Starting phenix.real_space_refine on Wed Apr 17 01:10:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jt1_22466/04_2024/7jt1_22466.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jt1_22466/04_2024/7jt1_22466.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jt1_22466/04_2024/7jt1_22466.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jt1_22466/04_2024/7jt1_22466.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jt1_22466/04_2024/7jt1_22466.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jt1_22466/04_2024/7jt1_22466.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.097 sd= 0.600 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 4655 5.49 5 S 143 5.16 5 C 73149 2.51 5 N 27165 2.21 5 O 40488 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "b GLU 34": "OE1" <-> "OE2" Residue "b ASP 83": "OD1" <-> "OD2" Residue "b GLU 99": "OE1" <-> "OE2" Residue "b ASP 167": "OD1" <-> "OD2" Residue "b GLU 184": "OE1" <-> "OE2" Residue "b ASP 263": "OD1" <-> "OD2" Residue "c ARG 13": "NH1" <-> "NH2" Residue "c ARG 33": "NH1" <-> "NH2" Residue "c ASP 43": "OD1" <-> "OD2" Residue "c ARG 59": "NH1" <-> "NH2" Residue "c GLU 64": "OE1" <-> "OE2" Residue "c ARG 77": "NH1" <-> "NH2" Residue "c ARG 83": "NH1" <-> "NH2" Residue "c ASP 108": "OD1" <-> "OD2" Residue "c ARG 169": "NH1" <-> "NH2" Residue "c ARG 184": "NH1" <-> "NH2" Residue "c ASP 200": "OD1" <-> "OD2" Residue "d GLU 2": "OE1" <-> "OE2" Residue "d ASP 7": "OD1" <-> "OD2" Residue "d PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 21": "NH1" <-> "NH2" Residue "d ASP 22": "OD1" <-> "OD2" Residue "d ARG 44": "NH1" <-> "NH2" Residue "d ARG 49": "NH1" <-> "NH2" Residue "d ARG 61": "NH1" <-> "NH2" Residue "d ARG 88": "NH1" <-> "NH2" Residue "d ARG 102": "NH1" <-> "NH2" Residue "d GLU 127": "OE1" <-> "OE2" Residue "d ASP 140": "OD1" <-> "OD2" Residue "d GLU 144": "OE1" <-> "OE2" Residue "d ASP 145": "OD1" <-> "OD2" Residue "d ASP 154": "OD1" <-> "OD2" Residue "d ARG 162": "NH1" <-> "NH2" Residue "d ASP 168": "OD1" <-> "OD2" Residue "d ARG 170": "NH1" <-> "NH2" Residue "d ASP 191": "OD1" <-> "OD2" Residue "e GLU 10": "OE1" <-> "OE2" Residue "e ARG 70": "NH1" <-> "NH2" Residue "e ARG 79": "NH1" <-> "NH2" Residue "e ARG 91": "NH1" <-> "NH2" Residue "e ARG 101": "NH1" <-> "NH2" Residue "e ARG 109": "NH1" <-> "NH2" Residue "e ARG 111": "NH1" <-> "NH2" Residue "e ASP 112": "OD1" <-> "OD2" Residue "e ARG 114": "NH1" <-> "NH2" Residue "e PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 132": "NH1" <-> "NH2" Residue "e GLU 133": "OE1" <-> "OE2" Residue "e ASP 152": "OD1" <-> "OD2" Residue "e GLU 163": "OE1" <-> "OE2" Residue "e PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 2": "NH1" <-> "NH2" Residue "f ASP 59": "OD1" <-> "OD2" Residue "f PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ASP 113": "OD1" <-> "OD2" Residue "f ARG 152": "NH1" <-> "NH2" Residue "f ARG 162": "NH1" <-> "NH2" Residue "f ARG 169": "NH1" <-> "NH2" Residue "g GLU 55": "OE1" <-> "OE2" Residue "g PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 114": "OE1" <-> "OE2" Residue "g GLU 137": "OE1" <-> "OE2" Residue "j ARG 13": "NH1" <-> "NH2" Residue "j ARG 37": "NH1" <-> "NH2" Residue "j ASP 71": "OD1" <-> "OD2" Residue "j ARG 96": "NH1" <-> "NH2" Residue "j GLU 102": "OE1" <-> "OE2" Residue "j ARG 120": "NH1" <-> "NH2" Residue "k ASP 80": "OD1" <-> "OD2" Residue "l GLU 10": "OE1" <-> "OE2" Residue "l ARG 21": "NH1" <-> "NH2" Residue "l ARG 33": "NH1" <-> "NH2" Residue "l ARG 41": "NH1" <-> "NH2" Residue "l ARG 47": "NH1" <-> "NH2" Residue "l TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ARG 60": "NH1" <-> "NH2" Residue "l ARG 78": "NH1" <-> "NH2" Residue "l GLU 115": "OE1" <-> "OE2" Residue "l ARG 126": "NH1" <-> "NH2" Residue "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 ARG 114": "NH1" <-> "NH2" Residue "n ARG 8": "NH1" <-> "NH2" Residue "n ARG 12": "NH1" <-> "NH2" Residue "n ARG 17": "NH1" <-> "NH2" Residue "n ARG 22": "NH1" <-> "NH2" Residue "n ARG 46": "NH1" <-> "NH2" Residue "n ARG 63": "NH1" <-> "NH2" Residue "n ARG 64": "NH1" <-> "NH2" Residue "n ARG 69": "NH1" <-> "NH2" Residue "n ARG 71": "NH1" <-> "NH2" Residue "n ASP 72": "OD1" <-> "OD2" Residue "n ARG 96": "NH1" <-> "NH2" Residue "n ASP 106": "OD1" <-> "OD2" Residue "n ARG 118": "NH1" <-> "NH2" Residue "o ARG 10": "NH1" <-> "NH2" Residue "o ARG 16": "NH1" <-> "NH2" Residue "o GLU 20": "OE1" <-> "OE2" Residue "o ARG 25": "NH1" <-> "NH2" Residue "o GLU 55": "OE1" <-> "OE2" Residue "o GLU 80": "OE1" <-> "OE2" Residue "o ARG 81": "NH1" <-> "NH2" Residue "o ARG 94": "NH1" <-> "NH2" Residue "o ARG 102": "NH1" <-> "NH2" Residue "o ARG 111": "NH1" <-> "NH2" Residue "p ARG 20": "NH1" <-> "NH2" Residue "p ARG 38": "NH1" <-> "NH2" Residue "p ARG 61": "NH1" <-> "NH2" Residue "p ASP 81": "OD1" <-> "OD2" 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 ARG 69": "NH1" <-> "NH2" Residue "q GLU 88": "OE1" <-> "OE2" Residue "r ARG 21": "NH1" <-> "NH2" Residue "r GLU 34": "OE1" <-> "OE2" Residue "r ARG 68": "NH1" <-> "NH2" Residue "r ARG 78": "NH1" <-> "NH2" Residue "r ARG 79": "NH1" <-> "NH2" Residue "r ARG 84": "NH1" <-> "NH2" Residue "s ASP 65": "OD1" <-> "OD2" Residue "s ASP 68": "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 18": "OE1" <-> "OE2" Residue "t PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t ARG 73": "NH1" <-> "NH2" Residue "t GLU 89": "OE1" <-> "OE2" Residue "u ARG 5": "NH1" <-> "NH2" Residue "u ARG 6": "NH1" <-> "NH2" Residue "u GLU 36": "OE1" <-> "OE2" Residue "u GLU 59": "OE1" <-> "OE2" Residue "u ARG 81": "NH1" <-> "NH2" Residue "u ARG 85": "NH1" <-> "NH2" Residue "u ARG 93": "NH1" <-> "NH2" Residue "v TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v ASP 43": "OD1" <-> "OD2" Residue "v ASP 76": "OD1" <-> "OD2" Residue "w GLU 13": "OE1" <-> "OE2" Residue "w PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y GLU 13": "OE1" <-> "OE2" Residue "y ARG 29": "NH1" <-> "NH2" Residue "y ARG 47": "NH1" <-> "NH2" Residue "y ARG 52": "NH1" <-> "NH2" Residue "y GLU 59": "OE1" <-> "OE2" Residue "z ARG 10": "NH1" <-> "NH2" Residue "z ARG 29": "NH1" <-> "NH2" Residue "z GLU 38": "OE1" <-> "OE2" Residue "z ARG 44": "NH1" <-> "NH2" Residue "z PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 9": "NH1" <-> "NH2" Residue "B ARG 15": "NH1" <-> "NH2" Residue "B ARG 39": "NH1" <-> "NH2" Residue "B TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 51": "NH1" <-> "NH2" Residue "C ARG 43": "NH1" <-> "NH2" Residue "C TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 3": "NH1" <-> "NH2" Residue "D ARG 12": "NH1" <-> "NH2" Residue "D ARG 14": "NH1" <-> "NH2" Residue "D ARG 19": "NH1" <-> "NH2" Residue "D ARG 21": "NH1" <-> "NH2" Residue "D ARG 33": "NH1" <-> "NH2" Residue "D ARG 41": "NH1" <-> "NH2" Residue "E ARG 12": "NH1" <-> "NH2" Residue "E ARG 29": "NH1" <-> "NH2" Residue "E ARG 39": "NH1" <-> "NH2" Residue "E ARG 41": "NH1" <-> "NH2" Residue "F ARG 12": "NH1" <-> "NH2" Residue "F ASP 20": "OD1" <-> "OD2" Residue "F ARG 24": "NH1" <-> "NH2" Residue "G PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 55": "OE1" <-> "OE2" Residue "G ASP 81": "OD1" <-> "OD2" Residue "G ASP 115": "OD1" <-> "OD2" Residue "G ASP 152": "OD1" <-> "OD2" Residue "G ASP 164": "OD1" <-> "OD2" Residue "G GLU 168": "OE1" <-> "OE2" Residue "G ARG 224": "NH1" <-> "NH2" Residue "H GLU 27": "OE1" <-> "OE2" Residue "H PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 30": "OD1" <-> "OD2" Residue "H ASP 35": "OD1" <-> "OD2" Residue "H ARG 106": "NH1" <-> "NH2" Residue "H GLU 109": "OE1" <-> "OE2" Residue "H ASP 117": "OD1" <-> "OD2" Residue "H ARG 130": "NH1" <-> "NH2" Residue "H GLU 151": "OE1" <-> "OE2" Residue "H ASP 182": "OD1" <-> "OD2" Residue "I GLU 56": "OE1" <-> "OE2" Residue "I TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 68": "OE1" <-> "OE2" Residue "I ASP 98": "OD1" <-> "OD2" Residue "I ASP 140": "OD1" <-> "OD2" Residue "I ASP 173": "OD1" <-> "OD2" Residue "I GLU 178": "OE1" <-> "OE2" Residue "I GLU 201": "OE1" <-> "OE2" Residue "J GLU 100": "OE1" <-> "OE2" Residue "J ASP 141": "OD1" <-> "OD2" Residue "J ARG 156": "NH1" <-> "NH2" Residue "K GLU 23": "OE1" <-> "OE2" Residue "K ASP 72": "OD1" <-> "OD2" Residue "K GLU 98": "OE1" <-> "OE2" Residue "L ASP 14": "OD1" <-> "OD2" Residue "L PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 89": "OE1" <-> "OE2" Residue "M ASP 4": "OD1" <-> "OD2" Residue "M ASP 53": "OD1" <-> "OD2" Residue "M GLU 57": "OE1" <-> "OE2" Residue "M ASP 89": "OD1" <-> "OD2" Residue "N PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 41": "OE1" <-> "OE2" Residue "N TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 96": "OE1" <-> "OE2" Residue "N ASP 106": "OD1" <-> "OD2" Residue "N GLU 111": "OE1" <-> "OE2" Residue "N ARG 123": "NH1" <-> "NH2" Residue "O ASP 14": "OD1" <-> "OD2" Residue "O PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 81": "OE1" <-> "OE2" Residue "P GLU 93": "OE1" <-> "OE2" Residue "Q ARG 55": "NH1" <-> "NH2" Residue "R ASP 67": "OD1" <-> "OD2" Residue "S ASP 39": "OD1" <-> "OD2" Residue "U TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 28": "NH1" <-> "NH2" Residue "U GLU 47": "OE1" <-> "OE2" Residue "U GLU 77": "OE1" <-> "OE2" Residue "V ASP 14": "OD1" <-> "OD2" Residue "V PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 59": "OE1" <-> "OE2" Residue "V GLU 79": "OE1" <-> "OE2" Residue "W ARG 11": "NH1" <-> "NH2" Residue "W GLU 34": "OE1" <-> "OE2" Residue "W TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 11": "OD1" <-> "OD2" Residue "X ASP 63": "OD1" <-> "OD2" Residue "X GLU 64": "OE1" <-> "OE2" Residue "Y GLU 14": "OE1" <-> "OE2" Residue "Z GLU 23": "OE1" <-> "OE2" Residue "Z ARG 66": "NH1" <-> "NH2" Residue "8 ARG 78": "NH1" <-> "NH2" Residue "8 GLU 97": "OE1" <-> "OE2" Residue "8 ARG 117": "NH1" <-> "NH2" Residue "9 ASP 12": "OD1" <-> "OD2" Residue "9 PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 ASP 42": "OD1" <-> "OD2" Residue "9 GLU 50": "OE1" <-> "OE2" Residue "9 ASP 67": "OD1" <-> "OD2" Residue "9 ARG 78": "NH1" <-> "NH2" Residue "9 ARG 90": "NH1" <-> "NH2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 145600 Number of models: 1 Model: "" Number of chains: 55 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': 92, 'rna2p_pyr': 50, 'rna3p_pur': 782, 'rna3p_pyr': 615} Link IDs: {'rna2p': 142, 'rna3p': 1396} Chain: "1" Number of atoms: 62315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2903, 62315 Classifications: {'RNA': 2903} Modifications used: {'5*END': 1, 'rna2p_pur': 216, 'rna2p_pyr': 95, 'rna3p_pur': 1458, 'rna3p_pyr': 1133} Link IDs: {'rna2p': 311, 'rna3p': 2591} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "2" Number of atoms: 2568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2568 Classifications: {'RNA': 120} Modifications used: {'5*END': 1, 'rna2p_pur': 4, 'rna2p_pyr': 3, 'rna3p_pur': 61, 'rna3p_pyr': 52} Link IDs: {'rna2p': 7, 'rna3p': 112} Chain: "5" Number of atoms: 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: 439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 439 Classifications: {'RNA': 20} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 16, 'rna3p_pyr': 3} Link IDs: {'rna2p': 1, 'rna3p': 18} Chain: "8" Number of atoms: 1016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1016 Classifications: {'peptide': 130} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 125} Chain: "9" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 641 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 2, 'TRANS': 78} Chain breaks: 1 Time building chain proxies: 56.46, per 1000 atoms: 0.39 Number of scatterers: 145600 At special positions: 0 Unit cell: (269.878, 246.954, 240.702, 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 143 16.00 P 4655 15.00 O 40488 8.00 N 27165 7.00 C 73149 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: 63.91 Conformation dependent library (CDL) restraints added in 6.8 seconds 11452 Ramachandran restraints generated. 5726 Oldfield, 0 Emsley, 5726 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10724 Finding SS restraints... Secondary structure from input PDB file: 176 helices and 71 sheets defined 32.8% alpha, 16.3% beta 1422 base pairs and 2576 stacking pairs defined. Time for finding SS restraints: 54.23 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 196 through 202 removed outlier: 3.817A pdb=" N MET b 200 " --> pdb=" O ALA b 197 " (cutoff:3.500A) Processing helix chain 'b' and resid 207 through 212 removed outlier: 3.736A pdb=" N ARG b 211 " --> pdb=" O ALA b 207 " (cutoff:3.500A) Processing helix chain 'c' and resid 61 through 72 removed outlier: 3.638A pdb=" N ALA c 71 " --> pdb=" O HIS c 67 " (cutoff:3.500A) Processing helix chain 'c' and resid 97 through 102 removed outlier: 3.811A pdb=" N LEU c 100 " --> pdb=" O SER c 97 " (cutoff:3.500A) Processing helix chain 'd' and resid 15 through 20 Processing helix chain 'd' and resid 24 through 38 removed outlier: 3.609A pdb=" N VAL d 31 " --> pdb=" O LEU d 27 " (cutoff:3.500A) Processing helix chain 'd' and resid 97 through 115 removed outlier: 3.546A pdb=" N GLU d 111 " --> pdb=" O SER d 107 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU d 112 " --> pdb=" O ILE d 108 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL d 113 " --> pdb=" O LEU d 109 " (cutoff:3.500A) Processing helix chain 'd' and resid 130 through 141 removed outlier: 3.752A pdb=" N LYS d 137 " --> pdb=" O LEU d 133 " (cutoff:3.500A) Processing helix chain 'd' and resid 154 through 160 removed outlier: 3.543A pdb=" N ALA d 160 " --> pdb=" O ASN d 156 " (cutoff:3.500A) Processing helix chain 'd' and resid 173 through 175 No H-bonds generated for 'chain 'd' and resid 173 through 175' Processing helix chain 'd' and resid 178 through 183 Processing helix chain 'd' and resid 190 through 200 Processing helix chain 'e' and resid 2 through 10 removed outlier: 3.660A pdb=" N TYR e 6 " --> pdb=" O LYS e 2 " (cutoff:3.500A) Processing helix chain 'e' and resid 10 through 16 Processing helix chain 'e' and resid 47 through 60 removed outlier: 3.576A pdb=" N ALA e 58 " --> pdb=" O ALA e 54 " (cutoff:3.500A) Processing helix chain 'e' and resid 93 through 105 removed outlier: 3.675A pdb=" N GLU e 97 " --> pdb=" O GLU e 93 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N PHE e 99 " --> pdb=" O MET e 95 " (cutoff:3.500A) Processing helix chain 'e' and resid 106 through 110 removed outlier: 3.508A pdb=" N ILE e 110 " --> pdb=" O VAL e 107 " (cutoff:3.500A) Processing helix chain 'e' and resid 161 through 169 removed outlier: 3.559A pdb=" N GLY e 165 " --> pdb=" O SER e 161 " (cutoff:3.500A) Processing helix chain 'e' and resid 170 through 173 removed outlier: 3.704A pdb=" N ASP e 173 " --> pdb=" O ALA e 170 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 170 through 173' Processing helix chain 'f' and resid 2 through 6 removed outlier: 3.863A pdb=" N ALA f 6 " --> pdb=" O ARG f 2 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 2 through 6' Processing helix chain 'f' and resid 59 through 80 removed outlier: 3.678A pdb=" N THR f 66 " --> pdb=" O ALA f 62 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA f 69 " --> pdb=" O GLY f 65 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR f 79 " --> pdb=" O VAL f 75 " (cutoff:3.500A) Processing helix chain 'f' and resid 136 through 151 removed outlier: 3.576A pdb=" N GLY f 141 " --> pdb=" O LYS f 137 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ARG f 151 " --> pdb=" O LEU f 147 " (cutoff:3.500A) Processing helix chain 'g' and resid 22 through 29 removed outlier: 3.622A pdb=" N ALA g 26 " --> pdb=" O LYS g 22 " (cutoff:3.500A) removed outlier: 3.585A 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 49 through 54 removed outlier: 3.541A pdb=" N GLU g 53 " --> pdb=" O ALA g 49 " (cutoff:3.500A) Processing helix chain 'g' and resid 54 through 69 removed outlier: 3.636A pdb=" N GLU g 60 " --> pdb=" O ALA g 56 " (cutoff:3.500A) Processing helix chain 'g' and resid 96 through 103 Processing helix chain 'j' and resid 24 through 38 removed outlier: 3.801A pdb=" N GLU j 31 " --> pdb=" O ARG j 27 " (cutoff:3.500A) Processing helix chain 'j' and resid 58 through 62 removed outlier: 3.597A pdb=" N LYS j 61 " --> pdb=" O ASN j 58 " (cutoff:3.500A) Processing helix chain 'j' and resid 67 through 72 removed outlier: 3.672A pdb=" N ASP j 71 " --> pdb=" O ASN j 67 " (cutoff:3.500A) Processing helix chain 'j' and resid 88 through 96 Processing helix chain 'j' and resid 98 through 107 removed outlier: 3.670A pdb=" N LYS j 106 " --> pdb=" O GLU j 102 " (cutoff:3.500A) Processing helix chain 'j' and resid 112 through 118 Processing helix chain 'j' and resid 132 through 136 Processing helix chain 'k' and resid 112 through 118 removed outlier: 3.649A pdb=" N ILE k 116 " --> pdb=" O PHE k 112 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER k 117 " --> pdb=" O MET k 113 " (cutoff:3.500A) Processing helix chain 'l' and resid 56 through 60 Processing helix chain 'l' and resid 129 through 137 removed outlier: 3.626A pdb=" N ALA l 133 " --> pdb=" O LYS l 129 " (cutoff:3.500A) Processing helix chain 'm' and resid 43 through 58 removed outlier: 3.514A pdb=" N MET m 53 " --> pdb=" O ALA m 49 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ARG m 55 " --> pdb=" O ARG m 51 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N ALA m 56 " --> pdb=" O ALA m 52 " (cutoff:3.500A) Processing helix chain 'm' and resid 109 through 122 removed outlier: 3.692A pdb=" N ALA m 122 " --> pdb=" O LYS m 118 " (cutoff:3.500A) Processing helix chain 'n' and resid 13 through 32 removed outlier: 3.507A pdb=" N PHE n 21 " --> pdb=" O ARG n 17 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG n 22 " --> pdb=" O GLN n 18 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ASN n 23 " --> pdb=" O ALA n 19 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG n 30 " --> pdb=" O GLY n 26 " (cutoff:3.500A) Processing helix chain 'n' and resid 38 through 57 removed outlier: 4.520A pdb=" N ARG n 46 " --> pdb=" O LYS n 42 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N VAL n 47 " --> pdb=" O GLU n 43 " (cutoff:3.500A) removed outlier: 3.511A 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 60 through 69 removed outlier: 3.561A pdb=" N ARG n 64 " --> pdb=" O VAL n 60 " (cutoff:3.500A) 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 21 removed outlier: 4.072A pdb=" N ARG o 7 " --> pdb=" O LYS o 3 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE o 8 " --> pdb=" O LYS o 4 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR o 12 " --> pdb=" O ILE o 8 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N ARG o 13 " --> pdb=" O ARG o 9 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ALA o 14 " --> pdb=" O ARG o 10 " (cutoff:3.500A) removed outlier: 3.541A 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 86 removed outlier: 3.515A pdb=" N ARG o 81 " --> pdb=" O ALA o 77 " (cutoff:3.500A) Processing helix chain 'o' and resid 101 through 113 Processing helix chain 'p' and resid 2 through 10 removed outlier: 3.682A pdb=" N GLU p 10 " --> pdb=" O GLN p 6 " (cutoff:3.500A) Processing helix chain 'p' and resid 52 through 55 Processing helix chain 'p' and resid 96 through 101 Processing helix chain 'q' and resid 5 through 18 removed outlier: 3.523A pdb=" N ALA q 11 " --> pdb=" O VAL q 7 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE q 16 " --> pdb=" O ARG q 12 " (cutoff:3.500A) Processing helix chain 'q' and resid 24 through 29 removed outlier: 3.657A pdb=" N SER q 28 " --> pdb=" O GLY q 25 " (cutoff:3.500A) Processing helix chain 'q' and resid 30 through 72 removed outlier: 4.014A pdb=" N GLN q 36 " --> pdb=" O ARG q 32 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ARG q 50 " --> pdb=" O TYR q 46 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N LYS q 53 " --> pdb=" O ARG q 49 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG q 57 " --> pdb=" O LYS q 53 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA q 67 " --> pdb=" O ARG q 63 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN q 71 " --> pdb=" O ALA q 67 " (cutoff:3.500A) Processing helix chain 'q' and resid 74 through 85 removed outlier: 3.533A pdb=" N GLY q 81 " --> pdb=" O LYS q 77 " (cutoff:3.500A) Processing helix chain 'q' and resid 90 through 101 removed outlier: 3.832A pdb=" N ASP q 96 " --> pdb=" O LYS q 92 " (cutoff:3.500A) Processing helix chain 'q' and resid 101 through 117 removed outlier: 3.901A pdb=" N ALA q 107 " --> pdb=" O VAL q 103 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU q 110 " --> pdb=" O THR q 106 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA q 117 " --> pdb=" O LYS q 113 " (cutoff:3.500A) Processing helix chain 's' and resid 13 through 22 removed outlier: 3.695A pdb=" N VAL s 17 " --> pdb=" O SER s 13 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU s 19 " --> pdb=" O GLN s 15 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N VAL s 20 " --> pdb=" O LYS s 16 " (cutoff:3.500A) Processing helix chain 's' and resid 29 through 37 removed outlier: 3.515A pdb=" N ASP s 34 " --> pdb=" O SER s 30 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU s 36 " --> pdb=" O ALA s 32 " (cutoff:3.500A) Processing helix chain 's' and