 87 LEU Chi-restraints excluded: chain O residue 98 VAL Chi-restraints excluded: chain P residue 29 THR Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain P residue 58 THR Chi-restraints excluded: chain P residue 69 CYS Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 112 VAL Chi-restraints excluded: chain P residue 115 ILE Chi-restraints excluded: chain Q residue 4 ASN Chi-restraints excluded: chain Q residue 23 LEU Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 57 THR Chi-restraints excluded: chain Q residue 58 ASN Chi-restraints excluded: chain Q residue 78 VAL Chi-restraints excluded: chain R residue 21 ILE Chi-restraints excluded: chain R residue 22 TYR Chi-restraints excluded: chain R residue 48 SER Chi-restraints excluded: chain R residue 88 LEU Chi-restraints excluded: chain S residue 26 LEU Chi-restraints excluded: chain S residue 33 VAL Chi-restraints excluded: chain S residue 73 LEU Chi-restraints excluded: chain T residue 31 LEU Chi-restraints excluded: chain T residue 60 SER Chi-restraints excluded: chain T residue 67 ASP Chi-restraints excluded: chain U residue 2 VAL Chi-restraints excluded: chain U residue 79 ASN Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain V residue 40 THR Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain W residue 30 ASN Chi-restraints excluded: chain W residue 70 THR Chi-restraints excluded: chain X residue 46 LEU Chi-restraints excluded: chain X residue 73 PHE Chi-restraints excluded: chain Y residue 3 ILE Chi-restraints excluded: chain Y residue 26 MET Chi-restraints excluded: chain Y residue 69 ASN Chi-restraints excluded: chain Z residue 42 THR Chi-restraints excluded: chain 8 residue 35 THR Chi-restraints excluded: chain 8 residue 46 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1016 random chunks: chunk 913 optimal weight: 20.0000 chunk 694 optimal weight: 10.0000 chunk 479 optimal weight: 5.9990 chunk 102 optimal weight: 0.1980 chunk 441 optimal weight: 10.0000 chunk 620 optimal weight: 20.0000 chunk 927 optimal weight: 20.0000 chunk 982 optimal weight: 20.0000 chunk 484 optimal weight: 50.0000 chunk 879 optimal weight: 30.0000 chunk 264 optimal weight: 0.0870 overall best weight: 5.2568 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 36 GLN d 92 HIS d 195 GLN ** f 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 28 ASN ** l 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 5 ASN ** v 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 3 GLN G 18 GLN ** G 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 68 HIS I 70 GLN ** I 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 145 ASN ** K 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 ASN ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 51 GLN T 45 HIS ** X 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.3686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 157481 Z= 0.213 Angle : 0.615 10.374 235693 Z= 0.318 Chirality : 0.036 0.317 30128 Planarity : 0.005 0.055 12572 Dihedral : 23.293 177.638 79037 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 17.96 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.01 % Favored : 90.85 % Rotamer: Outliers : 5.54 % Allowed : 21.14 % Favored : 73.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.42 (0.11), residues: 5651 helix: -0.51 (0.12), residues: 1783 sheet: -1.90 (0.16), residues: 921 loop : -2.23 (0.11), residues: 2947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 200 HIS 0.013 0.001 HIS Q 76 PHE 0.030 0.002 PHE g 46 TYR 0.027 0.002 TYR L 43 ARG 0.007 0.001 ARG e 91 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11302 Ramachandran restraints generated. 5651 Oldfield, 0 Emsley, 5651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11302 Ramachandran restraints generated. 5651 Oldfield, 0 Emsley, 5651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1332 residues out of total 4697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 260 poor density : 1072 time to evaluate : 6.524 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: b 82 TYR cc_start: 0.8534 (t80) cc_final: 0.8195 (t80) REVERT: b 113 ASP cc_start: 0.7495 (t70) cc_final: 0.7132 (t70) REVERT: b 116 GLN cc_start: 0.8228 (pt0) cc_final: 0.7919 (pt0) REVERT: b 152 GLN cc_start: 0.8001 (mm110) cc_final: 0.7300 (mt0) REVERT: b 250 GLN cc_start: 0.8258 (tm-30) cc_final: 0.7790 (tm-30) REVERT: c 94 GLN cc_start: 0.7807 (tm-30) cc_final: 0.7542 (tm-30) REVERT: c 128 ARG cc_start: 0.8056 (mtt90) cc_final: 0.7540 (mmm160) REVERT: c 168 GLU cc_start: 0.8760 (mm-30) cc_final: 0.7924 (pm20) REVERT: d 19 PHE cc_start: 0.8524 (m-10) cc_final: 0.8015 (m-10) REVERT: d 143 LEU cc_start: 0.8206 (mp) cc_final: 0.7964 (mp) REVERT: d 163 ASN cc_start: 0.5813 (OUTLIER) cc_final: 0.5239 (m110) REVERT: e 25 MET cc_start: 0.6002 (mmt) cc_final: 0.5531 (tpt) REVERT: e 122 ASP cc_start: 0.3971 (t0) cc_final: 0.3238 (m-30) REVERT: e 124 ARG cc_start: 0.8178 (mmt180) cc_final: 0.7284 (mmm160) REVERT: e 168 LEU cc_start: 0.7052 (mp) cc_final: 0.6786 (mp) REVERT: e 172 PHE cc_start: 0.7124 (m-80) cc_final: 0.6560 (m-80) REVERT: f 61 TRP cc_start: 0.7177 (OUTLIER) cc_final: 0.6748 (t-100) REVERT: f 94 ARG cc_start: 0.6762 (mmt-90) cc_final: 0.6194 (ttm170) REVERT: g 1 MET cc_start: 0.5093 (mmm) cc_final: 0.4581 (mmm) REVERT: g 60 GLU cc_start: 0.6430 (mm-30) cc_final: 0.6192 (mp0) REVERT: g 122 LEU cc_start: 0.4884 (mp) cc_final: 0.4637 (tt) REVERT: j 16 TYR cc_start: 0.8333 (m-80) cc_final: 0.7978 (m-80) REVERT: j 92 MET cc_start: 0.9006 (tpt) cc_final: 0.8767 (tpt) REVERT: j 108 MET cc_start: 0.8673 (mmp) cc_final: 0.7884 (mmm) REVERT: j 125 TYR cc_start: 0.7910 (m-10) cc_final: 0.7474 (m-10) REVERT: j 142 ILE cc_start: 0.7328 (tp) cc_final: 0.7095 (tt) REVERT: k 32 TYR cc_start: 0.8358 (m-10) cc_final: 0.7896 (m-10) REVERT: k 45 GLU cc_start: 0.7788 (mm-30) cc_final: 0.7347 (tm-30) REVERT: k 51 LYS cc_start: 0.8855 (mttm) cc_final: 0.8025 (mtmt) REVERT: k 88 ASN cc_start: 0.8644 (t0) cc_final: 0.8119 (t0) REVERT: k 110 GLU cc_start: 0.9116 (tm-30) cc_final: 0.8845 (tp30) REVERT: k 121 GLU cc_start: 0.7874 (mp0) cc_final: 0.7582 (mp0) REVERT: l 58 TYR cc_start: 0.8522 (p90) cc_final: 0.8233 (p90) REVERT: l 104 GLN cc_start: 0.8676 (mm110) cc_final: 0.8242 (mm110) REVERT: l 106 GLU cc_start: 0.8297 (mm-30) cc_final: 0.7994 (mm-30) REVERT: l 111 ILE cc_start: 0.8203 (mm) cc_final: 0.7887 (mm) REVERT: m 1 MET cc_start: 0.7458 (mmp) cc_final: 0.6968 (mmp) REVERT: m 22 GLN cc_start: 0.8376 (mm-40) cc_final: 0.8019 (mm-40) REVERT: m 44 ARG cc_start: 0.8703 (mtt180) cc_final: 0.8295 (mmt180) REVERT: m 90 GLU cc_start: 0.7816 (mm-30) cc_final: 0.7533 (mm-30) REVERT: m 96 ILE cc_start: 0.8657 (mp) cc_final: 0.8454 (mp) REVERT: n 4 ARG cc_start: 0.8678 (mmt180) cc_final: 0.8258 (mmm-85) REVERT: n 24 MET cc_start: 0.8662 (tpp) cc_final: 0.8198 (mmt) REVERT: n 43 GLU cc_start: 0.8789 (mm-30) cc_final: 0.8409 (tp30) REVERT: n 112 TYR cc_start: 0.8629 (m-80) cc_final: 0.8365 (m-80) REVERT: o 97 PHE cc_start: 0.8040 (m-80) cc_final: 0.7402 (m-80) REVERT: o 100 HIS cc_start: 0.7811 (OUTLIER) cc_final: 0.7469 (t-170) REVERT: o 104 GLN cc_start: 0.8993 (tt0) cc_final: 0.8668 (tm-30) REVERT: o 108 ASP cc_start: 0.8907 (m-30) cc_final: 0.8170 (m-30) REVERT: p 8 GLU cc_start: 0.8159 (pp20) cc_final: 0.7798 (pp20) REVERT: p 43 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7683 (tp30) REVERT: q 24 TYR cc_start: 0.8431 (t80) cc_final: 0.7941 (t80) REVERT: r 1 MET cc_start: 0.8062 (tpp) cc_final: 0.7735 (tpp) REVERT: r 16 GLU cc_start: 0.8925 (tm-30) cc_final: 0.8675 (tm-30) REVERT: r 23 GLU cc_start: 0.7796 (pp20) cc_final: 0.7316 (pp20) REVERT: r 24 LYS cc_start: 0.8562 (tttt) cc_final: 0.8031 (ttpt) REVERT: r 98 ILE cc_start: 0.8886 (mm) cc_final: 0.8610 (tt) REVERT: s 9 HIS cc_start: 0.8044 (m-70) cc_final: 0.7832 (m-70) REVERT: s 40 ASN cc_start: 0.8987 (p0) cc_final: 0.8659 (p0) REVERT: s 57 ASN cc_start: 0.9079 (m-40) cc_final: 0.8666 (t0) REVERT: s 100 THR cc_start: 0.8667 (OUTLIER) cc_final: 0.8463 (m) REVERT: t 1 MET cc_start: 0.4714 (mpp) cc_final: 0.2421 (ttp) REVERT: t 48 GLN cc_start: 0.8482 (mt0) cc_final: 0.8247 (mt0) REVERT: u 8 ASP cc_start: 0.7925 (t0) cc_final: 0.7538 (m-30) REVERT: u 9 GLU cc_start: 0.8443 (pm20) cc_final: 0.8178 (tp30) REVERT: u 11 ILE cc_start: 0.8008 (OUTLIER) cc_final: 0.7791 (pt) REVERT: u 65 GLN cc_start: 0.8310 (mt0) cc_final: 0.7807 (mt0) REVERT: u 68 ASN cc_start: 0.7699 (m110) cc_final: 0.6858 (m-40) REVERT: v 1 MET cc_start: 0.8532 (tmm) cc_final: 0.8277 (ppp) REVERT: v 11 GLU cc_start: 0.9024 (tt0) cc_final: 0.8082 (pm20) REVERT: v 12 GLN cc_start: 0.7741 (pt0) cc_final: 0.7324 (pt0) REVERT: v 88 HIS cc_start: 0.7543 (OUTLIER) cc_final: 0.7222 (t70) REVERT: w 33 ILE cc_start: 0.8504 (mt) cc_final: 0.8180 (mp) REVERT: w 40 LYS cc_start: 0.8155 (mmmm) cc_final: 0.7851 (mtmt) REVERT: w 51 ARG cc_start: 0.7309 (ptm-80) cc_final: 0.6468 (ptm160) REVERT: w 62 LYS cc_start: 0.8446 (mtpt) cc_final: 0.8105 (mttm) REVERT: w 79 GLU cc_start: 0.8121 (mm-30) cc_final: 0.7810 (mm-30) REVERT: x 22 ASN cc_start: 0.8372 (m110) cc_final: 0.7969 (m-40) REVERT: x 33 HIS cc_start: 0.5357 (m-70) cc_final: 0.5129 (m-70) REVERT: x 36 ARG cc_start: 0.7896 (ptt-90) cc_final: 0.6683 (ptm160) REVERT: x 75 GLU cc_start: 0.8503 (mm-30) cc_final: 0.7601 (mp0) REVERT: y 2 LYS cc_start: 0.6862 (pttt) cc_final: 0.6444 (pttp) REVERT: y 8 GLU cc_start: 0.7708 (mm-30) cc_final: 0.7358 (mm-30) REVERT: y 49 ASP cc_start: 0.8545 (m-30) cc_final: 0.8032 (m-30) REVERT: z 18 LYS cc_start: 0.8517 (mmtt) cc_final: 0.8139 (mmmt) REVERT: z 36 GLU cc_start: 0.6774 (mm-30) cc_final: 0.6435 (mm-30) REVERT: z 37 ARG cc_start: 0.7781 (mmt-90) cc_final: 0.6880 (mmt-90) REVERT: z 38 GLU cc_start: 0.9263 (pt0) cc_final: 0.8624 (mp0) REVERT: z 40 THR cc_start: 0.7900 (OUTLIER) cc_final: 0.7665 (p) REVERT: B 21 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.7921 (tt) REVERT: B 45 ASP cc_start: 0.8759 (t0) cc_final: 0.8293 (t0) REVERT: B 47 TYR cc_start: 0.8531 (m-80) cc_final: 0.8077 (m-10) REVERT: B 52 LYS cc_start: 0.8454 (tptm) cc_final: 0.8222 (tttp) REVERT: C 24 LYS cc_start: 0.7350 (ttpp) cc_final: 0.6777 (ttpp) REVERT: C 33 LEU cc_start: 0.7799 (mp) cc_final: 0.6700 (tp) REVERT: C 50 GLU cc_start: 0.8039 (pt0) cc_final: 0.7591 (pm20) REVERT: D 18 PHE cc_start: 0.8523 (t80) cc_final: 0.8247 (t80) REVERT: D 22 MET cc_start: 0.9163 (mmm) cc_final: 0.8935 (mmm) REVERT: E 21 PHE cc_start: 0.8264 (m-80) cc_final: 0.7928 (m-80) REVERT: G 26 MET cc_start: 0.7228 (tpp) cc_final: 0.6648 (ttm) REVERT: G 221 ARG cc_start: 0.8760 (mtp85) cc_final: 0.8483 (mtp85) REVERT: H 2 GLN cc_start: 0.7966 (pm20) cc_final: 0.7644 (pm20) REVERT: H 17 TRP cc_start: 0.7694 (m-90) cc_final: 0.7300 (m-10) REVERT: H 107 LYS cc_start: 0.8348 (mptt) cc_final: 0.7718 (mtmt) REVERT: H 125 ARG cc_start: 0.7809 (mtm110) cc_final: 0.7114 (mtt-85) REVERT: H 126 ARG cc_start: 0.6405 (mtt90) cc_final: 0.6118 (ptt180) REVERT: H 151 GLU cc_start: 0.6939 (tp30) cc_final: 0.6686 (tm-30) REVERT: H 184 ASN cc_start: 0.6264 (t0) cc_final: 0.5595 (t0) REVERT: I 70 GLN cc_start: 0.9327 (mt0) cc_final: 0.8967 (mt0) REVERT: I 90 LEU cc_start: 0.7588 (OUTLIER) cc_final: 0.6875 (pp) REVERT: I 189 ASP cc_start: 0.8119 (t0) cc_final: 0.7327 (p0) REVERT: I 195 ASN cc_start: 0.7385 (t0) cc_final: 0.7168 (t0) REVERT: I 205 LYS cc_start: 0.6095 (ptmt) cc_final: 0.5723 (ptpp) REVERT: J 25 LYS cc_start: 0.7996 (tmmt) cc_final: 0.7548 (tptt) REVERT: J 70 MET cc_start: 0.7735 (ttt) cc_final: 0.7056 (mmm) REVERT: J 81 GLN cc_start: 0.8380 (tp40) cc_final: 0.7355 (tt0) REVERT: J 87 VAL cc_start: 0.8046 (p) cc_final: 0.7724 (m) REVERT: J 100 GLU cc_start: 0.8415 (mm-30) cc_final: 0.7858 (tp30) REVERT: J 115 GLU cc_start: 0.7969 (mt-10) cc_final: 0.7737 (mt-10) REVERT: J 125 LYS cc_start: 0.6896 (tptp) cc_final: 0.6278 (tptt) REVERT: J 145 ASN cc_start: 0.8060 (OUTLIER) cc_final: 0.7698 (p0) REVERT: K 9 MET cc_start: 0.6708 (tpp) cc_final: 0.6236 (tpp) REVERT: K 21 MET cc_start: 0.7692 (mmm) cc_final: 0.7281 (tpp) REVERT: K 90 MET cc_start: 0.6551 (ttm) cc_final: 0.6048 (ttp) REVERT: K 91 ARG cc_start: 0.5728 (tpm170) cc_final: 0.5439 (mmm160) REVERT: L 24 LYS cc_start: 0.8737 (mmmt) cc_final: 0.8296 (mttt) REVERT: L 32 ASP cc_start: 0.7003 (m-30) cc_final: 0.6639 (m-30) REVERT: L 83 THR cc_start: 0.6784 (OUTLIER) cc_final: 0.6563 (m) REVERT: M 4 ASP cc_start: 0.7253 (t0) cc_final: 0.6690 (t0) REVERT: M 79 ARG cc_start: 0.8040 (mtm110) cc_final: 0.7592 (mtm-85) REVERT: M 90 GLU cc_start: 0.8105 (tp30) cc_final: 0.7883 (tp30) REVERT: M 110 MET cc_start: 0.6092 (ptp) cc_final: 0.5485 (pmm) REVERT: N 49 GLN cc_start: 0.7249 (mp10) cc_final: 0.7049 (mp10) REVERT: O 53 ILE cc_start: 0.6234 (tt) cc_final: 0.6031 (pt) REVERT: O 54 SER cc_start: 0.6738 (t) cc_final: 0.6521 (t) REVERT: O 66 GLU cc_start: 0.8314 (pt0) cc_final: 0.7688 (tm-30) REVERT: P 14 GLN cc_start: 0.8572 (pp30) cc_final: 0.8326 (pp30) REVERT: P 26 PHE cc_start: 0.8628 (m-10) cc_final: 0.8295 (m-80) REVERT: P 33 ILE cc_start: 0.7840 (mp) cc_final: 0.7613 (tp) REVERT: P 84 MET cc_start: 0.7821 (ttp) cc_final: 0.7232 (ttp) REVERT: R 71 GLU cc_start: 0.8835 (mt-10) cc_final: 0.8627 (mt-10) REVERT: R 88 LEU cc_start: 0.6143 (OUTLIER) cc_final: 0.5923 (mm) REVERT: S 88 MET cc_start: 0.8271 (mmm) cc_final: 0.8057 (mmm) REVERT: S 99 SER cc_start: 0.3375 (t) cc_final: 0.2811 (m) REVERT: U 31 ARG cc_start: 0.7750 (tmm-80) cc_final: 0.7128 (tmm-80) REVERT: U 40 ASN cc_start: 0.8599 (t0) cc_final: 0.8131 (t0) REVERT: U 48 GLU cc_start: 0.6124 (mt-10) cc_final: 0.5619 (tt0) REVERT: W 59 LYS cc_start: 0.8592 (pttp) cc_final: 0.7700 (tttp) REVERT: X 2 ARG cc_start: 0.7292 (mtt-85) cc_final: 0.7030 (mpp80) REVERT: X 43 MET cc_start: 0.4632 (mmp) cc_final: 0.4359 (mtm) REVERT: Y 22 SER cc_start: 0.8135 (p) cc_final: 0.7903 (m) REVERT: Y 23 ARG cc_start: 0.8554 (mmm-85) cc_final: 0.8163 (mmt-90) REVERT: Y 81 GLN cc_start: 0.8544 (tt0) cc_final: 0.8178 (tp40) REVERT: 8 84 ARG cc_start: 0.8290 (mmm160) cc_final: 0.7597 (ttp-170) REVERT: 8 131 MET cc_start: 0.6897 (ptp) cc_final: 0.6642 (ptp) outliers start: 260 outliers final: 182 residues processed: 1230 average time/residue: 1.2437 time to fit residues: 2678.0803 Evaluate side-chains 1187 residues out of total 4697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 195 poor density : 992 time to evaluate : 5.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 37 SER Chi-restraints excluded: chain b residue 173 LEU Chi-restraints excluded: chain b residue 191 LEU Chi-restraints excluded: chain b residue 222 THR Chi-restraints excluded: chain b residue 238 ASN Chi-restraints excluded: chain b residue 256 THR Chi-restraints excluded: chain c residue 24 VAL Chi-restraints excluded: chain c residue 103 ASP Chi-restraints excluded: chain c residue 112 THR Chi-restraints excluded: chain c residue 145 SER Chi-restraints excluded: chain c residue 171 THR Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain c residue 177 VAL Chi-restraints excluded: chain c residue 189 VAL Chi-restraints excluded: chain c residue 200 ASP Chi-restraints excluded: chain c residue 207 VAL Chi-restraints excluded: chain d residue 4 VAL Chi-restraints excluded: chain d residue 72 SER Chi-restraints excluded: chain d residue 112 LEU Chi-restraints excluded: chain d residue 113 VAL Chi-restraints excluded: chain d residue 163 ASN Chi-restraints excluded: chain e residue 11 VAL Chi-restraints excluded: chain e residue 35 LEU Chi-restraints excluded: chain e residue 84 ILE Chi-restraints excluded: chain f residue 24 THR Chi-restraints excluded: chain f residue 61 TRP Chi-restraints excluded: chain f residue 121 THR Chi-restraints excluded: chain f residue 126 THR Chi-restraints excluded: chain f residue 131 VAL Chi-restraints excluded: chain f residue 132 LEU Chi-restraints excluded: chain f residue 136 ASP Chi-restraints excluded: chain f residue 167 VAL Chi-restraints excluded: chain g residue 12 LEU Chi-restraints excluded: chain g residue 17 ASP Chi-restraints excluded: chain j residue 54 ILE Chi-restraints excluded: chain j residue 56 VAL Chi-restraints excluded: chain j residue 73 VAL Chi-restraints excluded: chain j residue 101 ILE Chi-restraints excluded: chain j residue 139 VAL Chi-restraints excluded: chain k residue 22 ILE Chi-restraints excluded: chain k residue 28 SER Chi-restraints excluded: chain k residue 77 ILE Chi-restraints excluded: chain k residue 85 VAL Chi-restraints excluded: chain k residue 90 ASN Chi-restraints excluded: chain l residue 7 SER Chi-restraints excluded: chain l residue 23 ILE Chi-restraints excluded: chain l residue 57 LEU Chi-restraints excluded: chain l residue 85 VAL Chi-restraints excluded: chain m residue 54 THR Chi-restraints excluded: chain m residue 73 ILE Chi-restraints excluded: chain m residue 135 VAL Chi-restraints excluded: chain n residue 13 ASN Chi-restraints excluded: chain n residue 14 SER Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 51 LEU Chi-restraints excluded: chain n residue 74 GLU Chi-restraints excluded: chain o residue 18 LEU Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 28 VAL Chi-restraints excluded: chain o residue 43 ASN Chi-restraints excluded: chain o residue 54 VAL Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain o residue 100 HIS Chi-restraints excluded: chain p residue 1 SER Chi-restraints excluded: chain p residue 26 GLU Chi-restraints excluded: chain p residue 29 VAL Chi-restraints excluded: chain p residue 43 GLU Chi-restraints excluded: chain p residue 47 ILE Chi-restraints excluded: chain p residue 65 ASN Chi-restraints excluded: chain p residue 85 VAL Chi-restraints excluded: chain q residue 3 VAL Chi-restraints excluded: chain q residue 17 LEU Chi-restraints excluded: chain q residue 33 VAL Chi-restraints excluded: chain q residue 86 SER Chi-restraints excluded: chain q residue 99 VAL Chi-restraints excluded: chain r residue 11 GLN Chi-restraints excluded: chain r residue 33 VAL Chi-restraints excluded: chain r residue 54 VAL Chi-restraints excluded: chain r residue 63 VAL Chi-restraints excluded: chain r residue 75 VAL Chi-restraints excluded: chain s residue 4 ILE Chi-restraints excluded: chain s residue 35 ILE Chi-restraints excluded: chain s residue 45 VAL Chi-restraints excluded: chain s residue 46 LEU Chi-restraints excluded: chain s residue 100 THR Chi-restraints excluded: chain t residue 55 VAL Chi-restraints excluded: chain t residue 58 VAL Chi-restraints excluded: chain t residue 62 VAL Chi-restraints excluded: chain t residue 63 VAL Chi-restraints excluded: chain u residue 11 ILE Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain u residue 51 LEU Chi-restraints excluded: chain v residue 8 VAL Chi-restraints excluded: chain v residue 24 ASN Chi-restraints excluded: chain v residue 45 ASP Chi-restraints excluded: chain v residue 66 ASP Chi-restraints excluded: chain v residue 86 LEU Chi-restraints excluded: chain v residue 88 HIS Chi-restraints excluded: chain w residue 42 HIS Chi-restraints excluded: chain w residue 60 ASP Chi-restraints excluded: chain w residue 71 LYS Chi-restraints excluded: chain x residue 24 THR Chi-restraints excluded: chain x residue 39 VAL Chi-restraints excluded: chain x residue 46 VAL Chi-restraints excluded: chain x residue 67 LEU Chi-restraints excluded: chain y residue 58 ASN Chi-restraints excluded: chain z residue 24 LEU Chi-restraints excluded: chain z residue 40 THR Chi-restraints excluded: chain z residue 56 VAL Chi-restraints excluded: chain B residue 5 ASN Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 196 ASP Chi-restraints excluded: chain H residue 28 PHE Chi-restraints excluded: chain H residue 50 SER Chi-restraints excluded: chain H residue 74 ILE Chi-restraints excluded: chain H residue 122 GLN Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 90 LEU Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 29 ILE Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 95 MET Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 145 ASN Chi-restraints excluded: chain J residue 147 ASN Chi-restraints excluded: chain K residue 7 VAL Chi-restraints excluded: chain K residue 73 GLU Chi-restraints excluded: chain K residue 76 THR Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain L residue 42 VAL Chi-restraints excluded: chain L residue 83 THR Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 74 ILE Chi-restraints excluded: chain M residue 78 SER Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain M residue 128 VAL Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain N residue 28 VAL Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 87 MET Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain O residue 42 LEU Chi-restraints excluded: chain O residue 98 VAL Chi-restraints excluded: chain P residue 29 THR Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain P residue 54 SER Chi-restraints excluded: chain P residue 69 CYS Chi-restraints excluded: chain P residue 71 ASP Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 115 ILE Chi-restraints excluded: chain Q residue 4 ASN Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 58 ASN Chi-restraints excluded: chain Q residue 78 VAL Chi-restraints excluded: chain R residue 21 ILE Chi-restraints excluded: chain R residue 48 SER Chi-restraints excluded: chain R residue 88 LEU Chi-restraints excluded: chain S residue 26 LEU Chi-restraints excluded: chain S residue 33 VAL Chi-restraints excluded: chain S residue 73 LEU Chi-restraints excluded: chain T residue 60 SER Chi-restraints excluded: chain T residue 67 ASP Chi-restraints excluded: chain U residue 2 VAL Chi-restraints excluded: chain U residue 66 THR Chi-restraints excluded: chain U residue 79 ASN Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain W residue 30 ASN Chi-restraints excluded: chain W residue 70 THR Chi-restraints excluded: chain X residue 11 ASP Chi-restraints excluded: chain X residue 18 VAL Chi-restraints excluded: chain X residue 46 LEU Chi-restraints excluded: chain X residue 73 PHE Chi-restraints excluded: chain Y residue 3 ILE Chi-restraints excluded: chain Y residue 11 ILE Chi-restraints excluded: chain Y residue 26 MET Chi-restraints excluded: chain Y residue 69 ASN Chi-restraints excluded: chain Z residue 42 THR Chi-restraints excluded: chain 8 residue 35 THR Chi-restraints excluded: chain 8 residue 46 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1016 random chunks: chunk 817 optimal weight: 10.0000 chunk 557 optimal weight: 40.0000 chunk 14 optimal weight: 10.0000 chunk 731 optimal weight: 20.0000 chunk 405 optimal weight: 20.0000 chunk 838 optimal weight: 30.0000 chunk 678 optimal weight: 30.0000 chunk 1 optimal weight: 9.9990 chunk 501 optimal weight: 0.0040 chunk 881 optimal weight: 20.0000 chunk 247 optimal weight: 30.0000 overall best weight: 10.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 114 HIS f 115 GLN f 142 GLN ** l 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 6 GLN p 14 GLN ** r 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 46 ASN ** x 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 119 HIS ** J 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 145 ASN ** K 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 19 ASN ** R 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 83 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.3964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.101 157481 Z= 0.357 Angle : 0.719 12.665 235693 Z= 0.366 Chirality : 0.040 0.344 30128 Planarity : 0.005 0.059 12572 Dihedral : 23.348 178.286 79037 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 22.80 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.40 % Favored : 88.48 % Rotamer: Outliers : 7.47 % Allowed : 20.97 % Favored : 71.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.11), residues: 5651 helix: -0.54 (0.12), residues: 1774 sheet: -1.90 (0.16), residues: 926 loop : -2.25 (0.11), residues: 2951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP H 200 HIS 0.015 0.002 HIS K 55 PHE 0.026 0.002 PHE M 44 TYR 0.029 0.002 TYR I 74 ARG 0.010 0.001 ARG e 91 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11302 Ramachandran restraints generated. 5651 Oldfield, 0 Emsley, 5651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11302 Ramachandran restraints generated. 5651 Oldfield, 0 Emsley, 5651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1351 residues out of total 4697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 351 poor density : 1000 time to evaluate : 6.472 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: b 82 TYR cc_start: 0.8678 (t80) cc_final: 0.8329 (t80) REVERT: b 113 ASP cc_start: 0.7526 (t70) cc_final: 0.7161 (t70) REVERT: b 116 GLN cc_start: 0.8137 (pt0) cc_final: 0.7823 (pt0) REVERT: b 152 GLN cc_start: 0.8122 (mm110) cc_final: 0.7817 (mm110) REVERT: c 94 GLN cc_start: 0.8014 (tm-30) cc_final: 0.7691 (tm-30) REVERT: c 108 ASP cc_start: 0.8391 (m-30) cc_final: 0.8156 (m-30) REVERT: c 128 ARG cc_start: 0.8157 (mtt90) cc_final: 0.7613 (mtp85) REVERT: c 168 GLU cc_start: 0.8743 (mm-30) cc_final: 0.7913 (pm20) REVERT: d 19 PHE cc_start: 0.8518 (m-80) cc_final: 0.7956 (m-10) REVERT: d 116 ASP cc_start: 0.8931 (OUTLIER) cc_final: 0.8419 (t0) REVERT: e 25 MET cc_start: 0.6008 (OUTLIER) cc_final: 0.5549 (tpt) REVERT: e 122 ASP cc_start: 0.3967 (t0) cc_final: 0.3336 (m-30) REVERT: e 124 ARG cc_start: 0.8214 (mmt180) cc_final: 0.7700 (tpp-160) REVERT: f 61 TRP cc_start: 0.7218 (OUTLIER) cc_final: 0.6502 (t-100) REVERT: f 94 ARG cc_start: 0.6751 (mmt-90) cc_final: 0.6169 (ttm170) REVERT: g 1 MET cc_start: 0.5315 (mmm) cc_final: 0.4797 (mmm) REVERT: g 46 PHE cc_start: 0.7415 (t80) cc_final: 0.7058 (t80) REVERT: g 55 GLU cc_start: 0.6591 (mm-30) cc_final: 0.6116 (mt-10) REVERT: j 92 MET cc_start: 0.9029 (tpt) cc_final: 0.8501 (tpt) REVERT: j 96 ARG cc_start: 0.8265 (mtp180) cc_final: 0.8041 (ttp-170) REVERT: j 108 MET cc_start: 0.8760 (mmp) cc_final: 0.8245 (mmm) REVERT: j 125 TYR cc_start: 0.7913 (m-80) cc_final: 0.7538 (m-10) REVERT: j 142 ILE cc_start: 0.7376 (tp) cc_final: 0.7139 (tt) REVERT: k 7 MET cc_start: 0.8913 (mmt) cc_final: 0.8447 (mmp) REVERT: k 32 TYR cc_start: 0.8535 (m-10) cc_final: 0.8171 (m-10) REVERT: k 45 GLU cc_start: 0.7792 (mm-30) cc_final: 0.7194 (tm-30) REVERT: k 88 ASN cc_start: 0.8665 (t0) cc_final: 0.8393 (t0) REVERT: k 105 ARG cc_start: 0.6409 (OUTLIER) cc_final: 0.6006 (tmt170) REVERT: k 110 GLU cc_start: 0.9212 (tm-30) cc_final: 0.8872 (tp30) REVERT: l 58 TYR cc_start: 0.8493 (p90) cc_final: 0.8292 (p90) REVERT: l 79 LEU cc_start: 0.9078 (tp) cc_final: 0.8856 (tp) REVERT: l 104 GLN cc_start: 0.8655 (mm110) cc_final: 0.8220 (mm-40) REVERT: l 106 GLU cc_start: 0.8308 (mm-30) cc_final: 0.8016 (mm-30) REVERT: m 1 MET cc_start: 0.7520 (mmp) cc_final: 0.7062 (mmp) REVERT: m 22 GLN cc_start: 0.8334 (mm-40) cc_final: 0.7933 (mm-40) REVERT: m 44 ARG cc_start: 0.8738 (mtt180) cc_final: 0.8335 (mmt180) REVERT: m 90 GLU cc_start: 0.7862 (mm-30) cc_final: 0.7548 (mm-30) REVERT: n 4 ARG cc_start: 0.8658 (mmt180) cc_final: 0.8095 (mmm-85) REVERT: n 20 MET cc_start: 0.8700 (ttp) cc_final: 0.8373 (ttp) REVERT: n 43 GLU cc_start: 0.8724 (mm-30) cc_final: 0.8391 (tp30) REVERT: n 49 GLU cc_start: 0.8694 (mt-10) cc_final: 0.8411 (mt-10) REVERT: n 106 ASP cc_start: 0.8273 (p0) cc_final: 0.8049 (p0) REVERT: o 97 PHE cc_start: 0.8077 (m-80) cc_final: 0.7497 (m-80) REVERT: o 100 HIS cc_start: 0.7718 (OUTLIER) cc_final: 0.7383 (t-170) REVERT: o 104 GLN cc_start: 0.8976 (tt0) cc_final: 0.8620 (tm-30) REVERT: p 8 GLU cc_start: 0.8288 (pp20) cc_final: 0.7716 (pp20) REVERT: p 12 MET cc_start: 0.7764 (mtt) cc_final: 0.7101 (mtt) REVERT: p 43 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7715 (tp30) REVERT: p 108 ARG cc_start: 0.6421 (mmt-90) cc_final: 0.6185 (mmt-90) REVERT: q 24 TYR cc_start: 0.8527 (t80) cc_final: 0.7905 (t80) REVERT: q 87 VAL cc_start: 0.8749 (t) cc_final: 0.8449 (t) REVERT: r 43 ASN cc_start: 0.8402 (p0) cc_final: 0.8006 (p0) REVERT: s 9 HIS cc_start: 0.8020 (m-70) cc_final: 0.7768 (m-70) REVERT: s 40 ASN cc_start: 0.9062 (p0) cc_final: 0.8717 (p0) REVERT: s 57 ASN cc_start: 0.9066 (m-40) cc_final: 0.8690 (t0) REVERT: s 59 GLU cc_start: 0.8896 (tt0) cc_final: 0.8414 (mt-10) REVERT: t 1 MET cc_start: 0.4745 (mpp) cc_final: 0.2665 (ttp) REVERT: u 8 ASP cc_start: 0.8044 (t0) cc_final: 0.7604 (m-30) REVERT: u 9 GLU cc_start: 0.8455 (pm20) cc_final: 0.8191 (tp30) REVERT: v 1 MET cc_start: 0.8594 (tmm) cc_final: 0.8346 (ppp) REVERT: v 5 ASN cc_start: 0.8933 (OUTLIER) cc_final: 0.8652 (p0) REVERT: v 11 GLU cc_start: 0.8986 (tt0) cc_final: 0.8015 (pm20) REVERT: v 12 GLN cc_start: 0.7721 (pt0) cc_final: 0.7249 (pt0) REVERT: v 35 GLU cc_start: 0.8094 (mt-10) cc_final: 0.7609 (mp0) REVERT: v 59 GLU cc_start: 0.6661 (OUTLIER) cc_final: 0.5228 (tt0) REVERT: v 88 HIS cc_start: 0.7603 (OUTLIER) cc_final: 0.7322 (t70) REVERT: w 33 ILE cc_start: 0.8371 (mt) cc_final: 0.8087 (mp) REVERT: w 40 LYS cc_start: 0.8075 (mmmm) cc_final: 0.7840 (mtmt) REVERT: w 51 ARG cc_start: 0.7322 (ptm-80) cc_final: 0.6373 (ptm160) REVERT: w 62 LYS cc_start: 0.8391 (mtpt) cc_final: 0.7782 (mmtt) REVERT: w 79 GLU cc_start: 0.7992 (mm-30) cc_final: 0.7707 (mm-30) REVERT: x 22 ASN cc_start: 0.8543 (m110) cc_final: 0.8199 (m-40) REVERT: x 33 HIS cc_start: 0.5489 (m-70) cc_final: 0.5281 (m-70) REVERT: x 36 ARG cc_start: 0.7947 (ptt-90) cc_final: 0.6838 (ptm160) REVERT: y 1 MET cc_start: 0.8208 (mmm) cc_final: 0.7294 (tpt) REVERT: y 5 GLU cc_start: 0.8594 (mt-10) cc_final: 0.8202 (mp0) REVERT: y 8 GLU cc_start: 0.7678 (mm-30) cc_final: 0.7432 (mm-30) REVERT: y 49 ASP cc_start: 0.8593 (m-30) cc_final: 0.8056 (m-30) REVERT: z 18 LYS cc_start: 0.8559 (mmtt) cc_final: 0.8166 (mmmt) REVERT: z 37 ARG cc_start: 0.7727 (mmt-90) cc_final: 0.7296 (mmt-90) REVERT: z 38 GLU cc_start: 0.9242 (pt0) cc_final: 0.8623 (mp0) REVERT: z 40 THR cc_start: 0.7896 (OUTLIER) cc_final: 0.7667 (p) REVERT: B 21 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.7954 (tt) REVERT: C 6 GLU cc_start: 0.7716 (mp0) cc_final: 0.7469 (mp0) REVERT: C 50 GLU cc_start: 0.8022 (pt0) cc_final: 0.7764 (pm20) REVERT: D 18 PHE cc_start: 0.8629 (t80) cc_final: 0.8314 (t80) REVERT: G 26 MET cc_start: 0.7295 (tpp) cc_final: 0.6854 (tpp) REVERT: G 221 ARG cc_start: 0.8816 (mtp85) cc_final: 0.8325 (mmt180) REVERT: H 2 GLN cc_start: 0.7895 (pm20) cc_final: 0.7526 (pm20) REVERT: H 17 TRP cc_start: 0.7764 (m-90) cc_final: 0.7327 (m-10) REVERT: H 107 LYS cc_start: 0.8386 (mptt) cc_final: 0.7760 (mtmt) REVERT: H 125 ARG cc_start: 0.7856 (mtm110) cc_final: 0.7195 (mtt-85) REVERT: H 126 ARG cc_start: 0.6505 (mtt90) cc_final: 0.6170 (ptt-90) REVERT: H 133 MET cc_start: 0.7775 (ttt) cc_final: 0.7215 (tmm) REVERT: H 184 ASN cc_start: 0.6253 (t0) cc_final: 0.5607 (t0) REVERT: I 90 LEU cc_start: 0.7444 (OUTLIER) cc_final: 0.6861 (pp) REVERT: I 189 ASP cc_start: 0.8058 (t0) cc_final: 0.7257 (p0) REVERT: I 205 LYS cc_start: 0.6030 (ptmt) cc_final: 0.5547 (ptpp) REVERT: J 13 LYS cc_start: 0.7383 (ptpt) cc_final: 0.7085 (pttt) REVERT: J 25 LYS cc_start: 0.8099 (tmmt) cc_final: 0.7560 (tptt) REVERT: J 70 MET cc_start: 0.7680 (ttt) cc_final: 0.6816 (mmm) REVERT: J 87 VAL cc_start: 0.8044 (p) cc_final: 0.7696 (m) REVERT: J 100 GLU cc_start: 0.8387 (mm-30) cc_final: 0.7860 (tp30) REVERT: J 125 LYS cc_start: 0.6816 (tptp) cc_final: 0.6276 (tptt) REVERT: K 1 MET cc_start: 0.4749 (mtp) cc_final: 0.4483 (ttm) REVERT: K 9 MET cc_start: 0.6814 (tpp) cc_final: 0.6537 (mmm) REVERT: K 33 GLU cc_start: 0.7426 (tm-30) cc_final: 0.7189 (tm-30) REVERT: K 88 MET cc_start: 0.6744 (mmm) cc_final: 0.6528 (mmm) REVERT: K 90 MET cc_start: 0.6699 (ttm) cc_final: 0.6187 (ttm) REVERT: K 91 ARG cc_start: 0.5837 (tpm170) cc_final: 0.5537 (mmm160) REVERT: L 24 LYS cc_start: 0.8793 (mmmt) cc_final: 0.8372 (mttt) REVERT: L 32 ASP cc_start: 0.7038 (m-30) cc_final: 0.6679 (m-30) REVERT: M 4 ASP cc_start: 0.7379 (t0) cc_final: 0.6854 (t0) REVERT: M 44 PHE cc_start: 0.8562 (m-80) cc_final: 0.8207 (m-80) REVERT: M 79 ARG cc_start: 0.8093 (mtm110) cc_final: 0.7619 (mtm-85) REVERT: M 90 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7789 (tp30) REVERT: M 110 MET cc_start: 0.5861 (ptp) cc_final: 0.5317 (pmm) REVERT: O 52 LEU cc_start: 0.5768 (mt) cc_final: 0.5529 (mp) REVERT: O 53 ILE cc_start: 0.6263 (tt) cc_final: 0.5960 (pt) REVERT: P 14 GLN cc_start: 0.8519 (pp30) cc_final: 0.8282 (pp30) REVERT: P 26 PHE cc_start: 0.8670 (m-10) cc_final: 0.8326 (m-80) REVERT: P 84 MET cc_start: 0.7793 (OUTLIER) cc_final: 0.7170 (ttp) REVERT: R 88 LEU cc_start: 0.6162 (OUTLIER) cc_final: 0.5962 (mm) REVERT: S 88 MET cc_start: 0.8404 (mmm) cc_final: 0.8202 (mmm) REVERT: U 31 ARG cc_start: 0.7904 (tmm-80) cc_final: 0.6854 (tmm-80) REVERT: U 40 ASN cc_start: 0.8611 (t0) cc_final: 0.8206 (t0) REVERT: W 34 GLU cc_start: 0.7855 (mt-10) cc_final: 0.7379 (pt0) REVERT: W 59 LYS cc_start: 0.8625 (pttp) cc_final: 0.7809 (tttp) REVERT: X 43 MET cc_start: 0.4657 (mmp) cc_final: 0.4378 (mtm) REVERT: Y 22 SER cc_start: 0.8198 (p) cc_final: 0.7979 (m) REVERT: Y 23 ARG cc_start: 0.8553 (mmm-85) cc_final: 0.8185 (mmt-90) REVERT: Z 18 PHE cc_start: 0.8130 (t80) cc_final: 0.7879 (t80) REVERT: 8 84 ARG cc_start: 0.8259 (mmm160) cc_final: 0.7498 (ttp-170) REVERT: 8 131 MET cc_start: 0.6792 (ptp) cc_final: 0.6516 (ptp) outliers start: 351 outliers final: 274 residues processed: 1210 average time/residue: 1.2388 time to fit residues: 2644.2637 Evaluate side-chains 1251 residues out of total 4697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 289 poor density : 962 time to evaluate : 6.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 15 VAL Chi-restraints excluded: chain b residue 19 VAL Chi-restraints excluded: chain b residue 37 SER Chi-restraints excluded: chain b residue 39 SER Chi-restraints excluded: chain b residue 52 HIS Chi-restraints excluded: chain b residue 53 ILE Chi-restraints excluded: chain b residue 63 ILE Chi-restraints excluded: chain b residue 173 LEU Chi-restraints excluded: chain b residue 222 THR Chi-restraints excluded: chain b residue 238 ASN Chi-restraints excluded: chain b residue 256 THR Chi-restraints excluded: chain c residue 24 VAL Chi-restraints excluded: chain c residue 51 THR Chi-restraints excluded: chain c residue 103 ASP Chi-restraints excluded: chain c residue 112 THR Chi-restraints excluded: chain c residue 139 SER Chi-restraints excluded: chain c residue 145 SER Chi-restraints excluded: chain c residue 171 THR Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain c residue 177 VAL Chi-restraints excluded: chain c residue 189 VAL Chi-restraints excluded: chain c residue 200 ASP Chi-restraints excluded: chain c residue 207 VAL Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 4 VAL Chi-restraints excluded: chain d residue 72 SER Chi-restraints excluded: chain d residue 84 THR Chi-restraints excluded: chain d residue 112 LEU Chi-restraints excluded: chain d residue 113 VAL Chi-restraints excluded: chain d residue 116 ASP Chi-restraints excluded: chain d residue 163 ASN Chi-restraints excluded: chain d residue 167 VAL Chi-restraints excluded: chain d residue 184 ASP Chi-restraints excluded: chain e residue 11 VAL Chi-restraints excluded: chain e residue 25 MET Chi-restraints excluded: chain e residue 26 GLN Chi-restraints excluded: chain e residue 35 LEU Chi-restraints excluded: chain e residue 84 ILE Chi-restraints excluded: chain f residue 24 THR Chi-restraints excluded: chain f residue 35 THR Chi-restraints excluded: chain f residue 44 HIS Chi-restraints excluded: chain f residue 61 TRP Chi-restraints excluded: chain f residue 103 ASN Chi-restraints excluded: chain f residue 121 THR Chi-restraints excluded: chain f residue 126 THR Chi-restraints excluded: chain f residue 131 VAL Chi-restraints excluded: chain f residue 132 LEU Chi-restraints excluded: chain f residue 136 ASP Chi-restraints excluded: chain f residue 167 VAL Chi-restraints excluded: chain g residue 12 LEU Chi-restraints excluded: chain g residue 17 ASP Chi-restraints excluded: chain g residue 127 GLU Chi-restraints excluded: chain j residue 45 THR Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 57 LEU Chi-restraints excluded: chain j residue 73 VAL Chi-restraints excluded: chain j residue 101 ILE Chi-restraints excluded: chain j residue 102 GLU Chi-restraints excluded: chain k residue 22 ILE Chi-restraints excluded: chain k residue 24 VAL Chi-restraints excluded: chain k residue 28 SER Chi-restraints excluded: chain k residue 56 ASP Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 77 ILE Chi-restraints excluded: chain k residue 85 VAL Chi-restraints excluded: chain k residue 86 LEU Chi-restraints excluded: chain k residue 87 LEU Chi-restraints excluded: chain k residue 90 ASN Chi-restraints excluded: chain k residue 105 ARG Chi-restraints excluded: chain l residue 7 SER Chi-restraints excluded: chain l residue 23 ILE Chi-restraints excluded: chain l residue 46 VAL Chi-restraints excluded: chain l residue 57 LEU Chi-restraints excluded: chain l residue 85 VAL Chi-restraints excluded: chain l residue 101 ILE Chi-restraints excluded: chain l residue 116 VAL Chi-restraints excluded: chain m residue 7 THR Chi-restraints excluded: chain m residue 26 VAL Chi-restraints excluded: chain m residue 54 THR Chi-restraints excluded: chain m residue 73 ILE Chi-restraints excluded: chain m residue 74 THR Chi-restraints excluded: chain m residue 104 GLU Chi-restraints excluded: chain m residue 135 VAL Chi-restraints excluded: chain n residue 13 ASN Chi-restraints excluded: chain n residue 14 SER Chi-restraints excluded: chain n residue 33 ILE Chi-restraints excluded: chain n residue 36 THR Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 51 LEU Chi-restraints excluded: chain n residue 60 VAL Chi-restraints excluded: chain n residue 83 LEU Chi-restraints excluded: chain o residue 18 LEU Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 28 VAL Chi-restraints excluded: chain o residue 43 ASN Chi-restraints excluded: chain o residue 54 VAL Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain o residue 93 ASP Chi-restraints excluded: chain o residue 100 HIS Chi-restraints excluded: chain p residue 1 SER Chi-restraints excluded: chain p residue 26 GLU Chi-restraints excluded: chain p residue 29 VAL Chi-restraints excluded: chain p residue 43 GLU Chi-restraints excluded: chain p residue 47 ILE Chi-restraints excluded: chain p residue 65 ASN Chi-restraints excluded: chain p residue 69 VAL Chi-restraints excluded: chain p residue 85 VAL Chi-restraints excluded: chain q residue 3 VAL Chi-restraints excluded: chain q residue 17 LEU Chi-restraints excluded: chain q residue 33 VAL Chi-restraints excluded: chain q residue 38 VAL Chi-restraints excluded: chain q residue 86 SER Chi-restraints excluded: chain q residue 99 VAL Chi-restraints excluded: chain q residue 103 VAL Chi-restraints excluded: chain r residue 11 GLN Chi-restraints excluded: chain r residue 14 VAL Chi-restraints excluded: chain r residue 22 LEU Chi-restraints excluded: chain r residue 33 VAL Chi-restraints excluded: chain r residue 46 GLU Chi-restraints excluded: chain r residue 54 VAL Chi-restraints excluded: chain r residue 63 VAL Chi-restraints excluded: chain r residue 64 VAL Chi-restraints excluded: chain r residue 75 VAL Chi-restraints excluded: chain r residue 94 THR Chi-restraints excluded: chain s residue 4 ILE Chi-restraints excluded: chain s residue 35 ILE Chi-restraints excluded: chain s residue 45 VAL Chi-restraints excluded: chain s residue 46 LEU Chi-restraints excluded: chain s residue 77 ASP Chi-restraints excluded: chain t residue 8 LEU Chi-restraints excluded: chain t residue 10 VAL Chi-restraints excluded: chain t residue 37 ASP Chi-restraints excluded: chain t residue 55 VAL Chi-restraints excluded: chain t residue 58 VAL Chi-restraints excluded: chain t residue 62 VAL Chi-restraints excluded: chain t residue 63 VAL Chi-restraints excluded: chain u residue 11 ILE Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain u residue 51 LEU Chi-restraints excluded: chain v residue 5 ASN Chi-restraints excluded: chain v residue 8 VAL Chi-restraints excluded: chain v residue 24 ASN Chi-restraints excluded: chain v residue 45 ASP Chi-restraints excluded: chain v residue 59 GLU Chi-restraints excluded: chain v residue 66 ASP Chi-restraints excluded: chain v residue 77 VAL Chi-restraints excluded: chain v residue 86 LEU Chi-restraints excluded: chain v residue 88 HIS 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 42 HIS Chi-restraints excluded: chain w residue 46 ASN Chi-restraints excluded: chain w residue 55 LEU Chi-restraints excluded: chain w residue 60 ASP Chi-restraints excluded: chain w residue 67 VAL Chi-restraints excluded: chain w residue 71 LYS Chi-restraints excluded: chain x residue 3 VAL Chi-restraints excluded: chain x residue 24 THR Chi-restraints excluded: chain x residue 39 VAL Chi-restraints excluded: chain x residue 46 VAL Chi-restraints excluded: chain x residue 47 THR Chi-restraints excluded: chain x residue 67 LEU Chi-restraints excluded: chain y residue 11 VAL Chi-restraints excluded: chain y residue 58 ASN Chi-restraints excluded: chain z residue 13 ILE Chi-restraints excluded: chain z residue 24 LEU Chi-restraints excluded: chain z residue 40 THR Chi-restraints excluded: chain z residue 56 VAL Chi-restraints excluded: chain B residue 5 ASN Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 30 HIS Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain G residue 66 ILE Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 146 SER Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 196 ASP Chi-restraints excluded: chain H residue 28 PHE Chi-restraints excluded: chain H residue 50 SER Chi-restraints excluded: chain H residue 74 ILE Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 122 GLN Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain H residue 197 VAL Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain I residue 90 LEU Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 95 MET Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 