resid 41 through 59 removed outlier: 3.582A pdb=" N VAL s 45 " --> pdb=" O LYS s 41 " (cutoff:3.500A) Processing helix chain 's' and resid 89 through 91 No H-bonds generated for 'chain 's' and resid 89 through 91' Processing helix chain 't' and resid 2 through 9 removed outlier: 3.657A pdb=" N ARG t 6 " --> pdb=" O ILE t 2 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS t 9 " --> pdb=" O GLU t 5 " (cutoff:3.500A) Processing helix chain 't' and resid 17 through 28 removed outlier: 3.520A pdb=" N SER t 21 " --> pdb=" O SER t 17 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR t 22 " --> pdb=" O GLU t 18 " (cutoff:3.500A) Processing helix chain 't' and resid 39 through 50 Processing helix chain 'v' and resid 13 through 22 Processing helix chain 'v' and resid 44 through 51 removed outlier: 3.729A pdb=" N ASN v 49 " --> pdb=" O ASP v 45 " (cutoff:3.500A) Processing helix chain 'v' and resid 53 through 58 removed outlier: 3.573A pdb=" N SER v 58 " --> pdb=" O GLU v 55 " (cutoff:3.500A) Processing helix chain 'x' and resid 52 through 61 Processing helix chain 'x' and resid 62 through 74 removed outlier: 3.611A pdb=" N GLU x 69 " --> pdb=" O THR x 65 " (cutoff:3.500A) Processing helix chain 'y' and resid 9 through 23 removed outlier: 3.593A pdb=" N ASN y 15 " --> pdb=" O VAL y 11 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ARG y 23 " --> pdb=" O LEU y 19 " (cutoff:3.500A) Processing helix chain 'y' and resid 25 through 34 removed outlier: 3.502A pdb=" N ALA y 32 " --> pdb=" O LEU y 28 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA y 33 " --> pdb=" O ARG y 29 " (cutoff:3.500A) Processing helix chain 'y' and resid 40 through 60 removed outlier: 3.630A pdb=" N LYS y 44 " --> pdb=" O SER y 40 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU y 56 " --> pdb=" O ARG y 52 " (cutoff:3.500A) Processing helix chain 'z' and resid 16 through 27 Processing helix chain 'z' and resid 40 through 48 Processing helix chain 'B' and resid 8 through 16 Processing helix chain 'D' and resid 8 through 14 Processing helix chain 'D' and resid 17 through 22 Processing helix chain 'D' and resid 24 through 38 Processing helix chain 'E' and resid 6 through 11 Processing helix chain 'E' and resid 36 through 43 Processing helix chain 'E' and resid 50 through 61 removed outlier: 4.170A pdb=" N GLY E 55 " --> pdb=" O LYS E 51 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N LEU E 56 " --> pdb=" O GLY E 52 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N CYS E 60 " --> pdb=" O LEU E 56 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 10 removed outlier: 3.812A pdb=" N LEU G 9 " --> pdb=" O MET G 5 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LYS G 10 " --> pdb=" O ARG G 6 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 5 through 10' Processing helix chain 'G' and resid 23 through 27 removed outlier: 3.826A pdb=" N LYS G 27 " --> pdb=" O PRO G 24 " (cutoff:3.500A) Processing helix chain 'G' and resid 33 through 37 removed outlier: 3.997A pdb=" N LYS G 36 " --> pdb=" O ALA G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 41 through 44 removed outlier: 3.794A pdb=" N LYS G 44 " --> pdb=" O ASN G 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 41 through 44' Processing helix chain 'G' and resid 45 through 61 removed outlier: 3.584A pdb=" N GLU G 51 " --> pdb=" O PRO G 47 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLU G 55 " --> pdb=" O GLU G 51 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU G 56 " --> pdb=" O ALA G 52 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER G 61 " --> pdb=" O ASN G 57 " (cutoff:3.500A) Processing helix chain 'G' and resid 75 through 85 removed outlier: 3.536A pdb=" N ALA G 83 " --> pdb=" O VAL G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 123 removed outlier: 3.527A pdb=" N VAL G 106 " --> pdb=" O ASN G 102 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N GLN G 108 " --> pdb=" O LYS G 104 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N SER G 109 " --> pdb=" O THR G 105 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR G 118 " --> pdb=" O LYS G 114 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLN G 121 " --> pdb=" O GLU G 117 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ASP G 122 " --> pdb=" O THR G 118 " (cutoff:3.500A) Processing helix chain 'G' and resid 124 through 127 removed outlier: 3.908A pdb=" N LYS G 127 " --> pdb=" O THR G 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 124 through 127' Processing helix chain 'G' and resid 129 through 146 removed outlier: 3.657A pdb=" N ASN G 145 " --> pdb=" O GLU G 141 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N SER G 146 " --> pdb=" O LYS G 142 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 176 removed outlier: 3.782A pdb=" N ILE G 172 " --> pdb=" O GLU G 168 " (cutoff:3.500A) Processing helix chain 'G' and resid 205 through 223 removed outlier: 3.722A pdb=" N THR G 210 " --> pdb=" O ILE G 206 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU G 211 " --> pdb=" O ARG G 207 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR G 212 " --> pdb=" O ALA G 208 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL G 220 " --> pdb=" O VAL G 216 " (cutoff:3.500A) Processing helix chain 'H' and resid 7 through 11 removed outlier: 3.759A pdb=" N LEU H 11 " --> pdb=" O GLY H 8 " (cutoff:3.500A) Processing helix chain 'H' and resid 27 through 44 removed outlier: 3.536A pdb=" N ASP H 33 " --> pdb=" O ALA H 29 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER H 34 " --> pdb=" O ASP H 30 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASP H 35 " --> pdb=" O ASN H 31 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LYS H 44 " --> pdb=" O GLN H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 72 through 77 Processing helix chain 'H' and resid 80 through 95 removed outlier: 3.543A pdb=" N VAL H 90 " --> pdb=" O LEU H 86 " (cutoff:3.500A) Processing helix chain 'H' and resid 107 through 110 Processing helix chain 'H' and resid 111 through 124 Processing helix chain 'H' and resid 128 through 142 removed outlier: 3.532A pdb=" N ARG H 135 " --> pdb=" O ARG H 131 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N MET H 141 " --> pdb=" O VAL H 137 " (cutoff:3.500A) Processing helix chain 'H' and resid 155 through 159 removed outlier: 3.692A pdb=" N ALA H 159 " --> pdb=" O LEU H 156 " (cutoff:3.500A) Processing helix chain 'I' and resid 8 through 15 removed outlier: 3.754A pdb=" N ARG I 13 " --> pdb=" O LYS I 9 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 65 removed outlier: 3.654A pdb=" N GLU I 56 " --> pdb=" O VAL I 52 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS I 57 " --> pdb=" O GLN I 53 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS I 59 " --> pdb=" O ARG I 55 " (cutoff:3.500A) Processing helix chain 'I' and resid 67 through 80 removed outlier: 3.583A pdb=" N LYS I 76 " --> pdb=" O ARG I 72 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG I 80 " --> pdb=" O LYS I 76 " (cutoff:3.500A) Processing helix chain 'I' and resid 84 through 92 removed outlier: 3.550A pdb=" N LEU I 89 " --> pdb=" O THR I 85 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N LEU I 90 " --> pdb=" O GLY I 86 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA I 91 " --> pdb=" O GLU I 87 " (cutoff:3.500A) Processing helix chain 'I' and resid 96 through 104 removed outlier: 3.644A pdb=" N TYR I 102 " --> pdb=" O ASP I 98 " (cutoff:3.500A) Processing helix chain 'I' and resid 109 through 118 removed outlier: 3.737A pdb=" N GLN I 115 " --> pdb=" O ALA I 111 " (cutoff:3.500A) Processing helix chain 'I' and resid 153 through 160 Processing helix chain 'I' and resid 161 through 164 Processing helix chain 'I' and resid 196 through 203 removed outlier: 3.731A pdb=" N TYR I 203 " --> pdb=" O ILE I 199 " (cutoff:3.500A) Processing helix chain 'J' and resid 54 through 60 Processing helix chain 'J' and resid 62 through 69 Processing helix chain 'J' and resid 75 through 79 removed outlier: 4.354A pdb=" N GLY J 78 " --> pdb=" O LEU J 75 " (cutoff:3.500A) Processing helix chain 'J' and resid 110 through 116 removed outlier: 3.817A pdb=" N VAL J 116 " --> pdb=" O ALA J 112 " (cutoff:3.500A) Processing helix chain 'J' and resid 131 through 145 removed outlier: 3.513A pdb=" N ILE J 140 " --> pdb=" O VAL J 136 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASP J 141 " --> pdb=" O ARG J 137 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASN J 145 " --> pdb=" O ASP J 141 " (cutoff:3.500A) Processing helix chain 'J' and resid 148 through 153 Processing helix chain 'J' and resid 161 through 165 removed outlier: 3.629A pdb=" N GLY J 165 " --> pdb=" O GLU J 162 " (cutoff:3.500A) Processing helix chain 'K' and resid 12 through 16 removed outlier: 3.603A pdb=" N GLU K 16 " --> pdb=" O ASP K 13 " (cutoff:3.500A) Processing helix chain 'K' and resid 17 through 30 removed outlier: 3.502A pdb=" N GLU K 23 " --> pdb=" O PRO K 19 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA K 28 " --> pdb=" O ARG K 24 " (cutoff:3.500A) Processing helix chain 'K' and resid 31 through 33 No H-bonds generated for 'chain 'K' and resid 31 through 33' Processing helix chain 'K' and resid 67 through 81 removed outlier: 3.676A pdb=" N ILE K 71 " --> pdb=" O PRO K 67 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR K 76 " --> pdb=" O ASP K 72 " (cutoff:3.500A) Processing helix chain 'L' and resid 19 through 27 removed outlier: 3.690A pdb=" N ASN L 27 " --> pdb=" O ALA L 23 " (cutoff:3.500A) Processing helix chain 'L' and resid 34 through 54 removed outlier: 3.810A pdb=" N SER L 40 " --> pdb=" O SER L 36 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR L 48 " --> pdb=" O SER L 44 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU L 49 " --> pdb=" O ALA L 45 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG L 52 " --> pdb=" O THR L 48 " (cutoff:3.500A) Processing helix chain 'L' and resid 56 through 66 removed outlier: 3.599A pdb=" N ALA L 64 " --> pdb=" O ALA L 60 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU L 66 " --> pdb=" O GLU L 62 " (cutoff:3.500A) Processing helix chain 'L' and resid 91 through 107 removed outlier: 3.713A pdb=" N ASN L 96 " --> pdb=" O PRO L 92 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N ALA L 97 " --> pdb=" O VAL L 93 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N TRP L 102 " --> pdb=" O LEU L 98 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE L 103 " --> pdb=" O ALA L 99 " (cutoff:3.500A) Processing helix chain 'L' and resid 114 through 127 removed outlier: 3.570A pdb=" N GLU L 122 " --> pdb=" O ARG L 118 " (cutoff:3.500A) Processing helix chain 'L' and resid 134 through 147 removed outlier: 3.530A pdb=" N ASP L 139 " --> pdb=" O LYS L 135 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL L 140 " --> pdb=" O LYS L 136 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 19 removed outlier: 3.661A pdb=" N GLN M 17 " --> pdb=" O ILE M 13 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA M 19 " --> pdb=" O ASN M 15 " (cutoff:3.500A) Processing helix chain 'M' and resid 29 through 42 Processing helix chain 'M' and resid 87 through 91 removed outlier: 3.541A pdb=" N LEU M 91 " --> pdb=" O LYS M 88 " (cutoff:3.500A) Processing helix chain 'M' and resid 93 through 98 Processing helix chain 'M' and resid 111 through 119 removed outlier: 4.011A pdb=" N GLN M 117 " --> pdb=" O ARG M 113 " (cutoff:3.500A) Processing helix chain 'N' and resid 34 through 38 removed outlier: 3.673A pdb=" N PHE N 38 " --> pdb=" O LEU N 34 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 34 through 38' Processing helix chain 'N' and resid 70 through 86 removed outlier: 3.809A pdb=" N THR N 83 " --> pdb=" O ARG N 79 " (cutoff:3.500A) Processing helix chain 'N' and resid 90 through 99 removed outlier: 4.089A pdb=" N GLU N 96 " --> pdb=" O SER N 92 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU N 97 " --> pdb=" O LEU N 93 " (cutoff:3.500A) Processing helix chain 'O' and resid 14 through 34 removed outlier: 3.603A pdb=" N ILE O 18 " --> pdb=" O ASP O 14 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASP O 19 " --> pdb=" O HIS O 15 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N GLN O 20 " --> pdb=" O ARG O 16 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA O 23 " --> pdb=" O ASP O 19 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR O 28 " --> pdb=" O GLU O 24 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N THR O 32 " --> pdb=" O THR O 28 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA O 34 " --> pdb=" O LYS O 30 " (cutoff:3.500A) Processing helix chain 'O' and resid 83 through 88 removed outlier: 3.591A pdb=" N LEU O 87 " --> pdb=" O THR O 83 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N MET O 88 " --> pdb=" O VAL O 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 83 through 88' Processing helix chain 'P' and resid 58 through 69 Processing helix chain 'P' and resid 93 through 101 Processing helix chain 'Q' and resid 2 through 9 removed outlier: 3.584A pdb=" N LEU Q 6 " --> pdb=" O THR Q 2 " (cutoff:3.500A) Processing helix chain 'R' and resid 2 through 6 removed outlier: 3.842A pdb=" N GLY R 5 " --> pdb=" O ARG R 2 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE R 6 " --> pdb=" O ILE R 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 2 through 6' Processing helix chain 'R' and resid 13 through 18 Processing helix chain 'R' and resid 25 through 37 Processing helix chain 'R' and resid 48 through 62 removed outlier: 3.834A pdb=" N THR R 54 " --> pdb=" O GLY R 50 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N PHE R 62 " --> pdb=" O GLU R 58 " (cutoff:3.500A) Processing helix chain 'R' and resid 64 through 81 removed outlier: 3.723A pdb=" N ARG R 70 " --> pdb=" O GLY R 66 " (cutoff:3.500A) Processing helix chain 'R' and resid 84 through 93 Processing helix chain 'R' and resid 105 through 110 Processing helix chain 'S' and resid 2 through 19 removed outlier: 3.673A pdb=" N GLU S 9 " --> pdb=" O MET S 5 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL S 10 " --> pdb=" O LYS S 6 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ARG S 12 " --> pdb=" O ARG S 8 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA S 14 " --> pdb=" O VAL S 10 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU S 15 " --> pdb=" O LYS S 11 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASP S 17 " --> pdb=" O VAL S 13 " (cutoff:3.500A) Processing helix chain 'S' and resid 24 through 29 Processing helix chain 'S' and resid 37 through 46 removed outlier: 3.671A pdb=" N ALA S 43 " --> pdb=" O ASP S 39 " (cutoff:3.500A) Processing helix chain 'S' and resid 47 through 49 No H-bonds generated for 'chain 'S' and resid 47 through 49' Processing helix chain 'S' and resid 79 through 88 Processing helix chain 'T' and resid 3 through 15 removed outlier: 4.212A pdb=" N SER T 12 " --> pdb=" O ALA T 8 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLU T 13 " --> pdb=" O LYS T 9 " (cutoff:3.500A) Processing helix chain 'T' and resid 23 through 44 removed outlier: 4.231A pdb=" N GLY T 40 " --> pdb=" O ASN T 36 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N HIS T 41 " --> pdb=" O HIS T 37 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLU T 44 " --> pdb=" O GLY T 40 " (cutoff:3.500A) Processing helix chain 'T' and resid 50 through 73 removed outlier: 3.643A pdb=" N GLY T 54 " --> pdb=" O HIS T 50 " (cutoff:3.500A) Processing helix chain 'T' and resid 73 through 85 removed outlier: 3.879A pdb=" N GLU T 82 " --> pdb=" O THR T 78 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU T 84 " --> pdb=" O LEU T 80 " (cutoff:3.500A) Processing helix chain 'U' and resid 53 through 62 removed outlier: 3.820A pdb=" N TRP U 60 " --> pdb=" O ARG U 56 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY U 62 " --> pdb=" O ALA U 58 " (cutoff:3.500A) Processing helix chain 'U' and resid 68 through 78 Processing helix chain 'W' and resid 24 through 30 removed outlier: 3.793A pdb=" N ASN W 30 " --> pdb=" O ALA W 26 " (cutoff:3.500A) Processing helix chain 'W' and resid 47 through 64 Processing helix chain 'X' and resid 11 through 23 removed outlier: 3.861A pdb=" N LYS X 17 " --> pdb=" O HIS X 13 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS X 20 " --> pdb=" O LYS X 16 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA X 21 " --> pdb=" O LYS X 17 " (cutoff:3.500A) Processing helix chain 'X' and resid 40 through 44 removed outlier: 3.642A pdb=" N ILE X 44 " --> pdb=" O PRO X 41 " (cutoff:3.500A) Processing helix chain 'X' and resid 69 through 74 removed outlier: 3.645A pdb=" N PHE X 73 " --> pdb=" O LEU X 70 " (cutoff:3.500A) Processing helix chain 'Y' and resid 7 through 41 removed outlier: 4.099A pdb=" N ILE Y 11 " --> pdb=" O LYS Y 7 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS Y 18 " --> pdb=" O GLU Y 14 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N HIS Y 19 " --> pdb=" O LYS Y 15 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA Y 21 " --> pdb=" O ARG Y 17 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER Y 22 " --> pdb=" O LYS Y 18 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N MET Y 27 " --> pdb=" O ARG Y 23 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE Y 30 " --> pdb=" O MET Y 26 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS Y 32 " --> pdb=" O ARG Y 28 " (cutoff:3.500A) Processing helix chain 'Y' and resid 42 through 62 Proline residue: Y 55 - end of helix removed outlier: 3.747A pdb=" N ARG Y 59 " --> pdb=" O PRO Y 55 " (cutoff:3.500A) Processing helix chain 'Y' and resid 69 through 85 removed outlier: 3.561A pdb=" N THR Y 79 " --> pdb=" O LYS Y 75 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU Y 85 " --> pdb=" O GLN Y 81 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 21 Processing helix chain 'Z' and resid 27 through 31 removed outlier: 3.587A pdb=" N GLU Z 30 " --> pdb=" O VAL Z 27 " (cutoff:3.500A) Processing helix chain 'Z' and resid 38 through 57 removed outlier: 3.586A pdb=" N LYS Z 48 " --> pdb=" O ARG Z 44 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA Z 49 " --> pdb=" O LYS Z 45 " (cutoff:3.500A) Processing helix chain 'Z' and resid 58 through 63 removed outlier: 3.570A pdb=" N ARG Z 61 " --> pdb=" O LYS Z 58 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLU Z 62 " --> pdb=" O LEU Z 59 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ASN Z 63 " --> pdb=" O ALA Z 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 58 through 63' Processing helix chain '8' and resid 26 through 30 removed outlier: 3.666A pdb=" N HIS 8 29 " --> pdb=" O GLY 8 26 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N VAL 8 30 " --> pdb=" O GLY 8 27 " (cutoff:3.500A) No H-bonds generated for 'chain '8' and resid 26 through 30' Processing helix chain '8' and resid 53 through 58 removed outlier: 3.518A pdb=" N LEU 8 57 " --> pdb=" O LYS 8 53 " (cutoff:3.500A) Processing helix chain '8' and resid 79 through 99 removed outlier: 3.514A pdb=" N VAL 8 92 " --> pdb=" O LEU 8 88 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLU 8 97 " --> pdb=" O ALA 8 93 " (cutoff:3.500A) Processing helix chain '8' and resid 117 through 122 Processing helix chain '9' and resid 49 through 57 removed outlier: 4.043A pdb=" N ARG 9 55 " --> pdb=" O TYR 9 51 " (cutoff:3.500A) Processing helix chain '9' and resid 79 through 99 Processing sheet with id=AA1, first strand: chain 'b' and resid 3 through 4 Processing sheet with id=AA2, first strand: chain 'b' and resid 33 through 34 Processing sheet with id=AA3, first strand: chain 'b' and resid 100 through 104 removed outlier: 7.000A pdb=" N ILE b 90 " --> pdb=" O LEU b 80 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N LEU b 80 " --> pdb=" O ILE b 90 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LEU b 92 " --> pdb=" O GLU b 78 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ILE b 73 " --> pdb=" O SER b 117 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N SER b 117 " --> pdb=" O ILE b 73 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'b' and resid 128 through 130 removed outlier: 6.433A pdb=" N THR b 172 " --> pdb=" O VAL b 164 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N ARG b 166 " --> pdb=" O TYR b 170 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N TYR b 170 " --> pdb=" O ARG b 166 " (cutoff:3.500A) removed outlier: 6.626A 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 6 removed outlier: 6.123A pdb=" N VAL c 109 " --> pdb=" O GLN c 173 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N GLN c 173 " --> pdb=" O VAL c 109 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N GLY c 111 " --> pdb=" O THR c 171 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N THR c 171 " --> pdb=" O GLY c 111 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ASP c 176 " --> pdb=" O LYS c 190 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LEU c 188 " --> pdb=" O VAL c 178 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N VAL c 180 " --> pdb=" O LEU c 186 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LEU c 186 " --> pdb=" O VAL c 180 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLY c 10 " --> pdb=" O VAL c 