120 HIS Chi-restraints excluded: chain J residue 135 VAL Chi-restraints excluded: chain J residue 147 ASN Chi-restraints excluded: chain K residue 7 VAL Chi-restraints excluded: chain K residue 13 ASP Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 73 GLU Chi-restraints excluded: chain K residue 76 THR Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain L residue 42 VAL Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 76 SER Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 74 ILE Chi-restraints excluded: chain M residue 90 GLU Chi-restraints excluded: chain M residue 102 VAL Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain M residue 128 VAL Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 24 ASN Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain N residue 28 VAL Chi-restraints excluded: chain N residue 53 LEU Chi-restraints excluded: chain N residue 67 LYS Chi-restraints excluded: chain N residue 87 MET Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain O residue 42 LEU Chi-restraints excluded: chain O residue 96 VAL Chi-restraints excluded: chain O residue 98 VAL Chi-restraints excluded: chain P residue 29 THR Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain P residue 54 SER Chi-restraints excluded: chain P residue 58 THR Chi-restraints excluded: chain P residue 69 CYS Chi-restraints excluded: chain P residue 71 ASP Chi-restraints excluded: chain P residue 83 VAL Chi-restraints excluded: chain P residue 84 MET Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 112 VAL Chi-restraints excluded: chain P residue 115 ILE Chi-restraints excluded: chain P residue 124 LYS Chi-restraints excluded: chain Q residue 4 ASN Chi-restraints excluded: chain Q residue 23 LEU Chi-restraints excluded: chain Q residue 34 THR Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 58 ASN Chi-restraints excluded: chain Q residue 78 VAL Chi-restraints excluded: chain R residue 13 HIS Chi-restraints excluded: chain R residue 21 ILE Chi-restraints excluded: chain R residue 22 TYR Chi-restraints excluded: chain R residue 48 SER Chi-restraints excluded: chain R residue 88 LEU Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain S residue 26 LEU Chi-restraints excluded: chain S residue 33 VAL Chi-restraints excluded: chain S residue 73 LEU Chi-restraints excluded: chain T residue 31 LEU Chi-restraints excluded: chain T residue 60 SER Chi-restraints excluded: chain T residue 67 ASP Chi-restraints excluded: chain U residue 2 VAL Chi-restraints excluded: chain U residue 57 ILE Chi-restraints excluded: chain U residue 66 THR Chi-restraints excluded: chain U residue 79 ASN Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain W residue 20 ILE Chi-restraints excluded: chain W residue 25 ILE Chi-restraints excluded: chain W residue 30 ASN Chi-restraints excluded: chain W residue 70 THR Chi-restraints excluded: chain X residue 11 ASP Chi-restraints excluded: chain X residue 46 LEU Chi-restraints excluded: chain X residue 48 ILE Chi-restraints excluded: chain X residue 65 MET Chi-restraints excluded: chain X residue 73 PHE Chi-restraints excluded: chain Y residue 3 ILE Chi-restraints excluded: chain Y residue 11 ILE Chi-restraints excluded: chain Y residue 69 ASN Chi-restraints excluded: chain Z residue 42 THR Chi-restraints excluded: chain 8 residue 35 THR Chi-restraints excluded: chain 8 residue 46 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1016 random chunks: chunk 330 optimal weight: 40.0000 chunk 884 optimal weight: 20.0000 chunk 194 optimal weight: 9.9990 chunk 576 optimal weight: 20.0000 chunk 242 optimal weight: 7.9990 chunk 983 optimal weight: 40.0000 chunk 816 optimal weight: 10.0000 chunk 455 optimal weight: 8.9990 chunk 81 optimal weight: 30.0000 chunk 325 optimal weight: 1.9990 chunk 516 optimal weight: 9.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 49 GLN f 114 HIS k 3 GLN k 93 GLN ** l 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 6 GLN p 11 GLN q 55 GLN ** r 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 68 ASN ** w 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 25 GLN y 31 GLN ** y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 14 HIS ** G 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 139 ASN I 70 GLN ** I 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.4330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 157481 Z= 0.289 Angle : 0.668 15.964 235693 Z= 0.342 Chirality : 0.038 0.339 30128 Planarity : 0.005 0.094 12572 Dihedral : 23.437 177.120 79037 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 20.88 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.91 % Favored : 89.97 % Rotamer: Outliers : 7.43 % Allowed : 22.42 % Favored : 70.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.32 (0.11), residues: 5651 helix: -0.42 (0.12), residues: 1776 sheet: -1.72 (0.17), residues: 910 loop : -2.22 (0.11), residues: 2965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 200 HIS 0.007 0.001 HIS x 19 PHE 0.020 0.002 PHE D 18 TYR 0.027 0.002 TYR j 16 ARG 0.009 0.001 ARG y 29 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11302 Ramachandran restraints generated. 5651 Oldfield, 0 Emsley, 5651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11302 Ramachandran restraints generated. 5651 Oldfield, 0 Emsley, 5651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1361 residues out of total 4697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 349 poor density : 1012 time to evaluate : 6.445 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: b 82 TYR cc_start: 0.8760 (t80) cc_final: 0.8326 (t80) REVERT: b 113 ASP cc_start: 0.7526 (t70) cc_final: 0.7088 (t70) REVERT: b 116 GLN cc_start: 0.8119 (pt0) cc_final: 0.7729 (pt0) REVERT: b 152 GLN cc_start: 0.8094 (mm110) cc_final: 0.7809 (mm110) REVERT: b 180 MET cc_start: 0.8017 (mpp) cc_final: 0.7601 (mpp) REVERT: c 83 ARG cc_start: 0.8302 (OUTLIER) cc_final: 0.7696 (mpp80) REVERT: c 94 GLN cc_start: 0.7929 (tm-30) cc_final: 0.7561 (tm-30) REVERT: c 128 ARG cc_start: 0.8140 (mtt90) cc_final: 0.7617 (mmm160) REVERT: c 145 SER cc_start: 0.9209 (OUTLIER) cc_final: 0.8472 (m) REVERT: d 19 PHE cc_start: 0.8560 (m-80) cc_final: 0.8086 (m-10) REVERT: d 116 ASP cc_start: 0.8878 (OUTLIER) cc_final: 0.8409 (t0) REVERT: e 25 MET cc_start: 0.6068 (OUTLIER) cc_final: 0.5639 (tpt) REVERT: e 122 ASP cc_start: 0.4099 (t0) cc_final: 0.3539 (m-30) REVERT: e 124 ARG cc_start: 0.8197 (mmt180) cc_final: 0.7486 (mmm-85) REVERT: f 61 TRP cc_start: 0.7092 (OUTLIER) cc_final: 0.6415 (t-100) REVERT: f 94 ARG cc_start: 0.6679 (mmt-90) cc_final: 0.6364 (tmt-80) REVERT: f 98 LYS cc_start: 0.6838 (OUTLIER) cc_final: 0.6607 (mtmm) REVERT: g 1 MET cc_start: 0.5308 (mmm) cc_final: 0.4732 (mmm) REVERT: g 46 PHE cc_start: 0.7520 (t80) cc_final: 0.7117 (t80) REVERT: g 55 GLU cc_start: 0.6736 (mm-30) cc_final: 0.6457 (mt-10) REVERT: g 62 LEU cc_start: 0.6564 (mt) cc_final: 0.6337 (tp) REVERT: j 92 MET cc_start: 0.9035 (tpt) cc_final: 0.8493 (tpt) REVERT: j 108 MET cc_start: 0.8776 (mmt) cc_final: 0.8223 (mmm) REVERT: j 125 TYR cc_start: 0.7924 (m-80) cc_final: 0.7583 (m-10) REVERT: k 7 MET cc_start: 0.9008 (mmt) cc_final: 0.8577 (mmp) REVERT: k 32 TYR cc_start: 0.8422 (m-10) cc_final: 0.8116 (m-10) REVERT: k 45 GLU cc_start: 0.7786 (mm-30) cc_final: 0.7169 (tm-30) REVERT: k 88 ASN cc_start: 0.8662 (t0) cc_final: 0.8105 (t0) REVERT: k 110 GLU cc_start: 0.9130 (tm-30) cc_final: 0.8773 (tp30) REVERT: l 106 GLU cc_start: 0.8304 (mm-30) cc_final: 0.7789 (mm-30) REVERT: m 1 MET cc_start: 0.7508 (mmp) cc_final: 0.7039 (mmp) REVERT: m 22 GLN cc_start: 0.8295 (mm-40) cc_final: 0.7998 (mm-40) REVERT: m 44 ARG cc_start: 0.8746 (mtt180) cc_final: 0.8317 (mmt180) REVERT: n 4 ARG cc_start: 0.8683 (mmt180) cc_final: 0.8086 (mmm-85) REVERT: n 24 MET cc_start: 0.8588 (OUTLIER) cc_final: 0.8344 (mmt) REVERT: n 43 GLU cc_start: 0.8713 (mm-30) cc_final: 0.8330 (tp30) REVERT: n 49 GLU cc_start: 0.8723 (mt-10) cc_final: 0.8466 (mt-10) REVERT: n 106 ASP cc_start: 0.8138 (p0) cc_final: 0.7862 (p0) REVERT: o 97 PHE cc_start: 0.8071 (m-80) cc_final: 0.7475 (m-80) REVERT: o 112 GLU cc_start: 0.9238 (pt0) cc_final: 0.8940 (pp20) REVERT: p 8 GLU cc_start: 0.8505 (pp20) cc_final: 0.7838 (pp20) REVERT: p 12 MET cc_start: 0.7630 (mtt) cc_final: 0.6987 (mtt) REVERT: p 14 GLN cc_start: 0.9253 (tp40) cc_final: 0.9044 (tp40) REVERT: p 43 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7787 (tp30) REVERT: p 108 ARG cc_start: 0.6555 (mmt-90) cc_final: 0.6325 (mmt-90) REVERT: q 24 TYR cc_start: 0.8487 (t80) cc_final: 0.8001 (t80) REVERT: r 1 MET cc_start: 0.7953 (tpt) cc_final: 0.7528 (mmm) REVERT: r 70 GLU cc_start: 0.8672 (pm20) cc_final: 0.8415 (pm20) REVERT: r 79 ARG cc_start: 0.8711 (ptp90) cc_final: 0.8324 (ptm-80) REVERT: r 98 ILE cc_start: 0.8836 (mm) cc_final: 0.8437 (tt) REVERT: s 9 HIS cc_start: 0.8090 (m-70) cc_final: 0.7845 (m-70) REVERT: s 40 ASN cc_start: 0.8986 (p0) cc_final: 0.8629 (p0) REVERT: s 57 ASN cc_start: 0.9058 (m-40) cc_final: 0.8648 (t0) REVERT: s 59 GLU cc_start: 0.8904 (tt0) cc_final: 0.8514 (mt-10) REVERT: s 66 ILE cc_start: 0.8884 (pt) cc_final: 0.8676 (pt) REVERT: t 1 MET cc_start: 0.4467 (mpp) cc_final: 0.2553 (ttp) REVERT: u 8 ASP cc_start: 0.8080 (t0) cc_final: 0.7538 (t0) REVERT: u 65 GLN cc_start: 0.8301 (mt0) cc_final: 0.7865 (mt0) REVERT: u 68 ASN cc_start: 0.7950 (m110) cc_final: 0.7456 (m-40) REVERT: v 1 MET cc_start: 0.8534 (tmm) cc_final: 0.8275 (ppp) REVERT: v 5 ASN cc_start: 0.9000 (p0) cc_final: 0.8718 (p0) REVERT: v 11 GLU cc_start: 0.8901 (tt0) cc_final: 0.7954 (pm20) REVERT: v 12 GLN cc_start: 0.7803 (pt0) cc_final: 0.7261 (pt0) REVERT: v 35 GLU cc_start: 0.8102 (mt-10) cc_final: 0.7613 (mp0) REVERT: v 88 HIS cc_start: 0.7547 (OUTLIER) cc_final: 0.7285 (t70) REVERT: w 33 ILE cc_start: 0.8353 (mt) cc_final: 0.8075 (mp) REVERT: w 40 LYS cc_start: 0.8167 (mmmm) cc_final: 0.7858 (mtmt) REVERT: w 51 ARG cc_start: 0.7282 (ptm-80) cc_final: 0.6364 (ptm160) REVERT: w 62 LYS cc_start: 0.8375 (mtpt) cc_final: 0.8041 (mttm) REVERT: w 77 SER cc_start: 0.8781 (t) cc_final: 0.8558 (t) REVERT: w 79 GLU cc_start: 0.8009 (mm-30) cc_final: 0.7641 (mm-30) REVERT: x 22 ASN cc_start: 0.8525 (m110) cc_final: 0.8161 (m-40) REVERT: x 36 ARG cc_start: 0.7996 (ptt-90) cc_final: 0.6825 (ptm160) REVERT: y 1 MET cc_start: 0.8139 (mmm) cc_final: 0.7216 (tpt) REVERT: y 5 GLU cc_start: 0.8514 (mt-10) cc_final: 0.8157 (mp0) REVERT: y 49 ASP cc_start: 0.8558 (m-30) cc_final: 0.8040 (m-30) REVERT: z 18 LYS cc_start: 0.8577 (mmtt) cc_final: 0.8125 (mmmt) REVERT: z 37 ARG cc_start: 0.7765 (mmt-90) cc_final: 0.6760 (tpp-160) REVERT: z 38 GLU cc_start: 0.9251 (pt0) cc_final: 0.8601 (mp0) REVERT: z 40 THR cc_start: 0.7842 (OUTLIER) cc_final: 0.7616 (p) REVERT: B 21 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8027 (tt) REVERT: B 31 LYS cc_start: 0.8768 (OUTLIER) cc_final: 0.8501 (mmtt) REVERT: D 18 PHE cc_start: 0.8652 (t80) cc_final: 0.8083 (t80) REVERT: E 53 ASP cc_start: 0.8447 (p0) cc_final: 0.8092 (m-30) REVERT: F 19 ARG cc_start: 0.7276 (ttm110) cc_final: 0.6889 (ttm110) REVERT: G 26 MET cc_start: 0.7237 (tpp) cc_final: 0.6533 (ttm) REVERT: G 221 ARG cc_start: 0.8817 (mtp85) cc_final: 0.8328 (mmt180) REVERT: H 2 GLN cc_start: 0.7740 (pm20) cc_final: 0.7520 (pm20) REVERT: H 5 HIS cc_start: 0.7296 (t-90) cc_final: 0.6802 (t-90) REVERT: H 17 TRP cc_start: 0.7816 (m-90) cc_final: 0.7375 (m-10) REVERT: H 125 ARG cc_start: 0.7896 (mtm110) cc_final: 0.7221 (mtt-85) REVERT: H 126 ARG cc_start: 0.6598 (mtt90) cc_final: 0.6191 (ptt180) REVERT: H 133 MET cc_start: 0.7829 (ttt) cc_final: 0.7318 (tmm) REVERT: H 138 GLN cc_start: 0.8372 (mp10) cc_final: 0.8117 (mp10) REVERT: H 182 ASP cc_start: 0.7902 (t0) cc_final: 0.7627 (t0) REVERT: H 184 ASN cc_start: 0.6196 (t0) cc_final: 0.5903 (t0) REVERT: I 90 LEU cc_start: 0.7494 (mm) cc_final: 0.7125 (tp) REVERT: I 123 MET cc_start: 0.7143 (mmm) cc_final: 0.6674 (mmm) REVERT: I 170 LEU cc_start: 0.6449 (OUTLIER) cc_final: 0.6065 (pp) REVERT: I 189 ASP cc_start: 0.8194 (t0) cc_final: 0.7415 (p0) REVERT: I 196 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7083 (mt-10) REVERT: I 205 LYS cc_start: 0.5878 (ptmt) cc_final: 0.5402 (ptpp) REVERT: J 25 LYS cc_start: 0.8105 (tmmt) cc_final: 0.7653 (tptt) REVERT: J 70 MET cc_start: 0.7588 (ttt) cc_final: 0.6721 (mmm) REVERT: J 87 VAL cc_start: 0.7930 (p) cc_final: 0.7595 (m) REVERT: J 100 GLU cc_start: 0.8341 (mm-30) cc_final: 0.7811 (tp30) REVERT: J 125 LYS cc_start: 0.6771 (tptp) cc_final: 0.6216 (tptt) REVERT: K 9 MET cc_start: 0.6854 (tpp) cc_final: 0.6556 (tpp) REVERT: K 33 GLU cc_start: 0.7634 (tm-30) cc_final: 0.7321 (tm-30) REVERT: K 41 ASP cc_start: 0.8553 (p0) cc_final: 0.8244 (t0) REVERT: K 90 MET cc_start: 0.6661 (ttm) cc_final: 0.6004 (ttp) REVERT: K 91 ARG cc_start: 0.5822 (tpm170) cc_final: 0.5413 (mmm160) REVERT: L 24 LYS cc_start: 0.8839 (mmmt) cc_final: 0.8385 (mttt) REVERT: L 32 ASP cc_start: 0.7038 (m-30) cc_final: 0.6684 (m-30) REVERT: M 4 ASP cc_start: 0.7500 (t0) cc_final: 0.6971 (t0) REVERT: M 79 ARG cc_start: 0.8117 (mtm110) cc_final: 0.7622 (mtm-85) REVERT: M 90 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7949 (tp30) REVERT: M 110 MET cc_start: 0.5763 (ptp) cc_final: 0.5386 (pmm) REVERT: P 26 PHE cc_start: 0.8608 (m-10) cc_final: 0.8261 (m-80) REVERT: U 31 ARG cc_start: 0.7880 (tmm-80) cc_final: 0.6817 (tmm-80) REVERT: U 40 ASN cc_start: 0.8604 (t0) cc_final: 0.8152 (t0) REVERT: W 59 LYS cc_start: 0.8523 (pttp) cc_final: 0.7713 (tptt) REVERT: X 43 MET cc_start: 0.4612 (mmp) cc_final: 0.4359 (mtm) REVERT: Y 22 SER cc_start: 0.8193 (p) cc_final: 0.7971 (m) REVERT: Y 23 ARG cc_start: 0.8508 (mmm-85) cc_final: 0.8122 (mmt-90) REVERT: 8 84 ARG cc_start: 0.8273 (mmm160) cc_final: 0.7478 (ttp-170) REVERT: 8 131 MET cc_start: 0.6981 (ptp) cc_final: 0.6580 (ptp) outliers start: 349 outliers final: 270 residues processed: 1228 average time/residue: 1.2187 time to fit residues: 2628.8597 Evaluate side-chains 1244 residues out of total 4697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 285 poor density : 959 time to evaluate : 6.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 15 VAL Chi-restraints excluded: chain b residue 19 VAL Chi-restraints excluded: chain b residue 37 SER Chi-restraints excluded: chain b residue 39 SER Chi-restraints excluded: chain b residue 52 HIS Chi-restraints excluded: chain b residue 53 ILE Chi-restraints excluded: chain b residue 63 ILE Chi-restraints excluded: chain b residue 86 ARG Chi-restraints excluded: chain b residue 173 LEU Chi-restraints excluded: chain b residue 222 THR Chi-restraints excluded: chain b residue 238 ASN Chi-restraints excluded: chain b residue 256 THR Chi-restraints excluded: chain c residue 24 VAL Chi-restraints excluded: chain c residue 61 THR Chi-restraints excluded: chain c residue 83 ARG Chi-restraints excluded: chain c residue 103 ASP Chi-restraints excluded: chain c residue 112 THR Chi-restraints excluded: chain c residue 122 VAL Chi-restraints excluded: chain c residue 145 SER Chi-restraints excluded: chain c residue 171 THR Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain c residue 177 VAL Chi-restraints excluded: chain c residue 189 VAL Chi-restraints excluded: chain c residue 200 ASP Chi-restraints excluded: chain c residue 207 VAL Chi-restraints excluded: chain d residue 4 VAL Chi-restraints excluded: chain d residue 72 SER Chi-restraints excluded: chain d residue 84 THR Chi-restraints excluded: chain d residue 113 VAL Chi-restraints excluded: chain d residue 116 ASP Chi-restraints excluded: chain d residue 131 THR Chi-restraints excluded: chain d residue 163 ASN Chi-restraints excluded: chain d residue 167 VAL Chi-restraints excluded: chain e residue 11 VAL Chi-restraints excluded: chain e residue 20 ASN Chi-restraints excluded: chain e residue 25 MET Chi-restraints excluded: chain e residue 26 GLN Chi-restraints excluded: chain e residue 35 LEU Chi-restraints excluded: chain e residue 84 ILE Chi-restraints excluded: chain f residue 24 THR Chi-restraints excluded: chain f residue 59 ASP Chi-restraints excluded: chain f residue 61 TRP Chi-restraints excluded: chain f residue 71 LEU Chi-restraints excluded: chain f residue 98 LYS Chi-restraints excluded: chain f residue 101 VAL Chi-restraints excluded: chain f residue 103 ASN Chi-restraints excluded: chain f residue 121 THR Chi-restraints excluded: chain f residue 126 THR Chi-restraints excluded: chain f residue 131 VAL Chi-restraints excluded: chain f residue 132 LEU Chi-restraints excluded: chain f residue 136 ASP Chi-restraints excluded: chain f residue 167 VAL Chi-restraints excluded: chain g residue 12 LEU Chi-restraints excluded: chain g residue 17 ASP Chi-restraints excluded: chain g residue 127 GLU Chi-restraints excluded: chain j residue 12 LYS Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 54 ILE Chi-restraints excluded: chain j residue 57 LEU Chi-restraints excluded: chain j residue 73 VAL Chi-restraints excluded: chain j residue 78 THR Chi-restraints excluded: chain j residue 101 ILE Chi-restraints excluded: chain k residue 22 ILE Chi-restraints excluded: chain k residue 24 VAL Chi-restraints excluded: chain k residue 28 SER Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 77 ILE Chi-restraints excluded: chain k residue 85 VAL Chi-restraints excluded: chain k residue 86 LEU Chi-restraints excluded: chain k residue 90 ASN Chi-restraints excluded: chain l residue 7 SER Chi-restraints excluded: chain l residue 23 ILE Chi-restraints excluded: chain l residue 46 VAL Chi-restraints excluded: chain l residue 57 LEU Chi-restraints excluded: chain l residue 85 VAL Chi-restraints excluded: chain l residue 101 ILE Chi-restraints excluded: chain l residue 116 VAL Chi-restraints excluded: chain m residue 73 ILE Chi-restraints excluded: chain m residue 74 THR Chi-restraints excluded: chain m residue 104 GLU Chi-restraints excluded: chain m residue 126 ILE Chi-restraints excluded: chain m residue 135 VAL Chi-restraints excluded: chain n residue 13 ASN Chi-restraints excluded: chain n residue 14 SER Chi-restraints excluded: chain n residue 24 MET Chi-restraints excluded: chain n residue 33 ILE Chi-restraints excluded: chain n residue 36 THR Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 51 LEU Chi-restraints excluded: chain n residue 83 LEU Chi-restraints excluded: chain n residue 99 LYS Chi-restraints excluded: chain o residue 18 LEU Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 28 VAL Chi-restraints excluded: chain o residue 35 ILE Chi-restraints excluded: chain o residue 43 ASN Chi-restraints excluded: chain o residue 54 VAL Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain o residue 93 ASP Chi-restraints excluded: chain p residue 1 SER Chi-restraints excluded: chain p residue 26 GLU Chi-restraints excluded: chain p residue 29 VAL Chi-restraints excluded: chain p residue 43 GLU Chi-restraints excluded: chain p residue 47 ILE Chi-restraints excluded: chain p residue 65 ASN Chi-restraints excluded: chain p residue 69 VAL Chi-restraints excluded: chain p residue 85 VAL Chi-restraints excluded: chain q residue 3 VAL Chi-restraints excluded: chain q residue 7 VAL Chi-restraints excluded: chain q residue 17 LEU Chi-restraints excluded: chain q residue 33 VAL Chi-restraints excluded: chain q residue 38 VAL Chi-restraints excluded: chain q residue 86 SER Chi-restraints excluded: chain q residue 99 VAL Chi-restraints excluded: chain q residue 103 VAL Chi-restraints excluded: chain r residue 11 GLN Chi-restraints excluded: chain r residue 14 VAL Chi-restraints excluded: chain r residue 22 LEU Chi-restraints excluded: chain r residue 33 VAL Chi-restraints excluded: chain r residue 37 GLU Chi-restraints excluded: chain r residue 54 VAL Chi-restraints excluded: chain r residue 63 VAL Chi-restraints excluded: chain r residue 64 VAL Chi-restraints excluded: chain r residue 75 VAL Chi-restraints excluded: chain r residue 94 THR Chi-restraints excluded: chain s residue 35 ILE Chi-restraints excluded: chain s residue 45 VAL Chi-restraints excluded: chain s residue 46 LEU Chi-restraints excluded: chain t residue 8 LEU Chi-restraints excluded: chain t residue 10 VAL Chi-restraints excluded: chain t residue 39 THR Chi-restraints excluded: chain t residue 58 VAL Chi-restraints excluded: chain t residue 62 VAL Chi-restraints excluded: chain t residue 63 VAL Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain u residue 51 LEU Chi-restraints excluded: chain u residue 69 VAL Chi-restraints excluded: chain v residue 8 VAL Chi-restraints excluded: chain v residue 24 ASN Chi-restraints excluded: chain v residue 45 ASP Chi-restraints excluded: chain v residue 61 LEU Chi-restraints excluded: chain v residue 66 ASP Chi-restraints excluded: chain v residue 86 LEU Chi-restraints excluded: chain v residue 88 HIS Chi-restraints excluded: chain w residue 42 HIS Chi-restraints excluded: chain w residue 46 ASN Chi-restraints excluded: chain w residue 60 ASP Chi-restraints excluded: chain w residue 71 LYS Chi-restraints excluded: chain x residue 3 VAL