26 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N GLU c 28 " --> pdb=" O LYS c 8 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N LYS c 8 " --> pdb=" O GLU c 28 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'c' and resid 32 through 33 Processing sheet with id=AA7, first strand: chain 'c' and resid 36 through 38 Processing sheet with id=AA8, first strand: chain 'c' and resid 117 through 118 Processing sheet with id=AA9, first strand: chain 'd' and resid 2 through 3 Processing sheet with id=AB1, first strand: chain 'd' and resid 118 through 121 removed outlier: 3.937A pdb=" N THR d 189 " --> pdb=" O ILE d 149 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG d 170 " --> pdb=" O ILE d 148 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'e' and resid 65 through 68 removed outlier: 3.845A pdb=" N GLY e 85 " --> pdb=" O THR e 67 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS e 32 " --> pdb=" O THR e 156 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'f' and resid 8 through 9 Processing sheet with id=AB4, first strand: chain 'f' and resid 15 through 18 removed outlier: 3.687A pdb=" N THR f 24 " --> pdb=" O LYS f 17 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'f' and resid 121 through 123 Processing sheet with id=AB6, first strand: chain 'f' and resid 94 through 98 Processing sheet with id=AB7, first strand: chain 'g' and resid 18 through 20 Processing sheet with id=AB8, first strand: chain 'g' and resid 77 through 78 removed outlier: 3.720A pdb=" N VAL g 130 " --> pdb=" O VAL g 142 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'j' and resid 123 through 124 removed outlier: 6.341A pdb=" N ILE j 54 " --> pdb=" O LYS j 123 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N TRP j 15 " --> pdb=" O GLN j 138 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'j' and resid 76 through 77 removed outlier: 3.523A pdb=" N HIS j 76 " --> pdb=" O LYS j 85 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'k' and resid 91 through 94 removed outlier: 3.559A pdb=" N ASN k 88 " --> pdb=" O SER k 91 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N GLN k 93 " --> pdb=" O LEU k 86 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N LEU k 86 " --> pdb=" O GLN k 93 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ALA k 83 " --> pdb=" O VAL k 63 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N LYS k 59 " --> pdb=" O LEU k 87 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ILE k 39 " --> pdb=" O VAL k 24 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N VAL k 24 " --> pdb=" O ILE k 39 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N ILE k 41 " --> pdb=" O ILE k 22 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N ILE k 22 " --> pdb=" O ILE k 41 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N ILE k 43 " --> pdb=" O MET k 20 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N MET k 20 " --> pdb=" O ILE k 43 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG k 18 " --> pdb=" O GLU k 45 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ARG k 17 " --> pdb=" O VAL k 10 " (cutoff:3.500A) removed outlier: 8.807A pdb=" N CYS k 84 " --> pdb=" O MET k 7 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ASN k 9 " --> pdb=" O CYS k 84 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N LEU k 86 " --> pdb=" O ASN k 9 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'l' and resid 74 through 78 removed outlier: 3.677A pdb=" N LYS l 109 " --> pdb=" O ALA l 75 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'l' and resid 89 through 90 removed outlier: 6.769A pdb=" N VAL l 90 " --> pdb=" O ARG l 123 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N VAL l 122 " --> pdb=" O GLU l 143 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'm' and resid 62 through 65 removed outlier: 6.390A pdb=" N LEU m 33 " --> pdb=" O LEU m 102 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N GLU m 104 " --> pdb=" O PHE m 31 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N PHE m 31 " --> pdb=" O GLU m 104 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'm' and resid 39 through 42 removed outlier: 5.446A pdb=" N VAL m 89 " --> pdb=" O GLU m 75 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N GLU m 75 " --> pdb=" O VAL m 89 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'n' and resid 33 through 37 removed outlier: 6.775A pdb=" N MET n 110 " --> pdb=" O CYS n 100 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'o' and resid 47 through 51 removed outlier: 4.110A pdb=" N VAL o 49 " --> pdb=" O VAL o 39 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG o 25 " --> pdb=" O ILE o 40 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'p' and resid 36 through 42 removed outlier: 6.647A pdb=" N THR p 24 " --> pdb=" O LYS p 86 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER p 82 " --> pdb=" O LYS p 28 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N TRP p 30 " --> pdb=" O VAL p 80 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N VAL p 80 " --> pdb=" O TRP p 30 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'p' and resid 45 through 50 removed outlier: 5.789A pdb=" N VAL p 46 " --> pdb=" O ARG p 61 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ARG p 61 " --> pdb=" O VAL p 46 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ALA p 48 " --> pdb=" O THR p 59 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'r' and resid 11 through 15 Processing sheet with id=AD3, first strand: chain 'r' and resid 19 through 23 removed outlier: 7.177A pdb=" N LYS r 60 " --> pdb=" O THR r 99 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'r' and resid 72 through 78 removed outlier: 4.213A pdb=" N TYR r 83 " --> pdb=" O ARG r 78 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 's' and resid 2 through 4 removed outlier: 3.718A pdb=" N THR s 3 " --> pdb=" O VAL s 107 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N SER s 101 " --> pdb=" O HIS s 9 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 's' and resid 2 through 4 removed outlier: 3.718A pdb=" N THR s 3 " --> pdb=" O VAL s 107 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N ASP s 94 " --> pdb=" O ARG s 84 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N ARG s 84 " --> pdb=" O ASP s 94 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ILE s 96 " --> pdb=" O MET s 82 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N MET s 82 " --> pdb=" O ILE s 96 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N LYS s 98 " --> pdb=" O PRO s 80 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N THR s 100 " --> pdb=" O GLU s 78 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N GLU s 78 " --> pdb=" O THR s 100 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N HIS s 102 " --> pdb=" O VAL s 76 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N VAL s 76 " --> pdb=" O HIS s 102 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N THR s 104 " --> pdb=" O ILE s 74 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ILE s 74 " --> pdb=" O THR s 104 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N VAL s 106 " --> pdb=" O THR s 72 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LYS s 27 " --> pdb=" O VAL s 71 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 't' and resid 11 through 14 removed outlier: 4.063A pdb=" N LYS t 81 " --> pdb=" O VAL t 34 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'u' and resid 63 through 65 removed outlier: 3.616A pdb=" N ILE u 64 " --> pdb=" O VAL u 33 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N LYS u 32 " --> pdb=" O VAL u 27 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N VAL u 27 " --> pdb=" O LYS u 32 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ILE u 34 " --> pdb=" O LYS u 25 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'u' and resid 40 through 42 Processing sheet with id=AE1, first strand: chain 'u' and resid 82 through 86 removed outlier: 3.623A pdb=" N PHE u 94 " --> pdb=" O GLY u 83 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'v' and resid 7 through 8 removed outlier: 8.790A pdb=" N LYS v 25 " --> pdb=" O GLN v 87 " (cutoff:3.500A) removed outlier: 10.359A pdb=" N ILE v 89 " --> pdb=" O LYS v 25 " (cutoff:3.500A) removed outlier: 8.624A pdb=" N PHE v 91 " --> pdb=" O PRO v 27 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ILE v 29 " --> pdb=" O PHE v 91 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N VAL v 92 " --> pdb=" O ALA v 74 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N ALA v 74 " --> pdb=" O VAL v 92 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'w' and resid 18 through 19 removed outlier: 6.877A pdb=" N LEU w 55 " --> pdb=" O ILE w 33 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'w' and resid 42 through 43 Processing sheet with id=AE5, first strand: chain 'x' and resid 12 through 14 Processing sheet with id=AE6, first strand: chain 'x' and resid 32 through 39 Processing sheet with id=AE7, first strand: chain 'z' and resid 34 through 38 removed outlier: 4.386A pdb=" N LYS z 5 " --> pdb=" O GLU z 57 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 28 through 29 Processing sheet with id=AE9, first strand: chain 'C' and resid 19 through 24 removed outlier: 3.709A pdb=" N LYS C 9 " --> pdb=" O ALA C 51 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLN C 44 " --> pdb=" O ASP C 39 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 14 through 15 Processing sheet with id=AF2, first strand: chain 'F' and resid 14 through 17 Processing sheet with id=AF3, first strand: chain 'G' and resid 89 through 91 removed outlier: 6.292A pdb=" N ILE G 66 " --> pdb=" O PHE G 89 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N VAL G 91 " --> pdb=" O ILE G 66 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N PHE G 68 " --> pdb=" O VAL G 91 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N LEU G 67 " --> pdb=" O PHE G 161 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N ILE G 163 " --> pdb=" O LEU G 67 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL G 69 " --> pdb=" O ILE G 163 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'H' and resid 19 through 20 removed outlier: 7.090A pdb=" N ILE H 63 " --> pdb=" O GLN H 99 " (cutoff:3.500A) removed outlier: 8.325A pdb=" N ASN H 101 " --> pdb=" O ILE H 63 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N VAL H 65 " --> pdb=" O ASN H 101 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N ALA H 103 " --> pdb=" O VAL H 65 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ILE H 67 " --> pdb=" O ALA H 103 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'H' and resid 165 through 170 removed outlier: 6.938A pdb=" N ASP H 180 " --> pdb=" O LYS H 203 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'I' and resid 127 through 128 Processing sheet with id=AF7, first strand: chain 'J' and resid 12 through 14 Processing sheet with id=AF8, first strand: chain 'J' and resid 18 through 21 Processing sheet with id=AF9, first strand: chain 'J' and resid 94 through 96 Processing sheet with id=AG1, first strand: chain 'K' and resid 2 through 3 Processing sheet with id=AG2, first strand: chain 'K' and resid 58 through 61 removed outlier: 3.641A pdb=" N MET K 9 " --> pdb=" O ARG K 86 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N ARG K 86 " --> pdb=" O MET K 9 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'L' and resid 72 through 75 removed outlier: 3.520A pdb=" N GLU L 73 " --> pdb=" O VAL L 88 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'M' and resid 23 through 24 removed outlier: 6.645A pdb=" N GLU M 59 " --> pdb=" O PHE M 48 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N PHE M 48 " --> pdb=" O GLU M 59 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR M 61 " --> pdb=" O GLU M 46 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'M' and resid 73 through 76 Processing sheet with id=AG6, first strand: chain 'M' and resid 73 through 76 removed outlier: 6.857A pdb=" N VAL M 102 " --> pdb=" O ILE M 125 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N TYR M 127 " --> pdb=" O ILE M 100 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ILE M 100 " --> pdb=" O TYR M 127 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'N' and resid 5 through 9 removed outlier: 3.610A pdb=" N THR N 65 " --> pdb=" O ARG N 17 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N LYS N 26 " --> pdb=" O LEU N 62 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N ILE N 64 " --> pdb=" O LYS N 26 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N VAL N 28 " --> pdb=" O ILE N 64 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N VAL N 66 " --> pdb=" O VAL N 28 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'O' and resid 71 through 73 Processing sheet with id=AG9, first strand: chain 'O' and resid 45 through 52 removed outlier: 3.946A pdb=" N ARG O 45 " --> pdb=" O THR O 69 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLU O 47 " --> pdb=" O ILE O 67 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASP O 63 " --> pdb=" O VAL O 51 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'P' and resid 40 through 44 removed outlier: 3.572A pdb=" N GLY P 42 " --> pdb=" O ILE P 33 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N ALA P 20 " --> pdb=" O MET P 84 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N LYS P 86 " --> pdb=" O ALA P 20 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ILE P 22 " --> pdb=" O LYS P 86 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N VAL P 83 " --> pdb=" O THR P 107 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ILE P 109 " --> pdb=" O VAL P 83 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N VAL P 85 " --> pdb=" O ILE P 109 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N ASP P 111 " --> pdb=" O VAL P 85 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'Q' and resid 29 through 31 removed outlier: 3.508A pdb=" N ILE Q 79 " --> pdb=" O GLY Q 31 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'Q' and resid 34 through 39 removed outlier: 4.546A pdb=" N VAL Q 36 " --> pdb=" O VAL Q 51 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL Q 51 " --> pdb=" O VAL Q 36 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N THR Q 38 " --> pdb=" O ARG Q 49 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N ARG Q 49 " --> pdb=" O THR Q 38 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'U' and resid 2 through 11 removed outlier: 3.725A pdb=" N GLU U 34 " --> pdb=" O VAL U 21 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'V' and resid 7 through 13 removed outlier: 7.295A pdb=" N GLN V 8 " --> pdb=" O GLU V 25 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N GLU V 25 " --> pdb=" O GLN V 8 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N VAL V 21 " --> pdb=" O VAL V 12 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N TRP V 72 " --> pdb=" O HIS V 44 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'X' and resid 31 through 32 removed outlier: 3.616A pdb=" N ILE X 48 " --> pdb=" O VAL X 59 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain '8' and resid 5 through 6 Processing sheet with id=AH8, first strand: chain '8' and resid 16 through 20 1540 hydrogen bonds defined for protein. 4257 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3559 hydrogen bonds 5764 hydrogen bond angles 0 basepair planarities 1422 basepair parallelities 2576 stacking parallelities Total time for adding SS restraints: 251.32 Time building geometry restraints manager: 69.45 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: 34975 1.35 - 1.48: 64933 1.48 - 1.61: 56878 1.61 - 1.74: 1166 1.74 - 1.88: 258 Bond restraints: 158210 Sorted by residual: bond pdb=" CA VAL e 107 " pdb=" CB VAL e 107 " ideal model delta sigma weight residual 1.534 1.577 -0.042 6.80e-03 2.16e+04 3.87e+01 bond pdb=" CA VAL J 55 " pdb=" CB VAL J 55 " ideal model delta sigma weight residual 1.537 1.558 -0.021 5.00e-03 4.00e+04 1.79e+01 bond pdb=" CA VAL r 51 " pdb=" CB VAL r 51 " ideal model delta sigma weight residual 1.539 1.566 -0.027 7.50e-03 1.78e+04 1.26e+01 bond pdb=" SD MET c 165 " pdb=" CE MET c 165 " ideal model delta sigma weight residual 1.791 1.875 -0.084 2.50e-02 1.60e+03 1.14e+01 bond pdb=" SD MET n 1 " pdb=" CE MET n 1 " ideal model delta sigma weight residual 1.791 1.873 -0.082 2.50e-02 1.60e+03 1.07e+01 ... (remaining 158205 not shown) Histogram of bond angle deviations from ideal: 98.58 - 105.66: 23671 105.66 - 112.74: 89380 112.74 - 119.82: 57248 119.82 - 126.90: 54318 126.90 - 133.98: 12076 Bond angle restraints: 236693 Sorted by residual: angle pdb=" N GLY G 32 " pdb=" CA GLY G 32 " pdb=" C GLY G 32 " ideal model delta sigma weight residual 112.33 132.49 -20.16 1.10e+00 8.26e-01 3.36e+02 angle pdb=" N LEU 9 63 " pdb=" CA LEU 9 63 " pdb=" C LEU 9 63 " ideal model delta sigma weight residual 113.12 99.51 13.61 1.25e+00 6.40e-01 1.19e+02 angle pdb=" N LEU N 97 " pdb=" CA LEU N 97 " pdb=" C LEU N 97 " ideal model delta sigma weight residual 113.23 100.16 13.07 1.24e+00 6.50e-01 1.11e+02 angle pdb=" N ASN c 149 " pdb=" CA ASN c 149 " pdb=" C ASN c 149 " ideal model delta sigma weight residual 109.60 124.48 -14.88 1.53e+00 4.27e-01 9.46e+01 angle pdb=" N LYS g 8 " pdb=" CA LYS g 8 " pdb=" C LYS g 8 " ideal model delta sigma weight residual 111.40 100.01 11.39 1.22e+00 6.72e-01 8.72e+01 ... (remaining 236688 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.35: 89895 35.35 - 70.70: 10156 70.70 - 106.05: 1295 106.05 - 141.40: 11 141.40 - 176.75: 11 Dihedral angle restraints: 101368 sinusoidal: 84753 harmonic: 16615 Sorted by residual: dihedral pdb=" C4' C 11914 " pdb=" C3' C 11914 " pdb=" C2' C 11914 " pdb=" C1' C 11914 " ideal model delta sinusoidal sigma weight residual 36.34 -37.28 73.62 1 3.10e+00 1.04e-01 7.17e+02 dihedral pdb=" O4' C 11914 " pdb=" C4' C 11914 " pdb=" C3' C 11914 " pdb=" C2' C 11914 " ideal model delta sinusoidal sigma weight residual -35.15 26.74 -61.89 1 4.00e+00 6.25e-02 3.17e+02 dihedral pdb=" O4' C 11914 " pdb=" C2' C 11914 " pdb=" C1' C 11914 " pdb=" C3' C 11914 " ideal model delta sinusoidal sigma weight residual -94.41 -35.97 -58.44 3 3.80e+00 6.93e-02 1.47e+02 ... (remaining 101365 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.119: 26312 0.119 - 0.238: 3687 0.238 - 0.356: 228 0.356 - 0.475: 19 0.475 - 0.594: 2 Chirality restraints: 30248 Sorted by residual: chirality pdb=" CA ALA G 33 " pdb=" N ALA G 33 " pdb=" C ALA G 33 " pdb=" CB ALA G 33 " both_signs ideal model delta sigma weight residual False 2.48 1.89 0.59 2.00e-01 2.50e+01 8.82e+00 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 -2.99 -0.58 2.00e-01 2.50e+01 8.38e+00 chirality pdb=" CA HIS 9 38 " pdb=" N HIS 9 38 " pdb=" C HIS 9 38 " pdb=" CB HIS 9 38 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.53e+00 ... (remaining 30245 not shown) Planarity restraints: 12684 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G 1 512 " 0.122 2.00e-02 2.50e+03 5.04e-02 7.64e+01 pdb=" N9 G 1 512 " -0.008 2.00e-02 2.50e+03 pdb=" C8 G 1 512 " -0.053 2.00e-02 2.50e+03 pdb=" N7 G 1 512 " -0.047 2.00e-02 2.50e+03 pdb=" C5 G 1 512 " -0.023 2.00e-02 2.50e+03 pdb=" C6 G 1 512 " 0.023 2.00e-02 2.50e+03 pdb=" O6 G 1 512 " 0.075 2.00e-02 2.50e+03 pdb=" N1 G 1 512 " 0.021 2.00e-02 2.50e+03 pdb=" C2 G 1 512 " -0.012 2.00e-02 2.50e+03 pdb=" N2 G 1 512 " -0.021 2.00e-02 2.50e+03 pdb=" N3 G 1 512 " -0.039 2.00e-02 2.50e+03 pdb=" C4 G 1 512 " -0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G 12061 " 0.118 2.00e-02 2.50e+03 5.03e-02 7.58e+01 pdb=" N9 G 12061 " -0.004 2.00e-02 2.50e+03 pdb=" C8 G 12061 " -0.052 2.00e-02 2.50e+03 pdb=" N7 G 12061 " -0.053 2.00e-02 2.50e+03 pdb=" C5 G 12061 " -0.026 2.00e-02 2.50e+03 pdb=" C6 G 12061 " 0.023 2.00e-02 2.50e+03 pdb=" O6 G 12061 " 0.077 2.00e-02 2.50e+03 pdb=" N1 G 12061 " 0.022 2.00e-02 2.50e+03 pdb=" C2 G 12061 " -0.012 2.00e-02 2.50e+03 pdb=" N2 G 12061 " -0.030 2.00e-02 2.50e+03 pdb=" N3 G 12061 " -0.030 2.00e-02 2.50e+03 pdb=" C4 G 12061 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A 1 196 " 0.105 2.00e-02 2.50e+03 4.60e-02 5.82e+01 pdb=" N9 A 1 196 " -0.005 2.00e-02 2.50e+03 pdb=" C8 A 1 196 " -0.039 2.00e-02 2.50e+03 pdb=" N7 A 1 196 " -0.037 2.00e-02 2.50e+03 pdb=" C5 A 1 196 " -0.025 2.00e-02 2.50e+03 pdb=" C6 A 1 196 " 0.016 2.00e-02 2.50e+03 pdb=" N6 A 1 196 " 0.069 2.00e-02 2.50e+03 pdb=" N1 A 1 196 " 0.012 2.00e-02 2.50e+03 pdb=" C2 A 1 196 " -0.018 2.00e-02 2.50e+03 pdb=" N3 A 1 196 " -0.041 2.00e-02 2.50e+03 pdb=" C4 A 1 196 " -0.039 2.00e-02 2.50e+03 ... (remaining 12681 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 21580 2.77 - 3.30: 134320 3.30 - 3.83: 301485 3.83 - 4.37: 369103 4.37 - 4.90: 488158 Nonbonded interactions: 1314646 Sorted by model distance: nonbonded pdb=" O PRO K 12 " pdb=" OG SER K 15 " model vdw 2.234 2.440 nonbonded pdb=" O VAL d 83 " pdb=" N PHE d 85 " model vdw 2.251 2.520 nonbonded pdb=" O HIS G 14 " pdb=" O PHE G 15 " model vdw 2.257 3.040 nonbonded pdb=" O LYS l 29 " pdb=" OG1 THR l 30 " model vdw 2.274 2.440 nonbonded pdb=" O ASP S 39 " pdb=" OD1 ASN S 42 " model vdw 2.304 3.040 ... (remaining 1314641 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.140 Extract box with map and model: 15.160 Check model and map are aligned: 1.620 Set scattering table: 1.000 Process input model: 531.210 Find NCS groups from input model: 2.820 Set up NCS constraints: 0.330 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 558.