Chi-restraints excluded: chain x residue 24 THR Chi-restraints excluded: chain x residue 39 VAL Chi-restraints excluded: chain x residue 46 VAL Chi-restraints excluded: chain x residue 47 THR Chi-restraints excluded: chain x residue 67 LEU Chi-restraints excluded: chain y residue 58 ASN Chi-restraints excluded: chain z residue 10 ARG Chi-restraints excluded: chain z residue 13 ILE Chi-restraints excluded: chain z residue 24 LEU Chi-restraints excluded: chain z residue 31 ILE Chi-restraints excluded: chain z residue 40 THR Chi-restraints excluded: chain z residue 56 VAL Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 5 ASN Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 36 LYS Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 30 HIS Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 20 ASP Chi-restraints excluded: chain G residue 8 MET Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 146 SER Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 196 ASP Chi-restraints excluded: chain H residue 28 PHE Chi-restraints excluded: chain H residue 50 SER Chi-restraints excluded: chain H residue 74 ILE Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 160 LEU Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain I residue 196 GLU Chi-restraints excluded: chain I residue 198 LEU Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 95 MET Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 135 VAL Chi-restraints excluded: chain J residue 147 ASN Chi-restraints excluded: chain K residue 7 VAL Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 68 GLN Chi-restraints excluded: chain K residue 73 GLU Chi-restraints excluded: chain K residue 76 THR Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain L residue 27 ASN Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain L residue 42 VAL Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 76 SER Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain M residue 26 MET Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 74 ILE Chi-restraints excluded: chain M residue 78 SER Chi-restraints excluded: chain M residue 90 GLU Chi-restraints excluded: chain M residue 100 ILE Chi-restraints excluded: chain M residue 102 VAL Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain M residue 113 ARG Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain N residue 28 VAL Chi-restraints excluded: chain N residue 53 LEU Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 67 LYS Chi-restraints excluded: chain N residue 87 MET Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain O residue 42 LEU Chi-restraints excluded: chain O residue 96 VAL Chi-restraints excluded: chain O residue 98 VAL Chi-restraints excluded: chain P residue 15 VAL Chi-restraints excluded: chain P residue 29 THR Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain P residue 54 SER Chi-restraints excluded: chain P residue 58 THR Chi-restraints excluded: chain P residue 69 CYS Chi-restraints excluded: chain P residue 71 ASP Chi-restraints excluded: chain P residue 83 VAL Chi-restraints excluded: chain P residue 84 MET Chi-restraints excluded: chain P residue 96 ILE Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 112 VAL Chi-restraints excluded: chain P residue 115 ILE Chi-restraints excluded: chain P residue 124 LYS Chi-restraints excluded: chain Q residue 4 ASN Chi-restraints excluded: chain Q residue 34 THR Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 57 THR Chi-restraints excluded: chain Q residue 58 ASN Chi-restraints excluded: chain Q residue 78 VAL Chi-restraints excluded: chain R residue 13 HIS Chi-restraints excluded: chain R residue 21 ILE Chi-restraints excluded: chain R residue 22 TYR Chi-restraints excluded: chain R residue 48 SER Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain S residue 26 LEU Chi-restraints excluded: chain S residue 33 VAL Chi-restraints excluded: chain S residue 73 LEU Chi-restraints excluded: chain T residue 60 SER Chi-restraints excluded: chain T residue 67 ASP Chi-restraints excluded: chain U residue 2 VAL Chi-restraints excluded: chain U residue 66 THR Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain U residue 79 ASN Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain W residue 20 ILE Chi-restraints excluded: chain W residue 30 ASN Chi-restraints excluded: chain W residue 70 THR Chi-restraints excluded: chain X residue 18 VAL Chi-restraints excluded: chain X residue 46 LEU Chi-restraints excluded: chain X residue 65 MET Chi-restraints excluded: chain X residue 73 PHE Chi-restraints excluded: chain Y residue 3 ILE Chi-restraints excluded: chain Y residue 11 ILE Chi-restraints excluded: chain Y residue 26 MET Chi-restraints excluded: chain Y residue 69 ASN Chi-restraints excluded: chain 8 residue 46 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1016 random chunks: chunk 947 optimal weight: 10.0000 chunk 110 optimal weight: 20.0000 chunk 560 optimal weight: 50.0000 chunk 717 optimal weight: 10.0000 chunk 556 optimal weight: 40.0000 chunk 827 optimal weight: 20.0000 chunk 548 optimal weight: 50.0000 chunk 979 optimal weight: 20.0000 chunk 612 optimal weight: 20.0000 chunk 597 optimal weight: 10.0000 chunk 452 optimal weight: 3.9990 overall best weight: 10.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 114 HIS k 93 GLN ** l 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 100 HIS ** r 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 48 GLN ** x 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 14 HIS ** G 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 167 HIS ** H 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 70 GLN ** I 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 51 HIS ** X 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.4462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.099 157481 Z= 0.384 Angle : 0.738 14.673 235693 Z= 0.373 Chirality : 0.040 0.349 30128 Planarity : 0.005 0.060 12572 Dihedral : 23.464 177.473 79036 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 23.71 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.48 % Favored : 88.39 % Rotamer: Outliers : 7.92 % Allowed : 23.40 % Favored : 68.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.41 (0.11), residues: 5651 helix: -0.49 (0.12), residues: 1768 sheet: -1.80 (0.17), residues: 936 loop : -2.27 (0.11), residues: 2947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 200 HIS 0.013 0.002 HIS x 33 PHE 0.040 0.002 PHE y 26 TYR 0.046 0.002 TYR j 16 ARG 0.010 0.001 ARG e 91 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11302 Ramachandran restraints generated. 5651 Oldfield, 0 Emsley, 5651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11302 Ramachandran restraints generated. 5651 Oldfield, 0 Emsley, 5651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1330 residues out of total 4697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 372 poor density : 958 time to evaluate : 6.478 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: b 82 TYR cc_start: 0.8801 (t80) cc_final: 0.8388 (t80) REVERT: b 86 ARG cc_start: 0.7746 (OUTLIER) cc_final: 0.6700 (mpp80) REVERT: b 113 ASP cc_start: 0.7531 (t70) cc_final: 0.7141 (t70) REVERT: b 116 GLN cc_start: 0.8039 (pt0) cc_final: 0.7782 (pt0) REVERT: b 152 GLN cc_start: 0.8093 (mm110) cc_final: 0.7850 (mm110) REVERT: b 180 MET cc_start: 0.7966 (mpp) cc_final: 0.7610 (mpp) REVERT: c 83 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.7704 (mpp80) REVERT: c 94 GLN cc_start: 0.7911 (tm-30) cc_final: 0.7017 (tm-30) REVERT: c 128 ARG cc_start: 0.8230 (mtt90) cc_final: 0.7672 (mmm160) REVERT: c 145 SER cc_start: 0.9244 (OUTLIER) cc_final: 0.8439 (m) REVERT: d 19 PHE cc_start: 0.8576 (m-80) cc_final: 0.8072 (m-10) REVERT: d 116 ASP cc_start: 0.8889 (OUTLIER) cc_final: 0.8427 (t0) REVERT: e 25 MET cc_start: 0.6107 (OUTLIER) cc_final: 0.5655 (tpt) REVERT: e 122 ASP cc_start: 0.4054 (t0) cc_final: 0.3496 (m-30) REVERT: f 61 TRP cc_start: 0.7188 (OUTLIER) cc_final: 0.6497 (t-100) REVERT: f 94 ARG cc_start: 0.6641 (mmt-90) cc_final: 0.6178 (ttm170) REVERT: g 1 MET cc_start: 0.5328 (mmm) cc_final: 0.4731 (mmm) REVERT: g 46 PHE cc_start: 0.7342 (t80) cc_final: 0.7016 (t80) REVERT: g 55 GLU cc_start: 0.6545 (mm-30) cc_final: 0.6322 (mm-30) REVERT: g 62 LEU cc_start: 0.6604 (mt) cc_final: 0.6385 (tp) REVERT: j 16 TYR cc_start: 0.8246 (m-80) cc_final: 0.8005 (m-80) REVERT: j 92 MET cc_start: 0.9036 (tpt) cc_final: 0.8547 (tpt) REVERT: j 96 ARG cc_start: 0.8292 (mtp180) cc_final: 0.8072 (ttp-170) REVERT: j 102 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.8138 (tp30) REVERT: j 108 MET cc_start: 0.8790 (mmt) cc_final: 0.8251 (mmm) REVERT: j 125 TYR cc_start: 0.7912 (m-80) cc_final: 0.7574 (m-10) REVERT: k 7 MET cc_start: 0.8956 (mmt) cc_final: 0.8466 (mmp) REVERT: k 32 TYR cc_start: 0.8512 (m-10) cc_final: 0.8205 (m-10) REVERT: k 45 GLU cc_start: 0.7797 (mm-30) cc_final: 0.7379 (tm-30) REVERT: k 88 ASN cc_start: 0.8692 (t0) cc_final: 0.8132 (t0) REVERT: k 105 ARG cc_start: 0.6393 (OUTLIER) cc_final: 0.6154 (tmt170) REVERT: k 110 GLU cc_start: 0.9181 (tm-30) cc_final: 0.8800 (tp30) REVERT: l 106 GLU cc_start: 0.8357 (mm-30) cc_final: 0.7853 (mm-30) REVERT: m 1 MET cc_start: 0.7560 (mmp) cc_final: 0.7086 (mmp) REVERT: m 22 GLN cc_start: 0.8372 (mm-40) cc_final: 0.8058 (mm-40) REVERT: m 44 ARG cc_start: 0.8821 (mtt180) cc_final: 0.8379 (mmt180) REVERT: n 4 ARG cc_start: 0.8679 (mmt180) cc_final: 0.8121 (mmm-85) REVERT: n 43 GLU cc_start: 0.8654 (mm-30) cc_final: 0.8313 (tp30) REVERT: n 49 GLU cc_start: 0.8659 (mt-10) cc_final: 0.8403 (mt-10) REVERT: n 106 ASP cc_start: 0.8206 (p0) cc_final: 0.7885 (p0) REVERT: o 97 PHE cc_start: 0.8118 (m-80) cc_final: 0.7496 (m-80) REVERT: o 100 HIS cc_start: 0.7820 (OUTLIER) cc_final: 0.7181 (t70) REVERT: o 112 GLU cc_start: 0.9261 (pt0) cc_final: 0.8937 (pp20) REVERT: p 8 GLU cc_start: 0.8517 (pp20) cc_final: 0.7835 (pp20) REVERT: p 12 MET cc_start: 0.7676 (mtt) cc_final: 0.7008 (mtt) REVERT: p 43 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7807 (tp30) REVERT: p 108 ARG cc_start: 0.6571 (mmt-90) cc_final: 0.6350 (mmt-90) REVERT: q 24 TYR cc_start: 0.8528 (t80) cc_final: 0.8037 (t80) REVERT: q 87 VAL cc_start: 0.8632 (t) cc_final: 0.8322 (t) REVERT: r 1 MET cc_start: 0.7883 (tpt) cc_final: 0.7433 (mmm) REVERT: r 70 GLU cc_start: 0.8707 (pm20) cc_final: 0.8468 (pm20) REVERT: r 98 ILE cc_start: 0.8862 (mm) cc_final: 0.8416 (tt) REVERT: s 9 HIS cc_start: 0.8003 (m-70) cc_final: 0.7759 (m-70) REVERT: s 40 ASN cc_start: 0.9028 (p0) cc_final: 0.8688 (p0) REVERT: s 57 ASN cc_start: 0.9058 (m-40) cc_final: 0.8652 (t0) REVERT: s 59 GLU cc_start: 0.8903 (tt0) cc_final: 0.8505 (mt-10) REVERT: t 1 MET cc_start: 0.4129 (mpp) cc_final: 0.2299 (ttp) REVERT: u 65 GLN cc_start: 0.8222 (mt0) cc_final: 0.7720 (mt0) REVERT: u 68 ASN cc_start: 0.7787 (m110) cc_final: 0.7122 (m-40) REVERT: v 5 ASN cc_start: 0.9002 (p0) cc_final: 0.8721 (p0) REVERT: v 11 GLU cc_start: 0.8919 (tt0) cc_final: 0.7947 (pm20) REVERT: v 12 GLN cc_start: 0.7823 (pt0) cc_final: 0.7332 (pt0) REVERT: v 35 GLU cc_start: 0.8106 (mt-10) cc_final: 0.7618 (mp0) REVERT: v 59 GLU cc_start: 0.6450 (OUTLIER) cc_final: 0.5284 (tt0) REVERT: v 88 HIS cc_start: 0.7589 (OUTLIER) cc_final: 0.7352 (t70) REVERT: w 33 ILE cc_start: 0.8369 (mt) cc_final: 0.8148 (mp) REVERT: w 40 LYS cc_start: 0.8190 (mmmm) cc_final: 0.7874 (mtmt) REVERT: w 51 ARG cc_start: 0.7261 (ptm-80) cc_final: 0.6580 (ptm160) REVERT: w 77 SER cc_start: 0.8715 (t) cc_final: 0.8462 (t) REVERT: w 79 GLU cc_start: 0.7977 (mm-30) cc_final: 0.7605 (mm-30) REVERT: x 22 ASN cc_start: 0.8576 (m110) cc_final: 0.8209 (m-40) REVERT: x 33 HIS cc_start: 0.5850 (m-70) cc_final: 0.5610 (m-70) REVERT: x 36 ARG cc_start: 0.8012 (ptt-90) cc_final: 0.6869 (ptm160) REVERT: y 1 MET cc_start: 0.8139 (mmm) cc_final: 0.7271 (tpt) REVERT: y 5 GLU cc_start: 0.8489 (mt-10) cc_final: 0.8162 (mp0) REVERT: y 49 ASP cc_start: 0.8582 (m-30) cc_final: 0.8055 (m-30) REVERT: z 10 ARG cc_start: 0.8498 (OUTLIER) cc_final: 0.7182 (mpp80) REVERT: z 18 LYS cc_start: 0.8597 (mmtt) cc_final: 0.8149 (mmmt) REVERT: z 37 ARG cc_start: 0.7738 (mmt-90) cc_final: 0.6917 (mmt-90) REVERT: z 38 GLU cc_start: 0.9252 (pt0) cc_final: 0.8612 (mp0) REVERT: z 40 THR cc_start: 0.7842 (t) cc_final: 0.7622 (p) REVERT: B 21 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8213 (tt) REVERT: B 31 LYS cc_start: 0.8760 (OUTLIER) cc_final: 0.8487 (mmtt) REVERT: C 50 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7538 (pm20) REVERT: D 18 PHE cc_start: 0.8518 (t80) cc_final: 0.8206 (t80) REVERT: F 19 ARG cc_start: 0.7296 (ttm110) cc_final: 0.6895 (ttm110) REVERT: G 95 TRP cc_start: 0.5259 (t-100) cc_final: 0.5054 (t-100) REVERT: G 221 ARG cc_start: 0.8818 (mtp85) cc_final: 0.8361 (mmt180) REVERT: H 2 GLN cc_start: 0.7836 (pm20) cc_final: 0.7509 (pm20) REVERT: H 17 TRP cc_start: 0.7869 (m-90) cc_final: 0.7440 (m-10) REVERT: H 126 ARG cc_start: 0.6721 (mtt90) cc_final: 0.6228 (ptt180) REVERT: H 133 MET cc_start: 0.7849 (ttt) cc_final: 0.7489 (tmm) REVERT: H 138 GLN cc_start: 0.8266 (mp10) cc_final: 0.7967 (mp10) REVERT: H 184 ASN cc_start: 0.6382 (t0) cc_final: 0.5746 (t0) REVERT: I 84 ASN cc_start: 0.8375 (t0) cc_final: 0.7804 (p0) REVERT: I 90 LEU cc_start: 0.7524 (mm) cc_final: 0.7156 (tp) REVERT: I 123 MET cc_start: 0.6903 (mmm) cc_final: 0.6443 (mmm) REVERT: I 196 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7074 (mt-10) REVERT: I 205 LYS cc_start: 0.5910 (ptmt) cc_final: 0.5609 (ptpp) REVERT: J 13 LYS cc_start: 0.7363 (ptpt) cc_final: 0.7083 (pttt) REVERT: J 25 LYS cc_start: 0.8229 (tmmt) cc_final: 0.7649 (tptt) REVERT: J 87 VAL cc_start: 0.7929 (p) cc_final: 0.7598 (m) REVERT: J 100 GLU cc_start: 0.8332 (mm-30) cc_final: 0.7788 (tp30) REVERT: J 125 LYS cc_start: 0.6800 (tptp) cc_final: 0.6294 (tptt) REVERT: K 9 MET cc_start: 0.6843 (tpp) cc_final: 0.6557 (tpp) REVERT: K 41 ASP cc_start: 0.8528 (p0) cc_final: 0.8213 (t0) REVERT: K 90 MET cc_start: 0.6730 (ttm) cc_final: 0.6191 (ttm) REVERT: K 91 ARG cc_start: 0.5933 (tpm170) cc_final: 0.5611 (mmm160) REVERT: L 24 LYS cc_start: 0.8843 (mmmt) cc_final: 0.8379 (mttt) REVERT: L 32 ASP cc_start: 0.7044 (m-30) cc_final: 0.6698 (m-30) REVERT: M 4 ASP cc_start: 0.7520 (t0) cc_final: 0.6975 (t0) REVERT: M 79 ARG cc_start: 0.8158 (mtm110) cc_final: 0.7648 (mtm-85) REVERT: M 90 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7973 (tp30) REVERT: M 110 MET cc_start: 0.5839 (ptp) cc_final: 0.5432 (pmm) REVERT: O 66 GLU cc_start: 0.8242 (pt0) cc_final: 0.7678 (tp30) REVERT: P 14 GLN cc_start: 0.8402 (pp30) cc_final: 0.7579 (mp10) REVERT: P 26 PHE cc_start: 0.8623 (m-10) cc_final: 0.8293 (m-80) REVERT: U 31 ARG cc_start: 0.7976 (tmm-80) cc_final: 0.6913 (tmm-80) REVERT: U 40 ASN cc_start: 0.8674 (t0) cc_final: 0.8305 (t0) REVERT: U 51 ARG cc_start: 0.8648 (tpp-160) cc_final: 0.8041 (tpp-160) REVERT: V 47 ASP cc_start: 0.6818 (OUTLIER) cc_final: 0.6316 (p0) REVERT: W 34 GLU cc_start: 0.7757 (mt-10) cc_final: 0.7184 (pt0) REVERT: W 59 LYS cc_start: 0.8533 (pttp) cc_final: 0.7721 (tptt) REVERT: X 43 MET cc_start: 0.4576 (mmp) cc_final: 0.4316 (mtm) REVERT: Y 22 SER cc_start: 0.8150 (p) cc_final: 0.7840 (m) REVERT: Y 23 ARG cc_start: 0.8487 (mmm-85) cc_final: 0.8000 (mmt90) REVERT: 8 84 ARG cc_start: 0.8268 (mmm160) cc_final: 0.7434 (ttp-170) REVERT: 8 85 GLU cc_start: 0.6799 (OUTLIER) cc_final: 0.6439 (pp20) REVERT: 8 131 MET cc_start: 0.7029 (ptp) cc_final: 0.6743 (ptp) outliers start: 372 outliers final: 318 residues processed: 1199 average time/residue: 1.1929 time to fit residues: 2519.7573 Evaluate side-chains 1272 residues out of total 4697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 338 poor density : 934 time to evaluate : 8.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 8 THR Chi-restraints excluded: chain b residue 15 VAL Chi-restraints excluded: chain b residue 19 VAL Chi-restraints excluded: chain b residue 37 SER Chi-restraints excluded: chain b residue 39 SER Chi-restraints excluded: chain b residue 52 HIS Chi-restraints excluded: chain b residue 53 ILE Chi-restraints excluded: chain b residue 63 ILE Chi-restraints excluded: chain b residue 86 ARG Chi-restraints excluded: chain b residue 133 ASN Chi-restraints excluded: chain b residue 173 LEU Chi-restraints excluded: chain b residue 222 THR Chi-restraints excluded: chain b residue 238 ASN Chi-restraints excluded: chain b residue 256 THR Chi-restraints excluded: chain b residue 265 PHE Chi-restraints excluded: chain c residue 24 VAL Chi-restraints excluded: chain c residue 51 THR Chi-restraints excluded: chain c residue 61 THR Chi-restraints excluded: chain c residue 73 VAL Chi-restraints excluded: chain c residue 83 ARG Chi-restraints excluded: chain c residue 103 ASP Chi-restraints excluded: chain c residue 109 VAL Chi-restraints excluded: chain c residue 112 THR Chi-restraints excluded: chain c residue 122 VAL Chi-restraints excluded: chain c residue 145 SER Chi-restraints excluded: chain c residue 171 THR Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain c residue 177 VAL Chi-restraints excluded: chain c residue 189 VAL Chi-restraints excluded: chain c residue 200 ASP Chi-restraints excluded: chain c residue 207 VAL Chi-restraints excluded: chain d residue 4 VAL Chi-restraints excluded: chain d residue 72 SER Chi-restraints excluded: chain d residue 84 THR Chi-restraints excluded: chain d residue 113 VAL Chi-restraints excluded: chain d residue 116 ASP Chi-restraints excluded: chain d residue 119 ILE Chi-restraints excluded: chain d residue 131 THR Chi-restraints excluded: chain d residue 163 ASN Chi-restraints excluded: chain d residue 167 VAL Chi-restraints excluded: chain d residue 184 ASP Chi-restraints excluded: chain e residue 11 VAL Chi-restraints excluded: chain e residue 20 ASN Chi-restraints excluded: chain e residue 25 MET Chi-restraints excluded: chain e residue 26 GLN Chi-restraints excluded: chain e residue 35 LEU Chi-restraints excluded: chain e residue 84 ILE Chi-restraints excluded: chain e residue 134 GLN Chi-restraints excluded: chain f residue 24 THR Chi-restraints excluded: chain f residue 35 THR Chi-restraints excluded: chain f residue 50 THR Chi-restraints excluded: chain f residue 59 ASP Chi-restraints excluded: chain f residue 61 TRP Chi-restraints excluded: chain f residue 71 LEU Chi-restraints excluded: chain f residue 101 VAL Chi-restraints excluded: chain f residue 103 ASN Chi-restraints excluded: chain f residue 121 THR Chi-restraints excluded: chain f residue 126 THR Chi-restraints excluded: chain f residue 131 VAL Chi-restraints excluded: chain f residue 132 LEU Chi-restraints excluded: chain f residue 136 ASP Chi-restraints excluded: chain f residue 167 VAL Chi-restraints excluded: chain g residue 12 LEU Chi-restraints excluded: chain g residue 17 ASP Chi-restraints excluded: chain g residue 40 THR Chi-restraints excluded: chain g residue 145 ASN Chi-restraints excluded: chain g residue 149 GLU Chi-restraints excluded: chain j residue 12 LYS Chi-restraints excluded: chain j residue 45 THR Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 57 LEU Chi-restraints excluded: chain j residue 73 VAL Chi-restraints excluded: chain j residue 78 THR Chi-restraints excluded: chain j residue 101 ILE Chi-restraints excluded: chain j residue 102 GLU Chi-restraints excluded: chain k residue 22 ILE Chi-restraints excluded: chain k residue 24 VAL Chi-restraints excluded: chain k residue 25 LEU Chi-restraints excluded: chain k residue 28 SER Chi-restraints excluded: chain k residue 56 ASP Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 77 ILE Chi-restraints excluded: chain k residue 85 VAL Chi-restraints excluded: chain k residue 86 LEU Chi-restraints excluded: chain k residue 90 ASN Chi-restraints excluded: chain k residue 105 ARG Chi-restraints excluded: chain l residue 7 SER Chi-restraints excluded: chain l residue 23 ILE Chi-restraints excluded: chain l residue 46 VAL Chi-restraints excluded: chain l residue 57 LEU Chi-restraints excluded: chain l residue 82 LEU Chi-restraints excluded: chain l residue 85 VAL Chi-restraints excluded: chain l residue 90 VAL Chi-restraints excluded: chain l residue 101 ILE Chi-restraints excluded: chain l residue 116 VAL Chi-restraints excluded: chain m residue 24 THR Chi-restraints excluded: chain m residue 26 VAL Chi-restraints excluded: chain m residue 41 LEU Chi-restraints excluded: chain m residue 42 THR Chi-restraints excluded: chain m residue 54 THR Chi-restraints excluded: chain m residue 73 ILE Chi-restraints excluded: chain m residue 74 THR Chi-restraints excluded: chain m residue 104 GLU Chi-restraints excluded: chain m residue 108 VAL Chi-restraints excluded: chain m residue 126 ILE Chi-restraints excluded: chain m residue 135 VAL Chi-restraints excluded: chain n residue 13 ASN Chi-restraints excluded: chain n residue 14 SER Chi-restraints excluded: chain n residue 24 MET Chi-restraints excluded: chain n residue 33 ILE Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 48 VAL Chi-restraints excluded: chain n residue 51 