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 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 0.084 158210 Z= 0.406 Angle : 0.989 20.161 236693 Z= 0.659 Chirality : 0.082 0.594 30248 Planarity : 0.008 0.081 12684 Dihedral : 22.461 176.753 90644 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 2.04 % Allowed : 10.83 % Favored : 87.13 % Rotamer: Outliers : 1.20 % Allowed : 7.58 % Favored : 91.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.23 (0.08), residues: 5726 helix: -4.15 (0.07), residues: 1709 sheet: -2.89 (0.14), residues: 980 loop : -3.28 (0.09), residues: 3037 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.006 TRP b 247 HIS 0.002 0.000 HIS c 134 PHE 0.044 0.005 PHE G 89 TYR 0.054 0.007 TYR 9 77 ARG 0.009 0.001 ARG V 5 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11452 Ramachandran restraints generated. 5726 Oldfield, 0 Emsley, 5726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11452 Ramachandran restraints generated. 5726 Oldfield, 0 Emsley, 5726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2352 residues out of total 4763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 2295 time to evaluate : 6.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 63 ILE cc_start: 0.8517 (mt) cc_final: 0.7728 (mt) REVERT: b 97 ASP cc_start: 0.7011 (p0) cc_final: 0.6580 (p0) REVERT: b 200 MET cc_start: 0.6701 (ttp) cc_final: 0.6483 (ttp) REVERT: b 266 ILE cc_start: 0.7990 (mm) cc_final: 0.7758 (mm) REVERT: d 2 GLU cc_start: 0.7561 (mm-30) cc_final: 0.7352 (tp30) REVERT: d 123 LYS cc_start: 0.8134 (tppt) cc_final: 0.7570 (mmtm) REVERT: d 168 ASP cc_start: 0.6828 (t0) cc_final: 0.6413 (t0) REVERT: f 100 ASN cc_start: 0.7815 (t0) cc_final: 0.7479 (t0) REVERT: f 108 PHE cc_start: 0.7981 (m-80) cc_final: 0.7767 (m-80) REVERT: f 116 LEU cc_start: 0.8264 (mm) cc_final: 0.7549 (mm) REVERT: g 137 GLU cc_start: 0.7037 (tm-30) cc_final: 0.6418 (tm-30) REVERT: j 103 ILE cc_start: 0.8569 (mt) cc_final: 0.8058 (mt) REVERT: j 119 PHE cc_start: 0.8470 (t80) cc_final: 0.7916 (t80) REVERT: k 5 GLN cc_start: 0.8026 (mm110) cc_final: 0.7638 (mm110) REVERT: k 20 MET cc_start: 0.7876 (ttp) cc_final: 0.7192 (ttp) REVERT: l 105 ILE cc_start: 0.8170 (mm) cc_final: 0.7823 (mm) REVERT: l 141 LYS cc_start: 0.8434 (mmmt) cc_final: 0.8228 (tppt) REVERT: m 91 TYR cc_start: 0.7707 (OUTLIER) cc_final: 0.7272 (p90) REVERT: m 95 LEU cc_start: 0.7729 (tp) cc_final: 0.7523 (tp) REVERT: n 67 PHE cc_start: 0.8390 (t80) cc_final: 0.7801 (t80) REVERT: n 75 ILE cc_start: 0.8537 (mm) cc_final: 0.8185 (mm) REVERT: n 95 THR cc_start: 0.8985 (p) cc_final: 0.8784 (p) REVERT: n 107 ASN cc_start: 0.7483 (t0) cc_final: 0.7133 (t0) REVERT: o 12 THR cc_start: 0.9090 (p) cc_final: 0.8838 (p) REVERT: o 76 LYS cc_start: 0.8568 (ttmm) cc_final: 0.8221 (mmtt) REVERT: o 97 PHE cc_start: 0.8732 (m-80) cc_final: 0.8195 (m-10) REVERT: p 93 LYS cc_start: 0.8411 (mttt) cc_final: 0.8197 (mttt) REVERT: q 8 ILE cc_start: 0.8319 (tp) cc_final: 0.8116 (tp) REVERT: q 54 ARG cc_start: 0.7070 (mtt90) cc_final: 0.6674 (mtt180) REVERT: q 61 ILE cc_start: 0.8971 (mm) cc_final: 0.8700 (mm) REVERT: q 65 ASN cc_start: 0.8256 (t0) cc_final: 0.7871 (t0) REVERT: q 84 LYS cc_start: 0.8237 (mttt) cc_final: 0.7928 (tttm) REVERT: r 32 THR cc_start: 0.9153 (t) cc_final: 0.8778 (t) REVERT: r 101 ILE cc_start: 0.8592 (mm) cc_final: 0.8355 (mt) REVERT: v 26 PHE cc_start: 0.8037 (p90) cc_final: 0.7827 (p90) REVERT: v 34 LYS cc_start: 0.8535 (mmtt) cc_final: 0.8250 (mmmt) REVERT: v 51 GLN cc_start: 0.8632 (pp30) cc_final: 0.8406 (pp30) REVERT: v 82 TYR cc_start: 0.8186 (p90) cc_final: 0.7826 (p90) REVERT: w 53 HIS cc_start: 0.7458 (m90) cc_final: 0.7102 (m170) REVERT: y 27 ASN cc_start: 0.8386 (t0) cc_final: 0.7989 (t0) REVERT: y 49 ASP cc_start: 0.8392 (t0) cc_final: 0.8086 (t0) REVERT: y 52 ARG cc_start: 0.8691 (ttm110) cc_final: 0.8447 (mtm-85) REVERT: z 30 ARG cc_start: 0.8398 (pmt170) cc_final: 0.7789 (ptt-90) REVERT: z 52 PHE cc_start: 0.8239 (p90) cc_final: 0.7972 (p90) REVERT: B 10 SER cc_start: 0.6926 (m) cc_final: 0.6633 (m) REVERT: C 24 LYS cc_start: 0.8029 (tttt) cc_final: 0.7690 (tttm) REVERT: C 33 LEU cc_start: 0.8404 (mt) cc_final: 0.8020 (mm) REVERT: E 39 ARG cc_start: 0.8073 (ttt180) cc_final: 0.7721 (ttt-90) REVERT: F 19 ARG cc_start: 0.8380 (ttm170) cc_final: 0.8095 (ttm170) REVERT: F 24 ARG cc_start: 0.8192 (mtt90) cc_final: 0.7989 (mtt-85) REVERT: F 32 LYS cc_start: 0.8597 (ptmt) cc_final: 0.8077 (ptmt) REVERT: G 29 PHE cc_start: 0.7913 (m-80) cc_final: 0.7254 (m-80) REVERT: G 139 GLU cc_start: 0.8077 (pt0) cc_final: 0.7240 (pt0) REVERT: G 151 LYS cc_start: 0.8584 (pttp) cc_final: 0.8193 (tptm) REVERT: G 213 LEU cc_start: 0.9075 (mt) cc_final: 0.8797 (pp) REVERT: H 45 GLU cc_start: 0.8276 (tm-30) cc_final: 0.7892 (tm-30) REVERT: I 39 GLN cc_start: 0.8559 (tt0) cc_final: 0.8278 (tt0) REVERT: I 195 ASN cc_start: 0.8499 (t0) cc_final: 0.8261 (t0) REVERT: J 77 ASN cc_start: 0.8602 (t0) cc_final: 0.8128 (t0) REVERT: J 92 ARG cc_start: 0.7395 (mmt90) cc_final: 0.7079 (mtt90) REVERT: J 100 GLU cc_start: 0.8075 (mm-30) cc_final: 0.7447 (tp30) REVERT: J 139 THR cc_start: 0.8921 (p) cc_final: 0.8395 (p) REVERT: K 25 TYR cc_start: 0.7471 (m-80) cc_final: 0.7125 (m-10) REVERT: L 30 MET cc_start: 0.7979 (ttp) cc_final: 0.7584 (ttp) REVERT: L 147 ASN cc_start: 0.7301 (t0) cc_final: 0.4959 (t0) REVERT: M 106 SER cc_start: 0.7977 (m) cc_final: 0.7142 (t) REVERT: N 8 THR cc_start: 0.8129 (t) cc_final: 0.7860 (t) REVERT: N 10 ARG cc_start: 0.6981 (mtm180) cc_final: 0.6579 (mtm180) REVERT: N 36 GLN cc_start: 0.8717 (tt0) cc_final: 0.8481 (tt0) REVERT: N 59 LYS cc_start: 0.8299 (mmmm) cc_final: 0.7985 (mmmm) REVERT: N 63 TYR cc_start: 0.6682 (t80) cc_final: 0.5700 (t80) REVERT: N 74 GLN cc_start: 0.8043 (mt0) cc_final: 0.7825 (mt0) REVERT: O 58 ASN cc_start: 0.9161 (m110) cc_final: 0.8789 (m-40) REVERT: P 26 PHE cc_start: 0.7677 (m-80) cc_final: 0.7393 (m-80) REVERT: P 112 VAL cc_start: 0.8639 (t) cc_final: 0.8420 (t) REVERT: Q 65 TYR cc_start: 0.7314 (t80) cc_final: 0.7063 (t80) REVERT: Q 114 SER cc_start: 0.8893 (m) cc_final: 0.8684 (m) REVERT: R 8 ILE cc_start: 0.5748 (mm) cc_final: 0.5349 (mm) REVERT: R 33 LEU cc_start: 0.8918 (mt) cc_final: 0.8407 (tp) REVERT: S 6 LYS cc_start: 0.9114 (mtpt) cc_final: 0.8910 (mmmm) REVERT: T 16 ARG cc_start: 0.7725 (mmp80) cc_final: 0.7482 (mmp80) REVERT: T 31 LEU cc_start: 0.9070 (mt) cc_final: 0.8838 (mt) REVERT: T 76 ARG cc_start: 0.8167 (mtm180) cc_final: 0.7772 (mtm-85) REVERT: T 83 ARG cc_start: 0.8079 (mtt180) cc_final: 0.7849 (ttm110) REVERT: U 5 ARG cc_start: 0.7454 (ptt-90) cc_final: 0.7140 (ptp90) REVERT: U 16 PHE cc_start: 0.8105 (t80) cc_final: 0.7886 (t80) REVERT: U 50 THR cc_start: 0.7566 (m) cc_final: 0.7264 (m) REVERT: U 67 ILE cc_start: 0.8924 (OUTLIER) cc_final: 0.8539 (pt) REVERT: V 37 ILE cc_start: 0.8385 (mm) cc_final: 0.7741 (mm) REVERT: V 69 THR cc_start: 0.8416 (p) cc_final: 0.7985 (t) REVERT: V 70 LYS cc_start: 0.7822 (ttpt) cc_final: 0.7325 (ttpt) REVERT: W 37 LYS cc_start: 0.8589 (mtpt) cc_final: 0.8137 (mtpp) REVERT: W 52 ARG cc_start: 0.8364 (mtm110) cc_final: 0.7867 (mtm110) REVERT: X 69 LYS cc_start: 0.8400 (mttt) cc_final: 0.7783 (mttt) REVERT: Y 8 LYS cc_start: 0.8887 (mtpt) cc_final: 0.8254 (mtmm) REVERT: Y 9 ARG cc_start: 0.8052 (mmm160) cc_final: 0.7606 (mmt-90) REVERT: Y 26 MET cc_start: 0.8237 (tpp) cc_final: 0.7746 (tpp) REVERT: Y 30 PHE cc_start: 0.8992 (m-10) cc_final: 0.8651 (m-80) REVERT: Y 54 GLN cc_start: 0.8900 (tt0) cc_final: 0.8420 (tm-30) REVERT: Y 78 LEU cc_start: 0.8001 (mp) cc_final: 0.7599 (mp) outliers start: 57 outliers final: 19 residues processed: 2330 average time/residue: 1.3638 time to fit residues: 5339.5014 Evaluate side-chains 1873 residues out of total 4763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 1852 time to evaluate : 6.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 119 VAL Chi-restraints excluded: chain c residue 109 VAL Chi-restraints excluded: chain d residue 83 VAL Chi-restraints excluded: chain e residue 30 VAL Chi-restraints excluded: chain e residue 112 ASP Chi-restraints excluded: chain e residue 156 THR Chi-restraints excluded: chain f residue 168 VAL Chi-restraints excluded: chain j residue 84 ILE Chi-restraints excluded: chain m residue 91 TYR Chi-restraints excluded: chain o residue 47 VAL Chi-restraints excluded: chain p residue 6 GLN Chi-restraints excluded: chain r residue 22 LEU Chi-restraints excluded: chain s residue 71 VAL Chi-restraints excluded: chain t residue 2 ILE Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain N residue 60 LEU Chi-restraints excluded: chain O residue 60 ASP Chi-restraints excluded: chain Q residue 73 LEU Chi-restraints excluded: chain U residue 67 ILE Chi-restraints excluded: chain V residue 77 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1025 random chunks: chunk 865 optimal weight: 20.0000 chunk 776 optimal weight: 10.0000 chunk 431 optimal weight: 5.9990 chunk 265 optimal weight: 10.0000 chunk 524 optimal weight: 20.0000 chunk 415 optimal weight: 5.9990 chunk 803 optimal weight: 30.0000 chunk 310 optimal weight: 20.0000 chunk 488 optimal weight: 20.0000 chunk 597 optimal weight: 10.0000 chunk 930 optimal weight: 10.0000 overall best weight: 8.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 45 ASN b 57 HIS b 59 GLN b 89 ASN b 250 GLN b 259 ASN ** c 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 164 GLN c 167 ASN ** d 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 30 GLN d 62 GLN d 163 ASN e 51 ASN ** f 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 100 ASN f 127 GLN g 18 GLN g 20 ASN g 28 ASN ** g 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 145 ASN j 67 ASN j 80 HIS j 135 GLN ** j 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 5 GLN l 38 GLN n 3 HIS ** n 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 62 ASN o 43 ASN o 98 GLN p 6 GLN p 11 GLN r 82 HIS s 40 ASN ** s 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 59 ASN u 44 HIS u 73 ASN v 44 HIS v 49 ASN ** v 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** x 16 ASN ** y 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 31 GLN ** y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 8 GLN B 41 HIS ** D 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 27 ASN E 30 HIS ** F 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 17 HIS G 176 ASN G 177 ASN H 68 HIS ** H 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 73 ASN I 125 ASN I 130 ASN J 96 GLN K 58 HIS ** K 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 129 ASN M 37 ASN ** N 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 GLN N 49 GLN N 74 GLN P 63 GLN ** P 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 4 ASN Q 19 ASN Q 28 GLN ** S 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 36 ASN T 41 HIS T 45 HIS T 61 GLN ** V 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 51 GLN ** Y 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 28 GLN 8 29 HIS ** 8 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 83 ASN ** 9 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 68 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.137 158210 Z= 0.409 Angle : 0.789 12.734 236693 Z= 0.405 Chirality : 0.045 0.762 30248 Planarity : 0.006 0.079 12684 Dihedral : 23.198 179.416 79198 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 20.65 Ramachandran Plot: Outliers : 0.35 % Allowed : 9.10 % Favored : 90.55 % Rotamer: Outliers : 5.92 % Allowed : 20.81 % Favored : 73.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.53 % 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: -3.73 (0.10), residues: 5726 helix: -2.08 (0.10), residues: 1776 sheet: -2.37 (0.15), residues: 999 loop : -2.78 (0.10), residues: 2951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP j 15 HIS 0.012 0.002 HIS v 44 PHE 0.029 0.003 PHE N 126 TYR 0.035 0.003 TYR L 43 ARG 0.015 0.001 ARG B 16 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11452 Ramachandran restraints generated. 5726 Oldfield, 0 Emsley, 5726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11452 Ramachandran restraints generated. 5726 Oldfield, 0 Emsley, 5726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2228 residues out of total 4763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 282 poor density : 1946 time to evaluate : 6.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 63 ILE cc_start: 0.8590 (mt) cc_final: 0.7660 (mt) REVERT: b 97 ASP cc_start: 0.7257 (p0) cc_final: 0.6875 (p0) REVERT: b 179 GLU cc_start: 0.6357 (tt0) cc_final: 0.6096 (tt0) REVERT: b 180 MET cc_start: 0.7730 (mmm) cc_final: 0.7492 (mmm) REVERT: b 263 ASP cc_start: 0.7224 (p0) cc_final: 0.6746 (p0) REVERT: e 33 ILE cc_start: 0.8281 (OUTLIER) cc_final: 0.7831 (tp) REVERT: f 100 ASN cc_start: 0.7751 (t0) cc_final: 0.7536 (t0) REVERT: g 137 GLU cc_start: 0.6793 (tm-30) cc_final: 0.6530 (tm-30) REVERT: j 44 TYR cc_start: 0.8408 (t80) cc_final: 0.8207 (t80) REVERT: n 42 LYS cc_start: 0.8865 (mmmm) cc_final: 0.8539 (mttm) REVERT: n 67 PHE cc_start: 0.8415 (t80) cc_final: 0.7611 (t80) REVERT: n 75 ILE cc_start: 0.8591 (mm) cc_final: 0.8156 (mm) REVERT: n 107 ASN cc_start: 0.7478 (t0) cc_final: 0.7264 (t0) REVERT: o 29 HIS cc_start: 0.8131 (t-90) cc_final: 0.7848 (t-90) REVERT: o 97 PHE cc_start: 0.8878 (m-80) cc_final: 0.8509 (m-10) REVERT: q 44 TYR cc_start: 0.8089 (m-80) cc_final: 0.7839 (m-80) REVERT: q 65 ASN cc_start: 0.8759 (t0) cc_final: 0.8255 (t0) REVERT: t 79 ASP cc_start: 0.8602 (t0) cc_final: 0.8212 (t0) REVERT: u 95 PHE cc_start: 0.7862 (m-80) cc_final: 0.7651 (m-80) REVERT: v 34 LYS cc_start: 0.8806 (mmtt) cc_final: 0.8452 (mmmt) REVERT: v 82 TYR cc_start: 0.8164 (p90) cc_final: 0.7931 (p90) REVERT: y 27 ASN cc_start: 0.8505 (t0) cc_final: 0.8175 (t0) REVERT: y 31 GLN cc_start: 0.8750 (tp-100) cc_final: 0.8515 (tp40) REVERT: z 30 ARG cc_start: 0.8449 (pmt170) cc_final: 0.8167 (ptt-90) REVERT: B 43 THR cc_start: 0.8849 (p) cc_final: 0.8606 (p) REVERT: C 5 ARG cc_start: 0.7684 (mtp85) cc_final: 0.7465 (mtp-110) REVERT: C 26 LYS cc_start: 0.8263 (pttp) cc_final: 0.7762 (ptmt) REVERT: E 44 ARG cc_start: 0.8828 (ttp-110) cc_final: 0.8566 (ttm-80) REVERT: G 14 HIS cc_start: 0.8700 (p-80) cc_final: 0.8452 (p-80) REVERT: G 30 ILE cc_start: 0.7741 (OUTLIER) cc_final: 0.7531 (mm) REVERT: G 151 LYS cc_start: 0.8638 (pttp) cc_final: 0.8297 (tttp) REVERT: H 28 PHE cc_start: 0.8515 (t80) cc_final: 0.8275 (t80) REVERT: H 31 ASN cc_start: 0.7458 (p0) cc_final: 0.7236 (p0) REVERT: H 67 ILE cc_start: 0.9310 (mm) cc_final: 0.9035 (mm) REVERT: H 122 GLN cc_start: 0.7973 (mm-40) cc_final: 0.7628 (mm-40) REVERT: H 165 GLU cc_start: 0.6285 (tm-30) cc_final: 0.6056 (tm-30) REVERT: J 11 GLN cc_start: 0.7957 (tm-30) cc_final: 0.7741 (tm-30) REVERT: J 61 LYS cc_start: 0.8826 (ttpt) cc_final: 0.8613 (ttpt) REVERT: K 25 TYR cc_start: 0.7571 (m-80) cc_final: 0.7294 (m-80) REVERT: K 55 HIS cc_start: 0.6847 (OUTLIER) cc_final: 0.6429 (m90) REVERT: L 30 MET cc_start: 0.8213 (ttp) cc_final: 0.7597 (ttp) REVERT: L 34 LYS cc_start: 0.8642 (OUTLIER) cc_final: 0.8420 (mtpt) REVERT: L 123 LEU cc_start: 0.9264 (mt) cc_final: 0.8942 (mp) REVERT: L 147 ASN cc_start: 0.7078 (t0) cc_final: 0.6760 (p0) REVERT: M 62 LEU cc_start: 0.8513 (mt) cc_final: 0.7698 (mt) REVERT: N 24 ASN cc_start: 0.9147 (p0) cc_final: 0.8931 (p0) REVERT: N 26 LYS cc_start: 0.8808 (mmmt) cc_final: 0.8527 (mmmt) REVERT: N 56 MET cc_start: 0.7114 (tmm) cc_final: 0.6888 (tmm) REVERT: N 74 GLN cc_start: 0.7956 (mt0) cc_final: 0.7735 (mt0) REVERT: N 114 LYS cc_start: 0.8762 (mptt) cc_final: 0.8505 (mptt) REVERT: O 47 GLU cc_start: 0.8485 (mm-30) cc_final: 0.7839 (mm-30) REVERT: R 8 ILE cc_start: 0.5801 (mm) cc_final: 0.5267 (mm) REVERT: R 32 ILE cc_start: 0.9177 (mm) cc_final: 0.8963 (mm) REVERT: R 33 LEU cc_start: 0.8838 (mt) cc_final: 0.8392 (tp) REVERT: S 38 GLU cc_start: 0.7280 (tm-30) cc_final: 0.7013 (tm-30) REVERT: S 42 ASN cc_start: 0.8987 (p0) cc_final: 0.8692 (p0) REVERT: T 16 ARG cc_start: 0.7775 (mmp80) cc_final: 0.7349 (mmp80) REVERT: T 25 GLU cc_start: 0.8090 (mp0) cc_final: 0.7597 (mp0) REVERT: T 31 LEU cc_start: 0.9158 (mt) cc_final: 0.8922 (mt) REVERT: T 68 TYR cc_start: 0.7943 (t80) cc_final: 0.7673 (t80) REVERT: U 32 PHE cc_start: 0.8338 (p90) cc_final: 0.8013 (p90) REVERT: U 34 GLU cc_start: 0.7044 (pp20) cc_final: 0.6674 (pp20) REVERT: U 60 TRP cc_start: 0.8157 (m100) cc_final: 0.7477 (m100) REVERT: V 24 ILE cc_start: 0.8568 (mm) cc_final: 0.8330 (tt) REVERT: V 68 LYS cc_start: 0.8420 (ttpt) cc_final: 0.8209 (ptmt) REVERT: V 70 LYS cc_start: 0.8082 (ttpt) cc_final: 0.7737 (ttpt) REVERT: W 37 LYS cc_start: 0.8565 (mtpt) cc_final: 0.8108 (mtpp) REVERT: Z 20 ARG cc_start: 0.8039 (mpp80) cc_final: 0.7498 (mpp80) REVERT: 8 103 LYS cc_start: 0.8203 (pttm) cc_final: 0.7827 (pttm) REVERT: 8 125 LYS cc_start: 0.8176 (mttt) cc_final: 0.7704 (mttt) REVERT: 9 48 LEU cc_start: 0.4445 (OUTLIER) cc_final: 0.4037 (pp) REVERT: 9 85 GLU cc_start: 0.8767 (mm-30) cc_final: 0.8409 (mm-30) outliers start: 282 outliers final: 185 residues processed: 2063 average time/residue: 1.3031 time to fit residues: 4602.9492 Evaluate side-chains 1959 residues out of total 4763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 1769 time to evaluate : 6.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 115 ILE Chi-restraints excluded: chain b residue 119 VAL Chi-restraints excluded: chain b residue 138 SER Chi-restraints excluded: chain b residue 153 LEU Chi-restraints excluded: chain b residue 164 VAL Chi-restraints excluded: chain b residue 194 VAL Chi-restraints excluded: chain b residue 215 VAL Chi-restraints excluded: chain c residue 13 ARG Chi-restraints excluded: chain c residue 26 VAL Chi-restraints excluded: chain c residue 91 THR Chi-restraints excluded: chain c residue 109 VAL Chi-restraints excluded: chain c residue 113 SER Chi-restraints excluded: chain c residue 122 VAL Chi-restraints excluded: chain c residue 197 THR Chi-restraints excluded: chain d residue 3 LEU Chi-restraints excluded: chain d residue 181 ILE Chi-restraints excluded: chain e residue 25 MET Chi-restraints excluded: chain e residue 30 VAL Chi-restraints excluded: chain e residue 33 ILE Chi-restraints excluded: chain e residue 50 ASP Chi-restraints excluded: chain e residue 84 ILE Chi-restraints excluded: chain e residue 102 LEU Chi-restraints excluded: chain e residue 146 ASP Chi-restraints excluded: chain e residue 156 THR Chi-restraints excluded: chain e residue 157 THR Chi-restraints excluded: chain e residue 158 THR Chi-restraints excluded: chain f residue 8 VAL Chi-restraints excluded: chain f residue 55 ASP Chi-restraints excluded: chain f residue 76 ILE Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 102 ILE Chi-restraints excluded: chain f residue 104 LEU Chi-restraints excluded: chain f residue 124 CYS Chi-restraints excluded: chain g residue 4 ILE Chi-restraints excluded: chain g residue 103 VAL Chi-restraints excluded: chain g residue 124 THR Chi-restraints excluded: chain g residue 146 VAL Chi-restraints excluded: chain j residue 140 LEU Chi-restraints excluded: chain k residue 56 ASP Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 61 VAL Chi-restraints excluded: chain k residue 103 VAL Chi-restraints excluded: chain l residue 23 ILE Chi-restraints excluded: chain l residue 77 ILE Chi-restraints excluded: chain l residue 89 VAL Chi-restraints excluded: chain l residue 93 ASN Chi-restraints excluded: chain l residue 111 ILE Chi-restraints excluded: chain l residue 142 ILE Chi-restraints excluded: chain m residue 5 LYS Chi-restraints excluded: chain m residue 26 VAL Chi-restraints excluded: chain m residue 30 SER Chi-restraints excluded: chain m residue 36 VAL Chi-restraints excluded: chain m residue 42 THR Chi-restraints excluded: chain m residue 74 THR Chi-restraints excluded: chain m residue 80 VAL Chi-restraints excluded: chain m residue 126 ILE Chi-restraints excluded: chain m residue 129 THR Chi-restraints excluded: chain n residue 28 LEU Chi-restraints excluded: chain n residue 29 VAL Chi-restraints excluded: chain n residue 33 ILE Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 38 LEU Chi-restraints excluded: chain n residue 53 THR 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 47 VAL Chi-restraints excluded: chain o residue 49 VAL Chi-restraints excluded: chain o residue 54 VAL Chi-restraints excluded: chain o residue 65 THR Chi-restraints excluded: chain o residue 91 SER Chi-restraints excluded: chain p residue 65 ASN Chi-restraints excluded: chain p residue 75 THR Chi-restraints excluded: chain p residue 83 ILE Chi-restraints excluded: chain p residue 85 VAL Chi-restraints excluded: chain q residue 82 LEU Chi-restraints excluded: chain r residue 22 LEU Chi-restraints excluded: chain r residue 27 ILE Chi-restraints excluded: chain r residue 41 ILE Chi-restraints excluded: chain r residue 43 ASN Chi-restraints excluded: chain r residue 51 VAL Chi-restraints excluded: chain r residue 79 ARG Chi-restraints excluded: chain s residue 71 VAL Chi-restraints excluded: chain s residue 72 THR Chi-restraints excluded: chain s residue 81 SER Chi-restraints excluded: chain s residue 96 ILE Chi-restraints excluded: chain t residue 2 ILE Chi-restraints excluded: chain t residue 22 THR Chi-restraints excluded: chain t residue 37 ASP Chi-restraints excluded: chain t residue 43 ILE Chi-restraints excluded: chain t residue 88 LYS Chi-restraints excluded: chain t residue 92 ASN Chi-restraints excluded: chain u residue 12 VAL Chi-restraints excluded: chain u residue 69 VAL Chi-restraints excluded: chain v residue 42 LEU Chi-restraints excluded: chain v residue 86 LEU Chi-restraints excluded: chain w residue 54 THR Chi-restraints excluded: chain w residue 73 ARG Chi-restraints excluded: chain w residue 76 ILE Chi-restraints excluded: chain x residue 1 SER Chi-restraints excluded: chain x residue 13 THR Chi-restraints excluded: chain x residue 50 VAL Chi-restraints excluded: chain x residue 67 LEU Chi-restraints excluded: chain z residue 48 ASN Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 27 ASN Chi-restraints excluded: chain G residue 30 ILE Chi-restraints excluded: chain G residue 49 PHE Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 104 GLU Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain H residue 148 ILE Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain I residue 49 ASP Chi-restraints excluded: chain I residue 88 ASN Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain I residue 164 ARG Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 71 ILE Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 120 HIS Chi-restraints excluded: chain J residue 145 ASN Chi-restraints excluded: chain K residue 7 VAL Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 55 HIS Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain L residue 34 LYS Chi-restraints excluded: chain M residue 2 MET Chi-restraints excluded: chain M residue 78 SER Chi-restraints excluded: chain M residue 89 ASP Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 105 THR Chi-restraints excluded: chain M residue 126 CYS Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain N residue 30 ASN Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 60 ASP Chi-restraints excluded: chain O residue 63 ASP Chi-restraints excluded: chain P residue 16 SER Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain P residue 85 VAL Chi-restraints excluded: chain P residue 95 THR Chi-restraints excluded: chain P residue 106 ILE Chi-restraints excluded: chain P residue 107 THR Chi-restraints excluded: chain Q residue 2 THR Chi-restraints excluded: chain Q residue 79 ILE Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain R residue 3 ILE Chi-restraints excluded: chain R residue 15 VAL Chi-restraints excluded: chain R residue 16 ILE Chi-restraints excluded: chain R residue 43 LYS Chi-restraints excluded: chain R residue 51 GLN Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain R residue 107 THR Chi-restraints excluded: chain S residue 41 TRP Chi-restraints excluded: chain S residue 66 THR Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain T residue 21 THR Chi-restraints excluded: chain T residue 32 THR Chi-restraints excluded: chain T residue 69 LEU Chi-restraints excluded: chain T residue 81 ILE Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain V residue 40 THR Chi-restraints excluded: chain V residue 47 ASP Chi-restraints excluded: chain W residue 24 ASP Chi-restraints excluded: chain W residue 46 THR Chi-restraints excluded: chain X residue 50 VAL Chi-restraints excluded: chain X residue 57 VAL Chi-restraints excluded: chain X residue 61 VAL Chi-restraints excluded: chain X residue 78 THR Chi-restraints excluded: chain Y residue 13 SER Chi-restraints excluded: chain Y residue 56 ILE Chi-restraints excluded: chain Z residue 27 VAL Chi-restraints excluded: chain 9 residue 37 ILE Chi-restraints excluded: chain 9 residue 48 LEU Chi-restraints excluded: chain 9 residue 61 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1025 random chunks: chunk 517 optimal weight: 5.9990 chunk 288 optimal weight: 2.9990 chunk 774 optimal weight: 8.9990 chunk 633 optimal weight: 10.0000 chunk 256 optimal weight: 2.9990 chunk 932 optimal weight: 10.0000 chunk 1007 optimal weight: 6.9990 chunk 830 optimal weight: 10.0000 chunk 924 optimal weight: 20.0000 chunk 317 optimal weight: 9.9990 chunk 748 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 126 ASN c 150 GLN c 167 ASN ** d 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 30 GLN d 62 GLN d 163 ASN ** f 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 87 GLN g 28 ASN g 133 GLN g 145 ASN k 5 GLN ** n 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 107 ASN p 51 ASN ** p 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 66 HIS s 9 HIS s 40 ASN ** s 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** x 16 ASN ** y 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 31 GLN y 58 ASN z 8 GLN D 26 ASN ** F 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 35 GLN H 68 HIS ** H 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 58 HIS ** K 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 68 GLN ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 37 ASN ** N 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 GLN ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 100 ASN ** P 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 158210 Z= 0.277 Angle : 0.658 13.824 236693 Z= 0.340 Chirality : 0.038 0.368 30248 Planarity : 0.005 0.079 12684 Dihedral : 23.251 179.839 79180 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 18.07 Ramachandran Plot: Outliers : 0.26 % Allowed : 9.64 % Favored : 90.10 % Rotamer: Outliers : 6.68 % Allowed : 22.59 % Favored : 70.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.04 (0.10), residues: 5726 helix: -1.23 (0.11), residues: 1779 sheet: -2.12 (0.15), residues: 1008 loop : -2.50 (0.10), residues: 2939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP j 15 HIS 0.010 0.001 HIS K 3 PHE 0.033 0.002 PHE K 78 TYR 0.027 0.003 TYR f 156 ARG 0.048 0.001 ARG T 76 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11452 Ramachandran restraints generated. 5726 Oldfield, 0 Emsley, 5726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11452 Ramachandran restraints generated. 5726 Oldfield, 0 Emsley, 5726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2195 residues out of total 4763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 318 poor density : 1877 time to evaluate : 6.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 97 ASP cc_start: 0.7143 (p0) cc_final: 0.6886 (p0) REVERT: b 180 MET cc_start: 0.7648 (mmm) cc_final: 0.7338 (mmm) REVERT: b 263 ASP cc_start: 0.7038 (p0) cc_final: 0.6659 (p0) REVERT: b 266 ILE cc_start: 0.8305 (mm) cc_final: 0.8000 (mm) REVERT: d 35 TYR cc_start: 0.8414 (t80) cc_final: 0.8201 (t80) REVERT: d 166 LYS cc_start: 0.9015 (mppt) cc_final: 0.8687 (mppt) REVERT: e 3 LEU cc_start: 0.8888 (mt) cc_final: 0.8574 (mt) REVERT: e 34 THR cc_start: 0.7970 (p) cc_final: 0.7746 (p) REVERT: g 116 ARG cc_start: 0.8555 (mmm-85) cc_final: 0.8230 (mmp80) REVERT: g 133 GLN cc_start: 0.8413 (OUTLIER) cc_final: 0.8084 (tm-30) REVERT: g 137 GLU cc_start: 0.6770 (tm-30) cc_final: 0.6450 (tm-30) REVERT: j 37 ARG cc_start: 0.7469 (ttt-90) cc_final: 0.7179 (ttt-90) REVERT: j 44 TYR cc_start: 0.8550 (t80) cc_final: 0.8312 (t80) REVERT: l 105 ILE cc_start: 0.8374 (mm) cc_final: 0.8018 (mm) REVERT: n 42 LYS cc_start: 0.8838 (mmmm) cc_final: 0.8494 (mttm) REVERT: n 43 GLU cc_start: 0.7181 (tp30) cc_final: 0.6927 (tp30) REVERT: n 67 PHE cc_start: 0.8387 (t80) cc_final: 0.7615 (t80) REVERT: n 75 ILE cc_start: 0.8627 (mm) cc_final: 0.8378 (mm) REVERT: n 107 ASN cc_start: 0.7411 (t0) cc_final: 0.7177 (t0) REVERT: o 29 HIS cc_start: 0.8125 (t-90) cc_final: 0.7886 (t-170) REVERT: o 76 LYS cc_start: 0.8701 (ttmm) cc_final: 0.8417 (tptt) REVERT: o 97 PHE cc_start: 0.8857 (m-80) cc_final: 0.8482 (m-80) REVERT: q 44 TYR cc_start: 0.8056 (m-80) cc_final: 0.7608 (m-80) REVERT: q 65 ASN cc_start: 0.8779 (t0) cc_final: 0.8333 (t0) REVERT: v 34 LYS cc_start: 0.8797 (mmtt) cc_final: 0.8436 (mmmt) REVERT: v 69 GLU cc_start: 0.8381 (mm-30) cc_final: 0.8054 (mm-30) REVERT: v 82 TYR cc_start: 0.8022 (p90) cc_final: 0.7802 (p90) REVERT: y 27 ASN cc_start: 0.8430 (t0) cc_final: 0.8144 (t0) REVERT: y 31 GLN cc_start: 0.8711 (tp40) cc_final: 0.8325 (tp-100) REVERT: B 17 SER cc_start: 0.7905 (t) cc_final: 0.7694 (p) REVERT: C 26 LYS cc_start: 0.8371 (pttp) cc_final: 0.7874 (ptmt) REVERT: E 41 ARG cc_start: 0.8092 (ttm-80) cc_final: 0.7513 (ttm-80) REVERT: G 26 MET cc_start: 0.7872 (tpp) cc_final: 0.7657 (tpp) REVERT: G 197 PHE cc_start: 0.8432 (m-80) cc_final: 0.8229 (m-10) REVERT: H 31 ASN cc_start: 0.7566 (p0) cc_final: 0.7361 (p0) REVERT: H 67 ILE cc_start: 0.9286 (mm) cc_final: 0.9009 (mm) REVERT: I 203 TYR cc_start: 0.8075 (m-80) cc_final: 0.7851 (m-80) REVERT: J 61 LYS cc_start: 0.8854 (ttpt) cc_final: 0.8640 (ttpt) REVERT: J 92 ARG cc_start: 0.7703 (mmt90) cc_final: 0.7342 (mtt90) REVERT: J 146 MET cc_start: 0.6531 (tmm) cc_final: 0.5350 (tmm) REVERT: K 24 ARG cc_start: 0.8457 (ttm110) cc_final: 0.7985 (ptm160) REVERT: K 25 TYR cc_start: 0.7605 (m-10) cc_final: 0.7233 (m-80) REVERT: K 55 HIS cc_start: 0.6846 (OUTLIER) cc_final: 0.6446 (m90) REVERT: L 30 MET cc_start: 0.8157 (ttp) cc_final: 0.7703 (ttp) REVERT: L 49 LEU cc_start: 0.8266 (tp) cc_final: 0.7926 (tt) REVERT: L 150 PHE cc_start: 0.6961 (m-80) cc_final: 0.6389 (t80) REVERT: M 9 MET cc_start: 0.8173 (ttp) cc_final: 0.7758 (ttp) REVERT: M 42 GLU cc_start: 0.7783 (tp30) cc_final: 0.7504 (tp30) REVERT: M 106 SER cc_start: 0.8127 (OUTLIER) cc_final: 0.7583 (t) REVERT: N 5 TYR cc_start: 0.6741 (m-80) cc_final: 0.6397 (m-80) REVERT: N 24 ASN cc_start: 0.9218 (p0) cc_final: 0.8998 (p0) REVERT: N 56 MET cc_start: 0.7178 (tmm) cc_final: 0.6917 (tmm) REVERT: N 88 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7213 (pm20) REVERT: N 114 LYS cc_start: 0.8669 (mptt) cc_final: 0.8330 (mptt) REVERT: P 52 ARG cc_start: 0.7436 (tpt90) cc_final: 0.7202 (mmm160) REVERT: P 92 ARG cc_start: 0.6179 (ttt-90) cc_final: 0.5942 (ttt-90) REVERT: R 8 ILE cc_start: 0.5729 (mm) cc_final: 0.5226 (mm) REVERT: R 33 LEU cc_start: 0.8711 (mt) cc_final: 0.8312 (tp) REVERT: S 38 GLU cc_start: 0.7274 (tm-30) cc_final: 0.7017 (tm-30) REVERT: S 42 ASN cc_start: 0.8947 (p0) cc_final: 0.8654 (p0) REVERT: T 16 ARG cc_start: 0.7639 (mmp80) cc_final: 0.7416 (mmp80) REVERT: T 68 TYR cc_start: 0.7721 (t80) cc_final: 0.7365 (t80) REVERT: T 76 ARG cc_start: 0.8223 (ttp-110) cc_final: 0.7908 (ttm110) REVERT: U 32 PHE cc_start: 0.8202 (p90) cc_final: 0.7848 (p90) REVERT: U 60 TRP cc_start: 0.8014 (m100) cc_final: 0.7470 (m100) REVERT: V 68 LYS cc_start: 0.8366 (ttpt) cc_final: 0.8133 (ptmt) REVERT: V 70 LYS cc_start: 0.8138 (ttpt) cc_final: 0.7166 (ttmm) REVERT: V 72 TRP cc_start: 0.7882 (m100) cc_final: 0.7449 (m100) REVERT: W 37 LYS cc_start: 0.8499 (mtpt) cc_final: 0.8019 (mtpp) REVERT: Y 12 GLN cc_start: 0.7852 (mt0) cc_final: 0.7646 (mp10) REVERT: Z 20 ARG cc_start: 0.8012 (mpp80) cc_final: 0.7261 (mpp80) REVERT: Z 33 ARG cc_start: 0.7746 (mtm-85) cc_final: 0.7295 (mtm-85) REVERT: 8 15 LEU cc_start: 0.8465 (tt) cc_final: 0.8234 (tp) REVERT: 8 103 LYS cc_start: 0.8319 (pttm) cc_final: 0.8026 (pttm) REVERT: 9 48 LEU cc_start: 0.4622 (OUTLIER) cc_final: 0.4159 (pp) outliers start: 318 outliers final: 229 residues processed: 2007 average time/residue: 1.2583 time to fit residues: 4327.5113 Evaluate side-chains 1997 residues out of total 4763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 234 poor density : 1763 time to evaluate : 6.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 119 VAL Chi-restraints excluded: chain b residue 138 SER Chi-restraints excluded: chain b residue 153 LEU Chi-restraints excluded: chain b residue 164 VAL Chi-restraints excluded: chain b residue 198 GLU Chi-restraints excluded: chain b residue 215 VAL Chi-restraints excluded: chain b residue 227 VAL Chi-restraints excluded: chain b residue 251 THR Chi-restraints excluded: chain c residue 2 ILE Chi-restraints excluded: chain c residue 13 ARG Chi-restraints excluded: chain c residue 18 ASP Chi-restraints excluded: chain c residue 26 VAL Chi-restraints excluded: chain c residue 91 THR Chi-restraints excluded: chain c residue 96 ILE Chi-restraints excluded: chain c residue 109 VAL Chi-restraints excluded: chain c residue 113 SER Chi-restraints excluded: chain c residue 176 ASP Chi-restraints excluded: chain c residue 177 VAL Chi-restraints excluded: chain d residue 163 ASN Chi-restraints excluded: chain d residue 169 VAL Chi-restraints excluded: chain d residue 181 ILE Chi-restraints excluded: chain d residue 189 THR Chi-restraints excluded: chain e residue 25 MET Chi-restraints excluded: chain e residue 30 VAL Chi-restraints excluded: chain e residue 50 ASP Chi-restraints excluded: chain e residue 84 ILE Chi-restraints excluded: chain e residue 102 LEU Chi-restraints excluded: chain e residue 112 ASP Chi-restraints excluded: chain e residue 156 THR Chi-restraints excluded: chain e residue 157 THR Chi-restraints excluded: chain e residue 158 THR Chi-restraints excluded: chain f residue 8 VAL Chi-restraints excluded: chain f residue 55 ASP Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 102 ILE Chi-restraints excluded: chain f residue 104 LEU Chi-restraints excluded: chain f residue 105 SER Chi-restraints excluded: chain f residue 120 ILE Chi-restraints excluded: chain f residue 124 CYS Chi-restraints excluded: chain g residue 4 ILE Chi-restraints excluded: chain g residue 37 VAL Chi-restraints excluded: chain g residue 86 ASP Chi-restraints excluded: chain g residue 103 VAL Chi-restraints excluded: chain g residue 124 THR Chi-restraints excluded: chain g residue 133 GLN Chi-restraints excluded: chain g residue 146 VAL Chi-restraints excluded: chain j residue 140 LEU Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 61 VAL Chi-restraints excluded: chain l residue 5 THR Chi-restraints excluded: chain l residue 23 ILE Chi-restraints excluded: chain l residue 77 ILE Chi-restraints excluded: chain l residue 89 VAL Chi-restraints excluded: chain l residue 93 ASN Chi-restraints excluded: chain l residue 111 ILE Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain l residue 142 ILE Chi-restraints excluded: chain m residue 5 LYS Chi-restraints excluded: chain m residue 25 ASP Chi-restraints excluded: chain m residue 26 VAL Chi-restraints excluded: chain m residue 30 SER Chi-restraints excluded: chain m residue 36 VAL Chi-restraints excluded: chain m residue 42 THR Chi-restraints excluded: chain m residue 74 THR Chi-restraints excluded: chain m residue 80 VAL Chi-restraints excluded: chain m residue 126 ILE Chi-restraints excluded: chain m residue 128 THR Chi-restraints excluded: chain m residue 129 THR Chi-restraints excluded: chain m residue 134 THR Chi-restraints excluded: chain n residue 14 SER Chi-restraints excluded: chain n residue 28 LEU Chi-restraints excluded: chain n residue 29 VAL Chi-restraints excluded: chain n residue 33 ILE Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 38 LEU Chi-restraints excluded: chain n residue 53 THR Chi-restraints excluded: chain o residue 28 VAL Chi-restraints excluded: chain o residue 35 ILE Chi-restraints excluded: chain o residue 47 VAL Chi-restraints excluded: chain o residue 49 VAL Chi-restraints excluded: chain o residue 63 LYS Chi-restraints excluded: chain o residue 65 THR Chi-restraints excluded: chain o residue 74 VAL Chi-restraints excluded: chain o residue 81 ARG Chi-restraints excluded: chain o residue 91 SER Chi-restraints excluded: chain p residue 15 ASP Chi-restraints excluded: chain p residue 65 ASN Chi-restraints excluded: chain p residue 75 THR Chi-restraints excluded: chain p residue 82 SER Chi-restraints excluded: chain p residue 85 VAL Chi-restraints excluded: chain q residue 82 LEU Chi-restraints excluded: chain q residue 94 LEU Chi-restraints excluded: chain r residue 22 LEU Chi-restraints excluded: chain r residue 27 ILE Chi-restraints excluded: chain r residue 43 ASN Chi-restraints excluded: chain r residue 51 VAL Chi-restraints excluded: chain r residue 64 VAL Chi-restraints excluded: chain r residue 66 HIS Chi-restraints excluded: chain r residue 94 THR Chi-restraints excluded: chain s residue 71 VAL Chi-restraints excluded: chain s residue 72 THR Chi-restraints excluded: chain s residue 81 SER Chi-restraints excluded: chain s residue 82 MET Chi-restraints excluded: chain s residue 96 ILE Chi-restraints excluded: chain s residue 107 VAL Chi-restraints excluded: chain t residue 2 ILE Chi-restraints excluded: chain t residue 22 THR Chi-restraints excluded: chain t residue 58 VAL Chi-restraints excluded: chain t residue 87 LEU Chi-restraints excluded: chain t residue 88 LYS Chi-restraints excluded: chain t residue 92 ASN Chi-restraints excluded: chain u residue 68 ASN Chi-restraints excluded: chain u residue 69 VAL Chi-restraints excluded: chain v residue 42 LEU Chi-restraints excluded: chain v residue 47 VAL Chi-restraints excluded: chain v residue 51 GLN Chi-restraints excluded: chain v residue 77 VAL Chi-restraints excluded: chain v residue 86 LEU Chi-restraints excluded: chain w residue 31 SER Chi-restraints excluded: chain w residue 39 THR Chi-restraints excluded: chain w residue 54 THR Chi-restraints excluded: chain w residue 73 ARG Chi-restraints excluded: chain w residue 76 ILE Chi-restraints excluded: chain x residue 4 CYS Chi-restraints excluded: chain x residue 12 VAL Chi-restraints excluded: chain x residue 13 THR Chi-restraints excluded: chain x residue 29 LEU Chi-restraints excluded: chain y residue 14 LEU Chi-restraints excluded: chain y residue 15 ASN Chi-restraints excluded: chain y residue 57 LEU Chi-restraints excluded: chain z residue 35 VAL Chi-restraints excluded: chain z residue 51 SER Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 13 ASN Chi-restraints excluded: chain G residue 49 PHE Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 198 VAL Chi-restraints excluded: chain G residue 204 ASP Chi-restraints excluded: chain H residue 13 ILE Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain H residue 104 GLU Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain H residue 148 ILE Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain I residue 49 ASP Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 164 ARG Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 71 ILE Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 120 HIS Chi-restraints excluded: chain J residue 145 ASN Chi-restraints excluded: chain K residue 7 VAL Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 55 HIS Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain L residue 34 LYS Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 117 LEU Chi-restraints excluded: chain M residue 2 MET Chi-restraints excluded: chain M residue 17 GLN Chi-restraints excluded: chain M residue 61 THR Chi-restraints excluded: chain M residue 98 LEU Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 105 THR Chi-restraints excluded: chain M residue 106 SER Chi-restraints excluded: chain M residue 126 CYS Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain N residue 30 ASN Chi-restraints excluded: chain N residue 88 GLU Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain O residue 17 LEU Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 60 ASP Chi-restraints excluded: chain O residue 63 ASP Chi-restraints excluded: chain O residue 73 LEU Chi-restraints excluded: chain P residue 16 SER Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain P residue 95 THR Chi-restraints excluded: chain P residue 106 ILE Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 89 LEU Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain R residue 3 ILE Chi-restraints excluded: chain R residue 15 VAL Chi-restraints excluded: chain R residue 16 ILE Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain S residue 41 TRP Chi-restraints excluded: chain S residue 66 THR Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain S residue 79 SER Chi-restraints excluded: chain T residue 21 THR Chi-restraints excluded: chain T residue 24 THR Chi-restraints excluded: chain T residue 32 THR Chi-restraints excluded: chain T residue 58 MET Chi-restraints excluded: chain T residue 81 ILE Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain V residue 40 THR Chi-restraints excluded: chain V residue 47 ASP Chi-restraints excluded: chain V residue 57 VAL Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain V residue 82 VAL Chi-restraints excluded: chain W residue 24 ASP Chi-restraints excluded: chain W residue 46 THR Chi-restraints excluded: chain W residue 49 LYS Chi-restraints excluded: chain X residue 50 VAL Chi-restraints excluded: chain X residue 57 VAL Chi-restraints excluded: chain X residue 72 GLU Chi-restraints excluded: chain X residue 78 THR Chi-restraints excluded: chain Y residue 13 SER Chi-restraints excluded: chain Y residue 52 GLU Chi-restraints excluded: chain Z residue 5 VAL Chi-restraints excluded: chain Z residue 42 THR Chi-restraints excluded: chain 8 residue 51 TYR Chi-restraints excluded: chain 9 residue 48 LEU Chi-restraints excluded: chain 9 residue 61 HIS Chi-restraints excluded: chain 9 residue 79 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1025 random chunks: chunk 921 optimal weight: 10.0000 chunk 701 optimal weight: 20.0000 chunk 483 optimal weight: 9.9990 chunk 103 optimal weight: 10.0000 chunk 445 optimal weight: 0.8980 chunk 626 optimal weight: 10.0000 chunk 935 optimal weight: 10.0000 chunk 990 optimal weight: 10.0000 chunk 488 optimal weight: 10.0000 chunk 886 optimal weight: 10.0000 chunk 267 optimal weight: 10.0000 overall best weight: 8.1794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 32 ASN c 126 ASN c 134 HIS c 136 ASN c 164 GLN c 167 ASN d 9 GLN ** d 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 30 GLN d 62 GLN ** d 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 163 ASN ** d 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 51 ASN ** f 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 28 ASN g 43 ASN g 145 ASN ** j 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 132 HIS k 5 GLN l 38 GLN ** n 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 55 GLN ** q 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 66 HIS s 61 ASN ** t 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 65 GLN ** v 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 8 GLN ** F 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 35 GLN ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 68 HIS ** H 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 82 HIS ** K 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 68 GLN ** N 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 GLN N 36 GLN ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 15 HIS ** P 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 45 HIS ** V 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.114 158210 Z= 0.388 Angle : 0.727 14.065 236693 Z= 0.371 Chirality : 0.040 0.341 30248 Planarity : 0.006 0.084 12684 Dihedral : 23.367 178.855 79180 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 22.26 Ramachandran Plot: Outliers : 0.26 % Allowed : 10.08 % Favored : 89.66 % Rotamer: Outliers : 8.04 % Allowed : 24.17 % Favored : 67.