LEU Chi-restraints excluded: chain n residue 60 VAL Chi-restraints excluded: chain n residue 83 LEU Chi-restraints excluded: chain n residue 99 LYS Chi-restraints excluded: chain n residue 100 CYS Chi-restraints excluded: chain o residue 2 ASP Chi-restraints excluded: chain o residue 18 LEU Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 28 VAL Chi-restraints excluded: chain o residue 35 ILE Chi-restraints excluded: chain o residue 43 ASN Chi-restraints excluded: chain o residue 54 VAL Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain o residue 93 ASP Chi-restraints excluded: chain o residue 100 HIS Chi-restraints excluded: chain p residue 1 SER Chi-restraints excluded: chain p residue 26 GLU Chi-restraints excluded: chain p residue 29 VAL Chi-restraints excluded: chain p residue 43 GLU Chi-restraints excluded: chain p residue 47 ILE Chi-restraints excluded: chain p residue 65 ASN Chi-restraints excluded: chain p residue 69 VAL Chi-restraints excluded: chain p residue 85 VAL Chi-restraints excluded: chain q residue 3 VAL Chi-restraints excluded: chain q residue 7 VAL Chi-restraints excluded: chain q residue 17 LEU Chi-restraints excluded: chain q residue 33 VAL Chi-restraints excluded: chain q residue 38 VAL Chi-restraints excluded: chain q residue 86 SER Chi-restraints excluded: chain q residue 99 VAL Chi-restraints excluded: chain q residue 103 VAL Chi-restraints excluded: chain r residue 11 GLN Chi-restraints excluded: chain r residue 14 VAL Chi-restraints excluded: chain r residue 20 VAL Chi-restraints excluded: chain r residue 22 LEU Chi-restraints excluded: chain r residue 33 VAL Chi-restraints excluded: chain r residue 54 VAL Chi-restraints excluded: chain r residue 63 VAL Chi-restraints excluded: chain r residue 64 VAL Chi-restraints excluded: chain r residue 75 VAL Chi-restraints excluded: chain r residue 94 THR Chi-restraints excluded: chain s residue 4 ILE Chi-restraints excluded: chain s residue 35 ILE Chi-restraints excluded: chain s residue 45 VAL Chi-restraints excluded: chain s residue 46 LEU Chi-restraints excluded: chain s residue 77 ASP Chi-restraints excluded: chain t residue 8 LEU Chi-restraints excluded: chain t residue 10 VAL Chi-restraints excluded: chain t residue 58 VAL Chi-restraints excluded: chain t residue 62 VAL Chi-restraints excluded: chain t residue 63 VAL Chi-restraints excluded: chain u residue 11 ILE Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain u residue 51 LEU Chi-restraints excluded: chain u residue 69 VAL Chi-restraints excluded: chain v residue 8 VAL Chi-restraints excluded: chain v residue 24 ASN Chi-restraints excluded: chain v residue 45 ASP Chi-restraints excluded: chain v residue 48 MET Chi-restraints excluded: chain v residue 59 GLU Chi-restraints excluded: chain v residue 61 LEU Chi-restraints excluded: chain v residue 64 VAL Chi-restraints excluded: chain v residue 66 ASP Chi-restraints excluded: chain v residue 86 LEU Chi-restraints excluded: chain v residue 88 HIS Chi-restraints excluded: chain w residue 19 VAL Chi-restraints excluded: chain w residue 27 VAL Chi-restraints excluded: chain w residue 42 HIS Chi-restraints excluded: chain w residue 60 ASP Chi-restraints excluded: chain w residue 67 VAL Chi-restraints excluded: chain w residue 71 LYS Chi-restraints excluded: chain x residue 3 VAL Chi-restraints excluded: chain x residue 24 THR Chi-restraints excluded: chain x residue 39 VAL Chi-restraints excluded: chain x residue 46 VAL Chi-restraints excluded: chain x residue 47 THR Chi-restraints excluded: chain x residue 67 LEU Chi-restraints excluded: chain x residue 76 LYS Chi-restraints excluded: chain y residue 58 ASN Chi-restraints excluded: chain z residue 10 ARG Chi-restraints excluded: chain z residue 13 ILE Chi-restraints excluded: chain z residue 24 LEU Chi-restraints excluded: chain z residue 31 ILE Chi-restraints excluded: chain z residue 56 VAL Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 5 ASN Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 36 LYS Chi-restraints excluded: chain C residue 4 ILE Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 30 HIS Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 20 ASP Chi-restraints excluded: chain G residue 8 MET Chi-restraints excluded: chain G residue 66 ILE Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 146 SER Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 196 ASP Chi-restraints excluded: chain H residue 28 PHE Chi-restraints excluded: chain H residue 50 SER Chi-restraints excluded: chain H residue 74 ILE Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain H residue 197 VAL Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain I residue 77 GLU Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 160 LEU Chi-restraints excluded: chain I residue 194 ILE Chi-restraints excluded: chain I residue 196 GLU Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 95 MET Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 135 VAL Chi-restraints excluded: chain J residue 147 ASN Chi-restraints excluded: chain K residue 7 VAL Chi-restraints excluded: chain K residue 13 ASP Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 68 GLN Chi-restraints excluded: chain K residue 76 THR Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain L residue 27 ASN Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain L residue 42 VAL Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 76 SER Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain L residue 115 MET Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain M residue 26 MET Chi-restraints excluded: chain M residue 42 GLU Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 74 ILE Chi-restraints excluded: chain M residue 78 SER Chi-restraints excluded: chain M residue 90 GLU Chi-restraints excluded: chain M residue 100 ILE Chi-restraints excluded: chain M residue 102 VAL Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain M residue 113 ARG Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain N residue 24 ASN Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain N residue 28 VAL Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain N residue 53 LEU Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 67 LYS Chi-restraints excluded: chain N residue 87 MET Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain O residue 42 LEU Chi-restraints excluded: chain O residue 53 ILE Chi-restraints excluded: chain O residue 96 VAL Chi-restraints excluded: chain O residue 98 VAL Chi-restraints excluded: chain P residue 29 THR Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain P residue 54 SER Chi-restraints excluded: chain P residue 58 THR Chi-restraints excluded: chain P residue 69 CYS Chi-restraints excluded: chain P residue 71 ASP Chi-restraints excluded: chain P residue 83 VAL Chi-restraints excluded: chain P residue 84 MET Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 112 VAL Chi-restraints excluded: chain P residue 115 ILE Chi-restraints excluded: chain P residue 124 LYS Chi-restraints excluded: chain Q residue 4 ASN Chi-restraints excluded: chain Q residue 34 THR Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 57 THR Chi-restraints excluded: chain Q residue 58 ASN Chi-restraints excluded: chain Q residue 78 VAL Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain Q residue 102 ASP Chi-restraints excluded: chain R residue 13 HIS Chi-restraints excluded: chain R residue 21 ILE Chi-restraints excluded: chain R residue 22 TYR Chi-restraints excluded: chain R residue 48 SER Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain S residue 26 LEU Chi-restraints excluded: chain S residue 33 VAL Chi-restraints excluded: chain S residue 73 LEU Chi-restraints excluded: chain T residue 19 ASN Chi-restraints excluded: chain T residue 60 SER Chi-restraints excluded: chain T residue 67 ASP Chi-restraints excluded: chain U residue 2 VAL Chi-restraints excluded: chain U residue 66 THR Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain U residue 79 ASN Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain V residue 47 ASP Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain W residue 20 ILE Chi-restraints excluded: chain W residue 30 ASN Chi-restraints excluded: chain W residue 70 THR Chi-restraints excluded: chain X residue 11 ASP Chi-restraints excluded: chain X residue 46 LEU Chi-restraints excluded: chain X residue 48 ILE Chi-restraints excluded: chain X residue 65 MET Chi-restraints excluded: chain X residue 73 PHE Chi-restraints excluded: chain Y residue 3 ILE Chi-restraints excluded: chain Y residue 11 ILE Chi-restraints excluded: chain Y residue 29 THR Chi-restraints excluded: chain Y residue 69 ASN Chi-restraints excluded: chain Z residue 42 THR Chi-restraints excluded: chain 8 residue 46 SER Chi-restraints excluded: chain 8 residue 85 GLU Chi-restraints excluded: chain 8 residue 94 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1016 random chunks: chunk 605 optimal weight: 20.0000 chunk 391 optimal weight: 20.0000 chunk 584 optimal weight: 40.0000 chunk 294 optimal weight: 8.9990 chunk 192 optimal weight: 5.9990 chunk 189 optimal weight: 20.0000 chunk 622 optimal weight: 20.0000 chunk 667 optimal weight: 50.0000 chunk 484 optimal weight: 0.5980 chunk 91 optimal weight: 20.0000 chunk 769 optimal weight: 10.0000 overall best weight: 9.1192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 62 GLN f 114 HIS ** k 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 100 HIS ** p 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 48 GLN w 46 ASN ** x 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 44 GLN G 14 HIS ** G 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 202 ASN ** H 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 39 GLN I 70 GLN ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 59 GLN S 65 GLN ** X 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.4801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 157481 Z= 0.332 Angle : 0.715 15.063 235693 Z= 0.364 Chirality : 0.040 0.348 30128 Planarity : 0.005 0.080 12572 Dihedral : 23.583 176.671 79036 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 23.18 Ramachandran Plot: Outliers : 0.11 % Allowed : 11.41 % Favored : 88.48 % Rotamer: Outliers : 7.58 % Allowed : 24.48 % Favored : 67.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.39 (0.11), residues: 5651 helix: -0.50 (0.12), residues: 1757 sheet: -1.75 (0.17), residues: 946 loop : -2.23 (0.11), residues: 2948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP r 92 HIS 0.043 0.002 HIS o 100 PHE 0.032 0.002 PHE v 2 TYR 0.032 0.002 TYR o 99 ARG 0.018 0.001 ARG o 102 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11302 Ramachandran restraints generated. 5651 Oldfield, 0 Emsley, 5651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11302 Ramachandran restraints generated. 5651 Oldfield, 0 Emsley, 5651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1332 residues out of total 4697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 356 poor density : 976 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: b 82 TYR cc_start: 0.8809 (t80) cc_final: 0.8336 (t80) REVERT: b 86 ARG cc_start: 0.7847 (OUTLIER) cc_final: 0.6674 (mpp80) REVERT: b 113 ASP cc_start: 0.7821 (t70) cc_final: 0.7357 (t70) REVERT: b 116 GLN cc_start: 0.8042 (pt0) cc_final: 0.7768 (pt0) REVERT: b 152 GLN cc_start: 0.8079 (mm110) cc_final: 0.7823 (mm110) REVERT: b 180 MET cc_start: 0.8092 (mpp) cc_final: 0.7713 (mpp) REVERT: c 83 ARG cc_start: 0.8306 (OUTLIER) cc_final: 0.7657 (mpp80) REVERT: c 94 GLN cc_start: 0.7765 (tm-30) cc_final: 0.6819 (tm-30) REVERT: c 128 ARG cc_start: 0.8225 (mtt90) cc_final: 0.7648 (mmm160) REVERT: c 145 SER cc_start: 0.9206 (OUTLIER) cc_final: 0.8422 (m) REVERT: d 19 PHE cc_start: 0.8602 (m-80) cc_final: 0.8097 (m-10) REVERT: d 116 ASP cc_start: 0.8926 (OUTLIER) cc_final: 0.8380 (t0) REVERT: e 25 MET cc_start: 0.6084 (OUTLIER) cc_final: 0.5848 (mmt) REVERT: e 122 ASP cc_start: 0.3929 (t0) cc_final: 0.3597 (m-30) REVERT: e 124 ARG cc_start: 0.8128 (mmt180) cc_final: 0.7367 (mmm-85) REVERT: f 61 TRP cc_start: 0.7131 (OUTLIER) cc_final: 0.6444 (t-100) REVERT: g 1 MET cc_start: 0.5411 (mmm) cc_final: 0.5005 (mmp) REVERT: g 46 PHE cc_start: 0.7264 (t80) cc_final: 0.7022 (t80) REVERT: g 55 GLU cc_start: 0.6332 (mm-30) cc_final: 0.6119 (mm-30) REVERT: g 62 LEU cc_start: 0.6555 (mt) cc_final: 0.6344 (tp) REVERT: j 92 MET cc_start: 0.9022 (tpt) cc_final: 0.8521 (tpt) REVERT: j 96 ARG cc_start: 0.8368 (mtp180) cc_final: 0.8063 (ttp-170) REVERT: j 108 MET cc_start: 0.8753 (mmt) cc_final: 0.8307 (mmm) REVERT: j 125 TYR cc_start: 0.7902 (m-80) cc_final: 0.7563 (m-10) REVERT: k 7 MET cc_start: 0.8976 (mmt) cc_final: 0.8480 (mmp) REVERT: k 32 TYR cc_start: 0.8469 (m-10) cc_final: 0.8143 (m-10) REVERT: k 45 GLU cc_start: 0.7823 (mm-30) cc_final: 0.7383 (tm-30) REVERT: k 88 ASN cc_start: 0.8712 (t0) cc_final: 0.8143 (t0) REVERT: k 105 ARG cc_start: 0.6584 (OUTLIER) cc_final: 0.6373 (tmt170) REVERT: k 110 GLU cc_start: 0.9155 (tm-30) cc_final: 0.8790 (tp30) REVERT: m 22 GLN cc_start: 0.8323 (mm-40) cc_final: 0.8012 (mm-40) REVERT: n 4 ARG cc_start: 0.8754 (mmt180) cc_final: 0.8199 (mmm-85) REVERT: n 49 GLU cc_start: 0.8632 (mt-10) cc_final: 0.8375 (mt-10) REVERT: n 106 ASP cc_start: 0.8120 (p0) cc_final: 0.7776 (p0) REVERT: o 97 PHE cc_start: 0.8145 (m-80) cc_final: 0.7652 (m-80) REVERT: o 104 GLN cc_start: 0.9074 (tt0) cc_final: 0.8645 (tm-30) REVERT: o 112 GLU cc_start: 0.9218 (pt0) cc_final: 0.8955 (pp20) REVERT: p 8 GLU cc_start: 0.8532 (pp20) cc_final: 0.7858 (pp20) REVERT: p 9 GLN cc_start: 0.9006 (tm-30) cc_final: 0.8778 (tm-30) REVERT: p 12 MET cc_start: 0.7624 (mtt) cc_final: 0.6887 (mtt) REVERT: p 43 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7792 (tp30) REVERT: q 24 TYR cc_start: 0.8553 (t80) cc_final: 0.8058 (t80) REVERT: q 87 VAL cc_start: 0.8523 (t) cc_final: 0.8235 (t) REVERT: r 70 GLU cc_start: 0.8862 (pm20) cc_final: 0.8597 (pm20) REVERT: r 79 ARG cc_start: 0.8742 (ptp90) cc_final: 0.8390 (ptm-80) REVERT: r 98 ILE cc_start: 0.8851 (mm) cc_final: 0.8547 (tp) REVERT: s 9 HIS cc_start: 0.8010 (m-70) cc_final: 0.7745 (m-70) REVERT: s 40 ASN cc_start: 0.9008 (p0) cc_final: 0.8661 (p0) REVERT: s 57 ASN cc_start: 0.9056 (m-40) cc_final: 0.8644 (t0) REVERT: s 59 GLU cc_start: 0.8835 (tt0) cc_final: 0.8420 (tm-30) REVERT: t 1 MET cc_start: 0.4185 (mpp) cc_final: 0.2258 (ttp) REVERT: v 1 MET cc_start: 0.8329 (ppp) cc_final: 0.8003 (ppp) REVERT: v 11 GLU cc_start: 0.8903 (tt0) cc_final: 0.7903 (pm20) REVERT: v 12 GLN cc_start: 0.7852 (pt0) cc_final: 0.7353 (pt0) REVERT: v 35 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7616 (mp0) REVERT: w 21 ARG cc_start: 0.8822 (mmp-170) cc_final: 0.8543 (mmp80) REVERT: w 33 ILE cc_start: 0.8366 (mt) cc_final: 0.8139 (mp) REVERT: w 40 LYS cc_start: 0.8147 (mmmm) cc_final: 0.7795 (mtmt) REVERT: w 51 ARG cc_start: 0.7229 (ptm-80) cc_final: 0.6870 (ptm160) REVERT: w 77 SER cc_start: 0.8684 (t) cc_final: 0.8475 (t) REVERT: w 79 GLU cc_start: 0.7874 (mm-30) cc_final: 0.7510 (mm-30) REVERT: x 22 ASN cc_start: 0.8569 (m110) cc_final: 0.8238 (m-40) REVERT: x 36 ARG cc_start: 0.8036 (ptt-90) cc_final: 0.6855 (ptm160) REVERT: y 1 MET cc_start: 0.8058 (mmm) cc_final: 0.7224 (tpt) REVERT: y 5 GLU cc_start: 0.8401 (mt-10) cc_final: 0.8139 (mp0) REVERT: y 49 ASP cc_start: 0.8569 (m-30) cc_final: 0.8044 (m-30) REVERT: z 18 LYS cc_start: 0.8599 (mmtt) cc_final: 0.8109 (mmmt) REVERT: z 37 ARG cc_start: 0.7693 (mmt-90) cc_final: 0.7252 (mmt-90) REVERT: z 38 GLU cc_start: 0.9248 (pt0) cc_final: 0.8578 (mp0) REVERT: z 40 THR cc_start: 0.7829 (OUTLIER) cc_final: 0.7611 (p) REVERT: B 21 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8246 (tt) REVERT: B 31 LYS cc_start: 0.8785 (OUTLIER) cc_final: 0.8530 (mmtt) REVERT: C 50 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7544 (pm20) REVERT: D 18 PHE cc_start: 0.8588 (t80) cc_final: 0.8251 (t80) REVERT: F 19 ARG cc_start: 0.7366 (ttm110) cc_final: 0.6986 (ttm110) REVERT: G 26 MET cc_start: 0.7181 (tpp) cc_final: 0.6860 (ttm) REVERT: G 221 ARG cc_start: 0.8797 (mtp85) cc_final: 0.8379 (mmt180) REVERT: H 17 TRP cc_start: 0.7776 (m-90) cc_final: 0.7388 (m-10) REVERT: H 71 ARG cc_start: 0.8094 (mtm180) cc_final: 0.7839 (mtm180) REVERT: H 125 ARG cc_start: 0.7895 (mtm110) cc_final: 0.7161 (mtt-85) REVERT: H 126 ARG cc_start: 0.6822 (mtt90) cc_final: 0.6282 (ptt180) REVERT: H 133 MET cc_start: 0.7821 (ttt) cc_final: 0.7455 (tmm) REVERT: H 138 GLN cc_start: 0.8242 (mp10) cc_final: 0.7949 (mp10) REVERT: H 182 ASP cc_start: 0.7854 (t0) cc_final: 0.7557 (t0) REVERT: H 184 ASN cc_start: 0.6071 (t0) cc_final: 0.5631 (t0) REVERT: I 74 TYR cc_start: 0.8926 (m-80) cc_final: 0.8620 (m-80) REVERT: I 90 LEU cc_start: 0.7759 (mm) cc_final: 0.7288 (tp) REVERT: I 123 MET cc_start: 0.6964 (mmm) cc_final: 0.6500 (mmm) REVERT: I 196 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7031 (mt-10) REVERT: I 205 LYS cc_start: 0.5875 (ptmt) cc_final: 0.5627 (ptpp) REVERT: J 25 LYS cc_start: 0.8225 (tmmt) cc_final: 0.7668 (tptt) REVERT: J 70 MET cc_start: 0.7459 (ttt) cc_final: 0.7007 (mmm) REVERT: J 87 VAL cc_start: 0.7904 (p) cc_final: 0.7588 (m) REVERT: J 100 GLU cc_start: 0.8258 (mm-30) cc_final: 0.7712 (tp30) REVERT: K 9 MET cc_start: 0.6787 (tpp) cc_final: 0.6559 (tpp) REVERT: K 38 ARG cc_start: 0.5847 (ttt180) cc_final: 0.5613 (ttm170) REVERT: K 56 LYS cc_start: 0.8040 (mptt) cc_final: 0.7809 (mptt) REVERT: K 90 MET cc_start: 0.6727 (ttm) cc_final: 0.6214 (ttp) REVERT: K 91 ARG cc_start: 0.5964 (tpm170) cc_final: 0.5649 (mmm160) REVERT: L 24 LYS cc_start: 0.8842 (mmmt) cc_final: 0.8347 (mttt) REVERT: L 32 ASP cc_start: 0.6850 (m-30) cc_final: 0.6463 (m-30) REVERT: L 143 MET cc_start: 0.8718 (tpt) cc_final: 0.8499 (tpt) REVERT: M 2 MET cc_start: 0.8311 (tpp) cc_final: 0.8000 (tpp) REVERT: M 4 ASP cc_start: 0.7696 (t0) cc_final: 0.7055 (t0) REVERT: M 79 ARG cc_start: 0.8166 (mtm110) cc_final: 0.7638 (mtm-85) REVERT: M 90 GLU cc_start: 0.8188 (tp30) cc_final: 0.7969 (tp30) REVERT: M 110 MET cc_start: 0.5969 (ptp) cc_final: 0.5643 (pmm) REVERT: P 14 GLN cc_start: 0.8454 (pp30) cc_final: 0.7649 (mp10) REVERT: P 26 PHE cc_start: 0.8635 (m-10) cc_final: 0.8340 (m-80) REVERT: Q 103 CYS cc_start: 0.6668 (t) cc_final: 0.6002 (t) REVERT: R 99 GLN cc_start: 0.4918 (mp10) cc_final: 0.4453 (mt0) REVERT: S 88 MET cc_start: 0.8272 (mmm) cc_final: 0.7950 (mmp) REVERT: T 48 ASP cc_start: 0.8114 (OUTLIER) cc_final: 0.7840 (m-30) REVERT: U 1 MET cc_start: 0.6608 (tpp) cc_final: 0.5866 (tpp) REVERT: U 31 ARG cc_start: 0.7871 (tmm-80) cc_final: 0.6856 (tmm-80) REVERT: U 40 ASN cc_start: 0.8652 (t0) cc_final: 0.8274 (t0) REVERT: U 51 ARG cc_start: 0.8685 (tpp-160) cc_final: 0.8463 (tpp-160) REVERT: V 47 ASP cc_start: 0.6716 (OUTLIER) cc_final: 0.6226 (p0) REVERT: X 2 ARG cc_start: 0.7297 (mtt-85) cc_final: 0.7051 (mpp80) REVERT: X 43 MET cc_start: 0.4562 (mmp) cc_final: 0.4314 (mtm) REVERT: Y 22 SER cc_start: 0.8198 (p) cc_final: 0.7931 (m) REVERT: Y 23 ARG cc_start: 0.8472 (mmm-85) cc_final: 0.7612 (mmp80) REVERT: 8 84 ARG cc_start: 0.8214 (mmm160) cc_final: 0.7337 (ttp-170) REVERT: 8 85 GLU cc_start: 0.6883 (OUTLIER) cc_final: 0.6527 (pp20) REVERT: 8 131 MET cc_start: 0.7076 (ptp) cc_final: 0.6792 (ptp) outliers start: 356 outliers final: 300 residues processed: 1206 average time/residue: 1.2677 time to fit residues: 2702.4451 Evaluate side-chains 1256 residues out of total 4697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 316 poor density : 940 time to evaluate : 6.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 8 THR Chi-restraints excluded: chain b residue 15 VAL Chi-restraints excluded: chain b residue 19 VAL Chi-restraints excluded: chain b residue 37 SER Chi-restraints excluded: chain b residue 39 SER Chi-restraints excluded: chain b residue 52 HIS Chi-restraints excluded: chain b residue 53 ILE Chi-restraints excluded: chain b residue 63 ILE Chi-restraints excluded: chain b residue 86 ARG Chi-restraints excluded: chain b residue 133 ASN Chi-restraints excluded: chain b residue 173 LEU Chi-restraints excluded: chain b residue 222 THR Chi-restraints excluded: chain b residue 238 ASN Chi-restraints excluded: chain b residue 256 THR Chi-restraints excluded: chain c residue 24 VAL Chi-restraints excluded: chain c residue 51 THR Chi-restraints excluded: chain c residue 73 VAL Chi-restraints excluded: chain c residue 83 ARG Chi-restraints excluded: chain c residue 103 ASP Chi-restraints excluded: chain c residue 112 THR Chi-restraints excluded: chain c residue 122 VAL Chi-restraints excluded: chain c residue 145 SER Chi-restraints excluded: chain c residue 171 THR Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain c residue 177 VAL Chi-restraints excluded: chain c residue 189 VAL Chi-restraints excluded: chain c residue 200 ASP Chi-restraints excluded: chain c residue 207 VAL Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 4 VAL Chi-restraints excluded: chain d residue 72 SER Chi-restraints excluded: chain d residue 84 THR Chi-restraints excluded: chain d residue 113 VAL Chi-restraints excluded: chain d residue 116 ASP Chi-restraints excluded: chain d residue 131 THR Chi-restraints excluded: chain d residue 163 ASN Chi-restraints excluded: chain d residue 167 VAL Chi-restraints excluded: chain e residue 11 VAL Chi-restraints excluded: chain e residue 20 ASN Chi-restraints excluded: chain e residue 25 MET Chi-restraints excluded: chain e residue 35 LEU Chi-restraints excluded: chain e residue 82 TYR Chi-restraints excluded: chain e residue 84 ILE Chi-restraints excluded: chain e residue 134 GLN Chi-restraints excluded: chain f residue 14 VAL Chi-restraints excluded: chain f residue 24 THR Chi-restraints excluded: chain f residue 59 ASP Chi-restraints excluded: chain f residue 61 TRP Chi-restraints excluded: chain f residue 101 VAL Chi-restraints excluded: chain f residue 103 ASN Chi-restraints excluded: chain f residue 121 THR Chi-restraints excluded: chain f residue 126 THR Chi-restraints excluded: chain f residue 131 VAL Chi-restraints excluded: chain f residue 132 LEU Chi-restraints excluded: chain f residue 136 ASP Chi-restraints excluded: chain f residue 167 VAL Chi-restraints excluded: chain g residue 17 ASP Chi-restraints excluded: chain g residue 40 THR Chi-restraints excluded: chain g residue 58 LEU Chi-restraints excluded: chain g residue 104 THR Chi-restraints excluded: chain g residue 145 ASN Chi-restraints excluded: chain j residue 45 THR Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 54 ILE Chi-restraints excluded: chain j residue 57 LEU Chi-restraints excluded: chain j residue 73 VAL Chi-restraints excluded: chain j residue 78 THR Chi-restraints excluded: chain j residue 101 ILE Chi-restraints excluded: chain k residue 9 ASN Chi-restraints excluded: chain k residue 22 ILE Chi-restraints excluded: chain k residue 24 VAL Chi-restraints excluded: chain k residue 28 SER Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 77 ILE Chi-restraints excluded: chain k residue 85 VAL Chi-restraints excluded: chain k residue 86 LEU Chi-restraints excluded: chain k residue 90 ASN Chi-restraints excluded: chain k residue 105 ARG Chi-restraints excluded: chain l residue 7 SER Chi-restraints excluded: chain l residue 23 ILE Chi-restraints excluded: chain l residue 46 VAL Chi-restraints excluded: chain l residue 57 LEU Chi-restraints excluded: chain l residue 82 LEU Chi-restraints excluded: chain l residue 85 VAL Chi-restraints excluded: chain l residue 90 VAL Chi-restraints excluded: chain l residue 101 ILE Chi-restraints excluded: chain l residue 116 VAL Chi-restraints excluded: chain m residue 24 THR Chi-restraints excluded: chain m residue 26 VAL Chi-restraints excluded: chain m residue 41 LEU Chi-restraints excluded: chain m residue 42 THR Chi-restraints excluded: chain m residue 54 THR Chi-restraints excluded: chain m residue 73 ILE Chi-restraints excluded: chain m residue 74 THR Chi-restraints excluded: chain m residue 104 GLU Chi-restraints excluded: chain m residue 126 ILE Chi-restraints excluded: chain m residue 135 VAL Chi-restraints excluded: chain n residue 13 ASN Chi-restraints excluded: chain n residue 14 SER Chi-restraints excluded: chain n residue 33 ILE Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 48 VAL Chi-restraints excluded: chain n residue 51 LEU Chi-restraints excluded: chain n residue 60 VAL Chi-restraints excluded: chain n residue 83 LEU Chi-restraints excluded: chain n residue 98 LEU Chi-restraints excluded: chain o residue 2 ASP Chi-restraints excluded: chain o residue 18 LEU Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 28 VAL Chi-restraints excluded: chain o residue 35 ILE Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain o residue 43 ASN Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain o residue 93 ASP Chi-restraints excluded: chain p residue 1 SER Chi-restraints excluded: chain p residue 26 GLU Chi-restraints excluded: chain p residue 29 VAL Chi-restraints excluded: chain p residue 43 GLU Chi-restraints excluded: chain p residue 47 ILE Chi-restraints excluded: chain p residue 65 ASN Chi-restraints excluded: chain p residue 69 VAL Chi-restraints excluded: chain p residue 96 LEU Chi-restraints excluded: chain q residue 3 VAL Chi-restraints excluded: chain q residue 7 VAL Chi-restraints excluded: chain q residue 17 LEU Chi-restraints excluded: chain q residue 33 VAL Chi-restraints excluded: chain q residue 38 VAL Chi-restraints excluded: chain q residue 86 SER Chi-restraints excluded: chain q residue 99 VAL Chi-restraints excluded: chain q residue 103 VAL Chi-restraints excluded: chain r residue 11 GLN Chi-restraints excluded: chain r residue 14 VAL Chi-restraints excluded: chain r residue 20 VAL Chi-restraints excluded: chain r residue 22 LEU Chi-restraints excluded: chain r residue 33 VAL Chi-restraints excluded: chain r residue 37 GLU Chi-restraints excluded: chain r residue 54 VAL Chi-restraints excluded: chain r residue 63 VAL Chi-restraints excluded: chain r residue 74 ILE Chi-restraints excluded: chain r residue 75 VAL Chi-restraints excluded: chain r residue 94 THR Chi-restraints excluded: chain s residue 4 ILE Chi-restraints excluded: chain s residue 35 ILE Chi-restraints excluded: chain s residue 45 VAL Chi-restraints excluded: chain s residue 46 LEU Chi-restraints excluded: chain s residue 77 ASP Chi-restraints excluded: chain t residue 8 LEU Chi-restraints excluded: chain t residue 10 VAL Chi-restraints excluded: chain t residue 58 VAL Chi-restraints excluded: chain t residue 62 VAL Chi-restraints excluded: chain t residue 63 VAL Chi-restraints excluded: chain u residue 11 ILE Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain u residue 51 LEU Chi-restraints excluded: chain u residue 69 VAL Chi-restraints excluded: chain v residue 8 VAL Chi-restraints excluded: chain v residue 24 ASN Chi-restraints excluded: chain v residue 45 ASP Chi-restraints excluded: chain v residue 61 LEU Chi-restraints excluded: chain v residue 64 VAL Chi-restraints excluded: chain v residue 66 ASP Chi-restraints excluded: chain v residue 86 LEU Chi-restraints excluded: chain v residue 90 ASP Chi-restraints excluded: chain w residue 27 VAL Chi-restraints excluded: chain w residue 42 HIS Chi-restraints excluded: chain w residue 46 ASN Chi-restraints excluded: chain w residue 55 LEU Chi-restraints excluded: chain w residue 60 ASP Chi-restraints excluded: chain w residue 67 VAL Chi-restraints excluded: chain w residue 71 LYS Chi-restraints excluded: chain x residue 3 VAL Chi-restraints excluded: chain x residue 24 THR Chi-restraints excluded: chain x residue 39 VAL Chi-restraints excluded: chain x residue 46 VAL Chi-restraints excluded: chain x residue 47 THR Chi-restraints excluded: chain x residue 67 LEU Chi-restraints excluded: chain y residue 12 GLU Chi-restraints excluded: chain y residue 58 ASN Chi-restraints excluded: chain z residue 10 ARG Chi-restraints excluded: chain z residue 13 ILE Chi-restraints excluded: chain z residue 24 LEU Chi-restraints excluded: chain z residue 31 ILE Chi-restraints excluded: chain z residue 40 THR Chi-restraints excluded: chain z residue 56 VAL Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 5 ASN Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 30 HIS Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 20 ASP Chi-restraints excluded: chain G residue 8 MET Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 146 SER Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 196 ASP Chi-restraints excluded: chain H residue 28 PHE Chi-restraints excluded: chain H residue 50 SER Chi-restraints excluded: chain H residue 74 ILE Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain H residue 197 VAL Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 28 ASP Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 160 LEU Chi-restraints excluded: chain I residue 194 ILE Chi-restraints excluded: chain I residue 196 GLU Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 95 MET Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 135 VAL Chi-restraints excluded: chain J residue 147 ASN Chi-restraints excluded: chain K residue 7 VAL Chi-restraints excluded: chain K residue 13 ASP Chi-restraints excluded: chain K residue 76 THR Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain L residue 27 ASN Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain L residue 42 VAL Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 76 SER Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain M residue 26 MET Chi-restraints excluded: chain M residue 42 GLU Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 74 ILE Chi-restraints excluded: chain M residue 78 SER Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain M residue 113 ARG Chi-restraints excluded: chain N residue 24 ASN Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain N residue 28 VAL Chi-restraints excluded: chain N residue 53 LEU Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 67 LYS Chi-restraints excluded: chain N residue 87 MET Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain O residue 42 LEU Chi-restraints excluded: chain O residue 53 ILE Chi-restraints excluded: chain O residue 96 VAL Chi-restraints excluded: chain O residue 98 VAL Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain P residue 54 SER Chi-restraints excluded: chain P residue 58 THR Chi-restraints excluded: chain P residue 69 CYS Chi-restraints excluded: chain P residue 71 ASP Chi-restraints excluded: chain P residue 83 VAL Chi-restraints excluded: chain P residue 84 MET Chi-restraints excluded: chain P residue 96 ILE Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 112 VAL Chi-restraints excluded: chain P residue 115 ILE Chi-restraints excluded: chain P residue 124 LYS Chi-restraints excluded: chain Q residue 4 ASN Chi-restraints excluded: chain Q residue 23 LEU Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 57 THR Chi-restraints excluded: chain Q residue 58 ASN Chi-restraints excluded: chain Q residue 78 VAL Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain Q residue 102 ASP Chi-restraints excluded: chain R residue 13 HIS Chi-restraints excluded: chain R residue 22 TYR Chi-restraints excluded: chain R residue 48 SER Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain R residue 107 THR Chi-restraints excluded: chain S residue 26 LEU Chi-restraints excluded: chain S residue 33 VAL Chi-restraints excluded: chain S residue 73 LEU Chi-restraints excluded: chain T residue 31 LEU Chi-restraints excluded: chain T residue 48 ASP Chi-restraints excluded: chain T residue 60 SER Chi-restraints excluded: chain T residue 67 ASP Chi-restraints excluded: chain U residue 2 VAL Chi-restraints excluded: chain U residue 66 THR Chi-restraints excluded: chain U residue 79 ASN Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain V residue 47 ASP Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain W residue 17 VAL Chi-restraints excluded: chain W residue 20 ILE Chi-restraints excluded: chain W residue 30 ASN Chi-restraints excluded: chain W residue 70 THR Chi-restraints excluded: chain X residue 11 ASP Chi-restraints excluded: chain X residue 46 LEU Chi-restraints excluded: chain X residue 65 MET Chi-restraints excluded: chain X residue 73 PHE Chi-restraints excluded: chain Y residue 3 ILE Chi-restraints excluded: chain Y residue 11 ILE Chi-restraints excluded: chain Y residue 29 THR Chi-restraints excluded: chain Y residue 69 ASN Chi-restraints excluded: chain Y residue 79 THR Chi-restraints excluded: chain Z residue 42 THR Chi-restraints excluded: chain 8 residue 46 SER Chi-restraints excluded: chain 8 residue 85 GLU Chi-restraints excluded: chain 8 residue 94 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1016 random chunks: chunk 890 optimal weight: 10.0000 chunk 938 optimal weight: 10.0000 chunk 855 optimal weight: 10.0000 chunk 912 optimal weight: 20.0000 chunk 937 optimal weight: 10.0000 chunk 549 optimal weight: 50.0000 chunk 397 optimal weight: 40.0000 chunk 716 optimal weight: 20.0000 chunk 280 optimal weight: 20.0000 chunk 824 optimal weight: 10.0000 chunk 863 optimal weight: 10.0000 overall best weight: 10.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 259 ASN f 114 HIS k 3 GLN k 93 GLN ** l 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 48 GLN u 68 ASN w 46 ASN ** y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 14 HIS ** G 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 70 GLN I 115 GLN ** I 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 96 GLN ** K 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 75 GLN ** N 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.4895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.093 157481 Z= 0.358 Angle : 0.737 14.621 235693 Z= 0.374 Chirality : 0.040 0.351 30128 Planarity : 0.005 0.063 12572 Dihedral : 23.611 176.691 79036 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 24.08 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.73 % Favored : 88.14 % Rotamer: Outliers : 7.66 % Allowed : 24.91 % Favored : 67.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.40 (0.11), residues: 5651 helix: -0.50 (0.12), residues: 1759 sheet: -1.74 (0.17), residues: 946 loop : -2.26 (0.11), residues: 2946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP r 92 HIS 0.012 0.002 HIS x 33 PHE 0.030 0.002 PHE y 26 TYR 0.028 0.002 TYR l 58 ARG 0.014 0.001 ARG R 91 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11302 Ramachandran restraints generated. 5651 Oldfield, 0 Emsley, 5651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11302 Ramachandran restraints generated. 5651 Oldfield, 0 Emsley, 5651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1301 residues out of total 4697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 360 poor density : 941 time to evaluate : 6.442 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: b 82 TYR cc_start: 0.8815 (t80) cc_final: 0.8341 (t80) REVERT: b 86 ARG cc_start: 0.7856 (OUTLIER) cc_final: 0.6703 (mpp80) REVERT: b 113 ASP cc_start: 0.7834 (t70) cc_final: 0.7374 (t70) REVERT: b 116 GLN cc_start: 0.8021 (pt0) cc_final: 0.7794 (pt0) REVERT: b 152 GLN cc_start: 0.8098 (mm110) cc_final: 0.7877 (mm110) REVERT: b 180 MET cc_start: 0.8102 (mpp) cc_final: 0.7739 (mpp) REVERT: c 83 ARG cc_start: 0.8317 (OUTLIER) cc_final: 0.7667 (mpp80) REVERT: c 94 GLN cc_start: 0.7775 (tm-30) cc_final: 0.6834 (tm-30) REVERT: c 128 ARG cc_start: 0.8224 (mtt90) cc_final: 0.7648 (mmm160) REVERT: c 145 SER cc_start: 0.9223 (OUTLIER) cc_final: 0.8427 (m) REVERT: d 19 PHE cc_start: 0.8605 (m-80) cc_final: 0.8158 (m-10) REVERT: d 116 ASP cc_start: 0.8936 (OUTLIER) cc_final: 0.8393 (t0) REVERT: e 25 MET cc_start: 0.6089 (OUTLIER) cc_final: 0.5849 (mmt) REVERT: e 122 ASP cc_start: 0.3966 (t0) cc_final: 0.3667 (m-30) REVERT: e 124 ARG cc_start: 0.8146 (mmt180) cc_final: 0.7405 (mmm-85) REVERT: f 61 TRP cc_start: 0.7135 (OUTLIER) cc_final: 0.6447 (t-100) REVERT: g 1 MET cc_start: 0.5424 (mmm) cc_final: 0.5016 (mmp) REVERT: g 46 PHE cc_start: 0.7204 (t80) cc_final: 0.6990 (t80) REVERT: g 62 LEU cc_start: 0.6568 (mt) cc_final: 0.6362 (tp) REVERT: j 92 MET cc_start: 0.9026 (tpt) cc_final: 0.8539 (tpt) REVERT: j 96 ARG cc_start: 0.8347 (mtp180) cc_final: 0.8094 (ttp-170) REVERT: j 108 MET cc_start: 0.8736 (mmt) cc_final: 0.8234 (mmm) REVERT: j 125 TYR cc_start: 0.7879 (m-80) cc_final: 0.7483 (m-10) REVERT: k 1 MET cc_start: 0.8485 (ttp) cc_final: 0.8141 (ttm) REVERT: k 7 MET cc_start: 0.8975 (mmt) cc_final: 0.8474 (mmp) REVERT: k 45 GLU cc_start: 0.7825 (mm-30) cc_final: 0.7420 (tm-30) REVERT: k 88 ASN cc_start: 0.8717 (t0) cc_final: 0.8144 (t0) REVERT: k 105 ARG cc_start: 0.6550 (OUTLIER) cc_final: 0.6335 (tmt170) REVERT: k 110 GLU cc_start: 0.9173 (tm-30) cc_final: 0.8802 (tp30) REVERT: l 82 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8365 (mp) REVERT: m 1 MET cc_start: 0.7466 (mmp) cc_final: 0.6874 (mmm) REVERT: m 22 GLN cc_start: 0.8317 (mm-40) cc_final: 0.8010 (mm-40) REVERT: m 44 ARG cc_start: 0.8843 (mtt180) cc_final: 0.8404 (mmt180) REVERT: n 4 ARG cc_start: 0.8746 (mmt180) cc_final: 0.8199 (mmm-85) REVERT: n 49 GLU cc_start: 0.8634 (mt-10) cc_final: 0.8382 (mt-10) REVERT: n 106 ASP cc_start: 0.8156 (p0) cc_final: 0.7806 (p0) REVERT: o 97 PHE cc_start: 0.8115 (m-80) cc_final: 0.7554 (m-80) REVERT: o 100 HIS cc_start: 0.7728 (OUTLIER) cc_final: 0.7338 (t-170) REVERT: o 104 GLN cc_start: 0.9059 (tt0) cc_final: 0.8597 (tm-30) REVERT: o 112 GLU cc_start: 0.9230 (pt0) cc_final: 0.8942 (pp20) REVERT: p 8 GLU cc_start: 0.8504 (pp20) cc_final: 0.7808 (pp20) REVERT: p 9 GLN cc_start: 0.9010 (tm-30) cc_final: 0.8806 (tm-30) REVERT: p 12 MET cc_start: 0.7616 (mtt) cc_final: 0.6885 (mtt) REVERT: p 43 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7800 (tp30) REVERT: q 24 TYR cc_start: 0.8595 (t80) cc_final: 0.8100 (t80) REVERT: q 87 VAL cc_start: 0.8614 (t) cc_final: 0.8318 (t) REVERT: r 70 GLU cc_start: 0.8861 (pm20) cc_final: 0.8596 (pm20) REVERT: r 98 ILE cc_start: 0.8864 (mm) cc_final: 0.8566 (tp) REVERT: s 1 MET cc_start: 0.7305 (OUTLIER) cc_final: 0.7027 (ttp) REVERT: s 9 HIS cc_start: 0.8007 (m-70) cc_final: 0.7745 (m-70) REVERT: s 40 ASN cc_start: 0.8994 (p0) cc_final: 0.8647 (p0) REVERT: s 57 ASN cc_start: 0.9017 (m-40) cc_final: 0.8605 (t0) REVERT: s 59 GLU cc_start: 0.8831 (tt0) cc_final: 0.8511 (mt-10) REVERT: s 62 ASP cc_start: 0.6961 (m-30) cc_final: 0.6580 (m-30) REVERT: t 1 MET cc_start: 0.4257 (mpp) cc_final: 0.2404 (ttp) REVERT: t 56 GLU cc_start: 0.8473 (tm-30) cc_final: 0.8198 (pm20) REVERT: v 1 MET cc_start: 0.8341 (ppp) cc_final: 0.7880 (ppp) REVERT: v 11 GLU cc_start: 0.8904 (tt0) cc_final: 0.7915 (pm20) REVERT: v 12 GLN cc_start: 0.7881 (pt0) cc_final: 0.7440 (pt0) REVERT: v 35 GLU cc_start: 0.8095 (mt-10) cc_final: 0.7622 (mp0) REVERT: v 59 GLU cc_start: 0.5906 (OUTLIER) cc_final: 0.5418 (tt0) REVERT: w 21 ARG cc_start: 0.8841 (mmp-170) cc_final: 0.8568 (mmp80) REVERT: w 33 ILE cc_start: 0.8337 (mt) cc_final: 0.8115 (mp) REVERT: w 39 THR cc_start: 0.8750 (OUTLIER) cc_final: 0.8546 (p) REVERT: w 40 LYS cc_start: 0.8161 (mmmm) cc_final: 0.7842 (mtmt) REVERT: w 51 ARG cc_start: 0.7206 (ptm-80) cc_final: 0.6959 (ptm160) REVERT: w 77 SER cc_start: 0.8753 (t) cc_final: 0.8469 (t) REVERT: w 79 GLU cc_start: 0.7910 (mm-30) cc_final: 0.7500 (mm-30) REVERT: x 22 ASN cc_start: 0.8566 (m110) cc_final: 0.8239 (m-40) REVERT: x 36 ARG cc_start: 0.8032 (ptt-90) cc_final: 0.6840 (ptm160) REVERT: y 1 MET cc_start: 0.8024 (mmm) cc_final: 0.7189 (tpt) REVERT: y 5 GLU cc_start: 0.8388 (mt-10) cc_final: 0.8116 (mp0) REVERT: y 36 GLN cc_start: 0.8346 (mt0) cc_final: 0.8011 (mp10) REVERT: y 49 ASP cc_start: 0.8573 (m-30) cc_final: 0.8053 (m-30) REVERT: z 10 ARG cc_start: 0.8510 (OUTLIER) cc_final: 0.7197 (mpp80) REVERT: z 18 LYS cc_start: 0.8603 (mmtt) cc_final: 0.8054 (mmmt) REVERT: z 37 ARG cc_start: 0.7681 (mmt-90) cc_final: 0.7226 (mmt-90) REVERT: z 38 GLU cc_start: 0.9259 (pt0) cc_final: 0.8588 (mp0) REVERT: z 40 THR cc_start: 0.7830 (OUTLIER) cc_final: 0.7615 (p) REVERT: B 21 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8229 (tt) REVERT: B 31 LYS cc_start: 0.8799 (OUTLIER) cc_final: 0.8548 (mmtt) REVERT: C 50 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7391 (pm20) REVERT: D 18 PHE cc_start: 0.8595 (t80) cc_final: 0.8274 (t80) REVERT: F 19 ARG cc_start: 0.7326 (ttm110) cc_final: 0.6952 (ttm110) REVERT: G 26 MET cc_start: 0.7274 (tpp) cc_final: 0.6879 (ttm) REVERT: G 95 TRP cc_start: 0.5117 (t-100) cc_final: 0.4917 (t-100) REVERT: G 221 ARG cc_start: 0.8806 (mtp85) cc_final: 0.8389 (mmt180) REVERT: H 17 TRP cc_start: 0.7761 (m-90) cc_final: 0.7375 (m-10) REVERT: H 126 ARG cc_start: 0.6836 (mtt90) cc_final: 0.6276 (ptt180) REVERT: H 133 MET cc_start: 0.7780 (ttt) cc_final: 0.7400 (tmm) REVERT: H 138 GLN cc_start: 0.8244 (mp10) cc_final: 0.7903 (mp10) REVERT: H 182 ASP cc_start: 0.7863 (t0) cc_final: 0.7570 (t0) REVERT: H 184 ASN cc_start: 0.6269 (t0) cc_final: 0.5680 (t0) REVERT: I 74 TYR cc_start: 0.8927 (m-80) cc_final: 0.8596 (m-80) REVERT: I 84 ASN cc_start: 0.8365 (t0) cc_final: 0.7770 (p0) REVERT: I 90 LEU cc_start: 0.7839 (mm) cc_final: 0.7345 (tp) REVERT: I 123 MET cc_start: 0.6994 (mmm) cc_final: 0.6461 (mmm) REVERT: I 189 ASP cc_start: 0.8089 (t0) cc_final: 0.7330 (p0) REVERT: I 196 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7028 (mt-10) REVERT: I 205 LYS cc_start: 0.5804 (ptmt) cc_final: 0.5566 (ptpp) REVERT: J 25 LYS cc_start: 0.8240 (tmmt) cc_final: 0.7679 (tptt) REVERT: J 70 MET cc_start: 0.7303 (ttt) cc_final: 0.6837 (mmm) REVERT: J 87 VAL cc_start: 0.7907 (p) cc_final: 0.7596 (m) REVERT: J 100 GLU cc_start: 0.8260 (mm-30) cc_final: 0.7702 (tp30) REVERT: K 88 MET cc_start: 0.6956 (mmm) cc_final: 0.6244 (mpp) REVERT: K 90 MET cc_start: 0.6708 (ttm) cc_final: 0.6195 (ttp) REVERT: K 91 ARG cc_start: 0.5995 (tpm170) cc_final: 0.5678 (mmm160) REVERT: L 24 LYS cc_start: 0.8853 (mmmt) cc_final: 0.8350 (mttt) REVERT: L 32 ASP cc_start: 0.7075 (m-30) cc_final: 0.6698 (m-30) REVERT: M 2 MET cc_start: 0.8270 (tpp) cc_final: 0.7963 (tpp) REVERT: M 4 ASP cc_start: 0.7712 (t0) cc_final: 0.7100 (t0) REVERT: M 31 LEU cc_start: 0.8827 (pp) cc_final: 0.8598 (tt) REVERT: M 79 ARG cc_start: 0.8166 (mtm110) cc_final: 0.7638 (mtm-85) REVERT: M 90 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7967 (tp30) REVERT: M 110 MET cc_start: 0.6089 (ptp) cc_final: 0.5737 (pmm) REVERT: P 14 GLN cc_start: 0.8436 (pp30) cc_final: 0.7639 (mp10) REVERT: P 26 PHE cc_start: 0.8645 (m-10) cc_final: 0.8349 (m-80) REVERT: Q 103 CYS cc_start: 0.6708 (t) cc_final: 0.6041 (t) REVERT: R 80 MET cc_start: 0.7698 (mmm) cc_final: 0.7075 (mmm) REVERT: R 99 GLN cc_start: 0.4871 (mp10) cc_final: 0.4417 (mt0) REVERT: S 88 MET cc_start: 0.8222 (mmm) cc_final: 0.7729 (mmt) REVERT: T 48 ASP cc_start: 0.8165 (OUTLIER) cc_final: 0.7863 (m-30) REVERT: U 1 MET cc_start: 0.6620 (tpp) cc_final: 0.5933 (tpp) REVERT: U 31 ARG cc_start: 0.7856 (tmm-80) cc_final: 0.6849 (tmm-80) REVERT: U 40 ASN cc_start: 0.8656 (t0) cc_final: 0.8281 (t0) REVERT: U 51 ARG cc_start: 0.8678 (tpp-160) cc_final: 0.8442 (tpp-160) REVERT: V 47 ASP cc_start: 0.6762 (OUTLIER) cc_final: 0.6216 (p0) REVERT: W 34 GLU cc_start: 0.7592 (mt-10) cc_final: 0.6990 (pt0) REVERT: W 42 ARG cc_start: 0.9042 (ptm160) cc_final: 0.8629 (ptt90) REVERT: X 43 MET cc_start: 0.4704 (mmp) cc_final: 0.4482 (mtm) REVERT: Y 22 SER cc_start: 0.8177 (p) cc_final: 0.7908 (m) REVERT: Y 23 ARG cc_start: 0.8476 (mmm-85) cc_final: 0.7674 (mmp80) REVERT: 8 50 GLU cc_start: 0.6623 (pp20) cc_final: 0.6345 (pp20) REVERT: 8 84 ARG cc_start: 0.8223 (mmm160) cc_final: 0.7337 (ttp-170) REVERT: 8 131 MET cc_start: 0.6942 (ptp) cc_final: 0.6676 (ptp) outliers start: 360 outliers final: 320 residues processed: 1169 average time/residue: 1.2191 time to fit residues: 2511.3103 Evaluate side-chains 1269 residues out of total 4697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 342 poor density : 927 time to evaluate : 6.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 8 THR Chi-restraints excluded: chain b residue 15 VAL Chi-restraints excluded: chain b residue 19 VAL Chi-restraints excluded: chain b residue 37 SER Chi-restraints excluded: chain b residue 39 SER Chi-restraints excluded: chain b residue 52 HIS Chi-restraints excluded: chain b residue 53 ILE Chi-restraints excluded: chain b residue 63 ILE Chi-restraints excluded: chain b residue 86 ARG Chi-restraints excluded: chain b residue 133 ASN Chi-restraints excluded: chain b residue 173 LEU Chi-restraints excluded: chain b residue 222 THR Chi-restraints excluded: chain b residue 238 ASN Chi-restraints excluded: chain b residue 256 THR Chi-restraints excluded: chain b residue 265 PHE Chi-restraints excluded: chain c residue 24 VAL Chi-restraints excluded: chain c residue 51 THR Chi-restraints excluded: chain c residue 73 VAL Chi-restraints excluded: chain c residue 83 ARG Chi-restraints excluded: chain c residue 103 ASP Chi-restraints excluded: chain c residue 112 THR Chi-restraints excluded: chain c residue 122 VAL Chi-restraints excluded: chain c residue 145 SER Chi-restraints excluded: chain c residue 167 ASN Chi-restraints excluded: chain c residue 171 THR Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain c residue 177 VAL Chi-restraints excluded: chain c residue 189 VAL Chi-restraints excluded: chain c residue 200 ASP Chi-restraints excluded: chain c residue 207 VAL Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 4 VAL Chi-restraints excluded: chain d residue 72 SER Chi-restraints excluded: chain d residue 84 THR Chi-restraints excluded: chain d residue 113 VAL Chi-restraints excluded: chain d residue 116 ASP Chi-restraints excluded: chain d residue 131 THR Chi-restraints excluded: chain d residue 163 ASN Chi-restraints excluded: chain d residue 167 VAL Chi-restraints excluded: chain e residue 11 VAL Chi-restraints excluded: chain e residue 20 ASN Chi-restraints excluded: chain e residue 25 MET Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 35 LEU Chi-restraints excluded: chain e residue 82 TYR Chi-restraints excluded: chain e residue 84 ILE Chi-restraints excluded: chain e residue 157 THR Chi-restraints excluded: chain f residue 14 VAL Chi-restraints excluded: chain f residue 24 THR Chi-restraints excluded: chain f residue 35 THR Chi-restraints excluded: chain f residue 59 ASP Chi-restraints excluded: chain f residue 61 TRP Chi-restraints excluded: chain f residue 71 LEU Chi-restraints excluded: chain f residue 101 VAL Chi-restraints excluded: chain f residue 103 ASN Chi-restraints excluded: chain f residue 121 THR Chi-restraints excluded: chain f residue 126 THR Chi-restraints excluded: chain f residue 131 VAL Chi-restraints excluded: chain f residue 132 LEU Chi-restraints excluded: chain f residue 136 ASP Chi-restraints excluded: chain f residue 167 VAL Chi-restraints excluded: chain g residue 12 LEU Chi-restraints excluded: chain g residue 17 ASP Chi-restraints excluded: chain g residue 40 THR Chi-restraints excluded: chain g residue 54 LEU Chi-restraints excluded: chain g residue 104 THR Chi-restraints excluded: chain g residue 127 GLU Chi-restraints excluded: chain g residue 145 ASN Chi-restraints excluded: chain j residue 10 THR Chi-restraints excluded: chain j residue 45 THR Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 54 ILE Chi-restraints excluded: chain j residue 57 LEU Chi-restraints excluded: chain j residue 73 VAL Chi-restraints excluded: chain j residue 78 THR Chi-restraints excluded: chain j residue 101 ILE Chi-restraints excluded: chain j residue 103 ILE Chi-restraints excluded: chain k residue 3 GLN Chi-restraints excluded: chain k residue 9 ASN Chi-restraints excluded: chain k residue 10 VAL Chi-restraints excluded: chain k residue 22 ILE Chi-restraints excluded: chain k residue 24 VAL Chi-restraints excluded: chain k residue 28 SER Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 77 ILE Chi-restraints excluded: chain k residue 85 VAL Chi-restraints excluded: chain k residue 86 LEU Chi-restraints excluded: chain k residue 90 ASN Chi-restraints excluded: chain k residue 105 ARG Chi-restraints excluded: chain l residue 7 SER Chi-restraints excluded: chain l residue 23 ILE Chi-restraints excluded: chain l residue 46 VAL Chi-restraints excluded: chain l residue 57 LEU Chi-restraints excluded: chain l residue 82 LEU Chi-restraints excluded: chain l residue 85 VAL Chi-restraints excluded: chain l residue 90 VAL Chi-restraints excluded: chain l residue 101 ILE Chi-restraints excluded: chain l residue 116 VAL Chi-restraints excluded: chain m residue 24 THR Chi-restraints excluded: chain m residue 26 VAL Chi-restraints excluded: chain m residue 41 LEU Chi-restraints excluded: chain m residue 42 THR Chi-restraints excluded: chain m residue 54 THR Chi-restraints excluded: chain m residue 73 ILE Chi-restraints excluded: chain m residue 74 THR Chi-restraints excluded: chain m residue 104 GLU Chi-restraints excluded: chain m residue 126 ILE Chi-restraints excluded: chain m residue 131 VAL Chi-restraints excluded: chain m residue 135 VAL Chi-restraints excluded: chain n residue 13 ASN Chi-restraints excluded: chain n residue 14 SER Chi-restraints excluded: chain n residue 33 ILE Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 48 VAL Chi-restraints excluded: chain n residue 51 LEU Chi-restraints excluded: chain n residue 60 VAL Chi-restraints excluded: chain n residue 83 LEU Chi-restraints excluded: chain n residue 98 LEU Chi-restraints excluded: chain n residue 100 CYS Chi-restraints excluded: chain o residue 18 LEU Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 28 VAL Chi-restraints excluded: chain o residue 35 ILE Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain o residue 43 ASN Chi-restraints excluded: chain o residue 54 VAL Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain o residue 93 ASP Chi-restraints excluded: chain o residue 100 HIS Chi-restraints excluded: chain p residue 1 SER Chi-restraints excluded: chain p residue 26 GLU Chi-restraints excluded: chain p residue 29 VAL Chi-restraints excluded: chain p residue 43 GLU Chi-restraints excluded: chain p residue 47 ILE Chi-restraints excluded: chain p residue 65 ASN Chi-restraints excluded: chain p residue 69 VAL Chi-restraints excluded: chain p residue 96 LEU Chi-restraints excluded: chain q residue 3 VAL Chi-restraints excluded: chain q residue 7 VAL Chi-restraints excluded: chain q residue 17 LEU Chi-restraints excluded: chain q residue 33 VAL Chi-restraints excluded: chain q residue 38 VAL Chi-restraints excluded: chain q residue 86 SER Chi-restraints excluded: chain q residue 99 VAL Chi-restraints excluded: chain q residue 103 VAL Chi-restraints excluded: chain r residue 11 GLN Chi-restraints excluded: chain r residue 14 VAL Chi-restraints excluded: chain r residue 20 VAL Chi-restraints excluded: chain r residue 22 LEU Chi-restraints excluded: chain r residue 33 VAL Chi-restraints excluded: chain r residue 54 VAL Chi-restraints excluded: chain r residue 63 VAL Chi-restraints excluded: chain r residue 75 VAL Chi-restraints excluded: chain r residue 94 THR Chi-restraints excluded: chain s residue 1 MET Chi-restraints excluded: chain s residue 4 ILE Chi-restraints excluded: chain s residue 35 ILE Chi-restraints excluded: chain s residue 45 VAL Chi-restraints excluded: chain s residue 46 LEU Chi-restraints excluded: chain s residue 77 ASP Chi-restraints excluded: chain t residue 8 LEU Chi-restraints excluded: chain t residue 10 VAL Chi-restraints excluded: chain t residue 58 VAL Chi-restraints excluded: chain t residue 62 VAL Chi-restraints excluded: chain t residue 63 VAL Chi-restraints excluded: chain u residue 11 ILE Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain u residue 51 LEU Chi-restraints excluded: chain u residue 69 VAL Chi-restraints excluded: chain v residue 8 VAL Chi-restraints excluded: chain v residue 24 ASN Chi-restraints excluded: chain v residue 45 ASP Chi-restraints excluded: chain v residue 48 MET Chi-restraints excluded: chain v residue 59 GLU Chi-restraints excluded: chain v residue 61 LEU Chi-restraints excluded: chain v residue 64 VAL Chi-restraints excluded: chain v residue 66 ASP Chi-restraints excluded: chain v residue 86 LEU Chi-restraints excluded: chain w residue 27 VAL Chi-restraints excluded: chain w residue 39 THR Chi-restraints excluded: chain w residue 42 HIS Chi-restraints excluded: chain w residue 55 LEU Chi-restraints excluded: chain w residue 60 ASP Chi-restraints excluded: chain w residue 67 VAL Chi-restraints excluded: chain w residue 71 LYS Chi-restraints excluded: chain x residue 3 VAL Chi-restraints excluded: chain x residue 24 THR Chi-restraints excluded: chain x residue 39 VAL Chi-restraints excluded: chain x residue 46 VAL Chi-restraints excluded: chain x residue 47 THR Chi-restraints excluded: chain x residue 67 LEU Chi-restraints excluded: chain y residue 12 GLU Chi-restraints excluded: chain y residue 58 ASN Chi-restraints excluded: chain z residue 10 ARG Chi-restraints excluded: chain z residue 13 ILE Chi-restraints excluded: chain z residue 24 LEU Chi-restraints excluded: chain z residue 31 ILE Chi-restraints excluded: chain z residue 40 THR Chi-restraints excluded: chain z residue 56 VAL Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 5 ASN Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 36 LYS Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain C residue 4 ILE Chi-restraints excluded: chain C residue 32 LYS Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 25 HIS Chi-restraints excluded: chain E residue 30 HIS Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 20 ASP Chi-restraints excluded: chain G residue 8 MET Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 146 SER Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 196 ASP Chi-restraints excluded: chain H residue 28 PHE Chi-restraints excluded: chain H residue 50 SER Chi-restraints excluded: chain H residue 74 ILE Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain H residue 197 VAL Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 28 ASP Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain I residue 77 GLU Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 160 LEU Chi-restraints excluded: chain I residue 194 ILE Chi-restraints excluded: chain I residue 196 GLU Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 29 ILE Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 95 MET Chi-restraints excluded: chain J residue 96 GLN Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 135 VAL Chi-restraints excluded: chain J residue 147 ASN Chi-restraints excluded: chain K residue 7 VAL Chi-restraints excluded: chain K residue 13 ASP Chi-restraints excluded: chain K residue 73 GLU Chi-restraints excluded: chain K residue 76 THR Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain L residue 27 ASN Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain L residue 42 VAL Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 76 SER Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain M residue 26 MET Chi-restraints excluded: chain M residue 42 GLU Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 74 ILE Chi-restraints excluded: chain M residue 78 SER Chi-restraints excluded: chain M residue 90 GLU Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain M residue 113 ARG Chi-restraints excluded: chain N residue 24 ASN Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain N residue 28 VAL Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain N residue 53 LEU Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 67 LYS Chi-restraints excluded: chain N residue 87 MET Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain O residue 42 LEU Chi-restraints excluded: chain O residue 96 VAL Chi-restraints excluded: chain O residue 98 VAL Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain P residue 54 SER Chi-restraints excluded: chain P residue 58 THR Chi-restraints excluded: chain P residue 69 CYS Chi-restraints excluded: chain P residue 71 ASP Chi-restraints excluded: chain P residue 83 VAL Chi-restraints excluded: chain P residue 84 MET Chi-restraints excluded: chain P residue 96 ILE Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 112 VAL Chi-restraints excluded: chain P residue 115 ILE Chi-restraints excluded: chain P residue 124 LYS Chi-restraints excluded: chain Q residue 4 ASN Chi-restraints excluded: chain Q residue 23 LEU Chi-restraints excluded: chain Q residue 34 THR Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 57 THR Chi-restraints excluded: chain Q residue 58 ASN Chi-restraints excluded: chain Q residue 78 VAL Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain Q residue 102 ASP Chi-restraints excluded: chain R residue 13 HIS Chi-restraints excluded: chain R residue 22 TYR Chi-restraints excluded: chain R residue 48 SER Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain R residue 107 THR Chi-restraints excluded: chain S residue 26 LEU Chi-restraints excluded: chain S residue 33 VAL Chi-restraints excluded: chain S residue 73 LEU Chi-restraints excluded: chain T residue 48 ASP Chi-restraints excluded: chain T residue 60 SER Chi-restraints excluded: chain T residue 67 ASP Chi-restraints excluded: chain U residue 2 VAL Chi-restraints excluded: chain U residue 66 THR Chi-restraints excluded: chain U residue 79 ASN Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain V residue 47 ASP Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain W residue 17 VAL Chi-restraints excluded: chain W residue 20 ILE Chi-restraints excluded: chain W residue 30 ASN Chi-restraints excluded: chain W residue 43 ILE Chi-restraints excluded: chain W residue 70 THR Chi-restraints excluded: chain X residue 11 ASP Chi-restraints excluded: chain X residue 46 LEU Chi-restraints excluded: chain X residue 65 MET Chi-restraints excluded: chain X residue 73 PHE Chi-restraints excluded: chain Y residue 3 ILE Chi-restraints excluded: chain Y residue 11 ILE Chi-restraints excluded: chain Y residue 29 THR Chi-restraints excluded: chain Y residue 34 VAL Chi-restraints excluded: chain Y residue 69 ASN Chi-restraints excluded: chain Y residue 79 THR Chi-restraints excluded: chain Z residue 42 THR Chi-restraints excluded: chain 8 residue 46 SER Chi-restraints excluded: chain 8 residue 94 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1016 random chunks: chunk 909 optimal weight: 50.0000 chunk 599 optimal weight: 30.0000 chunk 964 optimal weight: 10.0000 chunk 588 optimal weight: 40.0000 chunk 457 optimal weight: 10.0000 chunk 670 optimal weight: 30.0000 chunk 1012 optimal weight: 0.5980 chunk 931 optimal weight: 10.0000 chunk 806 optimal weight: 10.0000 chunk 83 optimal weight: 2.9990 chunk 622 optimal weight: 20.0000 overall best weight: 6.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 45 ASN ** b 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 259 ASN f 114 HIS ** l 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 48 GLN u 68 ASN ** y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 14 HIS ** G 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 139 ASN I 70 GLN ** I 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 96 GLN ** K 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 55 HIS ** L 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.4985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 157481 Z= 0.255 Angle : 0.657 14.626 235693 Z= 0.336 Chirality : 0.037 0.330 30128 Planarity : 0.005 0.068 12572 Dihedral : 23.580 175.958 79036 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 20.93 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.44 % Favored : 89.47 % Rotamer: Outliers : 6.81 % Allowed : 25.85 % Favored : 67.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.11), residues: 5651 helix: -0.30 (0.12), residues: 1745 sheet: -1.63 (0.17), residues: 927 loop : -2.16 (0.11), residues: 2979 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 200 HIS 0.008 0.001 HIS x 33 PHE 0.027 0.002 PHE y 26 TYR 0.023 0.002 TYR l 58 ARG 0.014 0.001 ARG y 29 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11302 Ramachandran restraints generated. 5651 Oldfield, 0 Emsley, 5651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11302 Ramachandran restraints generated. 5651 Oldfield, 0 Emsley, 5651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1302 residues out of total 4697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 320 poor density : 982 time to evaluate : 8.855 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: b 82 TYR cc_start: 0.8764 (t80) cc_final: 0.8303 (t80) REVERT: b 86 ARG cc_start: 0.7801 (OUTLIER) cc_final: 0.6686 (mpp80) REVERT: b 113 ASP cc_start: 0.7951 (t70) cc_final: 0.7483 (t70) REVERT: b 116 GLN cc_start: 0.8188 (pt0) cc_final: 0.7986 (pt0) REVERT: b 152 GLN cc_start: 0.8060 (mm110) cc_final: 0.7738 (mm110) REVERT: b 180 MET cc_start: 0.8046 (mpp) cc_final: 0.7653 (mpp) REVERT: b 269 ARG cc_start: 0.7898 (mmm160) cc_final: 0.7434 (mmt180) REVERT: c 83 ARG cc_start: 0.8251 (OUTLIER) cc_final: 0.7603 (mpp80) REVERT: c 94 GLN cc_start: 0.7765 (tm-30) cc_final: 0.6814 (tm-30) REVERT: c 128 ARG cc_start: 0.8202 (mtt90) cc_final: 0.7646 (mmm160) REVERT: c 145 SER cc_start: 0.9177 (OUTLIER) cc_final: 0.8515 (m) REVERT: d 19 PHE cc_start: 0.8642 (m-80) cc_final: 0.8210 (m-10) REVERT: d 116 ASP cc_start: 0.8930 (OUTLIER) cc_final: 0.8436 (t0) REVERT: d 163 ASN cc_start: 0.5417 (OUTLIER) cc_final: 0.5203 (t0) REVERT: e 25 MET cc_start: 0.6152 (OUTLIER) cc_final: 0.5926 (mmt) REVERT: e 122 ASP cc_start: 0.3813 (t0) cc_final: 0.3572 (m-30) REVERT: e 124 ARG cc_start: 0.8119 (mmt180) cc_final: 0.7342 (mmm-85) REVERT: f 61 TRP cc_start: 0.7085 (OUTLIER) cc_final: 0.6371 (t-100) REVERT: g 1 MET cc_start: 0.5340 (mmm) cc_final: 0.4992 (mmp) REVERT: g 62 LEU cc_start: 0.6577 (mt) cc_final: 0.6376 (tp) REVERT: j 92 MET cc_start: 0.9012 (tpt) cc_final: 0.8409 (tpt) REVERT: j 96 ARG cc_start: 0.8362 (mtp180) cc_final: 0.7950 (ttp-170) REVERT: j 108 MET cc_start: 0.8717 (mmt) cc_final: 0.8268 (mmm) REVERT: j 125 TYR cc_start: 0.7875 (m-80) cc_final: 0.7538 (m-10) REVERT: k 7 MET cc_start: 0.8978 (mmt) cc_final: 0.8485 (mmp) REVERT: k 32 TYR cc_start: 0.8289 (m-10) cc_final: 0.7964 (m-80) REVERT: k 45 GLU cc_start: 0.7809 (mm-30) cc_final: 0.7365 (tm-30) REVERT: k 88 ASN cc_start: 0.8726 (t0) cc_final: 0.8189 (t0) REVERT: k 105 ARG cc_start: 0.6620 (OUTLIER) cc_final: 0.6411 (tmt170) REVERT: k 110 GLU cc_start: 0.9116 (tm-30) cc_final: 0.8740 (tp30) REVERT: m 1 MET cc_start: 0.7440 (mmp) cc_final: 0.6823 (mmm) REVERT: m 44 ARG cc_start: 0.8789 (mtt180) cc_final: 0.8361 (mmt180) REVERT: n 4 ARG cc_start: 0.8738 (mmt180) cc_final: 0.8155 (mmm-85) REVERT: n 49 GLU cc_start: 0.8622 (mt-10) cc_final: 0.8386 (mt-10) REVERT: n 106 ASP cc_start: 0.8154 (p0) cc_final: 0.7823 (p0) REVERT: o 97 PHE cc_start: 0.8054 (m-80) cc_final: 0.7507 (m-80) REVERT: o 104 GLN cc_start: 0.9103 (tt0) cc_final: 0.8715 (tm-30) REVERT: o 108 ASP cc_start: 0.8774 (m-30) cc_final: 0.7886 (m-30) REVERT: o 112 GLU cc_start: 0.9250 (pt0) cc_final: 0.8965 (pp20) REVERT: p 8 GLU cc_start: 0.8518 (pp20) cc_final: 0.7819 (pp20) REVERT: p 9 GLN cc_start: 0.9004 (tm-30) cc_final: 0.8789 (tm-30) REVERT: p 12 MET cc_start: 0.7515 (mtt) cc_final: 0.6815 (mtt) REVERT: p 43 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7819 (tp30) REVERT: q 23 TYR cc_start: 0.7817 (m-80) cc_final: 0.7445 (m-80) REVERT: q 24 TYR cc_start: 0.8486 (t80) cc_final: 0.8074 (t80) REVERT: q 87 VAL cc_start: 0.8626 (t) cc_final: 0.8325 (t) REVERT: r 1 MET cc_start: 0.7979 (tpt) cc_final: 0.7539 (mmm) REVERT: r 92 TRP cc_start: 0.8728 (m100) cc_final: 0.8434 (m100) REVERT: r 98 ILE cc_start: 0.8851 (mm) cc_final: 0.8601 (tp) REVERT: s 1 MET cc_start: 0.7178 (mtt) cc_final: 0.4693 (ttp) REVERT: s 9 HIS cc_start: 0.8050 (m-70) cc_final: 0.7831 (m-70) REVERT: s 40 ASN cc_start: 0.8962 (p0) cc_final: 0.8615 (p0) REVERT: s 59 GLU cc_start: 0.8841 (tt0) cc_final: 0.8409 (mt-10) REVERT: s 62 ASP cc_start: 0.6884 (m-30) cc_final: 0.6464 (m-30) REVERT: t 1 MET cc_start: 0.4259 (mpp) cc_final: 0.2341 (ttp) REVERT: t 56 GLU cc_start: 0.8429 (tm-30) cc_final: 0.8144 (pm20) REVERT: v 1 MET cc_start: 0.8334 (ppp) cc_final: 0.7842 (ppp) REVERT: v 11 GLU cc_start: 0.8910 (tt0) cc_final: 0.7922 (pm20) REVERT: v 12 GLN cc_start: 0.7954 (pt0) cc_final: 0.7468 (pt0) REVERT: v 24 ASN cc_start: 0.8864 (OUTLIER) cc_final: 0.7740 (t0) REVERT: v 35 GLU cc_start: 0.8112 (mt-10) cc_final: 0.7629 (mp0) REVERT: v 59 GLU cc_start: 0.5886 (OUTLIER) cc_final: 0.5315 (tt0) REVERT: w 21 ARG cc_start: 0.8835 (mmp-170) cc_final: 0.8582 (mmp80) REVERT: w 33 ILE cc_start: 0.8361 (mt) cc_final: 0.8090 (mp) REVERT: w 39 THR cc_start: 0.8772 (OUTLIER) cc_final: 0.8523 (p) REVERT: w 40 LYS cc_start: 0.8147 (mmmm) cc_final: 0.7838 (mtmt) REVERT: w 51 ARG cc_start: 0.7288 (ptm-80) cc_final: 0.6938 (ptm160) REVERT: w 77 SER cc_start: 0.8740 (t) cc_final: 0.8529 (t) REVERT: w 79 GLU cc_start: 0.7858 (mm-30) cc_final: 0.7505 (mm-30) REVERT: x 22 ASN cc_start: 0.8480 (m110) cc_final: 0.8179 (m-40) REVERT: x 36 ARG cc_start: 0.8056 (ptt-90) cc_final: 0.6845 (ptm160) REVERT: y 1 MET cc_start: 0.8017 (mmm) cc_final: 0.7207 (tpt) REVERT: y 5 GLU cc_start: 0.8434 (mt-10) cc_final: 0.8124 (mp0) REVERT: y 49 ASP cc_start: 0.8536 (m-30) cc_final: 0.8000 (m-30) REVERT: z 18 LYS cc_start: 0.8585 (mmtt) cc_final: 0.8065 (mmmt) REVERT: z 37 ARG cc_start: 0.7826 (mmt-90) cc_final: 0.7334 (mmt-90) REVERT: z 38 GLU cc_start: 0.9266 (pt0) cc_final: 0.8584 (mp0) REVERT: z 40 THR cc_start: 0.7811 (OUTLIER) cc_final: 0.7594 (p) REVERT: B 21 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8248 (tt) REVERT: B 31 LYS cc_start: 0.8811 (OUTLIER) cc_final: 0.8548 (mmtt) REVERT: C 50 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7588 (pm20) REVERT: D 18 PHE cc_start: 0.8583 (t80) cc_final: 0.8108 (t80) REVERT: E 53 ASP cc_start: 0.8495 (p0) cc_final: 0.8067 (m-30) REVERT: F 19 ARG cc_start: 0.7321 (ttm110) cc_final: 0.6947 (ttm110) REVERT: G 26 MET cc_start: 0.7179 (tpp) cc_final: 0.6735 (ttm) REVERT: G 95 TRP cc_start: 0.5196 (t-100) cc_final: 0.4975 (t-100) REVERT: G 221 ARG cc_start: 0.8770 (mtp85) cc_final: 0.8348 (mmt180) REVERT: H 17 TRP cc_start: 0.7692 (m-90) cc_final: 0.7293 (m-10) REVERT: H 125 ARG cc_start: 0.7869 (mtm110) cc_final: 0.7096 (mtt-85) REVERT: H 126 ARG cc_start: 0.6834 (mtt90) cc_final: 0.6302 (ptt180) REVERT: H 133 MET cc_start: 0.7758 (ttt) cc_final: 0.7357 (tmm) REVERT: H 138 GLN cc_start: 0.8247 (mp10) cc_final: 0.7888 (mp10) REVERT: H 182 ASP cc_start: 0.7975 (t0) cc_final: 0.7699 (t0) REVERT: H 184 ASN cc_start: 0.6176 (t0) cc_final: 0.5582 (t0) REVERT: I 74 TYR cc_start: 0.8938 (m-80) cc_final: 0.8627 (m-80) REVERT: I 84 ASN cc_start: 0.8346 (t0) cc_final: 0.7872 (p0) REVERT: I 88 ASN cc_start: 0.7949 (m-40) cc_final: 0.7409 (m-40) REVERT: I 90 LEU cc_start: 0.7744 (mm) cc_final: 0.7167 (tp) REVERT: I 123 MET cc_start: 0.6936 (mmm) cc_final: 0.6304 (mmm) REVERT: I 189 ASP cc_start: 0.8271 (t0) cc_final: 0.7526 (p0) REVERT: I 196 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7059 (mt-10) REVERT: I 205 LYS cc_start: 0.5731 (ptmt) cc_final: 0.5494 (ptpp) REVERT: J 23 THR cc_start: 0.8672 (m) cc_final: 0.8236 (p) REVERT: J 25 LYS cc_start: 0.8224 (tmmt) cc_final: 0.7675 (tptt) REVERT: J 65 LYS cc_start: 0.9043 (mptt) cc_final: 0.8815 (mmtp) REVERT: J 70 MET cc_start: 0.7199 (ttt) cc_final: 0.6899 (mmm) REVERT: J 87 VAL cc_start: 0.7922 (p) cc_final: 0.7635 (m) REVERT: J 100 GLU cc_start: 0.8275 (mm-30) cc_final: 0.7762 (tp30) REVERT: K 9 MET cc_start: 0.7304 (mmm) cc_final: 0.6250 (tpp) REVERT: K 88 MET cc_start: 0.7122 (mmm) cc_final: 0.6499 (mpp) REVERT: K 90 MET cc_start: 0.6648 (ttm) cc_final: 0.6107 (ttm) REVERT: K 91 ARG cc_start: 0.5882 (tpm170) cc_final: 0.5532 (mmm160) REVERT: L 24 LYS cc_start: 0.8859 (mmmt) cc_final: 0.8404 (mttt) REVERT: L 32 ASP cc_start: 0.6948 (m-30) cc_final: 0.6564 (m-30) REVERT: M 2 MET cc_start: 0.8230 (tpp) cc_final: 0.7925 (tpp) REVERT: M 4 ASP cc_start: 0.7649 (t0) cc_final: 0.7002 (t0) REVERT: M 79 ARG cc_start: 0.8198 (mtm110) cc_final: 0.7692 (mtm-85) REVERT: M 90 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.8024 (tp30) REVERT: M 110 MET cc_start: 0.6192 (ptp) cc_final: 0.5794 (pmm) REVERT: N 112 ARG cc_start: 0.5316 (ttp-170) cc_final: 0.4997 (ttp-170) REVERT: P 14 GLN cc_start: 0.8460 (pp30) cc_final: 0.7601 (mp10) REVERT: P 26 PHE cc_start: 0.8629 (m-10) cc_final: 0.8323 (m-80) REVERT: Q 103 CYS cc_start: 0.6744 (t) cc_final: 0.6118 (t) REVERT: R 80 MET cc_start: 0.7706 (mmm) cc_final: 0.7068 (mmm) REVERT: R 99 GLN cc_start: 0.5127 (mp10) cc_final: 0.4554 (mt0) REVERT: T 48 ASP cc_start: 0.8143 (OUTLIER) cc_final: 0.7894 (m-30) REVERT: U 1 MET cc_start: 0.6653 (tpp) cc_final: 0.6181 (tpp) REVERT: U 31 ARG cc_start: 0.7851 (tmm-80) cc_final: 0.6837 (tmm-80) REVERT: U 40 ASN cc_start: 0.8684 (t0) cc_final: 0.8280 (t0) REVERT: U 51 ARG cc_start: 0.8629 (tpp-160) cc_final: 0.8405 (tpp-160) REVERT: V 56 ASP cc_start: 0.6730 (m-30) cc_final: 0.4700 (p0) REVERT: W 34 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7037 (pt0) REVERT: W 42 ARG cc_start: 0.9043 (ptm160) cc_final: 0.8622 (ptt90) REVERT: X 2 ARG cc_start: 0.7394 (mtt-85) cc_final: 0.7168 (mpp80) REVERT: X 43 MET cc_start: 0.4844 (mmp) cc_final: 0.4605 (mtm) REVERT: Y 22 SER cc_start: 0.8183 (p) cc_final: 0.7935 (m) REVERT: Y 23 ARG cc_start: 0.8421 (mmm-85) cc_final: 0.7644 (mmp80) REVERT: 8 50 GLU cc_start: 0.6575 (pp20) cc_final: 0.6330 (pp20) REVERT: 8 84 ARG cc_start: 0.8261 (mmm160) cc_final: 0.7399 (ttp-170) REVERT: 8 85 GLU cc_start: 0.6855 (OUTLIER) cc_final: 0.6493 (pp20) REVERT: 8 131 MET cc_start: 0.7093 (ptp) cc_final: 0.6833 (ptp) outliers start: 320 outliers final: 263 residues processed: 1184 average time/residue: 1.2313 time to fit residues: 2562.6497 Evaluate side-chains 1234 residues out of total 4697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 284 poor density : 950 time to evaluate : 6.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 19 VAL Chi-restraints excluded: chain b residue 37 SER Chi-restraints excluded: chain b residue 39 SER Chi-restraints excluded: chain b residue 52 HIS Chi-restraints excluded: chain b residue 53 ILE Chi-restraints excluded: chain b residue 63 ILE Chi-restraints excluded: chain b residue 86 ARG Chi-restraints excluded: chain b residue 133 ASN Chi-restraints excluded: chain b residue 173 LEU Chi-restraints excluded: chain b residue 238 ASN Chi-restraints excluded: chain b residue 256 THR Chi-restraints excluded: chain c residue 24 VAL Chi-restraints excluded: chain c residue 73 VAL Chi-restraints excluded: chain c residue 83 ARG Chi-restraints excluded: chain c residue 103 ASP Chi-restraints excluded: chain c residue 112 THR Chi-restraints excluded: chain c residue 122 VAL Chi-restraints excluded: chain c residue 145 SER Chi-restraints excluded: chain c residue 171 THR Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain c residue 177 VAL Chi-restraints excluded: chain c residue 189 VAL Chi-restraints excluded: chain c residue 200 ASP Chi-restraints excluded: chain c residue 207 VAL Chi-restraints excluded: chain d residue 4 VAL Chi-restraints excluded: chain d residue 72 SER Chi-restraints excluded: chain d residue 84 THR Chi-restraints excluded: chain d residue 113 VAL Chi-restraints excluded: chain d residue 116 ASP Chi-restraints excluded: chain d residue 163 ASN Chi-restraints excluded: chain e residue 11 VAL Chi-restraints excluded: chain e residue 20 ASN Chi-restraints excluded: chain e residue 25 MET Chi-restraints excluded: chain e residue 35 LEU Chi-restraints excluded: chain e residue 84 ILE Chi-restraints excluded: chain e residue 134 GLN Chi-restraints excluded: chain f residue 14 VAL Chi-restraints excluded: chain f residue 24 THR Chi-restraints excluded: chain f residue 35 THR Chi-restraints excluded: chain f residue 61 TRP Chi-restraints excluded: chain f residue 71 LEU Chi-restraints excluded: chain f residue 101 VAL Chi-restraints excluded: chain f residue 103 ASN Chi-restraints excluded: chain f residue 121 THR Chi-restraints excluded: chain f residue 126 THR Chi-restraints excluded: chain f residue 131 VAL Chi-restraints excluded: chain f residue 132 LEU Chi-restraints excluded: chain f residue 136 ASP Chi-restraints excluded: chain f residue 167 VAL Chi-restraints excluded: chain g residue 17 ASP Chi-restraints excluded: chain g residue 40 THR Chi-restraints excluded: chain g residue 104 THR Chi-restraints excluded: chain g residue 145 ASN Chi-restraints excluded: chain j residue 10 THR Chi-restraints excluded: chain j residue 45 THR Chi-restraints excluded: chain j residue 54 ILE Chi-restraints excluded: chain j residue 57 LEU Chi-restraints excluded: chain j residue 73 VAL Chi-restraints excluded: chain j residue 101 ILE Chi-restraints excluded: chain j residue 103 ILE Chi-restraints excluded: chain k residue 22 ILE Chi-restraints excluded: chain k residue 24 VAL Chi-restraints excluded: chain k residue 28 SER Chi-restraints excluded: chain k residue 77 ILE Chi-restraints excluded: chain k residue 86 LEU Chi-restraints excluded: chain k residue 90 ASN Chi-restraints excluded: chain k residue 105 ARG Chi-restraints excluded: chain l residue 7 SER Chi-restraints excluded: chain l residue 23 ILE Chi-restraints excluded: chain l residue 46 VAL Chi-restraints excluded: chain l residue 57 LEU Chi-restraints excluded: chain l residue 85 VAL Chi-restraints excluded: chain l residue 90 VAL Chi-restraints excluded: chain l residue 101 ILE Chi-restraints excluded: chain l residue 116 VAL Chi-restraints excluded: chain m residue 24 THR Chi-restraints excluded: chain m residue 41 LEU Chi-restraints excluded: chain m residue 42 THR Chi-restraints excluded: chain m residue 54 THR Chi-restraints excluded: chain m residue 73 ILE Chi-restraints excluded: chain m residue 74 THR Chi-restraints excluded: chain m residue 104 GLU Chi-restraints excluded: chain m residue 126 ILE Chi-restraints excluded: chain m residue 131 VAL Chi-restraints excluded: chain m residue 135 VAL Chi-restraints excluded: chain n residue 13 ASN Chi-restraints excluded: chain n residue 14 SER Chi-restraints excluded: chain n residue 33 ILE Chi-restraints excluded: chain n residue 36 THR Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 51 LEU Chi-restraints excluded: chain n residue 60 VAL Chi-restraints excluded: chain n residue 83 LEU Chi-restraints excluded: chain n residue 98 LEU Chi-restraints excluded: chain n residue 100 CYS Chi-restraints excluded: chain o residue 18 LEU Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 28 VAL Chi-restraints excluded: chain o residue 35 ILE Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain o residue 43 ASN Chi-restraints excluded: chain o residue 54 VAL Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain o residue 93 ASP Chi-restraints excluded: chain p residue 1 SER Chi-restraints excluded: chain p residue 26 GLU Chi-restraints excluded: chain p residue 29 VAL Chi-restraints excluded: chain p residue 43 GLU Chi-restraints excluded: chain p residue 47 ILE Chi-restraints excluded: chain p residue 65 ASN Chi-restraints excluded: chain p residue 69 VAL Chi-restraints excluded: chain q residue 3 VAL Chi-restraints excluded: chain q residue 7 VAL Chi-restraints excluded: chain q residue 17 LEU Chi-restraints excluded: chain q residue 33 VAL Chi-restraints excluded: chain q residue 38 VAL Chi-restraints excluded: chain q residue 86 SER Chi-restraints excluded: chain q residue 99 VAL Chi-restraints excluded: chain q residue 103 VAL Chi-restraints excluded: chain r residue 11 GLN Chi-restraints excluded: chain r residue 14 VAL Chi-restraints excluded: chain r residue 20 VAL Chi-restraints excluded: chain r residue 22 LEU Chi-restraints excluded: chain r residue 33 VAL Chi-restraints excluded: chain r residue 54 VAL Chi-restraints excluded: chain r residue 63 VAL Chi-restraints excluded: chain r residue 75 VAL Chi-restraints excluded: chain r residue 94 THR Chi-restraints excluded: chain s residue 4 ILE Chi-restraints excluded: chain s residue 35 ILE Chi-restraints excluded: chain s residue 45 VAL Chi-restraints excluded: chain s residue 46 LEU Chi-restraints excluded: chain s residue 77 ASP Chi-restraints excluded: chain t residue 8 LEU Chi-restraints excluded: chain t residue 10 VAL Chi-restraints excluded: chain t residue 58 VAL Chi-restraints excluded: chain t residue 62 VAL Chi-restraints excluded: chain t residue 63 VAL Chi-restraints excluded: chain u residue 11 ILE Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain u residue 51 LEU Chi-restraints excluded: chain u residue 69 VAL Chi-restraints excluded: chain v residue 8 VAL Chi-restraints excluded: chain v residue 24 ASN Chi-restraints excluded: chain v residue 48 MET Chi-restraints excluded: chain v residue 59 GLU Chi-restraints excluded: chain v residue 61 LEU Chi-restraints excluded: chain v residue 64 VAL Chi-restraints excluded: chain v residue 66 ASP Chi-restraints excluded: chain v residue 86 LEU Chi-restraints excluded: chain w residue 39 THR Chi-restraints excluded: chain w residue 42 HIS Chi-restraints excluded: chain w residue 55 LEU Chi-restraints excluded: chain w residue 60 ASP Chi-restraints excluded: chain w residue 67 VAL Chi-restraints excluded: chain w residue 71 LYS Chi-restraints excluded: chain x residue 3 VAL Chi-restraints excluded: chain x residue 24 THR Chi-restraints excluded: chain x residue 39 VAL Chi-restraints excluded: chain x residue 46 VAL Chi-restraints excluded: chain y residue 58 ASN Chi-restraints excluded: chain z residue 10 ARG Chi-restraints excluded: chain z residue 13 ILE Chi-restraints excluded: chain z residue 24 LEU Chi-restraints excluded: chain z residue 31 ILE Chi-restraints excluded: chain z residue 40 THR Chi-restraints excluded: chain z residue 56 VAL Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 5 ASN Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 36 LYS Chi-restraints excluded: chain C residue 32 LYS Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 25 HIS Chi-restraints excluded: chain E residue 30 HIS Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain F residue 20 ASP Chi-restraints excluded: chain G residue 8 MET Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 146 SER Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 196 ASP Chi-restraints excluded: chain H residue 28 PHE Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain H residue 197 VAL Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 28 ASP Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 146 GLU Chi-restraints excluded: chain I residue 160 LEU Chi-restraints excluded: chain I residue 194 ILE Chi-restraints excluded: chain I residue 196 GLU Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 29 ILE Chi-restraints excluded: chain J residue 94 PHE Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 147 ASN Chi-restraints excluded: chain K residue 7 VAL Chi-restraints excluded: chain K residue 13 ASP Chi-restraints excluded: chain K residue 76 THR Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain L residue 42 VAL Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 76 SER Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain L residue 145 GLU Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain M residue 26 MET Chi-restraints excluded: chain M residue 42 GLU Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 74 ILE Chi-restraints excluded: chain M residue 78 SER Chi-restraints excluded: chain M residue 90 GLU Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain M residue 113 ARG Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain N residue 28 VAL Chi-restraints excluded: chain N residue 53 LEU Chi-restraints excluded: chain N residue 67 LYS Chi-restraints excluded: chain N residue 87 MET Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain O residue 42 LEU Chi-restraints excluded: chain O residue 96 VAL Chi-restraints excluded: chain O residue 98 VAL Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain P residue 54 SER Chi-restraints excluded: chain P residue 58 THR Chi-restraints excluded: chain P residue 69 CYS Chi-restraints excluded: chain P residue 71 ASP Chi-restraints excluded: chain P residue 83 VAL Chi-restraints excluded: chain P residue 84 MET Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 112 VAL Chi-restraints excluded: chain P residue 115 ILE Chi-restraints excluded: chain P residue 124 LYS Chi-restraints excluded: chain Q residue 4 ASN Chi-restraints excluded: chain Q residue 34 THR Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 57 THR Chi-restraints excluded: chain Q residue 78 VAL Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain R residue 13 HIS Chi-restraints excluded: chain R residue 22 TYR Chi-restraints excluded: chain R residue 48 SER Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain S residue 26 LEU Chi-restraints excluded: chain S residue 33 VAL Chi-restraints excluded: chain S residue 73 LEU Chi-restraints excluded: chain T residue 48 ASP Chi-restraints excluded: chain T residue 60 SER Chi-restraints excluded: chain T residue 67 ASP Chi-restraints excluded: chain U residue 2 VAL Chi-restraints excluded: chain U residue 66 THR Chi-restraints excluded: chain U residue 79 ASN Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain W residue 17 VAL Chi-restraints excluded: chain W residue 20 ILE Chi-restraints excluded: chain W residue 30 ASN Chi-restraints excluded: chain W residue 34 GLU Chi-restraints excluded: chain W residue 70 THR Chi-restraints excluded: chain X residue 46 LEU Chi-restraints excluded: chain X residue 65 MET Chi-restraints excluded: chain X residue 73 PHE Chi-restraints excluded: chain Y residue 3 ILE Chi-restraints excluded: chain Y residue 11 ILE Chi-restraints excluded: chain Y residue 29 THR Chi-restraints excluded: chain Y residue 69 ASN Chi-restraints excluded: chain 8 residue 46 SER Chi-restraints excluded: chain 8 residue 85 GLU Chi-restraints excluded: chain 8 residue 94 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1016 random chunks: chunk 494 optimal weight: 10.0000 chunk 640 optimal weight: 50.0000 chunk 858 optimal weight: 10.0000 chunk 246 optimal weight: 20.0000 chunk 743 optimal weight: 20.0000 chunk 119 optimal weight: 9.9990 chunk 223 optimal weight: 20.0000 chunk 807 optimal weight: 20.0000 chunk 337 optimal weight: 7.9990 chunk 828 optimal weight: 10.0000 chunk 102 optimal weight: 30.0000 overall best weight: 9.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 45 ASN ** b 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 259 ASN f 114 HIS ** l 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 57 ASN ** y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 44 GLN G 14 HIS ** G 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 70 GLN ** I 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.086874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.063516 restraints weight = 638463.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.065085 restraints weight = 210277.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.066113 restraints weight = 119327.685| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.5043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 157481 Z= 0.351 Angle : 0.723 14.368 235693 Z= 0.365 Chirality : 0.040 0.401 30128 Planarity : 0.005 0.073 12572 Dihedral : 23.578 176.533 79036 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 23.00 Ramachandran Plot: Outliers : 0.11 % Allowed : 11.25 % Favored : 88.64 % Rotamer: Outliers : 6.94 % Allowed : 26.40 % Favored : 66.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.11), residues: 5651 helix: -0.37 (0.12), residues: 1756 sheet: -1.67 (0.17), residues: 958 loop : -2.23 (0.11), residues: 2937 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP r 92 HIS 0.010 0.002 HIS x 33 PHE 0.041 0.002 PHE e 99 TYR 0.029 0.002 TYR O 65 ARG 0.015 0.001 ARG M 14 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 38705.54 seconds wall clock time: 677 minutes 6.82 seconds (40626.82 seconds total)