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.53 % 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: -2.80 (0.10), residues: 5726 helix: -0.94 (0.12), residues: 1768 sheet: -1.96 (0.16), residues: 1018 loop : -2.42 (0.11), residues: 2940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP j 15 HIS 0.031 0.002 HIS r 66 PHE 0.036 0.002 PHE K 78 TYR 0.032 0.003 TYR g 25 ARG 0.015 0.001 ARG F 19 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11452 Ramachandran restraints generated. 5726 Oldfield, 0 Emsley, 5726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11452 Ramachandran restraints generated. 5726 Oldfield, 0 Emsley, 5726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2201 residues out of total 4763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 383 poor density : 1818 time to evaluate : 6.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 34 GLU cc_start: 0.7136 (pm20) cc_final: 0.6930 (pm20) REVERT: b 102 TYR cc_start: 0.8232 (OUTLIER) cc_final: 0.7994 (m-10) REVERT: b 263 ASP cc_start: 0.7106 (p0) cc_final: 0.6770 (p0) REVERT: c 64 GLU cc_start: 0.7798 (pt0) cc_final: 0.7598 (pt0) REVERT: d 35 TYR cc_start: 0.8703 (t80) cc_final: 0.8487 (t80) REVERT: e 35 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8664 (mp) REVERT: e 127 TYR cc_start: 0.8685 (t80) cc_final: 0.8436 (t80) REVERT: f 113 ASP cc_start: 0.8481 (p0) cc_final: 0.8157 (p0) REVERT: f 152 ARG cc_start: 0.8076 (ttm110) cc_final: 0.7703 (mmm160) REVERT: g 137 GLU cc_start: 0.6695 (tm-30) cc_final: 0.6394 (tm-30) REVERT: l 70 LYS cc_start: 0.8556 (OUTLIER) cc_final: 0.8342 (ttmm) REVERT: l 105 ILE cc_start: 0.8474 (mm) cc_final: 0.8198 (mm) REVERT: n 42 LYS cc_start: 0.8881 (mmmm) cc_final: 0.8491 (mttm) REVERT: n 71 ARG cc_start: 0.8331 (mmm160) cc_final: 0.8035 (mmm160) REVERT: n 107 ASN cc_start: 0.7492 (t0) cc_final: 0.7270 (t0) REVERT: o 29 HIS cc_start: 0.8258 (t-90) cc_final: 0.7931 (t-90) REVERT: o 97 PHE cc_start: 0.8887 (m-80) cc_final: 0.8473 (m-10) REVERT: q 65 ASN cc_start: 0.8760 (t0) cc_final: 0.8241 (t0) REVERT: r 1 MET cc_start: 0.7443 (tpt) cc_final: 0.7193 (tpt) REVERT: u 95 PHE cc_start: 0.7580 (m-80) cc_final: 0.7285 (m-80) REVERT: v 51 GLN cc_start: 0.8960 (OUTLIER) cc_final: 0.8434 (tm-30) REVERT: v 69 GLU cc_start: 0.8381 (mm-30) cc_final: 0.8019 (mm-30) REVERT: v 82 TYR cc_start: 0.8184 (p90) cc_final: 0.7861 (p90) REVERT: x 44 ARG cc_start: 0.6732 (OUTLIER) cc_final: 0.6340 (ptt180) REVERT: y 27 ASN cc_start: 0.8422 (t0) cc_final: 0.8184 (t0) REVERT: y 31 GLN cc_start: 0.8698 (tp40) cc_final: 0.8261 (tp40) REVERT: B 17 SER cc_start: 0.7931 (t) cc_final: 0.7688 (p) REVERT: C 5 ARG cc_start: 0.7867 (mtp85) cc_final: 0.7518 (mtp180) REVERT: C 26 LYS cc_start: 0.8297 (pttp) cc_final: 0.7799 (ptmt) REVERT: E 41 ARG cc_start: 0.8221 (ttm-80) cc_final: 0.7538 (ttm-80) REVERT: G 48 MET cc_start: 0.8350 (ptt) cc_final: 0.7599 (ptt) REVERT: G 99 MET cc_start: 0.7022 (mtp) cc_final: 0.6544 (ttp) REVERT: G 197 PHE cc_start: 0.8382 (m-80) cc_final: 0.8180 (m-10) REVERT: H 31 ASN cc_start: 0.7626 (p0) cc_final: 0.7412 (p0) REVERT: H 67 ILE cc_start: 0.9304 (mm) cc_final: 0.8998 (mm) REVERT: I 55 ARG cc_start: 0.7599 (mmm160) cc_final: 0.7213 (mmm160) REVERT: J 143 LEU cc_start: 0.9518 (mp) cc_final: 0.9315 (mp) REVERT: J 146 MET cc_start: 0.6592 (tmm) cc_final: 0.5494 (tmm) REVERT: K 24 ARG cc_start: 0.8571 (ttm110) cc_final: 0.8107 (ptm160) REVERT: K 25 TYR cc_start: 0.7675 (m-10) cc_final: 0.7267 (m-80) REVERT: K 33 GLU cc_start: 0.7717 (pp20) cc_final: 0.7484 (pp20) REVERT: L 30 MET cc_start: 0.8358 (ttp) cc_final: 0.7868 (ttp) REVERT: L 34 LYS cc_start: 0.8789 (OUTLIER) cc_final: 0.8542 (mtpt) REVERT: L 147 ASN cc_start: 0.7400 (t0) cc_final: 0.7159 (t0) REVERT: M 78 SER cc_start: 0.8310 (t) cc_final: 0.8101 (p) REVERT: M 106 SER cc_start: 0.8150 (OUTLIER) cc_final: 0.7706 (t) REVERT: N 5 TYR cc_start: 0.6866 (m-80) cc_final: 0.6516 (m-80) REVERT: N 26 LYS cc_start: 0.8395 (mmmt) cc_final: 0.8013 (mmmt) REVERT: N 56 MET cc_start: 0.7336 (tmm) cc_final: 0.7043 (tmm) REVERT: N 88 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7243 (pm20) REVERT: P 60 PHE cc_start: 0.8450 (t80) cc_final: 0.8143 (t80) REVERT: R 8 ILE cc_start: 0.6032 (mm) cc_final: 0.5590 (mm) REVERT: R 33 LEU cc_start: 0.8695 (mt) cc_final: 0.8305 (tp) REVERT: S 38 GLU cc_start: 0.7261 (tm-30) cc_final: 0.6940 (tm-30) REVERT: S 42 ASN cc_start: 0.8899 (p0) cc_final: 0.8557 (p0) REVERT: T 16 ARG cc_start: 0.7769 (mmp80) cc_final: 0.7369 (mmp80) REVERT: T 31 LEU cc_start: 0.8956 (mt) cc_final: 0.8672 (mt) REVERT: T 76 ARG cc_start: 0.8364 (ttp-110) cc_final: 0.7882 (ttm110) REVERT: U 5 ARG cc_start: 0.7356 (ptt-90) cc_final: 0.6654 (ptt-90) REVERT: U 23 ASP cc_start: 0.7959 (p0) cc_final: 0.7255 (p0) REVERT: U 31 ARG cc_start: 0.8971 (tmm-80) cc_final: 0.8652 (tmm-80) REVERT: U 32 PHE cc_start: 0.8303 (p90) cc_final: 0.7999 (p90) REVERT: U 34 GLU cc_start: 0.7034 (pp20) cc_final: 0.6606 (pp20) REVERT: U 60 TRP cc_start: 0.8091 (m100) cc_final: 0.7608 (m100) REVERT: V 68 LYS cc_start: 0.8412 (ttpt) cc_final: 0.8154 (ptmt) REVERT: V 78 VAL cc_start: 0.9230 (OUTLIER) cc_final: 0.8965 (p) REVERT: W 37 LYS cc_start: 0.8502 (mtpt) cc_final: 0.7990 (mtpp) REVERT: Y 12 GLN cc_start: 0.7795 (mt0) cc_final: 0.7572 (mp10) REVERT: Z 20 ARG cc_start: 0.8221 (mpp80) cc_final: 0.7228 (mpp80) REVERT: Z 61 ARG cc_start: 0.8535 (tmm160) cc_final: 0.8077 (ttp80) REVERT: 8 15 LEU cc_start: 0.8509 (tt) cc_final: 0.8255 (tp) REVERT: 8 80 GLN cc_start: 0.7289 (tt0) cc_final: 0.6904 (tt0) REVERT: 8 103 LYS cc_start: 0.8343 (pttm) cc_final: 0.8015 (pttm) REVERT: 9 48 LEU cc_start: 0.4569 (OUTLIER) cc_final: 0.3727 (pp) REVERT: 9 70 ILE cc_start: 0.4957 (OUTLIER) cc_final: 0.4704 (tt) outliers start: 383 outliers final: 293 residues processed: 1985 average time/residue: 1.2743 time to fit residues: 4371.8065 Evaluate side-chains 2029 residues out of total 4763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 304 poor density : 1725 time to evaluate : 6.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 18 VAL Chi-restraints excluded: chain b residue 102 TYR Chi-restraints excluded: chain b residue 115 ILE Chi-restraints excluded: chain b residue 119 VAL Chi-restraints excluded: chain b residue 138 SER Chi-restraints excluded: chain b residue 153 LEU Chi-restraints excluded: chain b residue 164 VAL Chi-restraints excluded: chain b residue 198 GLU Chi-restraints excluded: chain b residue 215 VAL Chi-restraints excluded: chain b residue 227 VAL Chi-restraints excluded: chain b residue 251 THR Chi-restraints excluded: chain c residue 2 ILE Chi-restraints excluded: chain c residue 13 ARG Chi-restraints excluded: chain c residue 18 ASP Chi-restraints excluded: chain c residue 26 VAL Chi-restraints excluded: chain c residue 32 ASN Chi-restraints excluded: chain c residue 91 THR Chi-restraints excluded: chain c residue 94 GLN Chi-restraints excluded: chain c residue 96 ILE Chi-restraints excluded: chain c residue 109 VAL Chi-restraints excluded: chain c residue 113 SER Chi-restraints excluded: chain c residue 122 VAL Chi-restraints excluded: chain c residue 176 ASP Chi-restraints excluded: chain c residue 177 VAL Chi-restraints excluded: chain c residue 197 THR Chi-restraints excluded: chain d residue 3 LEU Chi-restraints excluded: chain d residue 105 LEU Chi-restraints excluded: chain d residue 169 VAL Chi-restraints excluded: chain d residue 189 THR Chi-restraints excluded: chain e residue 4 HIS Chi-restraints excluded: chain e residue 25 MET Chi-restraints excluded: chain e residue 30 VAL Chi-restraints excluded: chain e residue 35 LEU Chi-restraints excluded: chain e residue 50 ASP Chi-restraints excluded: chain e residue 51 ASN Chi-restraints excluded: chain e residue 84 ILE Chi-restraints excluded: chain e residue 102 LEU Chi-restraints excluded: chain e residue 146 ASP Chi-restraints excluded: chain e residue 155 ILE Chi-restraints excluded: chain e residue 156 THR Chi-restraints excluded: chain e residue 157 THR Chi-restraints excluded: chain e residue 158 THR Chi-restraints excluded: chain f residue 8 VAL Chi-restraints excluded: chain f residue 55 ASP Chi-restraints excluded: chain f residue 73 SER Chi-restraints excluded: chain f residue 76 ILE Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 102 ILE Chi-restraints excluded: chain f residue 104 LEU Chi-restraints excluded: chain f residue 105 SER Chi-restraints excluded: chain f residue 120 ILE Chi-restraints excluded: chain f residue 168 VAL Chi-restraints excluded: chain g residue 4 ILE Chi-restraints excluded: chain g residue 31 VAL Chi-restraints excluded: chain g residue 37 VAL Chi-restraints excluded: chain g residue 43 ASN Chi-restraints excluded: chain g residue 86 ASP Chi-restraints excluded: chain g residue 103 VAL Chi-restraints excluded: chain g residue 124 THR Chi-restraints excluded: chain g residue 146 VAL Chi-restraints excluded: chain j residue 56 VAL Chi-restraints excluded: chain j residue 140 LEU Chi-restraints excluded: chain k residue 13 ASN Chi-restraints excluded: chain k residue 56 ASP Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 61 VAL Chi-restraints excluded: chain k residue 92 GLU Chi-restraints excluded: chain k residue 115 ILE Chi-restraints excluded: chain l residue 5 THR Chi-restraints excluded: chain l residue 23 ILE Chi-restraints excluded: chain l residue 42 SER Chi-restraints excluded: chain l residue 46 VAL Chi-restraints excluded: chain l residue 70 LYS Chi-restraints excluded: chain l residue 77 ILE Chi-restraints excluded: chain l residue 89 VAL Chi-restraints excluded: chain l residue 93 ASN Chi-restraints excluded: chain l residue 111 ILE Chi-restraints excluded: chain l residue 128 THR Chi-restraints excluded: chain l residue 136 GLU Chi-restraints excluded: chain l residue 142 ILE Chi-restraints excluded: chain m residue 5 LYS Chi-restraints excluded: chain m residue 26 VAL Chi-restraints excluded: chain m residue 30 SER Chi-restraints excluded: chain m residue 36 VAL Chi-restraints excluded: chain m residue 42 THR Chi-restraints excluded: chain m residue 74 THR Chi-restraints excluded: chain m residue 80 VAL Chi-restraints excluded: chain m residue 128 THR Chi-restraints excluded: chain m residue 129 THR Chi-restraints excluded: chain m residue 135 VAL Chi-restraints excluded: chain n residue 14 SER Chi-restraints excluded: chain n residue 28 LEU Chi-restraints excluded: chain n residue 29 VAL Chi-restraints excluded: chain n residue 33 ILE Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 38 LEU Chi-restraints excluded: chain n residue 53 THR Chi-restraints excluded: chain n residue 113 ILE Chi-restraints excluded: chain o residue 28 VAL Chi-restraints excluded: chain o residue 35 ILE Chi-restraints excluded: chain o residue 47 VAL Chi-restraints excluded: chain o residue 49 VAL Chi-restraints excluded: chain o residue 63 LYS Chi-restraints excluded: chain o residue 65 THR Chi-restraints excluded: chain o residue 81 ARG Chi-restraints excluded: chain o residue 83 LEU Chi-restraints excluded: chain o residue 91 SER Chi-restraints excluded: chain o residue 103 VAL Chi-restraints excluded: chain o residue 115 LEU Chi-restraints excluded: chain p residue 65 ASN Chi-restraints excluded: chain p residue 80 VAL Chi-restraints excluded: chain p residue 85 VAL Chi-restraints excluded: chain q residue 29 ARG Chi-restraints excluded: chain q residue 82 LEU Chi-restraints excluded: chain q residue 94 LEU Chi-restraints excluded: chain q residue 103 VAL Chi-restraints excluded: chain r residue 22 LEU Chi-restraints excluded: chain r residue 27 ILE Chi-restraints excluded: chain r residue 43 ASN Chi-restraints excluded: chain r residue 51 VAL Chi-restraints excluded: chain r residue 54 VAL Chi-restraints excluded: chain r residue 64 VAL Chi-restraints excluded: chain r residue 66 HIS Chi-restraints excluded: chain r residue 76 LYS Chi-restraints excluded: chain r residue 99 THR Chi-restraints excluded: chain s residue 30 SER Chi-restraints excluded: chain s residue 71 VAL Chi-restraints excluded: chain s residue 72 THR Chi-restraints excluded: chain s residue 81 SER Chi-restraints excluded: chain s residue 82 MET Chi-restraints excluded: chain s residue 96 ILE Chi-restraints excluded: chain s residue 107 VAL Chi-restraints excluded: chain t residue 2 ILE Chi-restraints excluded: chain t residue 22 THR Chi-restraints excluded: chain t residue 25 GLU Chi-restraints excluded: chain t residue 58 VAL Chi-restraints excluded: chain t residue 87 LEU Chi-restraints excluded: chain t residue 88 LYS Chi-restraints excluded: chain t residue 92 ASN Chi-restraints excluded: chain u residue 12 VAL Chi-restraints excluded: chain u residue 68 ASN Chi-restraints excluded: chain u residue 69 VAL Chi-restraints excluded: chain v residue 42 LEU Chi-restraints excluded: chain v residue 47 VAL Chi-restraints excluded: chain v residue 51 GLN Chi-restraints excluded: chain v residue 64 VAL Chi-restraints excluded: chain v residue 77 VAL Chi-restraints excluded: chain w residue 39 THR Chi-restraints excluded: chain w residue 54 THR Chi-restraints excluded: chain w residue 73 ARG Chi-restraints excluded: chain w residue 76 ILE Chi-restraints excluded: chain x residue 1 SER Chi-restraints excluded: chain x residue 4 CYS Chi-restraints excluded: chain x residue 12 VAL Chi-restraints excluded: chain x residue 13 THR Chi-restraints excluded: chain x residue 29 LEU Chi-restraints excluded: chain x residue 44 ARG Chi-restraints excluded: chain x residue 47 THR Chi-restraints excluded: chain x residue 48 LEU Chi-restraints excluded: chain y residue 14 LEU Chi-restraints excluded: chain y residue 15 ASN Chi-restraints excluded: chain y residue 57 LEU Chi-restraints excluded: chain z residue 6 ILE Chi-restraints excluded: chain z residue 40 THR Chi-restraints excluded: chain z residue 48 ASN Chi-restraints excluded: chain z residue 51 SER Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 13 ASN Chi-restraints excluded: chain G residue 5 MET Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 49 PHE Chi-restraints excluded: chain G residue 198 VAL Chi-restraints excluded: chain G residue 204 ASP Chi-restraints excluded: chain G residue 206 ILE Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain H residue 13 ILE Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 35 ASP Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain H residue 104 GLU Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain H residue 148 ILE Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain I residue 49 ASP Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 90 LEU Chi-restraints excluded: chain I residue 198 LEU Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 71 ILE Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 120 HIS 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 10 VAL Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain L residue 11 ILE Chi-restraints excluded: chain L residue 34 LYS Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 88 VAL Chi-restraints excluded: chain L residue 117 LEU Chi-restraints excluded: chain M residue 2 MET Chi-restraints excluded: chain M residue 17 GLN Chi-restraints excluded: chain M residue 98 LEU Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 105 THR Chi-restraints excluded: chain M residue 106 SER Chi-restraints excluded: chain M residue 126 CYS Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain N residue 30 ASN Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 88 GLU Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 117 LEU Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain P residue 16 SER Chi-restraints excluded: chain P residue 27 ASN Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain P residue 57 SER Chi-restraints excluded: chain P residue 58 THR Chi-restraints excluded: chain P residue 71 ASP Chi-restraints excluded: chain P residue 95 THR Chi-restraints excluded: chain P residue 106 ILE Chi-restraints excluded: chain P residue 107 THR Chi-restraints excluded: chain P residue 115 ILE Chi-restraints excluded: chain P residue 120 CYS Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 89 LEU Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain Q residue 111 GLN Chi-restraints excluded: chain Q residue 116 TYR Chi-restraints excluded: chain R residue 3 ILE Chi-restraints excluded: chain R residue 15 VAL Chi-restraints excluded: chain R residue 16 ILE Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 107 THR Chi-restraints excluded: chain S residue 41 TRP Chi-restraints excluded: chain S residue 45 LEU Chi-restraints excluded: chain S residue 66 THR Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain S residue 79 SER Chi-restraints excluded: chain S residue 85 GLU Chi-restraints excluded: chain S residue 99 SER Chi-restraints excluded: chain T residue 10 ILE Chi-restraints excluded: chain T residue 12 SER Chi-restraints excluded: chain T residue 21 THR Chi-restraints excluded: chain T residue 32 THR Chi-restraints excluded: chain T residue 69 LEU Chi-restraints excluded: chain T residue 81 ILE Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain V residue 11 VAL Chi-restraints excluded: chain V residue 40 THR Chi-restraints excluded: chain V residue 47 ASP Chi-restraints excluded: chain V residue 57 VAL Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain V residue 78 VAL Chi-restraints excluded: chain V residue 82 VAL Chi-restraints excluded: chain W residue 24 ASP Chi-restraints excluded: chain W residue 46 THR Chi-restraints excluded: chain W residue 49 LYS Chi-restraints excluded: chain X residue 14 LEU Chi-restraints excluded: chain X residue 35 ARG Chi-restraints excluded: chain X residue 48 ILE Chi-restraints excluded: chain X residue 50 VAL Chi-restraints excluded: chain X residue 57 VAL Chi-restraints excluded: chain X residue 60 PHE Chi-restraints excluded: chain X residue 72 GLU Chi-restraints excluded: chain X residue 78 THR Chi-restraints excluded: chain Y residue 13 SER Chi-restraints excluded: chain Y residue 52 GLU Chi-restraints excluded: chain Y residue 56 ILE Chi-restraints excluded: chain Z residue 5 VAL Chi-restraints excluded: chain Z residue 27 VAL Chi-restraints excluded: chain Z residue 42 THR Chi-restraints excluded: chain 8 residue 95 ILE Chi-restraints excluded: chain 9 residue 37 ILE Chi-restraints excluded: chain 9 residue 48 LEU Chi-restraints excluded: chain 9 residue 61 HIS Chi-restraints excluded: chain 9 residue 70 ILE Chi-restraints excluded: chain 9 residue 79 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1025 random chunks: chunk 825 optimal weight: 10.0000 chunk 562 optimal weight: 20.0000 chunk 14 optimal weight: 7.9990 chunk 737 optimal weight: 10.0000 chunk 408 optimal weight: 10.0000 chunk 845 optimal weight: 10.0000 chunk 684 optimal weight: 30.0000 chunk 1 optimal weight: 5.9990 chunk 505 optimal weight: 0.0870 chunk 889 optimal weight: 8.9990 chunk 250 optimal weight: 9.9990 overall best weight: 6.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 136 ASN c 167 ASN ** d 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 30 GLN d 62 GLN ** d 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 133 GLN g 135 HIS ** j 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 38 GLN ** n 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 107 ASN p 14 GLN ** q 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 71 ASN s 40 ASN ** t 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 65 GLN ** v 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 119 GLN ** G 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 68 HIS ** H 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 82 HIS ** K 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 68 GLN ** N 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 GLN N 36 GLN ** O 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 41 HIS T 45 HIS ** V 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.3348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 158210 Z= 0.319 Angle : 0.676 14.297 236693 Z= 0.347 Chirality : 0.038 0.322 30248 Planarity : 0.005 0.083 12684 Dihedral : 23.435 179.509 79178 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 20.95 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.68 % Favored : 90.08 % Rotamer: Outliers : 7.85 % Allowed : 26.50 % Favored : 65.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.53 % 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: -2.62 (0.10), residues: 5726 helix: -0.80 (0.12), residues: 1768 sheet: -1.85 (0.16), residues: 984 loop : -2.32 (0.11), residues: 2974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP e 96 HIS 0.017 0.002 HIS r 66 PHE 0.036 0.002 PHE K 78 TYR 0.030 0.002 TYR g 25 ARG 0.014 0.001 ARG F 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11452 Ramachandran restraints generated. 5726 Oldfield, 0 Emsley, 5726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11452 Ramachandran restraints generated. 5726 Oldfield, 0 Emsley, 5726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2178 residues out of total 4763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 374 poor density : 1804 time to evaluate : 6.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 102 TYR cc_start: 0.8203 (OUTLIER) cc_final: 0.7989 (m-10) REVERT: b 263 ASP cc_start: 0.7061 (p0) cc_final: 0.6727 (p0) REVERT: c 13 ARG cc_start: 0.8291 (OUTLIER) cc_final: 0.7666 (ptm160) REVERT: c 49 GLN cc_start: 0.7606 (tp40) cc_final: 0.7267 (tp40) REVERT: c 64 GLU cc_start: 0.7889 (pt0) cc_final: 0.7624 (pt0) REVERT: e 87 LYS cc_start: 0.6828 (OUTLIER) cc_final: 0.6391 (ptmm) REVERT: f 113 ASP cc_start: 0.8499 (p0) cc_final: 0.8080 (p0) REVERT: f 152 ARG cc_start: 0.8045 (ttm110) cc_final: 0.7702 (mmm160) REVERT: g 137 GLU cc_start: 0.6737 (tm-30) cc_final: 0.6345 (tm-30) REVERT: l 105 ILE cc_start: 0.8435 (mm) cc_final: 0.8210 (mm) REVERT: l 136 GLU cc_start: 0.7547 (OUTLIER) cc_final: 0.7117 (mp0) REVERT: n 42 LYS cc_start: 0.8830 (mmmm) cc_final: 0.8453 (mttm) REVERT: n 71 ARG cc_start: 0.8315 (mmm160) cc_final: 0.8038 (mmm160) REVERT: n 107 ASN cc_start: 0.7389 (t0) cc_final: 0.7126 (t0) REVERT: o 29 HIS cc_start: 0.8243 (t-90) cc_final: 0.7928 (t-90) REVERT: o 97 PHE cc_start: 0.8877 (m-80) cc_final: 0.8487 (m-10) REVERT: q 65 ASN cc_start: 0.8745 (t0) cc_final: 0.8389 (t0) REVERT: r 1 MET cc_start: 0.7379 (tpt) cc_final: 0.7116 (tpt) REVERT: u 95 PHE cc_start: 0.7650 (m-80) cc_final: 0.7308 (m-80) REVERT: v 51 GLN cc_start: 0.9052 (OUTLIER) cc_final: 0.8513 (tm-30) REVERT: v 69 GLU cc_start: 0.8383 (mm-30) cc_final: 0.8076 (mm-30) REVERT: v 82 TYR cc_start: 0.8119 (p90) cc_final: 0.7804 (p90) REVERT: x 44 ARG cc_start: 0.6642 (OUTLIER) cc_final: 0.6278 (ptt180) REVERT: y 1 MET cc_start: 0.8197 (tmm) cc_final: 0.7518 (tmm) REVERT: y 27 ASN cc_start: 0.8408 (t0) cc_final: 0.8155 (t0) REVERT: y 31 GLN cc_start: 0.8682 (tp40) cc_final: 0.8192 (tp-100) REVERT: z 28 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8465 (mp) REVERT: B 17 SER cc_start: 0.7898 (t) cc_final: 0.7635 (p) REVERT: C 5 ARG cc_start: 0.7853 (mtp85) cc_final: 0.7378 (mtp180) REVERT: C 26 LYS cc_start: 0.8351 (pttp) cc_final: 0.7823 (ptmt) REVERT: E 41 ARG cc_start: 0.8174 (ttm-80) cc_final: 0.7644 (ttm-80) REVERT: F 18 LYS cc_start: 0.8749 (OUTLIER) cc_final: 0.8520 (tptp) REVERT: F 19 ARG cc_start: 0.7989 (ttm170) cc_final: 0.7128 (ttm170) REVERT: G 99 MET cc_start: 0.7059 (mtp) cc_final: 0.6336 (ttp) REVERT: H 31 ASN cc_start: 0.7525 (p0) cc_final: 0.7230 (p0) REVERT: H 67 ILE cc_start: 0.9274 (mm) cc_final: 0.8968 (mm) REVERT: H 92 ASP cc_start: 0.8107 (OUTLIER) cc_final: 0.7554 (p0) REVERT: I 58 GLN cc_start: 0.7957 (mm110) cc_final: 0.7685 (tp40) REVERT: I 59 LYS cc_start: 0.8135 (ttmt) cc_final: 0.7859 (ttpt) REVERT: J 146 MET cc_start: 0.6596 (tmm) cc_final: 0.5466 (tmm) REVERT: K 25 TYR cc_start: 0.7628 (m-10) cc_final: 0.7258 (m-80) REVERT: L 30 MET cc_start: 0.8249 (ttp) cc_final: 0.7763 (ttp) REVERT: L 34 LYS cc_start: 0.8768 (OUTLIER) cc_final: 0.8497 (mtpt) REVERT: M 42 GLU cc_start: 0.8026 (tp30) cc_final: 0.7744 (tp30) REVERT: M 46 GLU cc_start: 0.7973 (mp0) cc_final: 0.7643 (mp0) REVERT: M 78 SER cc_start: 0.8424 (t) cc_final: 0.8161 (p) REVERT: M 106 SER cc_start: 0.8153 (OUTLIER) cc_final: 0.7860 (t) REVERT: N 5 TYR cc_start: 0.7000 (m-80) cc_final: 0.6566 (m-80) REVERT: N 37 TYR cc_start: 0.8038 (t80) cc_final: 0.7812 (t80) REVERT: N 56 MET cc_start: 0.7368 (tmm) cc_final: 0.7114 (tmm) REVERT: N 88 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7260 (pp20) REVERT: N 114 LYS cc_start: 0.8723 (mptt) cc_final: 0.8417 (mptt) REVERT: O 46 LYS cc_start: 0.8595 (mtmm) cc_final: 0.8308 (tptm) REVERT: R 8 ILE cc_start: 0.6062 (mm) cc_final: 0.5589 (mm) REVERT: R 33 LEU cc_start: 0.8659 (mt) cc_final: 0.8304 (tp) REVERT: S 38 GLU cc_start: 0.7185 (tm-30) cc_final: 0.6862 (tm-30) REVERT: S 42 ASN cc_start: 0.8899 (p0) cc_final: 0.8585 (p0) REVERT: T 16 ARG cc_start: 0.7826 (mmp80) cc_final: 0.7427 (mmp80) REVERT: T 66 LEU cc_start: 0.9140 (tp) cc_final: 0.8898 (tp) REVERT: T 76 ARG cc_start: 0.8360 (ttp-110) cc_final: 0.7818 (ttm110) REVERT: U 32 PHE cc_start: 0.8326 (p90) cc_final: 0.7954 (p90) REVERT: U 34 GLU cc_start: 0.6987 (pp20) cc_final: 0.6603 (pp20) REVERT: U 60 TRP cc_start: 0.7982 (m100) cc_final: 0.7626 (m100) REVERT: V 64 ARG cc_start: 0.8478 (mtm110) cc_final: 0.7959 (mtp-110) REVERT: V 66 LEU cc_start: 0.8964 (mm) cc_final: 0.8546 (mp) REVERT: V 68 LYS cc_start: 0.8402 (ttpt) cc_final: 0.8138 (ptmt) REVERT: W 37 LYS cc_start: 0.8488 (mtpt) cc_final: 0.7989 (mtpp) REVERT: W 52 ARG cc_start: 0.8455 (mtm110) cc_final: 0.7850 (mtm110) REVERT: Y 12 GLN cc_start: 0.7851 (mt0) cc_final: 0.7596 (mp10) REVERT: Y 26 MET cc_start: 0.8221 (tpp) cc_final: 0.7970 (tpp) REVERT: Y 27 MET cc_start: 0.8824 (ppp) cc_final: 0.8518 (ppp) REVERT: Z 3 ILE cc_start: 0.7102 (mm) cc_final: 0.6840 (mm) REVERT: Z 61 ARG cc_start: 0.8638 (tmm160) cc_final: 0.8249 (ttp80) REVERT: 8 72 ILE cc_start: 0.8644 (OUTLIER) cc_final: 0.8443 (tt) REVERT: 8 103 LYS cc_start: 0.8485 (pttm) cc_final: 0.8274 (pttp) REVERT: 9 48 LEU cc_start: 0.4239 (OUTLIER) cc_final: 0.3603 (pp) REVERT: 9 57 LEU cc_start: 0.7602 (mt) cc_final: 0.7319 (tt) outliers start: 374 outliers final: 287 residues processed: 1965 average time/residue: 1.2893 time to fit residues: 4363.0203 Evaluate side-chains 2040 residues out of total 4763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 301 poor density : 1739 time to evaluate : 6.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 18 VAL Chi-restraints excluded: chain b residue 102 TYR Chi-restraints excluded: chain b residue 119 VAL Chi-restraints excluded: chain b residue 138 SER Chi-restraints excluded: chain b residue 145 MET Chi-restraints excluded: chain b residue 153 LEU Chi-restraints excluded: chain b residue 164 VAL Chi-restraints excluded: chain b residue 198 GLU Chi-restraints excluded: chain b residue 215 VAL Chi-restraints excluded: chain b residue 227 VAL Chi-restraints excluded: chain b residue 251 THR Chi-restraints excluded: chain c residue 2 ILE Chi-restraints excluded: chain c residue 13 ARG Chi-restraints excluded: chain c residue 18 ASP Chi-restraints excluded: chain c residue 26 VAL Chi-restraints excluded: chain c residue 32 ASN Chi-restraints excluded: chain c residue 91 THR Chi-restraints excluded: chain c residue 94 GLN Chi-restraints excluded: chain c residue 109 VAL Chi-restraints excluded: chain c residue 113 SER Chi-restraints excluded: chain c residue 176 ASP Chi-restraints excluded: chain c residue 177 VAL Chi-restraints excluded: chain d residue 3 LEU Chi-restraints excluded: chain d residue 105 LEU Chi-restraints excluded: chain d residue 181 ILE Chi-restraints excluded: chain d residue 189 THR Chi-restraints excluded: chain e residue 4 HIS Chi-restraints excluded: chain e residue 6 TYR Chi-restraints excluded: chain e residue 25 MET Chi-restraints excluded: chain e residue 30 VAL Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 35 LEU Chi-restraints excluded: chain e residue 50 ASP Chi-restraints excluded: chain e residue 84 ILE Chi-restraints excluded: chain e residue 87 LYS Chi-restraints excluded: chain e residue 102 LEU Chi-restraints excluded: chain e residue 112 ASP Chi-restraints excluded: chain e residue 156 THR Chi-restraints excluded: chain e residue 157 THR Chi-restraints excluded: chain e residue 158 THR Chi-restraints excluded: chain e residue 168 LEU Chi-restraints excluded: chain f residue 8 VAL Chi-restraints excluded: chain f residue 35 THR Chi-restraints excluded: chain f residue 55 ASP Chi-restraints excluded: chain f residue 71 LEU Chi-restraints excluded: chain f residue 86 LEU Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 102 ILE Chi-restraints excluded: chain f residue 104 LEU Chi-restraints excluded: chain f residue 120 ILE Chi-restraints excluded: chain g residue 4 ILE Chi-restraints excluded: chain g residue 31 VAL Chi-restraints excluded: chain g residue 37 VAL Chi-restraints excluded: chain g residue 103 VAL Chi-restraints excluded: chain g residue 117 LEU Chi-restraints excluded: chain g residue 124 THR Chi-restraints excluded: chain g residue 133 GLN Chi-restraints excluded: chain g residue 143 ILE Chi-restraints excluded: chain g residue 146 VAL Chi-restraints excluded: chain j residue 56 VAL Chi-restraints excluded: chain j residue 140 LEU Chi-restraints excluded: chain k residue 56 ASP Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 61 VAL Chi-restraints excluded: chain k residue 92 GLU Chi-restraints excluded: chain k residue 115 ILE Chi-restraints excluded: chain l residue 23 ILE Chi-restraints excluded: chain l residue 46 VAL Chi-restraints excluded: chain l residue 77 ILE Chi-restraints excluded: chain l residue 89 VAL Chi-restraints excluded: chain l residue 93 ASN Chi-restraints excluded: chain l residue 136 GLU Chi-restraints excluded: chain l residue 142 ILE Chi-restraints excluded: chain m residue 5 LYS Chi-restraints excluded: chain m residue 25 ASP Chi-restraints excluded: chain m residue 26 VAL Chi-restraints excluded: chain m residue 30 SER Chi-restraints excluded: chain m residue 36 VAL Chi-restraints excluded: chain m residue 42 THR Chi-restraints excluded: chain m residue 74 THR Chi-restraints excluded: chain m residue 80 VAL Chi-restraints excluded: chain m residue 93 VAL Chi-restraints excluded: chain m residue 128 THR Chi-restraints excluded: chain m residue 129 THR Chi-restraints excluded: chain n residue 14 SER Chi-restraints excluded: chain n residue 28 LEU Chi-restraints excluded: chain n residue 33 ILE Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 38 LEU Chi-restraints excluded: chain n residue 53 THR Chi-restraints excluded: chain n residue 54 LEU Chi-restraints excluded: chain n residue 113 ILE Chi-restraints excluded: chain o residue 24 THR Chi-restraints excluded: chain o residue 28 VAL Chi-restraints excluded: chain o residue 35 ILE Chi-restraints excluded: chain o residue 47 VAL Chi-restraints excluded: chain o residue 49 VAL Chi-restraints excluded: chain o residue 65 THR Chi-restraints excluded: chain o residue 81 ARG Chi-restraints excluded: chain o residue 83 LEU Chi-restraints excluded: chain o residue 91 SER Chi-restraints excluded: chain o residue 115 LEU Chi-restraints excluded: chain p residue 65 ASN Chi-restraints excluded: chain p residue 80 VAL Chi-restraints excluded: chain p residue 85 VAL Chi-restraints excluded: chain q residue 82 LEU Chi-restraints excluded: chain q residue 94 LEU Chi-restraints excluded: chain q residue 116 LEU Chi-restraints excluded: chain r residue 22 LEU Chi-restraints excluded: chain r residue 27 ILE Chi-restraints excluded: chain r residue 43 ASN Chi-restraints excluded: chain r residue 51 VAL Chi-restraints excluded: chain r residue 64 VAL Chi-restraints excluded: chain r residue 66 HIS Chi-restraints excluded: chain r residue 99 THR Chi-restraints excluded: chain s residue 4 ILE Chi-restraints excluded: chain s residue 17 VAL Chi-restraints excluded: chain s residue 30 SER Chi-restraints excluded: chain s residue 39 THR Chi-restraints excluded: chain s residue 71 VAL Chi-restraints excluded: chain s residue 72 THR Chi-restraints excluded: chain s residue 81 SER Chi-restraints excluded: chain s residue 82 MET Chi-restraints excluded: chain s residue 96 ILE Chi-restraints excluded: chain s residue 107 VAL Chi-restraints excluded: chain t residue 1 MET Chi-restraints excluded: chain t residue 2 ILE Chi-restraints excluded: chain t residue 87 LEU Chi-restraints excluded: chain t residue 92 ASN Chi-restraints excluded: chain u residue 12 VAL Chi-restraints excluded: chain u residue 68 ASN Chi-restraints excluded: chain u residue 69 VAL Chi-restraints excluded: chain v residue 42 LEU Chi-restraints excluded: chain v residue 47 VAL Chi-restraints excluded: chain v residue 51 GLN Chi-restraints excluded: chain v residue 64 VAL Chi-restraints excluded: chain v residue 77 VAL Chi-restraints excluded: chain v residue 86 LEU Chi-restraints excluded: chain w residue 39 THR Chi-restraints excluded: chain w residue 54 THR Chi-restraints excluded: chain w residue 73 ARG Chi-restraints excluded: chain w residue 76 ILE Chi-restraints excluded: chain x residue 1 SER Chi-restraints excluded: chain x residue 4 CYS Chi-restraints excluded: chain x residue 12 VAL Chi-restraints excluded: chain x residue 13 THR Chi-restraints excluded: chain x residue 29 LEU Chi-restraints excluded: chain x residue 44 ARG Chi-restraints excluded: chain x residue 47 THR Chi-restraints excluded: chain x residue 48 LEU Chi-restraints excluded: chain y residue 14 LEU Chi-restraints excluded: chain y residue 15 ASN Chi-restraints excluded: chain y residue 57 LEU Chi-restraints excluded: chain z residue 28 LEU Chi-restraints excluded: chain z residue 40 THR Chi-restraints excluded: chain z residue 48 ASN Chi-restraints excluded: chain z residue 51 SER Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 13 ASN Chi-restraints excluded: chain F residue 18 LYS Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 49 PHE Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 198 VAL Chi-restraints excluded: chain G residue 204 ASP Chi-restraints excluded: chain G residue 206 ILE Chi-restraints excluded: chain H residue 13 ILE Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain H residue 148 ILE Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain I residue 49 ASP Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 90 LEU Chi-restraints excluded: chain I residue 104 MET Chi-restraints excluded: chain I residue 164 ARG Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 22 LYS Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 71 ILE Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 79 THR Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 120 HIS 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 10 VAL Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 38 ARG Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain L residue 11 ILE Chi-restraints excluded: chain L residue 34 LYS Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 117 LEU Chi-restraints excluded: chain M residue 2 MET Chi-restraints excluded: chain M residue 61 THR Chi-restraints excluded: chain M residue 62 LEU Chi-restraints excluded: chain M residue 98 LEU Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 105 THR Chi-restraints excluded: chain M residue 106 SER Chi-restraints excluded: chain M residue 126 CYS Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain N residue 30 ASN Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 88 GLU Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 117 LEU Chi-restraints excluded: chain O residue 17 LEU Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 51 VAL Chi-restraints excluded: chain O residue 56 HIS Chi-restraints excluded: chain O residue 63 ASP Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain P residue 27 ASN Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain P residue 57 SER Chi-restraints excluded: chain P residue 58 THR Chi-restraints excluded: chain P residue 85 VAL Chi-restraints excluded: chain P residue 95 THR Chi-restraints excluded: chain P residue 106 ILE Chi-restraints excluded: chain P residue 107 THR Chi-restraints excluded: chain P residue 109 ILE Chi-restraints excluded: chain P residue 115 ILE Chi-restraints excluded: chain P residue 120 CYS Chi-restraints excluded: chain Q residue 26 CYS Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 86 VAL Chi-restraints excluded: chain Q residue 89 LEU Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain Q residue 111 GLN Chi-restraints excluded: chain R residue 11 HIS Chi-restraints excluded: chain R residue 15 VAL Chi-restraints excluded: chain R residue 16 ILE Chi-restraints excluded: chain R residue 21 ILE Chi-restraints excluded: chain R residue 22 TYR Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 107 THR Chi-restraints excluded: chain S residue 41 TRP Chi-restraints excluded: chain S residue 66 THR Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain S residue 79 SER Chi-restraints excluded: chain S residue 99 SER Chi-restraints excluded: chain T residue 10 ILE Chi-restraints excluded: chain T residue 12 SER Chi-restraints excluded: chain T residue 21 THR Chi-restraints excluded: chain T residue 32 THR Chi-restraints excluded: chain T residue 81 ILE Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain V residue 11 VAL Chi-restraints excluded: chain V residue 16 MET Chi-restraints excluded: chain V residue 40 THR Chi-restraints excluded: chain V residue 47 ASP Chi-restraints excluded: chain V residue 69 THR Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain V residue 82 VAL Chi-restraints excluded: chain W residue 24 ASP Chi-restraints excluded: chain W residue 46 THR Chi-restraints excluded: chain W residue 49 LYS Chi-restraints excluded: chain X residue 14 LEU Chi-restraints excluded: chain X residue 35 ARG Chi-restraints excluded: chain X residue 50 VAL Chi-restraints excluded: chain X residue 57 VAL Chi-restraints excluded: chain X residue 72 GLU Chi-restraints excluded: chain X residue 78 THR Chi-restraints excluded: chain Y residue 13 SER Chi-restraints excluded: chain Y residue 52 GLU Chi-restraints excluded: chain Y residue 56 ILE Chi-restraints excluded: chain Z residue 5 VAL Chi-restraints excluded: chain Z residue 27 VAL Chi-restraints excluded: chain Z residue 42 THR Chi-restraints excluded: chain 8 residue 51 TYR Chi-restraints excluded: chain 8 residue 72 ILE Chi-restraints excluded: chain 8 residue 95 ILE Chi-restraints excluded: chain 8 residue 111 THR Chi-restraints excluded: chain 9 residue 37 ILE Chi-restraints excluded: chain 9 residue 48 LEU Chi-restraints excluded: chain 9 residue 61 HIS Chi-restraints excluded: chain 9 residue 79 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1025 random chunks: chunk 333 optimal weight: 9.9990 chunk 892 optimal weight: 10.0000 chunk 195 optimal weight: 10.0000 chunk 581 optimal weight: 20.0000 chunk 244 optimal weight: 9.9990 chunk 991 optimal weight: 10.0000 chunk 823 optimal weight: 10.0000 chunk 459 optimal weight: 8.9990 chunk 82 optimal weight: 7.9990 chunk 328 optimal weight: 6.9990 chunk 520 optimal weight: 7.9990 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 32 ASN c 136 ASN c 167 ASN ** d 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 30 GLN ** d 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 130 HIS l 104 GLN n 9 GLN ** n 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 107 ASN ** q 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 66 HIS s 40 ASN ** t 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 52 ASN u 65 GLN ** v 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 GLN ** F 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 35 GLN ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 119 GLN ** G 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 68 HIS ** H 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 82 HIS ** K 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 4 GLN ** N 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 GLN N 36 GLN ** O 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 27 GLN ** T 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 68 HIS ** Y 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.3600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.112 158210 Z= 0.398 Angle : 0.731 15.145 236693 Z= 0.372 Chirality : 0.041 0.316 30248 Planarity : 0.005 0.085 12684 Dihedral : 23.524 179.024 79178 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 24.06 Ramachandran Plot: Outliers : 0.23 % Allowed : 10.98 % Favored : 88.79 % Rotamer: Outliers : 8.65 % Allowed : 27.40 % Favored : 63.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.53 % 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: -2.66 (0.10), residues: 5726 helix: -0.84 (0.12), residues: 1784 sheet: -1.80 (0.16), residues: 1000 loop : -2.37 (0.11), residues: 2942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP G 103 HIS 0.010 0.002 HIS 8 62 PHE 0.035 0.002 PHE K 78 TYR 0.024 0.003 TYR j 75 ARG 0.011 0.001 ARG F 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11452 Ramachandran restraints generated. 5726 Oldfield, 0 Emsley, 5726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11452 Ramachandran restraints generated. 5726 Oldfield, 0 Emsley, 5726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2178 residues out of total 4763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 412 poor density : 1766 time to evaluate : 6.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 102 TYR cc_start: 0.8280 (OUTLIER) cc_final: 0.8057 (m-10) REVERT: b 186 ASP cc_start: 0.8551 (OUTLIER) cc_final: 0.8345 (t70) REVERT: c 49 GLN cc_start: 0.7633 (tp40) cc_final: 0.7343 (tp40) REVERT: c 64 GLU cc_start: 0.7957 (pt0) cc_final: 0.7637 (pt0) REVERT: e 32 LYS cc_start: 0.8848 (OUTLIER) cc_final: 0.8602 (tppt) REVERT: e 34 THR cc_start: 0.8259 (OUTLIER) cc_final: 0.7819 (p) REVERT: e 35 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8689 (tt) REVERT: e 87 LYS cc_start: 0.6728 (OUTLIER) cc_final: 0.6330 (ptmm) REVERT: f 152 ARG cc_start: 0.8072 (ttm110) cc_final: 0.7694 (mmm-85) REVERT: g 137 GLU cc_start: 0.6796 (tm-30) cc_final: 0.6451 (tm-30) REVERT: j 44 TYR cc_start: 0.8210 (t80) cc_final: 0.7888 (t80) REVERT: k 89 ASN cc_start: 0.7227 (m-40) cc_final: 0.7016 (p0) REVERT: k 105 ARG cc_start: 0.7082 (OUTLIER) cc_final: 0.6553 (ptt-90) REVERT: l 104 GLN cc_start: 0.7978 (OUTLIER) cc_final: 0.7676 (tp-100) REVERT: l 105 ILE cc_start: 0.8559 (mm) cc_final: 0.8321 (mm) REVERT: l 136 GLU cc_start: 0.7591 (mp0) cc_final: 0.6978 (mp0) REVERT: m 26 VAL cc_start: 0.8989 (OUTLIER) cc_final: 0.8667 (p) REVERT: m 95 LEU cc_start: 0.7676 (tp) cc_final: 0.7473 (mm) REVERT: n 42 LYS cc_start: 0.8859 (mmmm) cc_final: 0.8435 (mttm) REVERT: n 71 ARG cc_start: 0.8373 (mmm160) cc_final: 0.8170 (mmm160) REVERT: o 63 LYS cc_start: 0.8625 (pptt) cc_final: 0.8309 (pptt) REVERT: o 97 PHE cc_start: 0.8895 (m-80) cc_final: 0.8445 (m-10) REVERT: p 93 LYS cc_start: 0.8346 (mttt) cc_final: 0.8115 (mmtp) REVERT: q 65 ASN cc_start: 0.8861 (t0) cc_final: 0.8539 (t0) REVERT: r 1 MET cc_start: 0.7502 (tpt) cc_final: 0.7116 (tpt) REVERT: t 6 ARG cc_start: 0.7543 (mtt180) cc_final: 0.7297 (mtt180) REVERT: u 95 PHE cc_start: 0.7675 (m-80) cc_final: 0.7429 (m-80) REVERT: v 51 GLN cc_start: 0.9063 (OUTLIER) cc_final: 0.8522 (tm-30) REVERT: v 82 TYR cc_start: 0.8193 (p90) cc_final: 0.7853 (p90) REVERT: x 44 ARG cc_start: 0.6660 (OUTLIER) cc_final: 0.6296 (ptt180) REVERT: y 1 MET cc_start: 0.8380 (tmm) cc_final: 0.8161 (tmm) REVERT: y 27 ASN cc_start: 0.8430 (t0) cc_final: 0.8205 (t0) REVERT: y 31 GLN cc_start: 0.8671 (tp40) cc_final: 0.8287 (tp40) REVERT: y 52 ARG cc_start: 0.8623 (mtm-85) cc_final: 0.7638 (mtm-85) REVERT: z 28 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8522 (mp) REVERT: C 26 LYS cc_start: 0.8387 (pttp) cc_final: 0.7971 (ptmt) REVERT: E 41 ARG cc_start: 0.8154 (ttm-80) cc_final: 0.7603 (ttm-80) REVERT: F 19 ARG cc_start: 0.8039 (OUTLIER) cc_final: 0.7071 (ttm170) REVERT: G 5 MET cc_start: 0.7590 (mmm) cc_final: 0.7117 (tpt) REVERT: G 26 MET cc_start: 0.8184 (tpp) cc_final: 0.7909 (tpp) REVERT: G 77 GLU cc_start: 0.8779 (mm-30) cc_final: 0.8523 (tp30) REVERT: G 99 MET cc_start: 0.7059 (mtp) cc_final: 0.6549 (ttp) REVERT: G 144 GLU cc_start: 0.8725 (tp30) cc_final: 0.8194 (tm-30) REVERT: H 67 ILE cc_start: 0.9324 (mm) cc_final: 0.9024 (mm) REVERT: H 113 LYS cc_start: 0.8874 (OUTLIER) cc_final: 0.8663 (mmtm) REVERT: J 82 HIS cc_start: 0.6702 (p90) cc_final: 0.5725 (p-80) REVERT: J 146 MET cc_start: 0.6556 (tmm) cc_final: 0.6173 (tpp) REVERT: J 151 MET cc_start: 0.7868 (mmp) cc_final: 0.7582 (ptt) REVERT: K 24 ARG cc_start: 0.8578 (ttm110) cc_final: 0.8090 (ptm160) REVERT: K 25 TYR cc_start: 0.7608 (m-10) cc_final: 0.7241 (m-80) REVERT: L 30 MET cc_start: 0.8248 (ttp) cc_final: 0.7810 (ttp) REVERT: L 34 LYS cc_start: 0.8807 (OUTLIER) cc_final: 0.8583 (mtpt) REVERT: M 4 ASP cc_start: 0.6903 (m-30) cc_final: 0.6526 (m-30) REVERT: M 9 MET cc_start: 0.8395 (ttp) cc_final: 0.8148 (ttt) REVERT: M 42 GLU cc_start: 0.7940 (tp30) cc_final: 0.7312 (tp30) REVERT: M 46 GLU cc_start: 0.7943 (mp0) cc_final: 0.6693 (mp0) REVERT: M 78 SER cc_start: 0.8446 (t) cc_final: 0.8208 (p) REVERT: M 106 SER cc_start: 0.8133 (OUTLIER) cc_final: 0.7889 (t) REVERT: N 5 TYR cc_start: 0.7153 (m-80) cc_final: 0.6844 (m-80) REVERT: N 88 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7201 (pp20) REVERT: P 93 GLU cc_start: 0.6223 (tm-30) cc_final: 0.5949 (tm-30) REVERT: R 8 ILE cc_start: 0.6082 (mm) cc_final: 0.5668 (mm) REVERT: R 33 LEU cc_start: 0.8690 (mt) cc_final: 0.8318 (tp) REVERT: S 38 GLU cc_start: 0.7210 (tm-30) cc_final: 0.6896 (tm-30) REVERT: S 42 ASN cc_start: 0.8903 (p0) cc_final: 0.8589 (p0) REVERT: T 16 ARG cc_start: 0.7828 (mmp80) cc_final: 0.7333 (mmp80) REVERT: T 76 ARG cc_start: 0.8323 (ttp-110) cc_final: 0.8083 (ttp-110) REVERT: U 32 PHE cc_start: 0.8310 (p90) cc_final: 0.8004 (p90) REVERT: U 60 TRP cc_start: 0.8068 (m100) cc_final: 0.7632 (m100) REVERT: V 5 ARG cc_start: 0.7843 (ptm-80) cc_final: 0.7446 (ptm-80) REVERT: V 68 LYS cc_start: 0.8470 (ttpt) cc_final: 0.8173 (ptmt) REVERT: V 70 LYS cc_start: 0.8212 (ttpt) cc_final: 0.7754 (tttt) REVERT: W 52 ARG cc_start: 0.8441 (mtm110) cc_final: 0.7784 (mtm110) REVERT: Z 3 ILE cc_start: 0.7158 (mm) cc_final: 0.6920 (mm) REVERT: Z 61 ARG cc_start: 0.8645 (tmm160) cc_final: 0.8260 (ttp80) REVERT: 8 72 ILE cc_start: 0.8627 (OUTLIER) cc_final: 0.8421 (tt) REVERT: 8 103 LYS cc_start: 0.8589 (pttm) cc_final: 0.8365 (pttp) REVERT: 9 48 LEU cc_start: 0.4670 (OUTLIER) cc_final: 0.3926 (pp) outliers start: 412 outliers final: 318 residues processed: 1957 average time/residue: 1.1337 time to fit residues: 3846.2632 Evaluate side-chains 2050 residues out of total 4763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 337 poor density : 1713 time to evaluate : 5.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 102 TYR Chi-restraints excluded: chain b residue 115 ILE Chi-restraints excluded: chain b residue 119 VAL Chi-restraints excluded: chain b residue 138 SER Chi-restraints excluded: chain b residue 145 MET Chi-restraints excluded: chain b residue 153 LEU Chi-restraints excluded: chain b residue 164 VAL Chi-restraints excluded: chain b residue 186 ASP Chi-restraints excluded: chain b residue 198 GLU Chi-restraints excluded: chain b residue 215 VAL Chi-restraints excluded: chain b residue 227 VAL Chi-restraints excluded: chain b residue 251 THR Chi-restraints excluded: chain b residue 267 VAL Chi-restraints excluded: chain c residue 2 ILE Chi-restraints excluded: chain c residue 13 ARG Chi-restraints excluded: chain c residue 18 ASP Chi-restraints excluded: chain c residue 26 VAL Chi-restraints excluded: chain c residue 91 THR Chi-restraints excluded: chain c residue 94 GLN Chi-restraints excluded: chain c residue 109 VAL Chi-restraints excluded: chain c residue 113 SER Chi-restraints excluded: chain c residue 122 VAL Chi-restraints excluded: chain c residue 176 ASP Chi-restraints excluded: chain c residue 177 VAL Chi-restraints excluded: chain c residue 197 THR Chi-restraints excluded: chain d residue 48 THR Chi-restraints excluded: chain d residue 84 THR Chi-restraints excluded: chain d residue 105 LEU Chi-restraints excluded: chain d residue 181 ILE Chi-restraints excluded: chain d residue 189 THR Chi-restraints excluded: chain e residue 4 HIS Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 22 ASN Chi-restraints excluded: chain e residue 25 MET Chi-restraints excluded: chain e residue 30 VAL Chi-restraints excluded: chain e residue 32 LYS Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 35 LEU Chi-restraints excluded: chain e residue 50 ASP Chi-restraints excluded: chain e residue 84 ILE Chi-restraints excluded: chain e residue 87 LYS Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 102 LEU Chi-restraints excluded: chain e residue 156 THR Chi-restraints excluded: chain e residue 157 THR Chi-restraints excluded: chain e residue 158 THR Chi-restraints excluded: chain e residue 168 LEU Chi-restraints excluded: chain f residue 8 VAL Chi-restraints excluded: chain f residue 35 THR Chi-restraints excluded: chain f residue 55 ASP Chi-restraints excluded: chain f residue 71 LEU Chi-restraints excluded: chain f residue 73 SER Chi-restraints excluded: chain f residue 76 ILE Chi-restraints excluded: chain f residue 86 LEU Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 102 ILE Chi-restraints excluded: chain f residue 104 LEU Chi-restraints excluded: chain f residue 120 ILE Chi-restraints excluded: chain f residue 168 VAL Chi-restraints excluded: chain g residue 4 ILE Chi-restraints excluded: chain g residue 31 VAL Chi-restraints excluded: chain g residue 37 VAL Chi-restraints excluded: chain g residue 42 LYS Chi-restraints excluded: chain g residue 86 ASP Chi-restraints excluded: chain g residue 103 VAL Chi-restraints excluded: chain g residue 117 LEU Chi-restraints excluded: chain g residue 124 THR Chi-restraints excluded: chain g residue 143 ILE Chi-restraints excluded: chain g residue 146 VAL Chi-restraints excluded: chain j residue 56 VAL Chi-restraints excluded: chain j residue 84 ILE Chi-restraints excluded: chain j residue 140 LEU Chi-restraints excluded: chain k residue 56 ASP Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 61 VAL Chi-restraints excluded: chain k residue 103 VAL Chi-restraints excluded: chain k residue 105 ARG Chi-restraints excluded: chain k residue 115 ILE Chi-restraints excluded: chain l residue 5 THR Chi-restraints excluded: chain l residue 23 ILE Chi-restraints excluded: chain l residue 46 VAL Chi-restraints excluded: chain l residue 77 ILE Chi-restraints excluded: chain l residue 89 VAL Chi-restraints excluded: chain l residue 93 ASN Chi-restraints excluded: chain l residue 104 GLN Chi-restraints excluded: chain l residue 142 ILE Chi-restraints excluded: chain m residue 5 LYS Chi-restraints excluded: chain m residue 26 VAL Chi-restraints excluded: chain m residue 36 VAL Chi-restraints excluded: chain m residue 42 THR Chi-restraints excluded: chain m residue 74 THR Chi-restraints excluded: chain m residue 93 VAL Chi-restraints excluded: chain m residue 108 VAL Chi-restraints excluded: chain m residue 128 THR Chi-restraints excluded: chain m residue 129 THR Chi-restraints excluded: chain m residue 135 VAL Chi-restraints excluded: chain n residue 14 SER Chi-restraints excluded: chain n residue 28 LEU 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 37 THR Chi-restraints excluded: chain n residue 38 LEU Chi-restraints excluded: chain n residue 53 THR Chi-restraints excluded: chain n residue 54 LEU Chi-restraints excluded: chain n residue 113 ILE Chi-restraints excluded: chain o residue 2 ASP Chi-restraints excluded: chain o residue 4 LYS Chi-restraints excluded: chain o residue 24 THR Chi-restraints excluded: chain o residue 28 VAL Chi-restraints excluded: chain o residue 35 ILE Chi-restraints excluded: chain o residue 47 VAL Chi-restraints excluded: chain o residue 49 VAL Chi-restraints excluded: chain o residue 65 THR Chi-restraints excluded: chain o residue 81 ARG Chi-restraints excluded: chain o residue 83 LEU Chi-restraints excluded: chain o residue 91 SER Chi-restraints excluded: chain o residue 103 VAL Chi-restraints excluded: chain o residue 115 LEU Chi-restraints excluded: chain p residue 40 GLN Chi-restraints excluded: chain p residue 65 ASN Chi-restraints excluded: chain p residue 80 VAL Chi-restraints excluded: chain p residue 82 SER Chi-restraints excluded: chain p residue 85 VAL Chi-restraints excluded: chain q residue 29 ARG Chi-restraints excluded: chain q residue 82 LEU Chi-restraints excluded: chain q residue 94 LEU Chi-restraints excluded: chain q residue 103 VAL Chi-restraints excluded: chain q residue 116 LEU Chi-restraints excluded: chain r residue 22 LEU Chi-restraints excluded: chain r residue 41 ILE Chi-restraints excluded: chain r residue 43 ASN Chi-restraints excluded: chain r residue 51 VAL Chi-restraints excluded: chain r residue 64 VAL Chi-restraints excluded: chain r residue 66 HIS Chi-restraints excluded: chain r residue 99 THR Chi-restraints excluded: chain s residue 4 ILE Chi-restraints excluded: chain s residue 17 VAL Chi-restraints excluded: chain s residue 30 SER Chi-restraints excluded: chain s residue 39 THR Chi-restraints excluded: chain s residue 71 VAL Chi-restraints excluded: chain s residue 72 THR Chi-restraints excluded: chain s residue 81 SER Chi-restraints excluded: chain s residue 82 MET Chi-restraints excluded: chain s residue 85 ILE Chi-restraints excluded: chain s residue 96 ILE Chi-restraints excluded: chain s residue 107 VAL Chi-restraints excluded: chain t residue 1 MET Chi-restraints excluded: chain t residue 2 ILE Chi-restraints excluded: chain t residue 28 ASN Chi-restraints excluded: chain t residue 87 LEU Chi-restraints excluded: chain t residue 92 ASN Chi-restraints excluded: chain u residue 12 VAL Chi-restraints excluded: chain u residue 57 ILE Chi-restraints excluded: chain u residue 68 ASN Chi-restraints excluded: chain u residue 69 VAL Chi-restraints excluded: chain u residue 101 THR Chi-restraints excluded: chain v residue 42 LEU Chi-restraints excluded: chain v residue 47 VAL Chi-restraints excluded: chain v residue 51 GLN Chi-restraints excluded: chain v residue 64 VAL Chi-restraints excluded: chain v residue 72 VAL Chi-restraints excluded: chain v residue 77 VAL Chi-restraints excluded: chain w residue 31 SER Chi-restraints excluded: chain w residue 39 THR Chi-restraints excluded: chain w residue 54 THR Chi-restraints excluded: chain w residue 73 ARG Chi-restraints excluded: chain w residue 76 ILE Chi-restraints excluded: chain w residue 78 ILE Chi-restraints excluded: chain x residue 1 SER Chi-restraints excluded: chain x residue 4 CYS Chi-restraints excluded: chain x residue 12 VAL Chi-restraints excluded: chain x residue 13 THR Chi-restraints excluded: chain x residue 29 LEU Chi-restraints excluded: chain x residue 44 ARG Chi-restraints excluded: chain x residue 47 THR Chi-restraints excluded: chain x residue 48 LEU Chi-restraints excluded: chain y residue 14 LEU Chi-restraints excluded: chain y residue 15 ASN Chi-restraints excluded: chain y residue 57 LEU Chi-restraints excluded: chain z residue 28 LEU Chi-restraints excluded: chain z residue 40 THR Chi-restraints excluded: chain z residue 48 ASN Chi-restraints excluded: chain z residue 51 SER Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 13 ASN Chi-restraints excluded: chain F residue 19 ARG Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 49 PHE Chi-restraints excluded: chain G residue 119 GLN Chi-restraints excluded: chain G residue 198 VAL Chi-restraints excluded: chain G residue 204 ASP Chi-restraints excluded: chain G residue 206 ILE Chi-restraints excluded: chain H residue 13 ILE Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 35 ASP Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain H residue 148 ILE Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain H residue 185 THR Chi-restraints excluded: chain I residue 49 ASP Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 90 LEU Chi-restraints excluded: chain I residue 104 MET Chi-restraints excluded: chain I residue 164 ARG Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 71 ILE Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 79 THR Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 120 HIS 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 10 VAL Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 38 ARG Chi-restraints excluded: chain K residue 55 HIS Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain L residue 11 ILE Chi-restraints excluded: chain L residue 34 LYS Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 88 VAL Chi-restraints excluded: chain L residue 117 LEU Chi-restraints excluded: chain M residue 2 MET Chi-restraints excluded: chain M residue 62 LEU Chi-restraints excluded: chain M residue 98 LEU Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 105 THR Chi-restraints excluded: chain M residue 106 SER Chi-restraints excluded: chain M residue 126 CYS Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain N residue 30 ASN Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 88 GLU Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 117 LEU Chi-restraints excluded: chain O residue 17 LEU Chi-restraints excluded: chain O residue 24 GLU Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 51 VAL Chi-restraints excluded: chain O residue 56 HIS Chi-restraints excluded: chain O residue 60 ASP Chi-restraints excluded: chain O residue 63 ASP Chi-restraints excluded: chain O residue 73 LEU Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain P residue 16 SER Chi-restraints excluded: chain P residue 27 ASN Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain P residue 57 SER Chi-restraints excluded: chain P residue 58 THR Chi-restraints excluded: chain P residue 78 ILE Chi-restraints excluded: chain P residue 85 VAL Chi-restraints excluded: chain P residue 95 THR Chi-restraints excluded: chain P residue 106 ILE Chi-restraints excluded: chain P residue 107 THR Chi-restraints excluded: chain P residue 109 ILE Chi-restraints excluded: chain P residue 115 ILE Chi-restraints excluded: chain Q residue 19 ASN Chi-restraints excluded: chain Q residue 26 CYS Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 86 VAL Chi-restraints excluded: chain Q residue 89 LEU Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain Q residue 111 GLN Chi-restraints excluded: chain R residue 3 ILE Chi-restraints excluded: chain R residue 15 VAL Chi-restraints excluded: chain R residue 16 ILE Chi-restraints excluded: chain R residue 21 ILE Chi-restraints excluded: chain R residue 22 TYR Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 107 THR Chi-restraints excluded: chain S residue 41 TRP Chi-restraints excluded: chain S residue 66 THR Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain S residue 79 SER Chi-restraints excluded: chain S residue 99 SER Chi-restraints excluded: chain T residue 10 ILE Chi-restraints excluded: chain T residue 12 SER Chi-restraints excluded: chain T residue 21 THR Chi-restraints excluded: chain T residue 32 THR Chi-restraints excluded: chain T residue 35 ILE Chi-restraints excluded: chain T residue 69 LEU Chi-restraints excluded: chain T residue 81 ILE Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain V residue 11 VAL Chi-restraints excluded: chain V residue 16 MET Chi-restraints excluded: chain V residue 47 ASP Chi-restraints excluded: chain V residue 57 VAL Chi-restraints excluded: chain V residue 82 VAL Chi-restraints excluded: chain W residue 24 ASP Chi-restraints excluded: chain W residue 46 THR Chi-restraints excluded: chain W residue 49 LYS Chi-restraints excluded: chain X residue 12 LEU Chi-restraints excluded: chain X residue 14 LEU Chi-restraints excluded: chain X residue 35 ARG Chi-restraints excluded: chain X residue 50 VAL Chi-restraints excluded: chain X residue 57 VAL Chi-restraints excluded: chain X residue 72 GLU Chi-restraints excluded: chain X residue 78 THR Chi-restraints excluded: chain Y residue 13 SER Chi-restraints excluded: chain Y residue 56 ILE Chi-restraints excluded: chain Z residue 5 VAL Chi-restraints excluded: chain Z residue 27 VAL Chi-restraints excluded: chain Z residue 42 THR Chi-restraints excluded: chain 8 residue 51 TYR Chi-restraints excluded: chain 8 residue 72 ILE Chi-restraints excluded: chain 8 residue 95 ILE Chi-restraints excluded: chain 8 residue 111 THR Chi-restraints excluded: chain 9 residue 37 ILE Chi-restraints excluded: chain 9 residue 48 LEU Chi-restraints excluded: chain 9 residue 61 HIS Chi-restraints excluded: chain 9 residue 79 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1025 random chunks: chunk 956 optimal weight: 10.0000 chunk 111 optimal weight: 30.0000 chunk 565 optimal weight: 10.0000 chunk 724 optimal weight: 20.0000 chunk 561 optimal weight: 40.0000 chunk 834 optimal weight: 20.0000 chunk 553 optimal weight: 20.0000 chunk 987 optimal weight: 20.0000 chunk 618 optimal weight: 10.0000 chunk 602 optimal weight: 20.0000 chunk 456 optimal weight: 10.0000 overall best weight: 12.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: