Starting phenix.real_space_refine on Sat Mar 16 14:09:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jil_22345/03_2024/7jil_22345_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jil_22345/03_2024/7jil_22345.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jil_22345/03_2024/7jil_22345.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jil_22345/03_2024/7jil_22345.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jil_22345/03_2024/7jil_22345_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jil_22345/03_2024/7jil_22345_neut.pdb" } resolution = 2.8 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= -0.000 sd= 1.000 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 4327 5.49 5 S 118 5.16 5 C 66817 2.51 5 N 24679 2.21 5 O 36798 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 4": "NH1" <-> "NH2" Residue "B ARG 31": "NH1" <-> "NH2" Residue "B ARG 61": "NH1" <-> "NH2" Residue "B ARG 63": "NH1" <-> "NH2" Residue "B PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 82": "OE1" <-> "OE2" Residue "B TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 156": "NH1" <-> "NH2" Residue "B ARG 182": "NH1" <-> "NH2" Residue "B ARG 219": "NH1" <-> "NH2" Residue "B ASP 229": "OD1" <-> "OD2" Residue "B ARG 245": "NH1" <-> "NH2" Residue "B TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 107": "OD1" <-> "OD2" Residue "C PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 141": "NH1" <-> "NH2" Residue "D PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 45": "NH1" <-> "NH2" Residue "D ARG 62": "NH1" <-> "NH2" Residue "D PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 14": "NH1" <-> "NH2" Residue "E TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 143": "OE1" <-> "OE2" Residue "E ASP 145": "OD1" <-> "OD2" Residue "E ARG 151": "NH1" <-> "NH2" Residue "E PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 175": "OE1" <-> "OE2" Residue "E PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 3": "NH1" <-> "NH2" Residue "F PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 61": "NH1" <-> "NH2" Residue "F ARG 68": "NH1" <-> "NH2" Residue "F PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 140": "OD1" <-> "OD2" Residue "G PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 2": "OD1" <-> "OD2" Residue "J TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 26": "OE1" <-> "OE2" Residue "J TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 57": "OD1" <-> "OD2" Residue "J PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 125": "NH1" <-> "NH2" Residue "J ARG 143": "NH1" <-> "NH2" Residue "J ASP 149": "OD1" <-> "OD2" Residue "K ARG 23": "NH1" <-> "NH2" Residue "K ARG 70": "NH1" <-> "NH2" Residue "K ARG 71": "NH1" <-> "NH2" Residue "K TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 97": "NH1" <-> "NH2" Residue "K PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 104": "NH1" <-> "NH2" Residue "K GLU 105": "OE1" <-> "OE2" Residue "K PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 19": "NH1" <-> "NH2" Residue "L TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 61": "NH1" <-> "NH2" Residue "L PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 72": "NH1" <-> "NH2" Residue "L TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 94": "OD1" <-> "OD2" Residue "L GLU 111": "OE1" <-> "OE2" Residue "L PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 40": "OD1" <-> "OD2" Residue "M GLU 50": "OE1" <-> "OE2" Residue "M ARG 53": "NH1" <-> "NH2" Residue "M TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 137": "NH1" <-> "NH2" Residue "M PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 30": "OE1" <-> "OE2" Residue "N ARG 71": "NH1" <-> "NH2" Residue "N ASP 78": "OD1" <-> "OD2" Residue "N ARG 96": "NH1" <-> "NH2" Residue "N GLU 114": "OE1" <-> "OE2" Residue "O PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 45": "OD1" <-> "OD2" Residue "O ARG 93": "NH1" <-> "NH2" Residue "P PHE 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 35": "OE1" <-> "OE2" Residue "P ARG 40": "NH1" <-> "NH2" Residue "P ARG 51": "NH1" <-> "NH2" Residue "P ARG 52": "NH1" <-> "NH2" Residue "P PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 72": "OE1" <-> "OE2" Residue "P PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 3": "NH1" <-> "NH2" Residue "Q ARG 27": "NH1" <-> "NH2" Residue "Q TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 48": "NH1" <-> "NH2" Residue "Q ARG 50": "NH1" <-> "NH2" Residue "Q ARG 64": "NH1" <-> "NH2" Residue "Q PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 104": "OE1" <-> "OE2" Residue "Q PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 6": "OE1" <-> "OE2" Residue "R PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 79": "NH1" <-> "NH2" Residue "R TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 6": "NH1" <-> "NH2" Residue "S ASP 39": "OD1" <-> "OD2" Residue "S ARG 42": "NH1" <-> "NH2" Residue "S GLU 47": "OE1" <-> "OE2" Residue "S GLU 85": "OE1" <-> "OE2" Residue "S PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 104": "NH1" <-> "NH2" Residue "S ARG 115": "NH1" <-> "NH2" Residue "T ARG 6": "NH1" <-> "NH2" Residue "T GLU 16": "OE1" <-> "OE2" Residue "T PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 83": "NH1" <-> "NH2" Residue "U PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 139": "OE1" <-> "OE2" Residue "V PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 73": "NH1" <-> "NH2" Residue "W TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 3": "NH1" <-> "NH2" Residue "X ASP 6": "OD1" <-> "OD2" Residue "X ARG 11": "NH1" <-> "NH2" Residue "X ARG 27": "NH1" <-> "NH2" Residue "X PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 44": "OD1" <-> "OD2" Residue "X PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 47": "NH1" <-> "NH2" Residue "Z ARG 10": "NH1" <-> "NH2" Residue "Z ARG 29": "NH1" <-> "NH2" Residue "4 TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 35": "OE1" <-> "OE2" Residue "4 ASP 44": "OD1" <-> "OD2" Residue "5 ARG 7": "NH1" <-> "NH2" Residue "5 ARG 9": "NH1" <-> "NH2" Residue "5 ARG 22": "NH1" <-> "NH2" Residue "5 ARG 25": "NH1" <-> "NH2" Residue "a ASP 21": "OD1" <-> "OD2" Residue "a GLU 37": "OE1" <-> "OE2" Residue "a ASP 39": "OD1" <-> "OD2" Residue "a TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 52": "NH1" <-> "NH2" Residue "c TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 58": "OE1" <-> "OE2" Residue "d ARG 11": "NH1" <-> "NH2" Residue "d PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 29": "NH1" <-> "NH2" Residue "d ARG 40": "NH1" <-> "NH2" Residue "d ARG 50": "NH1" <-> "NH2" Residue "e ARG 13": "NH1" <-> "NH2" Residue "e PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 40": "NH1" <-> "NH2" Residue "e ASP 54": "OD1" <-> "OD2" Residue "f ARG 10": "NH1" <-> "NH2" Residue "f ARG 19": "NH1" <-> "NH2" Residue "f TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 88": "OE1" <-> "OE2" Residue "h GLU 89": "OE1" <-> "OE2" Residue "h GLU 97": "OE1" <-> "OE2" Residue "h PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 124": "OE1" <-> "OE2" Residue "h GLU 146": "OE1" <-> "OE2" Residue "h PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ASP 180": "OD1" <-> "OD2" Residue "h ASP 182": "OD1" <-> "OD2" Residue "h GLU 187": "OE1" <-> "OE2" Residue "h TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 3": "NH1" <-> "NH2" Residue "i ARG 13": "NH1" <-> "NH2" Residue "i PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i GLU 54": "OE1" <-> "OE2" Residue "i PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 70": "NH1" <-> "NH2" Residue "i GLU 74": "OE1" <-> "OE2" Residue "i GLU 85": "OE1" <-> "OE2" Residue "i GLU 92": "OE1" <-> "OE2" Residue "i PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 143": "NH1" <-> "NH2" Residue "i GLU 150": "OE1" <-> "OE2" Residue "i GLU 153": "OE1" <-> "OE2" Residue "i TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ASP 171": "OD1" <-> "OD2" Residue "i GLU 188": "OE1" <-> "OE2" Residue "j PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ARG 154": "NH1" <-> "NH2" Residue "j GLU 168": "OE1" <-> "OE2" Residue "k PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ARG 80": "NH1" <-> "NH2" Residue "k ARG 87": "NH1" <-> "NH2" Residue "l ARG 2": "NH1" <-> "NH2" Residue "l PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ASP 32": "OD1" <-> "OD2" Residue "l ASP 44": "OD1" <-> "OD2" Residue "l ARG 94": "NH1" <-> "NH2" Residue "l ASP 96": "OD1" <-> "OD2" Residue "l TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 125": "OE1" <-> "OE2" Residue "l ARG 140": "NH1" <-> "NH2" Residue "m ASP 4": "OD1" <-> "OD2" Residue "m ASP 8": "OD1" <-> "OD2" Residue "m TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ASP 66": "OD1" <-> "OD2" Residue "n PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ARG 78": "NH1" <-> "NH2" Residue "n ASP 105": "OD1" <-> "OD2" Residue "n ARG 107": "NH1" <-> "NH2" Residue "n ARG 120": "NH1" <-> "NH2" Residue "n ARG 122": "NH1" <-> "NH2" Residue "n PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ASP 18": "OD1" <-> "OD2" Residue "o GLU 22": "OE1" <-> "OE2" Residue "o PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ARG 124": "NH1" <-> "NH2" Residue "p ARG 126": "NH1" <-> "NH2" Residue "q ARG 9": "NH1" <-> "NH2" Residue "q ARG 54": "NH1" <-> "NH2" Residue "q TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ARG 3": "NH1" <-> "NH2" Residue "r ASP 11": "OD1" <-> "OD2" Residue "r TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r GLU 50": "OE1" <-> "OE2" Residue "r GLU 59": "OE1" <-> "OE2" Residue "r GLU 72": "OE1" <-> "OE2" Residue "r TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ARG 92": "NH1" <-> "NH2" Residue "s ARG 38": "NH1" <-> "NH2" Residue "s TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t ASP 48": "OD1" <-> "OD2" Residue "t GLU 52": "OE1" <-> "OE2" Residue "t ARG 87": "NH1" <-> "NH2" Residue "u TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ARG 29": "NH1" <-> "NH2" Residue "u TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ARG 71": "NH1" <-> "NH2" Residue "v TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v GLU 52": "OE1" <-> "OE2" Residue "v ARG 63": "NH1" <-> "NH2" Residue "w TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w ARG 34": "NH1" <-> "NH2" Residue "w TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w GLU 57": "OE1" <-> "OE2" Residue "w TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x GLU 21": "OE1" <-> "OE2" Residue "x PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z ARG 46": "NH1" <-> "NH2" Residue "z TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 132739 Number of models: 1 Model: "" Number of chains: 54 Chain: "B" Number of atoms: 2018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2018 Classifications: {'peptide': 271} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 19, 'TRANS': 251} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 39 Chain: "C" Number of atoms: 1456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1456 Classifications: {'peptide': 204} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 198} Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 9, 'ASN:plan1': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 61 Chain: "D" Number of atoms: 1484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1484 Classifications: {'peptide': 206} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 5, 'TRANS': 200} Unresolved non-hydrogen bonds: 125 Unresolved non-hydrogen angles: 154 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 14, 'ASN:plan1': 6, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 93 Chain: "E" Number of atoms: 1284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1284 Classifications: {'peptide': 174} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 6, 'TRANS': 167} Chain breaks: 1 Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 123 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ARG:plan': 4, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 61 Chain: "F" Number of atoms: 1251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1251 Classifications: {'peptide': 176} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 6, 'TRANS': 169} Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 108 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 4, 'ASN:plan1': 2, 'HIS:plan': 1, 'GLU:plan': 9, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 68 Chain: "G" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 360 Classifications: {'peptide': 50} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 3, 'TRANS': 46} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 16 Chain: "J" Number of atoms: 1112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1112 Classifications: {'peptide': 150} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 6, 'TRANS': 143} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 30 Chain: "K" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 885 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 3, 'TRANS': 117} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ASN:plan1': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 39 Chain: "L" Number of atoms: 1052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1052 Classifications: {'peptide': 150} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 3, 'TRANS': 146} Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ASN:plan1': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 47 Chain: "M" Number of atoms: 1056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1056 Classifications: {'peptide': 139} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 7, 'TRANS': 131} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 48 Chain: "N" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 980 Classifications: {'peptide': 125} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 122} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "O" Number of atoms: 846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 846 Classifications: {'peptide': 115} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 1, 'TRANS': 113} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "P" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 848 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 3, 'TRANS': 108} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 51 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 25 Chain: "Q" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 904 Classifications: {'peptide': 113} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 111} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "R" Number of atoms: 768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 768 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 1, 'TRANS': 102} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'GLU:plan': 5, 'ASN:plan1': 2, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 41 Chain: "S" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 964 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 4, 'TRANS': 123} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "T" Number of atoms: 647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 647 Classifications: {'peptide': 85} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 82} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "U" Number of atoms: 679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 679 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain breaks: 2 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 41 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 34 Chain: "V" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 881 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 6, 'TRANS': 117} Chain breaks: 1 Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 59 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ASN:plan1': 3, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 48 Chain: "W" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 569 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 72} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "X" Number of atoms: 586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 586 Classifications: {'peptide': 76} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 1, 'TRANS': 74} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "Y" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 359 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 2, 'TRANS': 48} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "Z" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 400 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 2, 'TRANS': 53} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'GLU:plan': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 19 Chain: "1" Number of atoms: 58828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2742, 58828 Classifications: {'RNA': 2742} Modifications used: {'rna2p_pur': 254, 'rna2p_pyr': 136, 'rna3p_pur': 1338, 'rna3p_pyr': 1014} Link IDs: {'rna2p': 390, 'rna3p': 2351} Chain breaks: 11 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen planarities: 1 Chain: "2" Number of atoms: 31599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1475, 31599 Classifications: {'RNA': 1475} Modifications used: {'rna2p_pur': 106, 'rna2p_pyr': 81, 'rna3p_pur': 728, 'rna3p_pyr': 560} Link IDs: {'rna2p': 187, 'rna3p': 1287} Chain breaks: 6 Chain: "3" Number of atoms: 2339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 2339 Classifications: {'RNA': 110} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 9, 'rna3p_pur': 50, 'rna3p_pyr': 48} Link IDs: {'rna2p': 12, 'rna3p': 97} Chain: "4" Number of atoms: 286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 286 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 2, 'TRANS': 33} Chain: "5" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 231 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "a" Number of atoms: 404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 404 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 3, 'TRANS': 48} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "b" Number of atoms: 475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 475 Classifications: {'peptide': 59} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 2, 'TRANS': 56} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "c" Number of atoms: 415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 415 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 3, 'TRANS': 50} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "d" Number of atoms: 416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 416 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 48} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "e" Number of atoms: 506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 506 Classifications: {'peptide': 64} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'TRANS': 63} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "f" Number of atoms: 305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 305 Classifications: {'peptide': 38} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 36} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "h" Number of atoms: 1551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1551 Classifications: {'peptide': 206} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 4, 'TRANS': 201} Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 4, 'HIS:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 46 Chain: "i" Number of atoms: 1540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1540 Classifications: {'peptide': 194} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 8, 'TRANS': 185} Chain breaks: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "j" Number of atoms: 1107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1107 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 4, 'TRANS': 154} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 6, 'HIS:plan': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 47 Chain: "k" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 815 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 1, 'TRANS': 105} Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 13, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 61 Chain: "l" Number of atoms: 1052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1052 Classifications: {'peptide': 133} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 6, 'TRANS': 126} Chain breaks: 3 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 21 Chain: "m" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 961 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 5, 'TRANS': 125} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 36 Chain: "n" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 757 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain breaks: 3 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "o" Number of atoms: 451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 451 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 52} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "p" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 823 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 6, 'TRANS': 110} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 48 Planarities with less than four sites: {'GLU:plan': 8, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 38 Chain: "q" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 922 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 114} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "r" Number of atoms: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 859 Classifications: {'peptide': 113} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 3, 'TRANS': 109} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "s" Number of atoms: 615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 615 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 4, 'TRANS': 76} Chain breaks: 1 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 20 Chain: "t" Number of atoms: 694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 694 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'TRANS': 87} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 41 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "u" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 653 Classifications: {'peptide': 85} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 4, 'TRANS': 80} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 13 Chain: "v" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 77} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "w" Number of atoms: 525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 525 Classifications: {'peptide': 65} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 62} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 13 Chain: "x" Number of atoms: 603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 603 Classifications: {'peptide': 78} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 4, 'TRANS': 73} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "y" Number of atoms: 550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 550 Classifications: {'peptide': 70} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'TRANS': 69} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "z" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 429 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain breaks: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "w" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 50.60, per 1000 atoms: 0.38 Number of scatterers: 132739 At special positions: 0 Unit cell: (232.841, 233.914, 278.98, 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 118 16.00 P 4327 15.00 O 36798 8.00 N 24679 7.00 C 66817 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: 50.36 Conformation dependent library (CDL) restraints added in 6.1 seconds 10360 Ramachandran restraints generated. 5180 Oldfield, 0 Emsley, 5180 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9812 Finding SS restraints... Warning! O2 atom is missing from residue U 1 472 Was trying to link: A 11286 N6 with U 1 472 O2, Saenger class: 21 Warning! O2 atom is missing from residue U 1 472 Was trying to link: A 11286 N6 with U 1 472 O2, Saenger class: 24 Secondary structure from input PDB file: 152 helices and 71 sheets defined 29.8% alpha, 16.1% beta 1301 base pairs and 2276 stacking pairs defined. Time for finding SS restraints: 43.41 Creating SS restraints... Processing helix chain 'B' and resid 30 through 32 No H-bonds generated for 'chain 'B' and resid 30 through 32' Processing helix chain 'B' and resid 207 through 214 removed outlier: 4.348A pdb=" N THR B 211 " --> pdb=" O LYS B 207 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ARG B 212 " --> pdb=" O ALA B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 225 Processing helix chain 'B' and resid 264 through 268 removed outlier: 3.618A pdb=" N TYR B 267 " --> pdb=" O SER B 264 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE B 268 " --> pdb=" O ASN B 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 264 through 268' Processing helix chain 'C' and resid 61 through 70 removed outlier: 3.811A pdb=" N LYS C 70 " --> pdb=" O GLY C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 124 Processing helix chain 'D' and resid 20 through 25 Processing helix chain 'D' and resid 29 through 44 Processing helix chain 'D' and resid 102 through 121 removed outlier: 3.534A pdb=" N ARG D 107 " --> pdb=" O LYS D 103 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS D 117 " --> pdb=" O ALA D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 142 Processing helix chain 'D' and resid 161 through 167 Processing helix chain 'D' and resid 180 through 182 No H-bonds generated for 'chain 'D' and resid 180 through 182' Processing helix chain 'D' and resid 183 through 190 removed outlier: 3.711A pdb=" N THR D 190 " --> pdb=" O ALA D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 205 removed outlier: 3.750A pdb=" N GLU D 205 " --> pdb=" O GLU D 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 21 removed outlier: 3.890A pdb=" N GLU E 9 " --> pdb=" O PRO E 5 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N ILE E 16 " --> pdb=" O LYS E 12 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N SER E 17 " --> pdb=" O SER E 13 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU E 21 " --> pdb=" O SER E 17 " (cutoff:3.500A) Processing helix chain 'E' and resid 27 through 31 removed outlier: 3.949A pdb=" N VAL E 31 " --> pdb=" O VAL E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 64 removed outlier: 4.567A pdb=" N ASP E 58 " --> pdb=" O ASP E 54 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LYS E 62 " --> pdb=" O ASP E 58 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ILE E 63 " --> pdb=" O GLU E 59 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR E 64 " --> pdb=" O LEU E 60 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 109 Processing helix chain 'E' and resid 170 through 175 Processing helix chain 'F' and resid 59 through 79 removed outlier: 4.309A pdb=" N GLY F 65 " --> pdb=" O ARG F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 140 through 153 Processing helix chain 'J' and resid 29 through 43 removed outlier: 4.089A pdb=" N LYS J 36 " --> pdb=" O ARG J 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 63 through 67 Processing helix chain 'J' and resid 72 through 77 Processing helix chain 'J' and resid 94 through 98 removed outlier: 3.592A pdb=" N GLN J 98 " --> pdb=" O ALA J 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 94 through 98' Processing helix chain 'J' and resid 99 through 101 No H-bonds generated for 'chain 'J' and resid 99 through 101' Processing helix chain 'J' and resid 102 through 111 removed outlier: 4.462A pdb=" N VAL J 106 " --> pdb=" O PRO J 102 " (cutoff:3.500A) Processing helix chain 'J' and resid 117 through 122 Processing helix chain 'J' and resid 123 through 127 Processing helix chain 'K' and resid 103 through 107 Processing helix chain 'K' and resid 111 through 116 Processing helix chain 'L' and resid 38 through 42 removed outlier: 3.652A pdb=" N ARG L 42 " --> pdb=" O ALA L 39 " (cutoff:3.500A) Processing helix chain 'L' and resid 57 through 62 removed outlier: 3.524A pdb=" N VAL L 62 " --> pdb=" O LEU L 58 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 89 removed outlier: 3.657A pdb=" N ASN L 89 " --> pdb=" O LEU L 85 " (cutoff:3.500A) Processing helix chain 'L' and resid 133 through 144 removed outlier: 3.694A pdb=" N ALA L 138 " --> pdb=" O ALA L 134 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA L 142 " --> pdb=" O ALA L 138 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA L 143 " --> pdb=" O ALA L 139 " (cutoff:3.500A) Processing helix chain 'M' and resid 46 through 59 removed outlier: 3.655A pdb=" N TYR M 59 " --> pdb=" O ALA M 55 " (cutoff:3.500A) Processing helix chain 'M' and resid 112 through 125 removed outlier: 3.827A pdb=" N GLU M 118 " --> pdb=" O SER M 114 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLN M 125 " --> pdb=" O ARG M 121 " (cutoff:3.500A) Processing helix chain 'N' and resid 13 through 31 removed outlier: 3.770A pdb=" N LYS N 18 " --> pdb=" O THR N 14 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N CYS N 26 " --> pdb=" O ALA N 22 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER N 27 " --> pdb=" O ASN N 23 " (cutoff:3.500A) Processing helix chain 'N' and resid 38 through 55 removed outlier: 3.585A pdb=" N GLN N 46 " --> pdb=" O LYS N 42 " (cutoff:3.500A) Proline residue: N 50 - end of helix Processing helix chain 'N' and resid 59 through 71 removed outlier: 3.570A pdb=" N ARG N 64 " --> pdb=" O THR N 60 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR N 69 " --> pdb=" O ILE N 65 " (cutoff:3.500A) Processing helix chain 'N' and resid 72 through 81 Processing helix chain 'N' and resid 82 through 88 removed outlier: 3.521A pdb=" N GLY N 88 " --> pdb=" O ALA N 84 " (cutoff:3.500A) Processing helix chain 'N' and resid 117 through 119 No H-bonds generated for 'chain 'N' and resid 117 through 119' Processing helix chain 'O' and resid 6 through 18 removed outlier: 3.509A pdb=" N ILE O 12 " --> pdb=" O ARG O 8 " (cutoff:3.500A) Processing helix chain 'O' and resid 65 through 82 Processing helix chain 'O' and resid 100 through 112 removed outlier: 3.781A pdb=" N ALA O 112 " --> pdb=" O GLY O 108 " (cutoff:3.500A) Processing helix chain 'P' and resid 5 through 13 removed outlier: 3.656A pdb=" N GLU P 11 " --> pdb=" O PHE P 7 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL P 13 " --> pdb=" O GLN P 9 " (cutoff:3.500A) Processing helix chain 'Q' and resid 6 through 19 removed outlier: 3.714A pdb=" N ARG Q 11 " --> pdb=" O SER Q 7 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ARG Q 14 " --> pdb=" O LYS Q 10 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS Q 16 " --> pdb=" O ALA Q 12 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE Q 17 " --> pdb=" O ARG Q 13 " (cutoff:3.500A) Processing helix chain 'Q' and resid 25 through 29 removed outlier: 4.009A pdb=" N LYS Q 29 " --> pdb=" O GLY Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 31 through 48 removed outlier: 4.157A pdb=" N ASN Q 37 " --> pdb=" O THR Q 33 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS Q 41 " --> pdb=" O ASN Q 37 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG Q 48 " --> pdb=" O SER Q 44 " (cutoff:3.500A) Processing helix chain 'Q' and resid 52 through 70 removed outlier: 3.558A pdb=" N PHE Q 57 " --> pdb=" O ASN Q 53 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ARG Q 58 " --> pdb=" O LYS Q 54 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N SER Q 59 " --> pdb=" O ARG Q 55 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU Q 60 " --> pdb=" O ASN Q 56 " (cutoff:3.500A) Processing helix chain 'Q' and resid 71 through 73 No H-bonds generated for 'chain 'Q' and resid 71 through 73' Processing helix chain 'Q' and resid 75 through 85 Processing helix chain 'Q' and resid 91 through 102 Processing helix chain 'Q' and resid 102 through 114 Processing helix chain 'S' and resid 5 through 14 Processing helix chain 'S' and resid 30 through 42 removed outlier: 3.540A pdb=" N MET S 34 " --> pdb=" O SER S 30 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU S 36 " --> pdb=" O ARG S 32 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N VAL S 37 " --> pdb=" O LYS S 33 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASP S 39 " --> pdb=" O ARG S 35 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LEU S 40 " --> pdb=" O LEU S 36 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL S 41 " --> pdb=" O VAL S 37 " (cutoff:3.500A) Processing helix chain 'S' and resid 47 through 55 Processing helix chain 'S' and resid 64 through 79 removed outlier: 3.509A pdb=" N LEU S 68 " --> pdb=" O LEU S 64 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU S 69 " --> pdb=" O GLU S 65 " (cutoff:3.500A) Processing helix chain 'T' and resid 10 through 20 removed outlier: 3.714A pdb=" N GLU T 16 " --> pdb=" O LYS T 12 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLU T 18 " --> pdb=" O THR T 14 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N VAL T 19 " --> pdb=" O LYS T 15 " (cutoff:3.500A) Processing helix chain 'T' and resid 32 through 45 removed outlier: 3.530A pdb=" N LYS T 38 " --> pdb=" O VAL T 34 " (cutoff:3.500A) Processing helix chain 'V' and resid 15 through 24 removed outlier: 3.680A pdb=" N THR V 19 " --> pdb=" O GLY V 15 " (cutoff:3.500A) Processing helix chain 'X' and resid 52 through 63 removed outlier: 3.635A pdb=" N LYS X 57 " --> pdb=" O ARG X 53 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR X 58 " --> pdb=" O SER X 54 " (cutoff:3.500A) Processing helix chain 'X' and resid 63 through 73 removed outlier: 3.992A pdb=" N SER X 73 " --> pdb=" O LYS X 69 " (cutoff:3.500A) Processing helix chain 'X' and resid 74 through 76 No H-bonds generated for 'chain 'X' and resid 74 through 76' Processing helix chain 'Y' and resid 17 through 22 Processing helix chain 'Y' and resid 24 through 35 removed outlier: 5.352A pdb=" N MET Y 30 " --> pdb=" O ALA Y 26 " (cutoff:3.500A) Processing helix chain 'Y' and resid 41 through 60 removed outlier: 3.566A pdb=" N SER Y 45 " --> pdb=" O LEU Y 41 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA Y 51 " --> pdb=" O ARG Y 47 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 26 removed outlier: 3.629A pdb=" N LEU Z 23 " --> pdb=" O GLN Z 19 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU Z 24 " --> pdb=" O LYS Z 20 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU Z 26 " --> pdb=" O GLY Z 22 " (cutoff:3.500A) Processing helix chain 'Z' and resid 42 through 50 removed outlier: 3.806A pdb=" N MET Z 46 " --> pdb=" O ALA Z 42 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N ASN Z 48 " --> pdb=" O LEU Z 44 " (cutoff:3.500A) Processing helix chain '5' and resid 3 through 8 removed outlier: 4.354A pdb=" N ARG 5 7 " --> pdb=" O SER 5 3 " (cutoff:3.500A) Processing helix chain '5' and resid 9 through 24 removed outlier: 3.730A pdb=" N ARG 5 17 " --> pdb=" O ALA 5 13 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS 5 18 " --> pdb=" O THR 5 14 " (cutoff:3.500A) Processing helix chain 'd' and resid 13 through 18 Processing helix chain 'd' and resid 18 through 23 Processing helix chain 'd' and resid 28 through 39 removed outlier: 4.062A pdb=" N LEU d 32 " --> pdb=" O GLY d 28 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA d 33 " --> pdb=" O ARG d 29 " (cutoff:3.500A) Processing helix chain 'd' and resid 44 through 48 Processing helix chain 'e' and resid 7 through 13 removed outlier: 3.865A pdb=" N ARG e 13 " --> pdb=" O SER e 9 " (cutoff:3.500A) Processing helix chain 'e' and resid 37 through 44 Processing helix chain 'e' and resid 51 through 62 removed outlier: 4.495A pdb=" N LYS e 56 " --> pdb=" O LYS e 52 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N SER e 57 " --> pdb=" O THR e 53 " (cutoff:3.500A) Processing helix chain 'f' and resid 30 through 33 Processing helix chain 'h' and resid 8 through 12 removed outlier: 3.938A pdb=" N ARG h 11 " --> pdb=" O ILE h 8 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LEU h 12 " --> pdb=" O GLY h 9 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 8 through 12' Processing helix chain 'h' and resid 28 through 46 removed outlier: 3.576A pdb=" N ASP h 35 " --> pdb=" O LYS h 31 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG h 39 " --> pdb=" O ASP h 35 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS h 40 " --> pdb=" O HIS h 36 " (cutoff:3.500A) Processing helix chain 'h' and resid 71 through 77 removed outlier: 4.015A pdb=" N ILE h 75 " --> pdb=" O ARG h 71 " (cutoff:3.500A) Processing helix chain 'h' and resid 80 through 94 removed outlier: 3.591A pdb=" N LYS h 85 " --> pdb=" O GLN h 81 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N LEU h 86 " --> pdb=" O GLU h 82 " (cutoff:3.500A) Processing helix chain 'h' and resid 113 through 126 Processing helix chain 'h' and resid 130 through 142 removed outlier: 4.450A pdb=" N LYS h 134 " --> pdb=" O ARG h 130 " (cutoff:3.500A) Processing helix chain 'i' and resid 7 through 14 removed outlier: 3.820A pdb=" N ILE i 11 " --> pdb=" O PRO i 7 " (cutoff:3.500A) Processing helix chain 'i' and resid 46 through 63 removed outlier: 3.860A pdb=" N ALA i 58 " --> pdb=" O GLU i 54 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N TYR i 62 " --> pdb=" O ALA i 58 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLY i 63 " --> pdb=" O LYS i 59 " (cutoff:3.500A) Processing helix chain 'i' and resid 65 through 77 Processing helix chain 'i' and resid 82 through 93 Processing helix chain 'i' and resid 94 through 102 Processing helix chain 'i' and resid 107 through 115 removed outlier: 3.765A pdb=" N GLN i 113 " --> pdb=" O ARG i 109 " (cutoff:3.500A) Processing helix chain 'i' and resid 116 through 118 No H-bonds generated for 'chain 'i' and resid 116 through 118' Processing helix chain 'i' and resid 149 through 156 removed outlier: 4.342A pdb=" N GLU i 153 " --> pdb=" O LEU i 149 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG i 154 " --> pdb=" O GLU i 150 " (cutoff:3.500A) Processing helix chain 'i' and resid 191 through 201 removed outlier: 3.631A pdb=" N ILE i 195 " --> pdb=" O LYS i 191 " (cutoff:3.500A) Processing helix chain 'j' and resid 61 through 74 Processing helix chain 'j' and resid 115 through 125 removed outlier: 4.300A pdb=" N SER j 119 " --> pdb=" O GLY j 115 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL j 120 " --> pdb=" O ALA j 116 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY j 125 " --> pdb=" O LEU j 121 " (cutoff:3.500A) Processing helix chain 'j' and resid 138 through 152 removed outlier: 3.705A pdb=" N VAL j 143 " --> pdb=" O PRO j 139 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N LYS j 144 " --> pdb=" O HIS j 140 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLN j 152 " --> pdb=" O ASP j 148 " (cutoff:3.500A) Processing helix chain 'j' and resid 155 through 164 Processing helix chain 'k' and resid 15 through 31 removed outlier: 3.746A pdb=" N VAL k 23 " --> pdb=" O VAL k 19 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N THR k 24 " --> pdb=" O LYS k 20 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS k 25 " --> pdb=" O GLU k 21 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE k 29 " --> pdb=" O LYS k 25 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU k 30 " --> pdb=" O PHE k 26 " (cutoff:3.500A) Processing helix chain 'k' and resid 68 through 72 removed outlier: 3.521A pdb=" N VAL k 71 " --> pdb=" O ALA k 68 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU k 72 " --> pdb=" O GLY k 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 68 through 72' Processing helix chain 'k' and resid 73 through 81 removed outlier: 3.761A pdb=" N PHE k 79 " --> pdb=" O PHE k 75 " (cutoff:3.500A) Processing helix chain 'k' and resid 97 through 106 Processing helix chain 'l' and resid 15 through 18 removed outlier: 3.577A pdb=" N ASN l 18 " --> pdb=" O PRO l 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 15 through 18' Processing helix chain 'l' and resid 19 through 30 removed outlier: 4.134A pdb=" N THR l 23 " --> pdb=" O ASP l 19 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG l 24 " --> pdb=" O GLN l 20 " (cutoff:3.500A) Processing helix chain 'l' and resid 35 through 49 Processing helix chain 'l' and resid 60 through 68 removed outlier: 4.193A pdb=" N TRP l 64 " --> pdb=" O SER l 60 " (cutoff:3.500A) Processing helix chain 'l' and resid 97 through 110 removed outlier: 5.896A pdb=" N MET l 103 " --> pdb=" O ILE l 99 " (cutoff:3.500A) Processing helix chain 'l' and resid 117 through 122 Processing helix chain 'l' and resid 136 through 148 removed outlier: 3.847A pdb=" N ARG l 140 " --> pdb=" O ALA l 136 " (cutoff:3.500A) Processing helix chain 'm' and resid 4 through 20 removed outlier: 3.529A pdb=" N VAL m 13 " --> pdb=" O TYR m 9 " (cutoff:3.500A) Processing helix chain 'm' and resid 29 through 43 Processing helix chain 'm' and resid 96 through 101 Processing helix chain 'm' and resid 115 through 120 removed outlier: 3.614A pdb=" N LYS m 119 " --> pdb=" O GLY m 115 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLN m 120 " --> pdb=" O LYS m 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 115 through 120' Processing helix chain 'n' and resid 39 through 44 Processing helix chain 'n' and resid 69 through 84 Processing helix chain 'o' and resid 16 through 25 Processing helix chain 'p' and resid 57 through 73 removed outlier: 3.709A pdb=" N CYS p 68 " --> pdb=" O ALA p 64 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS p 70 " --> pdb=" O GLU p 66 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N VAL p 71 " --> pdb=" O ASP p 67 " (cutoff:3.500A) Processing helix chain 'p' and resid 74 through 76 No H-bonds generated for 'chain 'p' and resid 74 through 76' Processing helix chain 'p' and resid 91 through 100 removed outlier: 3.920A pdb=" N ILE p 95 " --> pdb=" O ARG p 91 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N SER p 97 " --> pdb=" O SER p 93 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ILE p 98 " --> pdb=" O ALA p 94 " (cutoff:3.500A) Processing helix chain 'q' and resid 3 through 10 Processing helix chain 'q' and resid 115 through 119 removed outlier: 4.088A pdb=" N GLY q 118 " --> pdb=" O SER q 115 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ALA q 119 " --> pdb=" O LYS q 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'q' and resid 115 through 119' Processing helix chain 'r' and resid 14 through 20 Processing helix chain 'r' and resid 26 through 38 Processing helix chain 'r' and resid 49 through 61 removed outlier: 3.717A pdb=" N GLU r 59 " --> pdb=" O THR r 55 " (cutoff:3.500A) Processing helix chain 'r' and resid 66 through 82 Processing helix chain 'r' and resid 85 through 94 Processing helix chain 'r' and resid 106 through 111 Processing helix chain 's' and resid 3 through 17 removed outlier: 3.641A pdb=" N GLU s 10 " --> pdb=" O MET s 6 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL s 11 " --> pdb=" O LYS s 7 " (cutoff:3.500A) Processing helix chain 's' and resid 68 through 78 Processing helix chain 't' and resid 4 through 14 Processing helix chain 't' and resid 23 through 40 removed outlier: 3.633A pdb=" N LEU t 38 " --> pdb=" O ARG t 34 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLU t 40 " --> pdb=" O SER t 36 " (cutoff:3.500A) Processing helix chain 't' and resid 40 through 45 removed outlier: 3.729A pdb=" N LYS t 44 " --> pdb=" O GLU t 40 " (cutoff:3.500A) Processing helix chain 't' and resid 48 through 73 removed outlier: 3.606A pdb=" N SER t 54 " --> pdb=" O ASN t 50 " (cutoff:3.500A) Processing helix chain 't' and resid 73 through 85 removed outlier: 3.612A pdb=" N TYR t 77 " --> pdb=" O ASP t 73 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG t 78 " --> pdb=" O ILE t 74 " (cutoff:3.500A) Processing helix chain 'u' and resid 52 through 63 removed outlier: 3.858A pdb=" N VAL u 57 " --> pdb=" O LEU u 53 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LYS u 58 " --> pdb=" O ASP u 54 " (cutoff:3.500A) Processing helix chain 'u' and resid 67 through 74 Processing helix chain 'u' and resid 79 through 84 Processing helix chain 'w' and resid 33 through 38 removed outlier: 3.673A pdb=" N SER w 38 " --> pdb=" O ARG w 34 " (cutoff:3.500A) Processing helix chain 'w' and resid 63 through 68 removed outlier: 3.922A pdb=" N THR w 67 " --> pdb=" O PRO w 63 " (cutoff:3.500A) Processing helix chain 'w' and resid 70 through 87 removed outlier: 3.702A pdb=" N LYS w 76 " --> pdb=" O LYS w 72 " (cutoff:3.500A) Processing helix chain 'x' and resid 12 through 26 removed outlier: 3.735A pdb=" N GLU x 21 " --> pdb=" O LYS x 17 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASN x 22 " --> pdb=" O LYS x 18 " (cutoff:3.500A) Processing helix chain 'x' and resid 64 through 69 removed outlier: 3.571A pdb=" N VAL x 67 " --> pdb=" O GLU x 64 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N GLY x 68 " --> pdb=" O ASN x 65 " (cutoff:3.500A) Processing helix chain 'y' and resid 6 through 34 removed outlier: 3.740A pdb=" N ARG y 10 " --> pdb=" O SER y 6 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ILE y 11 " --> pdb=" O ALA y 7 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N ARG y 12 " --> pdb=" O LEU y 8 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N GLU y 15 " --> pdb=" O ILE y 11 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LYS y 16 " --> pdb=" O ARG y 12 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU y 20 " --> pdb=" O LYS y 16 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR y 28 " --> pdb=" O GLN y 24 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA y 31 " --> pdb=" O THR y 27 " (cutoff:3.500A) Processing helix chain 'y' and resid 47 through 49 No H-bonds generated for 'chain 'y' and resid 47 through 49' Processing helix chain 'y' and resid 50 through 61 removed outlier: 4.135A pdb=" N MET y 54 " --> pdb=" O THR y 50 " (cutoff:3.500A) Processing helix chain 'y' and resid 65 through 77 removed outlier: 3.603A pdb=" N THR y 77 " --> pdb=" O LYS y 73 " (cutoff:3.500A) Processing helix chain 'z' and resid 12 through 26 Processing helix chain 'z' and resid 31 through 36 removed outlier: 3.630A pdb=" N ARG z 35 " --> pdb=" O GLN z 31 " (cutoff:3.500A) Processing helix chain 'z' and resid 40 through 45 Processing helix chain 'z' and resid 45 through 50 removed outlier: 3.924A pdb=" N ILE z 49 " --> pdb=" O LYS z 45 " (cutoff:3.500A) Processing helix chain 'z' and resid 50 through 58 removed outlier: 3.718A pdb=" N TYR z 54 " --> pdb=" O GLN z 50 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 4 through 5 Processing sheet with id=AA2, first strand: chain 'B' and resid 34 through 35 Processing sheet with id=AA3, first strand: chain 'B' and resid 101 through 102 removed outlier: 6.841A pdb=" N LEU B 93 " --> pdb=" O LYS B 79 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 129 through 131 removed outlier: 6.334A pdb=" N LEU B 164 " --> pdb=" O LYS B 175 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N LYS B 175 " --> pdb=" O LEU B 164 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA B 166 " --> pdb=" O THR B 173 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 105 through 106 removed outlier: 3.940A pdb=" N ARG C 176 " --> pdb=" O LYS C 190 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N VAL C 188 " --> pdb=" O LEU C 178 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL C 26 " --> pdb=" O GLY C 10 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLY C 10 " --> pdb=" O VAL C 26 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 79 through 82 removed outlier: 3.973A pdb=" N GLN C 36 " --> pdb=" O GLN C 49 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N GLY C 51 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N VAL C 34 " --> pdb=" O GLY C 51 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 109 through 111 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 3 through 6 removed outlier: 3.905A pdb=" N VAL D 5 " --> pdb=" O ARG D 15 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ARG D 15 " --> pdb=" O VAL D 5 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 46 through 47 removed outlier: 3.714A pdb=" N GLY D 47 " --> pdb=" O ARG D 95 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 123 through 126 removed outlier: 6.386A pdb=" N ILE D 124 " --> pdb=" O LEU D 195 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LEU D 154 " --> pdb=" O VAL D 194 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N LEU D 196 " --> pdb=" O LEU D 154 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N VAL D 156 " --> pdb=" O LEU D 196 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N SER D 153 " --> pdb=" O ASN D 175 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N VAL D 177 " --> pdb=" O SER D 153 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N PHE D 155 " --> pdb=" O VAL D 177 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'E' and resid 34 through 36 Processing sheet with id=AB4, first strand: chain 'F' and resid 16 through 19 Processing sheet with id=AB5, first strand: chain 'F' and resid 41 through 44 Processing sheet with id=AB6, first strand: chain 'F' and resid 123 through 125 Processing sheet with id=AB7, first strand: chain 'F' and resid 94 through 97 removed outlier: 6.322A pdb=" N ASN F 111 " --> pdb=" O LYS 4 18 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N ILE 4 20 " --> pdb=" O ASN F 111 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N VAL F 113 " --> pdb=" O ILE 4 20 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N MET 4 22 " --> pdb=" O VAL F 113 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N GLU F 115 " --> pdb=" O MET 4 22 " (cutoff:3.500A) removed outlier: 9.449A pdb=" N LYS 4 24 " --> pdb=" O GLU F 115 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL 4 23 " --> pdb=" O ILE 4 32 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 18 through 19 Processing sheet with id=AB9, first strand: chain 'J' and resid 22 through 23 Processing sheet with id=AC1, first strand: chain 'J' and resid 78 through 80 removed outlier: 3.516A pdb=" N TYR J 79 " --> pdb=" O LEU J 92 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'K' and resid 7 through 10 removed outlier: 6.466A pdb=" N VAL K 40 " --> pdb=" O ILE K 22 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N VAL K 24 " --> pdb=" O LYS K 38 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N LYS K 38 " --> pdb=" O VAL K 24 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N THR K 59 " --> pdb=" O LEU K 87 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ALA K 83 " --> pdb=" O VAL K 63 " (cutoff:3.500A) removed outlier: 8.404A pdb=" N CYS K 84 " --> pdb=" O ARG K 7 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N LYS K 9 " --> pdb=" O CYS K 84 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N LEU K 86 " --> pdb=" O LYS K 9 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 69 through 70 removed outlier: 3.769A pdb=" N ILE P 69 " --> pdb=" O SER P 66 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN P 50 " --> pdb=" O THR P 61 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ARG P 63 " --> pdb=" O VAL P 48 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N VAL P 48 " --> pdb=" O ARG P 63 " (cutoff:3.500A) removed outlier: 8.860A pdb=" N MET P 65 " --> pdb=" O GLY P 46 " (cutoff:3.500A) removed outlier: 9.248A pdb=" N GLY P 46 " --> pdb=" O MET P 65 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N PHE P 30 " --> pdb=" O LYS P 84 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N LYS P 84 " --> pdb=" O PHE P 30 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 114 through 115 Processing sheet with id=AC5, first strand: chain 'L' and resid 127 through 129 Processing sheet with id=AC6, first strand: chain 'M' and resid 66 through 68 removed outlier: 6.701A pdb=" N ILE M 104 " --> pdb=" O SER M 36 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N SER M 36 " --> pdb=" O ILE M 104 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N PHE M 106 " --> pdb=" O ILE M 34 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'M' and resid 42 through 45 Processing sheet with id=AC8, first strand: chain 'N' and resid 36 through 37 removed outlier: 4.590A pdb=" N GLY N 101 " --> pdb=" O MET N 110 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'N' and resid 95 through 96 Processing sheet with id=AD1, first strand: chain 'O' and resid 48 through 55 removed outlier: 5.824A pdb=" N THR O 50 " --> pdb=" O ASP O 44 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ASP O 44 " --> pdb=" O THR O 50 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU O 52 " --> pdb=" O LEU O 42 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'R' and resid 2 through 5 removed outlier: 3.807A pdb=" N LEU R 40 " --> pdb=" O ILE R 4 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'R' and resid 19 through 23 removed outlier: 3.742A pdb=" N GLN R 65 " --> pdb=" O GLN R 95 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL R 97 " --> pdb=" O VAL R 63 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N VAL R 63 " --> pdb=" O VAL R 97 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N GLU R 99 " --> pdb=" O ALA R 61 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N ALA R 61 " --> pdb=" O GLU R 99 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE R 101 " --> pdb=" O VAL R 59 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N VAL R 59 " --> pdb=" O ILE R 101 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'R' and resid 72 through 78 removed outlier: 3.972A pdb=" N TYR R 83 " --> pdb=" O LYS R 78 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'S' and resid 21 through 27 removed outlier: 3.827A pdb=" N ASN S 26 " --> pdb=" O ASN S 121 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ASN S 121 " --> pdb=" O ASN S 26 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU S 93 " --> pdb=" O VAL S 126 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'S' and resid 102 through 108 removed outlier: 3.810A pdb=" N ARG S 112 " --> pdb=" O ALA S 108 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'T' and resid 4 through 7 removed outlier: 3.580A pdb=" N ARG T 6 " --> pdb=" O VAL T 26 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LYS T 78 " --> pdb=" O VAL T 27 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLN T 83 " --> pdb=" O SER T 50 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N SER T 50 " --> pdb=" O GLN T 83 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'T' and resid 61 through 62 Processing sheet with id=AD9, first strand: chain 'U' and resid 66 through 67 removed outlier: 6.598A pdb=" N LYS U 35 " --> pdb=" O VAL U 29 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N VAL U 29 " --> pdb=" O LYS U 35 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ILE U 37 " --> pdb=" O LEU U 27 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N ILE U 11 " --> pdb=" O ILE U 74 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ILE U 74 " --> pdb=" O ILE U 11 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LEU U 73 " --> pdb=" O THR U 82 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'U' and resid 43 through 47 Processing sheet with id=AE2, first strand: chain 'V' and resid 4 through 7 Processing sheet with id=AE3, first strand: chain 'V' and resid 9 through 10 removed outlier: 3.656A pdb=" N ILE V 89 " --> pdb=" O PRO V 29 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N GLN V 78 " --> pdb=" O LEU V 87 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ILE V 89 " --> pdb=" O ASP V 76 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ASP V 76 " --> pdb=" O ILE V 89 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N PHE V 91 " --> pdb=" O LEU V 74 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N LEU V 74 " --> pdb=" O PHE V 91 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N GLN V 93 " --> pdb=" O ALA V 72 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ALA V 72 " --> pdb=" O GLN V 93 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'V' and resid 100 through 105 Processing sheet with id=AE5, first strand: chain 'W' and resid 22 through 23 removed outlier: 3.676A pdb=" N GLY W 22 " --> pdb=" O ARG W 39 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU W 59 " --> pdb=" O ILE W 37 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'W' and resid 30 through 31 Processing sheet with id=AE7, first strand: chain 'X' and resid 13 through 16 Processing sheet with id=AE8, first strand: chain 'X' and resid 37 through 40 removed outlier: 3.595A pdb=" N ARG X 45 " --> pdb=" O LEU X 40 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'Z' and resid 34 through 37 Processing sheet with id=AF1, first strand: chain 'a' and resid 11 through 14 Processing sheet with id=AF2, first strand: chain 'b' and resid 27 through 29 Processing sheet with id=AF3, first strand: chain 'b' and resid 43 through 44 removed outlier: 6.498A pdb=" N MET b 49 " --> pdb=" O VAL b 56 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'c' and resid 27 through 33 removed outlier: 3.508A pdb=" N ARG c 52 " --> pdb=" O ASN c 47 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'e' and resid 15 through 16 Processing sheet with id=AF6, first strand: chain 'f' and resid 2 through 3 removed outlier: 7.203A pdb=" N LYS f 2 " --> pdb=" O ARG f 36 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF6 Processing sheet with id=AF7, first strand: chain 'f' and resid 15 through 18 Processing sheet with id=AF8, first strand: chain 'h' and resid 53 through 57 Processing sheet with id=AF9, first strand: chain 'h' and resid 53 through 57 removed outlier: 7.923A pdb=" N PHE h 103 " --> pdb=" O VAL h 65 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N ILE h 67 " --> pdb=" O PHE h 103 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'h' and resid 168 through 169 removed outlier: 3.806A pdb=" N GLU h 169 " --> pdb=" O ILE h 148 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ILE h 148 " --> pdb=" O GLU h 169 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N VAL h 199 " --> pdb=" O ALA h 184 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA h 184 " --> pdb=" O VAL h 199 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'i' and resid 120 through 122 Processing sheet with id=AG3, first strand: chain 'j' and resid 18 through 30 removed outlier: 5.262A pdb=" N ASP j 19 " --> pdb=" O GLY j 46 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N GLY j 46 " --> pdb=" O ASP j 19 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N LEU j 21 " --> pdb=" O VAL j 44 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N VAL j 44 " --> pdb=" O LEU j 21 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N SER j 23 " --> pdb=" O ILE j 42 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'j' and resid 91 through 93 Processing sheet with id=AG5, first strand: chain 'k' and resid 41 through 52 removed outlier: 6.371A pdb=" N TYR k 60 " --> pdb=" O TRP k 43 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N LEU k 45 " --> pdb=" O GLY k 58 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N GLY k 58 " --> pdb=" O LEU k 45 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N LYS k 47 " --> pdb=" O LYS k 56 " (cutoff:3.500A) removed outlier: 8.363A pdb=" N LYS k 56 " --> pdb=" O LYS k 47 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE k 59 " --> pdb=" O LEU k 10 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N HIS k 3 " --> pdb=" O LEU k 93 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ARG k 87 " --> pdb=" O ILE k 9 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'l' and resid 76 through 77 Processing sheet with id=AG7, first strand: chain 'm' and resid 23 through 27 removed outlier: 3.842A pdb=" N SER m 47 " --> pdb=" O ALA m 62 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'm' and resid 77 through 79 removed outlier: 6.859A pdb=" N ILE m 105 " --> pdb=" O ILE m 128 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N TYR m 130 " --> pdb=" O ILE m 103 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ILE m 103 " --> pdb=" O TYR m 130 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'n' and resid 5 through 7 Processing sheet with id=AH1, first strand: chain 'o' and resid 9 through 11 Processing sheet with id=AH2, first strand: chain 'p' and resid 39 through 44 removed outlier: 6.280A pdb=" N VAL p 39 " --> pdb=" O ASN p 34 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N ASN p 34 " --> pdb=" O VAL p 39 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'p' and resid 79 through 80 Processing sheet with id=AH4, first strand: chain 'q' and resid 79 through 82 removed outlier: 6.627A pdb=" N ARG q 54 " --> pdb=" O THR q 35 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N VAL q 37 " --> pdb=" O VAL q 52 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N VAL q 52 " --> pdb=" O VAL q 37 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N THR q 39 " --> pdb=" O ARG q 50 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N ARG q 50 " --> pdb=" O THR q 39 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N TYR q 95 " --> pdb=" O ASN q 64 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'u' and resid 35 through 36 removed outlier: 3.692A pdb=" N GLU u 35 " --> pdb=" O ALA u 22 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA u 22 " --> pdb=" O GLU u 35 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N VAL u 3 " --> pdb=" O GLN u 65 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'u' and resid 40 through 41 Processing sheet with id=AH7, first strand: chain 'v' and resid 40 through 50 removed outlier: 8.355A pdb=" N SER v 23 " --> pdb=" O ASN v 18 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N ASN v 18 " --> pdb=" O SER v 23 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N VAL v 25 " --> pdb=" O THR v 16 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N VAL v 29 " --> pdb=" O ILE v 12 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N ILE v 12 " --> pdb=" O VAL v 29 " (cutoff:3.500A) removed outlier: 13.473A pdb=" N LYS v 31 " --> pdb=" O GLU v 10 " (cutoff:3.500A) removed outlier: 16.889A pdb=" N GLU v 10 " --> pdb=" O LYS v 31 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N CYS v 75 " --> pdb=" O THR v 67 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'x' and resid 31 through 33 removed outlier: 3.711A pdb=" N GLN x 47 " --> pdb=" O VAL x 62 " (cutoff:3.500A) 1313 hydrogen bonds defined for protein. 3681 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3274 hydrogen bonds 5190 hydrogen bond angles 0 basepair planarities 1301 basepair parallelities 2276 stacking parallelities Total time for adding SS restraints: 198.87 Time building geometry restraints manager: 54.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 14178 1.32 - 1.45: 62929 1.45 - 1.57: 58496 1.57 - 1.69: 8631 1.69 - 1.81: 210 Bond restraints: 144444 Sorted by residual: bond pdb=" C1' U 21517 " pdb=" N1 U 21517 " ideal model delta sigma weight residual 1.480 1.570 -0.090 1.50e-02 4.44e+03 3.64e+01 bond pdb=" O3' C 21226 " pdb=" P G 21227 " ideal model delta sigma weight residual 1.607 1.552 0.055 1.50e-02 4.44e+03 1.35e+01 bond pdb=" O3' G 21503 " pdb=" P A 21504 " ideal model delta sigma weight residual 1.607 1.657 -0.050 1.50e-02 4.44e+03 1.10e+01 bond pdb=" O3' A 21139 " pdb=" P C 21140 " ideal model delta sigma weight residual 1.607 1.656 -0.049 1.50e-02 4.44e+03 1.05e+01 bond pdb=" O3' C 12464 " pdb=" P C 12465 " ideal model delta sigma weight residual 1.607 1.561 0.046 1.50e-02 4.44e+03 9.44e+00 ... (remaining 144439 not shown) Histogram of bond angle deviations from ideal: 98.79 - 105.84: 23311 105.84 - 112.89: 83969 112.89 - 119.94: 50739 119.94 - 126.99: 47733 126.99 - 134.04: 10743 Bond angle restraints: 216495 Sorted by residual: angle pdb=" O3' G 21203 " pdb=" C3' G 21203 " pdb=" C2' G 21203 " ideal model delta sigma weight residual 113.70 124.39 -10.69 1.50e+00 4.44e-01 5.08e+01 angle pdb=" C4' C 1 895 " pdb=" C3' C 1 895 " pdb=" O3' C 1 895 " ideal model delta sigma weight residual 113.00 102.69 10.31 1.50e+00 4.44e-01 4.73e+01 angle pdb=" C4' A 1 897 " pdb=" C3' A 1 897 " pdb=" O3' A 1 897 " ideal model delta sigma weight residual 113.00 121.61 -8.61 1.50e+00 4.44e-01 3.30e+01 angle pdb=" C4' G 21203 " pdb=" C3' G 21203 " pdb=" O3' G 21203 " ideal model delta sigma weight residual 113.00 121.46 -8.46 1.50e+00 4.44e-01 3.18e+01 angle pdb=" C3' C 21225 " pdb=" O3' C 21225 " pdb=" P C 21226 " ideal model delta sigma weight residual 120.20 128.52 -8.32 1.50e+00 4.44e-01 3.08e+01 ... (remaining 216490 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 81145 35.99 - 71.97: 9435 71.97 - 107.96: 1073 107.96 - 143.95: 22 143.95 - 179.93: 60 Dihedral angle restraints: 91735 sinusoidal: 76534 harmonic: 15201 Sorted by residual: dihedral pdb=" O4' U 11689 " pdb=" C1' U 11689 " pdb=" N1 U 11689 " pdb=" C2 U 11689 " ideal model delta sinusoidal sigma weight residual 200.00 24.10 175.90 1 1.50e+01 4.44e-03 8.52e+01 dihedral pdb=" O4' U 2 748 " pdb=" C1' U 2 748 " pdb=" N1 U 2 748 " pdb=" C2 U 2 748 " ideal model delta sinusoidal sigma weight residual -160.00 15.37 -175.37 1 1.50e+01 4.44e-03 8.52e+01 dihedral pdb=" O4' U 11815 " pdb=" C1' U 11815 " pdb=" N1 U 11815 " pdb=" C2 U 11815 " ideal model delta sinusoidal sigma weight residual 200.00 31.36 168.64 1 1.50e+01 4.44e-03 8.45e+01 ... (remaining 91732 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.145: 27799 0.145 - 0.290: 159 0.290 - 0.435: 2 0.435 - 0.580: 0 0.580 - 0.725: 2 Chirality restraints: 27962 Sorted by residual: chirality pdb=" C3' G 21203 " pdb=" C4' G 21203 " pdb=" O3' G 21203 " pdb=" C2' G 21203 " both_signs ideal model delta sigma weight residual False -2.48 -1.75 -0.72 2.00e-01 2.50e+01 1.31e+01 chirality pdb=" C3' A 1 897 " pdb=" C4' A 1 897 " pdb=" O3' A 1 897 " pdb=" C2' A 1 897 " both_signs ideal model delta sigma weight residual False -2.48 -1.88 -0.60 2.00e-01 2.50e+01 9.05e+00 chirality pdb=" CA SER O 34 " pdb=" N SER O 34 " pdb=" C SER O 34 " pdb=" CB SER O 34 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.05e+00 ... (remaining 27959 not shown) Planarity restraints: 11174 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G 1 470 " -0.045 2.00e-02 2.50e+03 1.90e-02 1.08e+01 pdb=" N9 G 1 470 " 0.041 2.00e-02 2.50e+03 pdb=" C8 G 1 470 " 0.009 2.00e-02 2.50e+03 pdb=" N7 G 1 470 " -0.005 2.00e-02 2.50e+03 pdb=" C5 G 1 470 " -0.003 2.00e-02 2.50e+03 pdb=" C6 G 1 470 " -0.012 2.00e-02 2.50e+03 pdb=" O6 G 1 470 " -0.002 2.00e-02 2.50e+03 pdb=" N1 G 1 470 " -0.009 2.00e-02 2.50e+03 pdb=" C2 G 1 470 " 0.000 2.00e-02 2.50e+03 pdb=" N2 G 1 470 " 0.002 2.00e-02 2.50e+03 pdb=" N3 G 1 470 " 0.014 2.00e-02 2.50e+03 pdb=" C4 G 1 470 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G 1 25 " 0.041 2.00e-02 2.50e+03 1.75e-02 9.19e+00 pdb=" N9 G 1 25 " -0.041 2.00e-02 2.50e+03 pdb=" C8 G 1 25 " -0.004 2.00e-02 2.50e+03 pdb=" N7 G 1 25 " -0.000 2.00e-02 2.50e+03 pdb=" C5 G 1 25 " -0.000 2.00e-02 2.50e+03 pdb=" C6 G 1 25 " 0.004 2.00e-02 2.50e+03 pdb=" O6 G 1 25 " 0.012 2.00e-02 2.50e+03 pdb=" N1 G 1 25 " 0.005 2.00e-02 2.50e+03 pdb=" C2 G 1 25 " -0.002 2.00e-02 2.50e+03 pdb=" N2 G 1 25 " -0.003 2.00e-02 2.50e+03 pdb=" N3 G 1 25 " -0.006 2.00e-02 2.50e+03 pdb=" C4 G 1 25 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A 11767 " -0.040 2.00e-02 2.50e+03 1.78e-02 8.73e+00 pdb=" N9 A 11767 " 0.041 2.00e-02 2.50e+03 pdb=" C8 A 11767 " 0.002 2.00e-02 2.50e+03 pdb=" N7 A 11767 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A 11767 " 0.003 2.00e-02 2.50e+03 pdb=" C6 A 11767 " -0.007 2.00e-02 2.50e+03 pdb=" N6 A 11767 " -0.010 2.00e-02 2.50e+03 pdb=" N1 A 11767 " -0.002 2.00e-02 2.50e+03 pdb=" C2 A 11767 " 0.002 2.00e-02 2.50e+03 pdb=" N3 A 11767 " 0.007 2.00e-02 2.50e+03 pdb=" C4 A 11767 " 0.005 2.00e-02 2.50e+03 ... (remaining 11171 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 936 2.57 - 3.15: 95724 3.15 - 3.74: 244305 3.74 - 4.32: 353778 4.32 - 4.90: 484574 Nonbonded interactions: 1179317 Sorted by model distance: nonbonded pdb=" O2' G 12653 " pdb=" O6 G 12662 " model vdw 1.991 2.440 nonbonded pdb=" O2' A 11116 " pdb=" O2' U 11137 " model vdw 2.113 2.440 nonbonded pdb=" O2' U 21222 " pdb=" OG1 THR l 37 " model vdw 2.114 2.440 nonbonded pdb=" O THR B 88 " pdb=" ND2 ASN B 197 " model vdw 2.121 2.520 nonbonded pdb=" O2' A 2 710 " pdb=" OP2 U 2 712 " model vdw 2.142 2.440 ... (remaining 1179312 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.640 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: 0.070 Extract box with map and model: 14.820 Check model and map are aligned: 1.440 Set scattering table: 0.900 Process input model: 433.580 Find NCS groups from input model: 2.690 Set up NCS constraints: 0.290 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: 0.010 Load rotamer database and sin/cos tables:11.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 466.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 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 : 0.002 0.090 144444 Z= 0.135 Angle : 0.482 10.691 216495 Z= 0.276 Chirality : 0.033 0.725 27962 Planarity : 0.003 0.041 11174 Dihedral : 22.853 179.933 81923 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.94 % Favored : 89.98 % Rotamer: Outliers : 2.15 % Allowed : 17.17 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.96 (0.10), residues: 5180 helix: -1.83 (0.12), residues: 1480 sheet: -2.39 (0.14), residues: 1025 loop : -3.25 (0.09), residues: 2675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP h 22 HIS 0.013 0.001 HIS y 65 PHE 0.011 0.001 PHE x 74 TYR 0.011 0.001 TYR h 129 ARG 0.006 0.000 ARG s 69 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10360 Ramachandran restraints generated. 5180 Oldfield, 0 Emsley, 5180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10360 Ramachandran restraints generated. 5180 Oldfield, 0 Emsley, 5180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1211 residues out of total 4485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 1126 time to evaluate : 5.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 163 GLN cc_start: 0.7989 (mt0) cc_final: 0.7605 (mt0) REVERT: B 165 MET cc_start: 0.7758 (mmm) cc_final: 0.7543 (mmp) REVERT: C 81 GLU cc_start: 0.7747 (tt0) cc_final: 0.7536 (tt0) REVERT: L 104 ASN cc_start: 0.8960 (m-40) cc_final: 0.8684 (m110) REVERT: O 33 ARG cc_start: 0.9077 (OUTLIER) cc_final: 0.8572 (ttp-170) REVERT: Q 111 ASN cc_start: 0.8359 (m-40) cc_final: 0.8144 (m-40) REVERT: V 108 ILE cc_start: 0.7985 (mm) cc_final: 0.7687 (mm) REVERT: Z 10 ARG cc_start: 0.7457 (mtp180) cc_final: 0.7221 (mtp85) REVERT: b 10 LYS cc_start: 0.7816 (ptpp) cc_final: 0.7560 (ptpp) REVERT: h 87 LYS cc_start: 0.5866 (mmmt) cc_final: 0.5165 (mtpt) REVERT: i 60 TYR cc_start: 0.7285 (m-80) cc_final: 0.7060 (m-80) REVERT: j 37 PHE cc_start: 0.7161 (m-80) cc_final: 0.6463 (m-80) REVERT: j 172 LYS cc_start: 0.6979 (mmpt) cc_final: 0.6713 (mmtm) REVERT: l 153 PHE cc_start: 0.7598 (m-10) cc_final: 0.7384 (m-10) REVERT: o 7 ILE cc_start: 0.4997 (OUTLIER) cc_final: 0.4688 (pt) REVERT: o 47 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.7840 (tt) REVERT: p 55 LYS cc_start: 0.8414 (mtmt) cc_final: 0.8192 (mttt) REVERT: q 26 SER cc_start: 0.8949 (p) cc_final: 0.8733 (t) REVERT: r 45 ILE cc_start: 0.6568 (tp) cc_final: 0.6202 (tt) REVERT: w 83 ARG cc_start: 0.8701 (OUTLIER) cc_final: 0.7962 (mtp180) REVERT: y 67 ASN cc_start: 0.7728 (m-40) cc_final: 0.7328 (m110) REVERT: y 71 ASN cc_start: 0.7718 (m-40) cc_final: 0.7483 (m110) outliers start: 85 outliers final: 23 residues processed: 1187 average time/residue: 1.9286 time to fit residues: 3278.7571 Evaluate side-chains 897 residues out of total 4485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 870 time to evaluate : 5.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 130 ASN Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 75 SER Chi-restraints excluded: chain O residue 33 ARG Chi-restraints excluded: chain U residue 44 VAL Chi-restraints excluded: chain V residue 95 PHE Chi-restraints excluded: chain W residue 81 ILE Chi-restraints excluded: chain Y residue 41 LEU Chi-restraints excluded: chain d residue 41 HIS Chi-restraints excluded: chain d residue 43 LEU Chi-restraints excluded: chain h residue 46 LEU Chi-restraints excluded: chain h residue 69 THR Chi-restraints excluded: chain h residue 90 LEU Chi-restraints excluded: chain i residue 126 VAL Chi-restraints excluded: chain j residue 134 GLN Chi-restraints excluded: chain l residue 23 THR Chi-restraints excluded: chain l residue 29 LEU Chi-restraints excluded: chain l residue 31 TRP Chi-restraints excluded: chain n residue 39 THR Chi-restraints excluded: chain o residue 7 ILE Chi-restraints excluded: chain o residue 47 LEU Chi-restraints excluded: chain q residue 73 ASN Chi-restraints excluded: chain w residue 83 ARG Chi-restraints excluded: chain z residue 58 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 942 random chunks: chunk 795 optimal weight: 0.5980 chunk 713 optimal weight: 3.9990 chunk 396 optimal weight: 10.0000 chunk 243 optimal weight: 30.0000 chunk 481 optimal weight: 10.0000 chunk 381 optimal weight: 10.0000 chunk 738 optimal weight: 9.9990 chunk 285 optimal weight: 10.0000 chunk 448 optimal weight: 10.0000 chunk 549 optimal weight: 10.0000 chunk 855 optimal weight: 0.0670 overall best weight: 4.9326 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 GLN B 46 GLN C 40 ASN C 59 HIS C 109 GLN C 118 GLN C 131 GLN C 136 GLN C 137 HIS D 29 ASN D 49 HIS D 80 ASN E 30 GLN E 138 GLN F 35 GLN F 111 ASN F 146 GLN ** G 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 117 ASN K 82 ASN L 130 HIS M 22 GLN M 38 HIS M 125 GLN N 102 ASN N 119 ASN O 10 GLN O 41 GLN P 78 ASN P 88 ASN R 95 GLN S 73 ASN S 74 ASN U 67 GLN V 40 HIS V 58 HIS V 78 GLN V 88 HIS V 93 GLN W 29 GLN W 40 GLN X 20 HIS X 23 ASN X 62 ASN Z 19 GLN b 3 HIS b 19 HIS b 26 GLN c 36 ASN ** c 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 17 HIS e 51 HIS i 51 GLN i 68 GLN ** i 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 128 ASN i 185 GLN i 193 GLN j 25 ASN j 89 HIS j 91 GLN j 127 HIS j 134 GLN j 157 HIS k 2 ASN k 11 ASN k 18 GLN k 53 GLN l 20 GLN l 88 GLN l 114 ASN m 21 HIS n 5 HIS n 25 ASN o 55 HIS p 34 ASN p 100 ASN q 5 GLN q 14 GLN q 46 ASN q 72 HIS r 8 ASN r 100 GLN s 37 GLN s 50 ASN s 78 ASN u 62 GLN u 83 HIS v 54 ASN w 74 GLN w 86 HIS y 24 GLN y 25 HIS y 65 HIS y 79 HIS Total number of N/Q/H flips: 92 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.1321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 144444 Z= 0.308 Angle : 0.573 10.624 216495 Z= 0.295 Chirality : 0.035 0.303 27962 Planarity : 0.004 0.052 11174 Dihedral : 23.130 179.918 72722 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.89 % Favored : 89.05 % Rotamer: Outliers : 6.09 % Allowed : 23.01 % Favored : 70.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.29 (0.10), residues: 5180 helix: -1.17 (0.13), residues: 1500 sheet: -2.05 (0.15), residues: 983 loop : -2.90 (0.10), residues: 2697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP l 64 HIS 0.012 0.001 HIS k 96 PHE 0.019 0.002 PHE 4 33 TYR 0.017 0.002 TYR m 2 ARG 0.015 0.001 ARG K 71 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10360 Ramachandran restraints generated. 5180 Oldfield, 0 Emsley, 5180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10360 Ramachandran restraints generated. 5180 Oldfield, 0 Emsley, 5180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1124 residues out of total 4485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 241 poor density : 883 time to evaluate : 5.693 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 44 GLN cc_start: 0.8303 (OUTLIER) cc_final: 0.7945 (mm110) REVERT: E 66 GLN cc_start: 0.8641 (OUTLIER) cc_final: 0.8410 (tt0) REVERT: E 136 ARG cc_start: 0.6427 (OUTLIER) cc_final: 0.5806 (mpp80) REVERT: J 42 ARG cc_start: 0.8420 (OUTLIER) cc_final: 0.7951 (tpt170) REVERT: L 56 MET cc_start: 0.7809 (mmt) cc_final: 0.7484 (mmt) REVERT: L 104 ASN cc_start: 0.9047 (m-40) cc_final: 0.8790 (m110) REVERT: P 73 ARG cc_start: 0.8137 (mtt-85) cc_final: 0.7936 (mmm160) REVERT: V 108 ILE cc_start: 0.8012 (mm) cc_final: 0.7763 (mm) REVERT: V 131 LYS cc_start: 0.8757 (ttmm) cc_final: 0.7555 (pmtt) REVERT: W 68 LYS cc_start: 0.8446 (OUTLIER) cc_final: 0.8224 (ttmm) REVERT: X 70 LYS cc_start: 0.8334 (OUTLIER) cc_final: 0.7865 (ttpt) REVERT: a 3 LYS cc_start: 0.7722 (OUTLIER) cc_final: 0.7485 (ptpt) REVERT: c 20 SER cc_start: 0.7742 (OUTLIER) cc_final: 0.7308 (t) REVERT: e 30 SER cc_start: 0.8324 (OUTLIER) cc_final: 0.8091 (t) REVERT: e 61 GLN cc_start: 0.8359 (OUTLIER) cc_final: 0.8013 (mt0) REVERT: f 8 LYS cc_start: 0.8442 (OUTLIER) cc_final: 0.7889 (mtmt) REVERT: h 87 LYS cc_start: 0.5922 (mmmt) cc_final: 0.5225 (mtpt) REVERT: h 129 TYR cc_start: 0.4644 (OUTLIER) cc_final: 0.1927 (t80) REVERT: h 195 MET cc_start: 0.7376 (ttm) cc_final: 0.7126 (ttm) REVERT: j 56 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8438 (tp) REVERT: l 30 MET cc_start: 0.8169 (mtp) cc_final: 0.7896 (mtt) REVERT: l 122 LEU cc_start: 0.8196 (tm) cc_final: 0.7934 (tp) REVERT: l 137 VAL cc_start: 0.8583 (OUTLIER) cc_final: 0.8380 (t) REVERT: l 153 PHE cc_start: 0.7684 (m-10) cc_final: 0.7404 (m-10) REVERT: m 20 ASN cc_start: 0.8564 (OUTLIER) cc_final: 0.8286 (m-40) REVERT: n 7 ILE cc_start: 0.7902 (mp) cc_final: 0.7486 (mt) REVERT: n 102 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8087 (pp) REVERT: o 47 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.7877 (tt) REVERT: q 29 GLN cc_start: 0.8769 (mp10) cc_final: 0.8511 (mp10) REVERT: r 45 ILE cc_start: 0.6540 (tp) cc_final: 0.6154 (tt) REVERT: s 19 LYS cc_start: 0.6847 (ptpt) cc_final: 0.6599 (ptpt) REVERT: w 83 ARG cc_start: 0.8777 (OUTLIER) cc_final: 0.8050 (mtp180) REVERT: y 67 ASN cc_start: 0.7912 (m-40) cc_final: 0.7337 (m110) REVERT: y 71 ASN cc_start: 0.7767 (m-40) cc_final: 0.7533 (m110) REVERT: y 76 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8218 (mm) outliers start: 241 outliers final: 127 residues processed: 1015 average time/residue: 1.7546 time to fit residues: 2630.0455 Evaluate side-chains 956 residues out of total 4485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 810 time to evaluate : 5.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 103 TYR Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain E residue 66 GLN Chi-restraints excluded: chain E residue 67 LYS Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 130 ASN Chi-restraints excluded: chain E residue 136 ARG Chi-restraints excluded: chain F residue 4 ILE Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 39 ASP Chi-restraints excluded: chain F residue 133 ILE Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 15 THR Chi-restraints excluded: chain J residue 35 SER Chi-restraints excluded: chain J residue 42 ARG Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 115 VAL Chi-restraints excluded: chain L residue 46 SER Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain M residue 122 LEU Chi-restraints excluded: chain M residue 134 VAL Chi-restraints excluded: chain N residue 14 THR Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 55 SER Chi-restraints excluded: chain N residue 109 ASP Chi-restraints excluded: chain O residue 3 LEU Chi-restraints excluded: chain O residue 19 THR Chi-restraints excluded: chain O residue 55 SER Chi-restraints excluded: chain O residue 65 THR Chi-restraints excluded: chain O residue 104 SER Chi-restraints excluded: chain P residue 61 THR Chi-restraints excluded: chain Q residue 7 SER Chi-restraints excluded: chain Q residue 77 SER Chi-restraints excluded: chain Q residue 113 VAL Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 48 THR Chi-restraints excluded: chain R residue 67 LEU Chi-restraints excluded: chain S residue 46 VAL Chi-restraints excluded: chain S residue 63 LYS Chi-restraints excluded: chain S residue 105 LEU Chi-restraints excluded: chain T residue 17 SER Chi-restraints excluded: chain T residue 89 THR Chi-restraints excluded: chain U residue 2 ILE Chi-restraints excluded: chain U residue 44 VAL Chi-restraints excluded: chain U residue 65 SER Chi-restraints excluded: chain U residue 97 SER Chi-restraints excluded: chain V residue 3 SER Chi-restraints excluded: chain V residue 95 PHE Chi-restraints excluded: chain W residue 55 LYS Chi-restraints excluded: chain W residue 68 LYS Chi-restraints excluded: chain W residue 77 SER Chi-restraints excluded: chain W residue 81 ILE Chi-restraints excluded: chain X residue 4 VAL Chi-restraints excluded: chain X residue 70 LYS Chi-restraints excluded: chain Y residue 41 LEU Chi-restraints excluded: chain Y residue 45 SER Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain 4 residue 23 VAL Chi-restraints excluded: chain 4 residue 28 THR Chi-restraints excluded: chain 4 residue 34 VAL Chi-restraints excluded: chain a residue 3 LYS Chi-restraints excluded: chain a residue 29 THR Chi-restraints excluded: chain b residue 27 ILE Chi-restraints excluded: chain c residue 20 SER Chi-restraints excluded: chain d residue 2 SER Chi-restraints excluded: chain d residue 43 LEU Chi-restraints excluded: chain d residue 46 SER Chi-restraints excluded: chain e residue 8 SER Chi-restraints excluded: chain e residue 9 SER Chi-restraints excluded: chain e residue 30 SER Chi-restraints excluded: chain e residue 61 GLN Chi-restraints excluded: chain f residue 8 LYS Chi-restraints excluded: chain h residue 46 LEU Chi-restraints excluded: chain h residue 69 THR Chi-restraints excluded: chain h residue 90 LEU Chi-restraints excluded: chain h residue 115 VAL Chi-restraints excluded: chain h residue 129 TYR Chi-restraints excluded: chain h residue 148 ILE Chi-restraints excluded: chain h residue 151 LEU Chi-restraints excluded: chain h residue 206 VAL Chi-restraints excluded: chain i residue 53 MET Chi-restraints excluded: chain i residue 126 VAL Chi-restraints excluded: chain j residue 56 LEU Chi-restraints excluded: chain j residue 78 VAL Chi-restraints excluded: chain j residue 106 SER Chi-restraints excluded: chain j residue 111 VAL Chi-restraints excluded: chain j residue 133 SER Chi-restraints excluded: chain j residue 134 GLN Chi-restraints excluded: chain j residue 165 VAL Chi-restraints excluded: chain k residue 7 VAL Chi-restraints excluded: chain k residue 31 THR Chi-restraints excluded: chain l residue 2 ARG Chi-restraints excluded: chain l residue 29 LEU Chi-restraints excluded: chain l residue 31 TRP Chi-restraints excluded: chain l residue 41 VAL Chi-restraints excluded: chain l residue 71 VAL Chi-restraints excluded: chain l residue 137 VAL Chi-restraints excluded: chain m residue 20 ASN Chi-restraints excluded: chain m residue 63 LEU Chi-restraints excluded: chain m residue 107 SER Chi-restraints excluded: chain n residue 4 ILE Chi-restraints excluded: chain n residue 47 LEU Chi-restraints excluded: chain n residue 102 LEU Chi-restraints excluded: chain o residue 47 LEU Chi-restraints excluded: chain p residue 22 SER Chi-restraints excluded: chain q residue 19 SER Chi-restraints excluded: chain q residue 22 VAL Chi-restraints excluded: chain q residue 73 ASN Chi-restraints excluded: chain q residue 104 THR Chi-restraints excluded: chain r residue 19 LEU Chi-restraints excluded: chain r residue 25 VAL Chi-restraints excluded: chain r residue 56 LEU Chi-restraints excluded: chain r residue 97 VAL Chi-restraints excluded: chain r residue 108 THR Chi-restraints excluded: chain s residue 46 VAL Chi-restraints excluded: chain t residue 33 TYR Chi-restraints excluded: chain v residue 32 VAL Chi-restraints excluded: chain v residue 53 THR Chi-restraints excluded: chain v residue 65 SER Chi-restraints excluded: chain w residue 83 ARG Chi-restraints excluded: chain w residue 90 MET Chi-restraints excluded: chain x residue 5 LEU Chi-restraints excluded: chain x residue 39 MET Chi-restraints excluded: chain y residue 36 ARG Chi-restraints excluded: chain y residue 70 SER Chi-restraints excluded: chain y residue 76 LEU Chi-restraints excluded: chain y residue 78 LYS Chi-restraints excluded: chain z residue 58 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 942 random chunks: chunk 475 optimal weight: 10.0000 chunk 265 optimal weight: 8.9990 chunk 711 optimal weight: 10.0000 chunk 582 optimal weight: 10.0000 chunk 235 optimal weight: 10.0000 chunk 856 optimal weight: 7.9990 chunk 925 optimal weight: 7.9990 chunk 763 optimal weight: 20.0000 chunk 849 optimal weight: 0.7980 chunk 292 optimal weight: 8.9990 chunk 687 optimal weight: 20.0000 overall best weight: 6.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 58 HIS C 40 ASN C 67 HIS C 136 GLN ** D 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 206 ASN E 27 ASN G 33 GLN K 4 GLN M 38 HIS N 119 ASN P 78 ASN Q 56 ASN V 58 HIS W 29 GLN X 20 HIS Z 52 HIS c 47 ASN c 56 HIS i 68 GLN ** i 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 128 ASN j 25 ASN j 91 GLN k 2 ASN k 18 GLN k 53 GLN n 5 HIS n 25 ASN o 14 HIS p 34 ASN p 100 ASN ** p 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 14 HIS r 91 HIS s 78 ASN u 62 GLN x 28 ASN y 24 GLN y 65 HIS Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.104 144444 Z= 0.423 Angle : 0.675 11.670 216495 Z= 0.348 Chirality : 0.041 0.343 27962 Planarity : 0.005 0.059 11174 Dihedral : 23.154 179.792 72710 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.10 % Allowed : 11.58 % Favored : 88.32 % Rotamer: Outliers : 8.45 % Allowed : 23.11 % Favored : 68.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.99 (0.11), residues: 5180 helix: -0.97 (0.13), residues: 1516 sheet: -1.80 (0.16), residues: 965 loop : -2.73 (0.10), residues: 2699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP l 64 HIS 0.008 0.002 HIS y 65 PHE 0.025 0.002 PHE 4 33 TYR 0.021 0.002 TYR m 130 ARG 0.010 0.001 ARG i 101 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10360 Ramachandran restraints generated. 5180 Oldfield, 0 Emsley, 5180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10360 Ramachandran restraints generated. 5180 Oldfield, 0 Emsley, 5180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1170 residues out of total 4485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 334 poor density : 836 time to evaluate : 5.839 Fit side-chains revert: symmetry clash REVERT: B 116 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8421 (pp) REVERT: B 229 ASP cc_start: 0.7133 (m-30) cc_final: 0.6878 (m-30) REVERT: C 70 LYS cc_start: 0.8600 (mtpm) cc_final: 0.8383 (mmtm) REVERT: C 157 LYS cc_start: 0.8797 (OUTLIER) cc_final: 0.8478 (mttp) REVERT: D 44 GLN cc_start: 0.8339 (OUTLIER) cc_final: 0.7932 (mm110) REVERT: E 23 PHE cc_start: 0.8199 (OUTLIER) cc_final: 0.7633 (t80) REVERT: E 66 GLN cc_start: 0.8603 (OUTLIER) cc_final: 0.8365 (tt0) REVERT: E 143 GLU cc_start: 0.7389 (OUTLIER) cc_final: 0.7091 (mt-10) REVERT: J 42 ARG cc_start: 0.8584 (OUTLIER) cc_final: 0.7617 (tpt170) REVERT: L 56 MET cc_start: 0.7911 (mmt) cc_final: 0.7647 (mmt) REVERT: L 104 ASN cc_start: 0.9094 (m-40) cc_final: 0.8854 (m110) REVERT: M 69 LYS cc_start: 0.8798 (OUTLIER) cc_final: 0.7980 (mmpt) REVERT: P 73 ARG cc_start: 0.8202 (mtt-85) cc_final: 0.8002 (mmm160) REVERT: P 114 LYS cc_start: 0.8229 (OUTLIER) cc_final: 0.7841 (ttmm) REVERT: V 131 LYS cc_start: 0.8746 (ttmm) cc_final: 0.7611 (pmtt) REVERT: W 68 LYS cc_start: 0.8470 (OUTLIER) cc_final: 0.8202 (ttmm) REVERT: W 70 GLN cc_start: 0.7983 (tm-30) cc_final: 0.7777 (tm-30) REVERT: X 70 LYS cc_start: 0.8390 (OUTLIER) cc_final: 0.7906 (ttpt) REVERT: a 3 LYS cc_start: 0.7779 (OUTLIER) cc_final: 0.7449 (ptpt) REVERT: a 43 TYR cc_start: 0.7267 (OUTLIER) cc_final: 0.6865 (p90) REVERT: c 20 SER cc_start: 0.8020 (OUTLIER) cc_final: 0.7486 (t) REVERT: e 61 GLN cc_start: 0.8403 (OUTLIER) cc_final: 0.8027 (mt0) REVERT: h 87 LYS cc_start: 0.6015 (mmmt) cc_final: 0.5384 (mtpt) REVERT: h 129 TYR cc_start: 0.5464 (OUTLIER) cc_final: 0.2593 (t80) REVERT: h 141 MET cc_start: 0.6866 (tpp) cc_final: 0.6559 (tpt) REVERT: h 156 LEU cc_start: 0.7729 (mt) cc_final: 0.7308 (mp) REVERT: h 202 MET cc_start: 0.7592 (OUTLIER) cc_final: 0.7226 (tpt) REVERT: i 66 GLU cc_start: 0.7282 (OUTLIER) cc_final: 0.6977 (tt0) REVERT: i 67 LYS cc_start: 0.8209 (OUTLIER) cc_final: 0.7518 (ttmt) REVERT: i 74 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7137 (mp0) REVERT: j 56 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8510 (tp) REVERT: l 30 MET cc_start: 0.8206 (mtp) cc_final: 0.7972 (mtt) REVERT: l 89 ILE cc_start: 0.8831 (OUTLIER) cc_final: 0.8626 (tt) REVERT: l 116 LYS cc_start: 0.7862 (OUTLIER) cc_final: 0.6619 (tppt) REVERT: l 122 LEU cc_start: 0.8365 (tm) cc_final: 0.8108 (tp) REVERT: l 153 PHE cc_start: 0.7805 (m-10) cc_final: 0.7556 (m-10) REVERT: m 20 ASN cc_start: 0.8612 (OUTLIER) cc_final: 0.8356 (m-40) REVERT: m 71 GLU cc_start: 0.7551 (OUTLIER) cc_final: 0.7004 (tm-30) REVERT: n 7 ILE cc_start: 0.7963 (mp) cc_final: 0.7524 (mt) REVERT: n 102 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8162 (pp) REVERT: o 47 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.7932 (tt) REVERT: q 29 GLN cc_start: 0.8878 (mp10) cc_final: 0.8674 (mp10) REVERT: q 51 LYS cc_start: 0.7814 (OUTLIER) cc_final: 0.6671 (mttt) REVERT: r 45 ILE cc_start: 0.6647 (tp) cc_final: 0.6282 (tt) REVERT: v 6 ASN cc_start: 0.8058 (m-40) cc_final: 0.7692 (m110) REVERT: w 83 ARG cc_start: 0.8818 (OUTLIER) cc_final: 0.8043 (mtp180) REVERT: y 67 ASN cc_start: 0.8022 (m-40) cc_final: 0.7557 (m-40) REVERT: y 71 ASN cc_start: 0.7793 (m-40) cc_final: 0.7509 (m110) outliers start: 334 outliers final: 176 residues processed: 1029 average time/residue: 1.7821 time to fit residues: 2720.0046 Evaluate side-chains 1011 residues out of total 4485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 205 poor density : 806 time to evaluate : 5.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 103 TYR Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 56 ASN Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 153 SER Chi-restraints excluded: chain C residue 157 LYS Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain E residue 23 PHE Chi-restraints excluded: chain E residue 27 ASN Chi-restraints excluded: chain E residue 29 MET Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 66 GLN Chi-restraints excluded: chain E residue 67 LYS Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 104 GLU Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 130 ASN Chi-restraints excluded: chain E residue 143 GLU Chi-restraints excluded: chain F residue 4 ILE Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 39 ASP Chi-restraints excluded: chain F residue 79 SER Chi-restraints excluded: chain F residue 109 SER Chi-restraints excluded: chain F residue 133 ILE Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 15 THR Chi-restraints excluded: chain J residue 35 SER Chi-restraints excluded: chain J residue 42 ARG Chi-restraints excluded: chain J residue 58 ASN Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 117 ASN Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 115 VAL Chi-restraints excluded: chain L residue 46 SER Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain L residue 95 SER Chi-restraints excluded: chain L residue 148 VAL Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 69 LYS Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain M residue 122 LEU Chi-restraints excluded: chain M residue 134 VAL Chi-restraints excluded: chain N residue 14 THR Chi-restraints excluded: chain N residue 55 SER Chi-restraints excluded: chain N residue 60 THR Chi-restraints excluded: chain N residue 78 ASP Chi-restraints excluded: chain O residue 4 THR Chi-restraints excluded: chain O residue 19 THR Chi-restraints excluded: chain O residue 55 SER Chi-restraints excluded: chain O residue 65 THR Chi-restraints excluded: chain O residue 114 LEU Chi-restraints excluded: chain P residue 61 THR Chi-restraints excluded: chain P residue 85 ILE Chi-restraints excluded: chain P residue 114 LYS Chi-restraints excluded: chain Q residue 77 SER Chi-restraints excluded: chain Q residue 83 VAL Chi-restraints excluded: chain Q residue 113 VAL Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 48 THR Chi-restraints excluded: chain R residue 67 LEU Chi-restraints excluded: chain S residue 34 MET Chi-restraints excluded: chain S residue 94 ILE Chi-restraints excluded: chain S residue 124 THR Chi-restraints excluded: chain T residue 13 VAL Chi-restraints excluded: chain T residue 47 THR Chi-restraints excluded: chain T residue 77 ILE Chi-restraints excluded: chain T residue 89 THR Chi-restraints excluded: chain U residue 2 ILE Chi-restraints excluded: chain U residue 44 VAL Chi-restraints excluded: chain U residue 65 SER Chi-restraints excluded: chain U residue 97 SER Chi-restraints excluded: chain V residue 3 SER Chi-restraints excluded: chain V residue 14 VAL Chi-restraints excluded: chain V residue 77 ILE Chi-restraints excluded: chain V residue 95 PHE Chi-restraints excluded: chain V residue 102 MET Chi-restraints excluded: chain W residue 55 LYS Chi-restraints excluded: chain W residue 68 LYS Chi-restraints excluded: chain W residue 77 SER Chi-restraints excluded: chain W residue 81 ILE Chi-restraints excluded: chain X residue 4 VAL Chi-restraints excluded: chain X residue 70 LYS Chi-restraints excluded: chain Y residue 41 LEU Chi-restraints excluded: chain Y residue 45 SER Chi-restraints excluded: chain Z residue 6 VAL Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain 4 residue 22 MET Chi-restraints excluded: chain 4 residue 34 VAL Chi-restraints excluded: chain a residue 3 LYS Chi-restraints excluded: chain a residue 29 THR Chi-restraints excluded: chain a residue 43 TYR Chi-restraints excluded: chain b residue 27 ILE Chi-restraints excluded: chain c residue 20 SER Chi-restraints excluded: chain c residue 31 THR Chi-restraints excluded: chain d residue 2 SER Chi-restraints excluded: chain d residue 42 LYS Chi-restraints excluded: chain d residue 43 LEU Chi-restraints excluded: chain d residue 46 SER Chi-restraints excluded: chain e residue 8 SER Chi-restraints excluded: chain e residue 9 SER Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 42 LEU Chi-restraints excluded: chain e residue 61 GLN Chi-restraints excluded: chain f residue 1 MET Chi-restraints excluded: chain h residue 5 THR Chi-restraints excluded: chain h residue 46 LEU Chi-restraints excluded: chain h residue 69 THR Chi-restraints excluded: chain h residue 90 LEU Chi-restraints excluded: chain h residue 129 TYR Chi-restraints excluded: chain h residue 148 ILE Chi-restraints excluded: chain h residue 202 MET Chi-restraints excluded: chain h residue 206 VAL Chi-restraints excluded: chain i residue 19 ILE Chi-restraints excluded: chain i residue 66 GLU Chi-restraints excluded: chain i residue 67 LYS Chi-restraints excluded: chain i residue 74 GLU Chi-restraints excluded: chain i residue 126 VAL Chi-restraints excluded: chain j residue 45 VAL Chi-restraints excluded: chain j residue 56 LEU Chi-restraints excluded: chain j residue 78 VAL Chi-restraints excluded: chain j residue 106 SER Chi-restraints excluded: chain j residue 111 VAL Chi-restraints excluded: chain j residue 133 SER Chi-restraints excluded: chain j residue 134 GLN Chi-restraints excluded: chain j residue 165 VAL Chi-restraints excluded: chain k residue 3 HIS Chi-restraints excluded: chain k residue 7 VAL Chi-restraints excluded: chain k residue 31 THR Chi-restraints excluded: chain k residue 39 SER Chi-restraints excluded: chain k residue 45 LEU Chi-restraints excluded: chain k residue 72 LEU Chi-restraints excluded: chain k residue 79 PHE Chi-restraints excluded: chain l residue 23 THR Chi-restraints excluded: chain l residue 29 LEU Chi-restraints excluded: chain l residue 31 TRP Chi-restraints excluded: chain l residue 41 VAL Chi-restraints excluded: chain l residue 71 VAL Chi-restraints excluded: chain l residue 89 ILE Chi-restraints excluded: chain l residue 116 LYS Chi-restraints excluded: chain m residue 20 ASN Chi-restraints excluded: chain m residue 71 GLU Chi-restraints excluded: chain m residue 107 SER Chi-restraints excluded: chain m residue 112 LEU Chi-restraints excluded: chain n residue 4 ILE Chi-restraints excluded: chain n residue 39 THR Chi-restraints excluded: chain n residue 47 LEU Chi-restraints excluded: chain n residue 102 LEU Chi-restraints excluded: chain n residue 108 MET Chi-restraints excluded: chain o residue 47 LEU Chi-restraints excluded: chain p residue 22 SER Chi-restraints excluded: chain p residue 24 THR Chi-restraints excluded: chain p residue 31 SER Chi-restraints excluded: chain p residue 44 SER Chi-restraints excluded: chain p residue 95 ILE Chi-restraints excluded: chain p residue 105 VAL Chi-restraints excluded: chain p residue 106 THR Chi-restraints excluded: chain q residue 19 SER Chi-restraints excluded: chain q residue 22 VAL Chi-restraints excluded: chain q residue 51 LYS Chi-restraints excluded: chain q residue 73 ASN Chi-restraints excluded: chain q residue 102 LEU Chi-restraints excluded: chain r residue 19 LEU Chi-restraints excluded: chain r residue 25 VAL Chi-restraints excluded: chain r residue 97 VAL Chi-restraints excluded: chain r residue 108 THR Chi-restraints excluded: chain s residue 46 VAL Chi-restraints excluded: chain u residue 27 SER Chi-restraints excluded: chain u residue 85 LEU Chi-restraints excluded: chain v residue 27 SER Chi-restraints excluded: chain v residue 32 VAL Chi-restraints excluded: chain v residue 53 THR Chi-restraints excluded: chain v residue 57 ASN Chi-restraints excluded: chain v residue 65 SER Chi-restraints excluded: chain v residue 71 SER Chi-restraints excluded: chain w residue 79 VAL Chi-restraints excluded: chain w residue 83 ARG Chi-restraints excluded: chain w residue 87 LEU Chi-restraints excluded: chain x residue 5 LEU Chi-restraints excluded: chain x residue 39 MET Chi-restraints excluded: chain x residue 45 VAL Chi-restraints excluded: chain x residue 51 VAL Chi-restraints excluded: chain y residue 70 SER Chi-restraints excluded: chain y residue 78 LYS Chi-restraints excluded: chain z residue 3 ILE Chi-restraints excluded: chain z residue 58 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 942 random chunks: chunk 846 optimal weight: 30.0000 chunk 644 optimal weight: 10.0000 chunk 444 optimal weight: 7.9990 chunk 94 optimal weight: 10.0000 chunk 408 optimal weight: 8.9990 chunk 575 optimal weight: 10.0000 chunk 860 optimal weight: 0.9990 chunk 910 optimal weight: 20.0000 chunk 449 optimal weight: 10.0000 chunk 815 optimal weight: 8.9990 chunk 245 optimal weight: 3.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 ASN C 40 ASN C 83 GLN C 136 GLN D 80 ASN D 206 ASN E 27 ASN ** F 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 33 GLN K 4 GLN M 38 HIS N 119 ASN O 47 ASN Q 56 ASN S 26 ASN T 55 ASN V 58 HIS W 29 GLN X 20 HIS ** i 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 128 ASN k 11 ASN k 18 GLN l 70 ASN l 120 GLN n 5 HIS n 25 ASN p 100 ASN ** p 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 78 ASN u 61 HIS u 62 GLN y 24 GLN y 65 HIS Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 144444 Z= 0.374 Angle : 0.637 11.613 216495 Z= 0.329 Chirality : 0.040 0.333 27962 Planarity : 0.005 0.075 11174 Dihedral : 23.135 179.904 72710 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.70 % Favored : 88.24 % Rotamer: Outliers : 7.89 % Allowed : 25.08 % Favored : 67.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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 (0.11), residues: 5180 helix: -0.82 (0.13), residues: 1523 sheet: -1.63 (0.16), residues: 956 loop : -2.62 (0.10), residues: 2701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP x 34 HIS 0.011 0.001 HIS k 96 PHE 0.026 0.002 PHE 4 46 TYR 0.018 0.002 TYR u 76 ARG 0.009 0.001 ARG i 143 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10360 Ramachandran restraints generated. 5180 Oldfield, 0 Emsley, 5180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10360 Ramachandran restraints generated. 5180 Oldfield, 0 Emsley, 5180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1141 residues out of total 4485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 312 poor density : 829 time to evaluate : 5.643 Fit side-chains revert: symmetry clash REVERT: B 116 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8496 (pp) REVERT: B 229 ASP cc_start: 0.7116 (m-30) cc_final: 0.6855 (m-30) REVERT: C 157 LYS cc_start: 0.8822 (OUTLIER) cc_final: 0.8518 (mttp) REVERT: D 44 GLN cc_start: 0.8370 (OUTLIER) cc_final: 0.7969 (mm110) REVERT: E 23 PHE cc_start: 0.8120 (OUTLIER) cc_final: 0.7566 (t80) REVERT: E 66 GLN cc_start: 0.8681 (OUTLIER) cc_final: 0.8454 (tt0) REVERT: L 104 ASN cc_start: 0.9085 (m-40) cc_final: 0.8829 (m110) REVERT: M 69 LYS cc_start: 0.8739 (OUTLIER) cc_final: 0.7989 (mmpt) REVERT: V 20 LYS cc_start: 0.8710 (OUTLIER) cc_final: 0.8370 (mttt) REVERT: V 131 LYS cc_start: 0.8742 (ttmm) cc_final: 0.7625 (pmtt) REVERT: W 68 LYS cc_start: 0.8466 (OUTLIER) cc_final: 0.8204 (ttmm) REVERT: W 70 GLN cc_start: 0.7954 (tm-30) cc_final: 0.7683 (tm-30) REVERT: X 70 LYS cc_start: 0.8379 (OUTLIER) cc_final: 0.7958 (ttpt) REVERT: a 43 TYR cc_start: 0.7385 (OUTLIER) cc_final: 0.7057 (p90) REVERT: c 20 SER cc_start: 0.8054 (OUTLIER) cc_final: 0.7545 (t) REVERT: e 61 GLN cc_start: 0.8375 (OUTLIER) cc_final: 0.7994 (mt0) REVERT: h 129 TYR cc_start: 0.5438 (OUTLIER) cc_final: 0.2844 (t80) REVERT: h 165 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.6929 (mt-10) REVERT: h 202 MET cc_start: 0.7553 (tmm) cc_final: 0.7197 (tpt) REVERT: i 66 GLU cc_start: 0.7193 (OUTLIER) cc_final: 0.6904 (tt0) REVERT: i 67 LYS cc_start: 0.8174 (OUTLIER) cc_final: 0.7535 (ttmt) REVERT: j 56 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8527 (tp) REVERT: k 79 PHE cc_start: 0.8767 (OUTLIER) cc_final: 0.7666 (t80) REVERT: l 30 MET cc_start: 0.8263 (mtp) cc_final: 0.8000 (mtt) REVERT: l 89 ILE cc_start: 0.8839 (OUTLIER) cc_final: 0.8613 (mp) REVERT: l 122 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8185 (tp) REVERT: l 153 PHE cc_start: 0.7804 (m-10) cc_final: 0.7525 (m-10) REVERT: m 71 GLU cc_start: 0.7652 (OUTLIER) cc_final: 0.7101 (tm-30) REVERT: n 7 ILE cc_start: 0.8018 (mp) cc_final: 0.7637 (mt) REVERT: n 102 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8203 (pp) REVERT: o 47 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.7885 (tt) REVERT: r 45 ILE cc_start: 0.6774 (tp) cc_final: 0.6441 (tt) REVERT: v 6 ASN cc_start: 0.8184 (m-40) cc_final: 0.7858 (m-40) REVERT: w 83 ARG cc_start: 0.8808 (OUTLIER) cc_final: 0.7985 (mtp180) REVERT: y 67 ASN cc_start: 0.8091 (m-40) cc_final: 0.7640 (m-40) REVERT: y 71 ASN cc_start: 0.7742 (m-40) cc_final: 0.7461 (m110) outliers start: 312 outliers final: 190 residues processed: 1017 average time/residue: 1.7548 time to fit residues: 2639.2867 Evaluate side-chains 1008 residues out of total 4485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 214 poor density : 794 time to evaluate : 5.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 103 TYR Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 56 ASN Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 153 SER Chi-restraints excluded: chain C residue 157 LYS Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain E residue 23 PHE Chi-restraints excluded: chain E residue 27 ASN Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 66 GLN Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 130 ASN Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain F residue 4 ILE Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 39 ASP Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 79 SER Chi-restraints excluded: chain F residue 133 ILE Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 15 THR Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 35 SER Chi-restraints excluded: chain J residue 58 ASN Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 117 ASN Chi-restraints excluded: chain J residue 133 SER Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 115 VAL Chi-restraints excluded: chain L residue 46 SER Chi-restraints excluded: chain L residue 82 THR Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain L residue 148 VAL Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 31 MET Chi-restraints excluded: chain M residue 58 ARG Chi-restraints excluded: chain M residue 69 LYS Chi-restraints excluded: chain M residue 84 ARG Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain M residue 129 VAL Chi-restraints excluded: chain M residue 134 VAL Chi-restraints excluded: chain N residue 14 THR Chi-restraints excluded: chain N residue 55 SER Chi-restraints excluded: chain N residue 60 THR Chi-restraints excluded: chain N residue 114 GLU Chi-restraints excluded: chain O residue 19 THR Chi-restraints excluded: chain O residue 30 SER Chi-restraints excluded: chain O residue 65 THR Chi-restraints excluded: chain O residue 114 LEU Chi-restraints excluded: chain P residue 61 THR Chi-restraints excluded: chain Q residue 77 SER Chi-restraints excluded: chain Q residue 113 VAL Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 48 THR Chi-restraints excluded: chain R residue 67 LEU Chi-restraints excluded: chain S residue 7 GLU Chi-restraints excluded: chain S residue 34 MET Chi-restraints excluded: chain S residue 46 VAL Chi-restraints excluded: chain S residue 94 ILE Chi-restraints excluded: chain S residue 126 VAL Chi-restraints excluded: chain T residue 13 VAL Chi-restraints excluded: chain T residue 47 THR Chi-restraints excluded: chain T residue 49 VAL Chi-restraints excluded: chain T residue 77 ILE Chi-restraints excluded: chain T residue 89 THR Chi-restraints excluded: chain U residue 2 ILE Chi-restraints excluded: chain U residue 44 VAL Chi-restraints excluded: chain U residue 65 SER Chi-restraints excluded: chain U residue 69 SER Chi-restraints excluded: chain U residue 97 SER Chi-restraints excluded: chain V residue 3 SER Chi-restraints excluded: chain V residue 20 LYS Chi-restraints excluded: chain V residue 30 CYS Chi-restraints excluded: chain V residue 95 PHE Chi-restraints excluded: chain W residue 55 LYS Chi-restraints excluded: chain W residue 68 LYS Chi-restraints excluded: chain W residue 77 SER Chi-restraints excluded: chain W residue 81 ILE Chi-restraints excluded: chain X residue 4 VAL Chi-restraints excluded: chain X residue 68 LEU Chi-restraints excluded: chain X residue 70 LYS Chi-restraints excluded: chain Y residue 41 LEU Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain 4 residue 34 VAL Chi-restraints excluded: chain 4 residue 37 ILE Chi-restraints excluded: chain a residue 29 THR Chi-restraints excluded: chain a residue 43 TYR Chi-restraints excluded: chain b residue 27 ILE Chi-restraints excluded: chain c residue 20 SER Chi-restraints excluded: chain c residue 43 ILE Chi-restraints excluded: chain d residue 2 SER Chi-restraints excluded: chain d residue 42 LYS Chi-restraints excluded: chain d residue 43 LEU Chi-restraints excluded: chain d residue 46 SER Chi-restraints excluded: chain e residue 8 SER Chi-restraints excluded: chain e residue 9 SER Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 30 SER Chi-restraints excluded: chain e residue 42 LEU Chi-restraints excluded: chain e residue 61 GLN Chi-restraints excluded: chain h residue 5 THR Chi-restraints excluded: chain h residue 46 LEU Chi-restraints excluded: chain h residue 47 SER Chi-restraints excluded: chain h residue 69 THR Chi-restraints excluded: chain h residue 84 ASP Chi-restraints excluded: chain h residue 90 LEU Chi-restraints excluded: chain h residue 129 TYR Chi-restraints excluded: chain h residue 148 ILE Chi-restraints excluded: chain h residue 165 GLU Chi-restraints excluded: chain h residue 206 VAL Chi-restraints excluded: chain i residue 19 ILE Chi-restraints excluded: chain i residue 66 GLU Chi-restraints excluded: chain i residue 67 LYS Chi-restraints excluded: chain i residue 121 THR Chi-restraints excluded: chain i residue 126 VAL Chi-restraints excluded: chain i residue 167 THR Chi-restraints excluded: chain j residue 56 LEU Chi-restraints excluded: chain j residue 78 VAL Chi-restraints excluded: chain j residue 106 SER Chi-restraints excluded: chain j residue 111 VAL Chi-restraints excluded: chain j residue 133 SER Chi-restraints excluded: chain j residue 134 GLN Chi-restraints excluded: chain j residue 165 VAL Chi-restraints excluded: chain j residue 170 VAL Chi-restraints excluded: chain k residue 3 HIS Chi-restraints excluded: chain k residue 7 VAL Chi-restraints excluded: chain k residue 31 THR Chi-restraints excluded: chain k residue 39 SER Chi-restraints excluded: chain k residue 45 LEU Chi-restraints excluded: chain k residue 79 PHE Chi-restraints excluded: chain k residue 108 LEU Chi-restraints excluded: chain l residue 23 THR Chi-restraints excluded: chain l residue 29 LEU Chi-restraints excluded: chain l residue 31 TRP Chi-restraints excluded: chain l residue 41 VAL Chi-restraints excluded: chain l residue 71 VAL Chi-restraints excluded: chain l residue 89 ILE Chi-restraints excluded: chain l residue 122 LEU Chi-restraints excluded: chain m residue 58 SER Chi-restraints excluded: chain m residue 63 LEU Chi-restraints excluded: chain m residue 71 GLU Chi-restraints excluded: chain m residue 107 SER Chi-restraints excluded: chain n residue 4 ILE Chi-restraints excluded: chain n residue 39 THR Chi-restraints excluded: chain n residue 47 LEU Chi-restraints excluded: chain n residue 102 LEU Chi-restraints excluded: chain o residue 47 LEU Chi-restraints excluded: chain p residue 22 SER Chi-restraints excluded: chain p residue 24 THR Chi-restraints excluded: chain p residue 31 SER Chi-restraints excluded: chain p residue 44 SER Chi-restraints excluded: chain p residue 95 ILE Chi-restraints excluded: chain p residue 105 VAL Chi-restraints excluded: chain p residue 106 THR Chi-restraints excluded: chain q residue 18 LYS Chi-restraints excluded: chain q residue 19 SER Chi-restraints excluded: chain q residue 22 VAL Chi-restraints excluded: chain q residue 73 ASN Chi-restraints excluded: chain q residue 104 THR Chi-restraints excluded: chain r residue 19 LEU Chi-restraints excluded: chain r residue 25 VAL Chi-restraints excluded: chain r residue 97 VAL Chi-restraints excluded: chain r residue 108 THR Chi-restraints excluded: chain s residue 46 VAL Chi-restraints excluded: chain s residue 75 MET Chi-restraints excluded: chain t residue 33 TYR Chi-restraints excluded: chain t residue 36 SER Chi-restraints excluded: chain u residue 27 SER Chi-restraints excluded: chain u residue 30 ASP Chi-restraints excluded: chain u residue 51 LEU Chi-restraints excluded: chain u residue 85 LEU Chi-restraints excluded: chain v residue 27 SER Chi-restraints excluded: chain v residue 32 VAL Chi-restraints excluded: chain v residue 53 THR Chi-restraints excluded: chain v residue 65 SER Chi-restraints excluded: chain v residue 71 SER Chi-restraints excluded: chain w residue 55 VAL Chi-restraints excluded: chain w residue 83 ARG Chi-restraints excluded: chain w residue 87 LEU Chi-restraints excluded: chain w residue 89 LEU Chi-restraints excluded: chain w residue 90 MET Chi-restraints excluded: chain x residue 5 LEU Chi-restraints excluded: chain x residue 39 MET Chi-restraints excluded: chain x residue 45 VAL Chi-restraints excluded: chain y residue 50 THR Chi-restraints excluded: chain y residue 70 SER Chi-restraints excluded: chain y residue 78 LYS Chi-restraints excluded: chain z residue 58 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 942 random chunks: chunk 758 optimal weight: 0.9990 chunk 516 optimal weight: 10.0000 chunk 13 optimal weight: 0.9990 chunk 677 optimal weight: 20.0000 chunk 375 optimal weight: 7.9990 chunk 777 optimal weight: 9.9990 chunk 629 optimal weight: 10.0000 chunk 1 optimal weight: 0.9990 chunk 464 optimal weight: 10.0000 chunk 817 optimal weight: 20.0000 chunk 229 optimal weight: 7.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 40 ASN C 83 GLN C 136 GLN D 80 ASN E 27 ASN E 30 GLN ** F 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 33 GLN K 4 GLN M 38 HIS N 61 HIS N 119 ASN O 47 ASN P 10 ASN Q 56 ASN S 26 ASN V 58 HIS W 29 GLN X 20 HIS Z 19 GLN ** i 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 128 ASN j 138 ASN k 18 GLN l 70 ASN p 34 ASN p 100 ASN ** p 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 78 ASN u 41 ASN u 62 GLN x 69 HIS y 24 GLN y 65 HIS Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 144444 Z= 0.239 Angle : 0.569 11.911 216495 Z= 0.297 Chirality : 0.035 0.296 27962 Planarity : 0.004 0.077 11174 Dihedral : 23.105 179.527 72710 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.93 % Favored : 89.03 % Rotamer: Outliers : 7.23 % Allowed : 26.27 % Favored : 66.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.57 (0.11), residues: 5180 helix: -0.60 (0.13), residues: 1526 sheet: -1.47 (0.16), residues: 965 loop : -2.51 (0.10), residues: 2689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP x 34 HIS 0.010 0.001 HIS y 65 PHE 0.029 0.001 PHE 4 46 TYR 0.025 0.002 TYR h 183 ARG 0.010 0.000 ARG E 128 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10360 Ramachandran restraints generated. 5180 Oldfield, 0 Emsley, 5180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10360 Ramachandran restraints generated. 5180 Oldfield, 0 Emsley, 5180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1116 residues out of total 4485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 286 poor density : 830 time to evaluate : 5.647 Fit side-chains revert: symmetry clash REVERT: B 116 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8375 (pp) REVERT: B 229 ASP cc_start: 0.7116 (m-30) cc_final: 0.6851 (m-30) REVERT: C 157 LYS cc_start: 0.8790 (OUTLIER) cc_final: 0.8505 (mttm) REVERT: D 44 GLN cc_start: 0.8290 (OUTLIER) cc_final: 0.7925 (mm110) REVERT: E 23 PHE cc_start: 0.8063 (OUTLIER) cc_final: 0.7390 (t80) REVERT: E 66 GLN cc_start: 0.8614 (OUTLIER) cc_final: 0.8366 (tt0) REVERT: J 113 MET cc_start: 0.8665 (mtt) cc_final: 0.8303 (mtt) REVERT: L 104 ASN cc_start: 0.9067 (m-40) cc_final: 0.8812 (m110) REVERT: M 58 ARG cc_start: 0.7755 (OUTLIER) cc_final: 0.7135 (mtp180) REVERT: M 69 LYS cc_start: 0.8688 (OUTLIER) cc_final: 0.7858 (mmpt) REVERT: V 20 LYS cc_start: 0.8702 (OUTLIER) cc_final: 0.8339 (mttt) REVERT: V 131 LYS cc_start: 0.8770 (ttmm) cc_final: 0.7615 (pmtt) REVERT: X 70 LYS cc_start: 0.8426 (OUTLIER) cc_final: 0.7996 (ttpt) REVERT: a 3 LYS cc_start: 0.7737 (OUTLIER) cc_final: 0.7427 (ptpt) REVERT: c 20 SER cc_start: 0.8103 (OUTLIER) cc_final: 0.7650 (t) REVERT: e 61 GLN cc_start: 0.8301 (OUTLIER) cc_final: 0.7944 (mt0) REVERT: h 129 TYR cc_start: 0.5357 (OUTLIER) cc_final: 0.2704 (t80) REVERT: h 156 LEU cc_start: 0.7229 (mp) cc_final: 0.6510 (mt) REVERT: h 165 GLU cc_start: 0.7489 (OUTLIER) cc_final: 0.6885 (mt-10) REVERT: h 202 MET cc_start: 0.7583 (tmm) cc_final: 0.7290 (tpt) REVERT: i 66 GLU cc_start: 0.7231 (OUTLIER) cc_final: 0.6827 (tt0) REVERT: i 67 LYS cc_start: 0.8167 (OUTLIER) cc_final: 0.7579 (ttmt) REVERT: i 154 ARG cc_start: 0.7132 (OUTLIER) cc_final: 0.5877 (mtp85) REVERT: j 153 MET cc_start: 0.7775 (OUTLIER) cc_final: 0.7380 (mtt) REVERT: l 30 MET cc_start: 0.8208 (mtp) cc_final: 0.7973 (mtt) REVERT: l 89 ILE cc_start: 0.8765 (OUTLIER) cc_final: 0.8554 (mp) REVERT: l 122 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.8124 (tp) REVERT: l 153 PHE cc_start: 0.7760 (m-10) cc_final: 0.7494 (m-10) REVERT: m 71 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.7083 (tm-30) REVERT: n 7 ILE cc_start: 0.7913 (mp) cc_final: 0.7503 (mt) REVERT: n 102 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8190 (pp) REVERT: o 47 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7886 (tt) REVERT: r 17 ILE cc_start: 0.6720 (mt) cc_final: 0.6367 (mm) REVERT: r 45 ILE cc_start: 0.6795 (tp) cc_final: 0.6417 (tt) REVERT: s 19 LYS cc_start: 0.6654 (ptpt) cc_final: 0.6373 (ptpt) REVERT: v 6 ASN cc_start: 0.8057 (m-40) cc_final: 0.7707 (m-40) REVERT: w 83 ARG cc_start: 0.8770 (OUTLIER) cc_final: 0.6972 (mtp180) REVERT: x 36 ARG cc_start: 0.8457 (OUTLIER) cc_final: 0.8051 (ptm160) REVERT: y 67 ASN cc_start: 0.7903 (m-40) cc_final: 0.7457 (m-40) REVERT: y 71 ASN cc_start: 0.7726 (m-40) cc_final: 0.7449 (m110) REVERT: y 77 THR cc_start: 0.8929 (OUTLIER) cc_final: 0.8716 (t) outliers start: 286 outliers final: 168 residues processed: 1005 average time/residue: 1.7324 time to fit residues: 2567.1754 Evaluate side-chains 994 residues out of total 4485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 800 time to evaluate : 5.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 103 TYR Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 56 ASN Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 153 SER Chi-restraints excluded: chain C residue 157 LYS Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain E residue 23 PHE Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 66 GLN Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 130 ASN Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain F residue 4 ILE Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 79 SER Chi-restraints excluded: chain F residue 133 ILE Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 35 SER Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 133 SER Chi-restraints excluded: chain K residue 115 VAL Chi-restraints excluded: chain L residue 46 SER Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain L residue 148 VAL Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 58 ARG Chi-restraints excluded: chain M residue 69 LYS Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain M residue 134 VAL Chi-restraints excluded: chain N residue 55 SER Chi-restraints excluded: chain N residue 60 THR Chi-restraints excluded: chain N residue 114 GLU Chi-restraints excluded: chain O residue 4 THR Chi-restraints excluded: chain O residue 19 THR Chi-restraints excluded: chain O residue 30 SER Chi-restraints excluded: chain O residue 43 ILE Chi-restraints excluded: chain O residue 65 THR Chi-restraints excluded: chain P residue 61 THR Chi-restraints excluded: chain P residue 111 ILE Chi-restraints excluded: chain Q residue 77 SER Chi-restraints excluded: chain Q residue 113 VAL Chi-restraints excluded: chain R residue 4 ILE Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 48 THR Chi-restraints excluded: chain R residue 67 LEU Chi-restraints excluded: chain S residue 7 GLU Chi-restraints excluded: chain S residue 34 MET Chi-restraints excluded: chain S residue 46 VAL Chi-restraints excluded: chain S residue 94 ILE Chi-restraints excluded: chain T residue 13 VAL Chi-restraints excluded: chain T residue 49 VAL Chi-restraints excluded: chain T residue 89 THR Chi-restraints excluded: chain U residue 2 ILE Chi-restraints excluded: chain U residue 44 VAL Chi-restraints excluded: chain U residue 65 SER Chi-restraints excluded: chain U residue 69 SER Chi-restraints excluded: chain U residue 71 ILE Chi-restraints excluded: chain U residue 97 SER Chi-restraints excluded: chain V residue 3 SER Chi-restraints excluded: chain V residue 20 LYS Chi-restraints excluded: chain V residue 30 CYS Chi-restraints excluded: chain V residue 95 PHE Chi-restraints excluded: chain V residue 102 MET Chi-restraints excluded: chain W residue 55 LYS Chi-restraints excluded: chain W residue 77 SER Chi-restraints excluded: chain W residue 81 ILE Chi-restraints excluded: chain X residue 4 VAL Chi-restraints excluded: chain X residue 55 THR Chi-restraints excluded: chain X residue 68 LEU Chi-restraints excluded: chain X residue 70 LYS Chi-restraints excluded: chain Y residue 41 LEU Chi-restraints excluded: chain Y residue 45 SER Chi-restraints excluded: chain Z residue 6 VAL Chi-restraints excluded: chain 4 residue 34 VAL Chi-restraints excluded: chain 4 residue 37 ILE Chi-restraints excluded: chain 5 residue 18 LYS Chi-restraints excluded: chain a residue 3 LYS Chi-restraints excluded: chain a residue 29 THR Chi-restraints excluded: chain b residue 27 ILE Chi-restraints excluded: chain c residue 20 SER Chi-restraints excluded: chain c residue 31 THR Chi-restraints excluded: chain c residue 43 ILE Chi-restraints excluded: chain d residue 2 SER Chi-restraints excluded: chain d residue 25 SER Chi-restraints excluded: chain d residue 43 LEU Chi-restraints excluded: chain d residue 46 SER Chi-restraints excluded: chain e residue 8 SER Chi-restraints excluded: chain e residue 9 SER Chi-restraints excluded: chain e residue 30 SER Chi-restraints excluded: chain e residue 42 LEU Chi-restraints excluded: chain e residue 61 GLN Chi-restraints excluded: chain f residue 29 LYS Chi-restraints excluded: chain h residue 5 THR Chi-restraints excluded: chain h residue 46 LEU Chi-restraints excluded: chain h residue 90 LEU Chi-restraints excluded: chain h residue 98 VAL Chi-restraints excluded: chain h residue 129 TYR Chi-restraints excluded: chain h residue 165 GLU Chi-restraints excluded: chain h residue 206 VAL Chi-restraints excluded: chain i residue 19 ILE Chi-restraints excluded: chain i residue 66 GLU Chi-restraints excluded: chain i residue 67 LYS Chi-restraints excluded: chain i residue 121 THR Chi-restraints excluded: chain i residue 126 VAL Chi-restraints excluded: chain i residue 154 ARG Chi-restraints excluded: chain i residue 167 THR Chi-restraints excluded: chain j residue 78 VAL Chi-restraints excluded: chain j residue 111 VAL Chi-restraints excluded: chain j residue 133 SER Chi-restraints excluded: chain j residue 134 GLN Chi-restraints excluded: chain j residue 153 MET Chi-restraints excluded: chain j residue 165 VAL Chi-restraints excluded: chain k residue 3 HIS Chi-restraints excluded: chain k residue 7 VAL Chi-restraints excluded: chain k residue 31 THR Chi-restraints excluded: chain k residue 39 SER Chi-restraints excluded: chain k residue 72 LEU Chi-restraints excluded: chain l residue 8 LYS Chi-restraints excluded: chain l residue 23 THR Chi-restraints excluded: chain l residue 29 LEU Chi-restraints excluded: chain l residue 31 TRP Chi-restraints excluded: chain l residue 41 VAL Chi-restraints excluded: chain l residue 71 VAL Chi-restraints excluded: chain l residue 89 ILE Chi-restraints excluded: chain l residue 122 LEU Chi-restraints excluded: chain m residue 71 GLU Chi-restraints excluded: chain m residue 107 SER Chi-restraints excluded: chain n residue 4 ILE Chi-restraints excluded: chain n residue 39 THR Chi-restraints excluded: chain n residue 47 LEU Chi-restraints excluded: chain n residue 102 LEU Chi-restraints excluded: chain o residue 47 LEU Chi-restraints excluded: chain p residue 22 SER Chi-restraints excluded: chain p residue 24 THR Chi-restraints excluded: chain p residue 31 SER Chi-restraints excluded: chain p residue 95 ILE Chi-restraints excluded: chain p residue 106 THR Chi-restraints excluded: chain q residue 19 SER Chi-restraints excluded: chain q residue 22 VAL Chi-restraints excluded: chain q residue 73 ASN Chi-restraints excluded: chain q residue 104 THR Chi-restraints excluded: chain r residue 19 LEU Chi-restraints excluded: chain r residue 25 VAL Chi-restraints excluded: chain r residue 97 VAL Chi-restraints excluded: chain r residue 108 THR Chi-restraints excluded: chain t residue 36 SER Chi-restraints excluded: chain u residue 30 ASP Chi-restraints excluded: chain u residue 51 LEU Chi-restraints excluded: chain v residue 32 VAL Chi-restraints excluded: chain v residue 53 THR Chi-restraints excluded: chain v residue 71 SER Chi-restraints excluded: chain w residue 52 LEU Chi-restraints excluded: chain w residue 55 VAL Chi-restraints excluded: chain w residue 83 ARG Chi-restraints excluded: chain w residue 87 LEU Chi-restraints excluded: chain w residue 89 LEU Chi-restraints excluded: chain x residue 5 LEU Chi-restraints excluded: chain x residue 36 ARG Chi-restraints excluded: chain x residue 45 VAL Chi-restraints excluded: chain y residue 50 THR Chi-restraints excluded: chain y residue 70 SER Chi-restraints excluded: chain y residue 77 THR Chi-restraints excluded: chain z residue 58 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 942 random chunks: chunk 306 optimal weight: 20.0000 chunk 819 optimal weight: 1.9990 chunk 179 optimal weight: 0.3980 chunk 534 optimal weight: 10.0000 chunk 224 optimal weight: 0.8980 chunk 911 optimal weight: 5.9990 chunk 756 optimal weight: 9.9990 chunk 421 optimal weight: 10.0000 chunk 75 optimal weight: 0.8980 chunk 301 optimal weight: 10.0000 chunk 478 optimal weight: 8.9990 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 40 ASN C 83 GLN C 136 GLN C 174 ASN D 80 ASN E 138 GLN ** F 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 4 GLN ** L 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 38 HIS N 119 ASN P 10 ASN Q 56 ASN S 73 ASN W 29 GLN X 20 HIS Z 19 GLN i 30 ASN i 89 GLN i 128 ASN i 133 HIS k 11 ASN k 18 GLN n 25 ASN p 34 ASN p 100 ASN ** p 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 78 ASN u 62 GLN x 69 HIS y 24 GLN y 65 HIS Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 144444 Z= 0.156 Angle : 0.543 11.195 216495 Z= 0.285 Chirality : 0.033 0.278 27962 Planarity : 0.004 0.073 11174 Dihedral : 23.118 179.520 72708 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.77 % Favored : 89.19 % Rotamer: Outliers : 6.07 % Allowed : 27.53 % Favored : 66.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.41 (0.11), residues: 5180 helix: -0.40 (0.14), residues: 1512 sheet: -1.42 (0.16), residues: 973 loop : -2.43 (0.11), residues: 2695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J 20 HIS 0.010 0.001 HIS y 65 PHE 0.034 0.001 PHE 4 46 TYR 0.034 0.001 TYR h 183 ARG 0.009 0.000 ARG W 73 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10360 Ramachandran restraints generated. 5180 Oldfield, 0 Emsley, 5180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10360 Ramachandran restraints generated. 5180 Oldfield, 0 Emsley, 5180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1052 residues out of total 4485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 240 poor density : 812 time to evaluate : 5.744 Fit side-chains revert: symmetry clash REVERT: B 116 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8298 (pp) REVERT: B 229 ASP cc_start: 0.7105 (m-30) cc_final: 0.6833 (m-30) REVERT: C 157 LYS cc_start: 0.8767 (OUTLIER) cc_final: 0.8491 (mttm) REVERT: D 44 GLN cc_start: 0.8239 (OUTLIER) cc_final: 0.7898 (mm110) REVERT: E 23 PHE cc_start: 0.8033 (OUTLIER) cc_final: 0.7519 (t80) REVERT: L 104 ASN cc_start: 0.9044 (m-40) cc_final: 0.8802 (m110) REVERT: V 20 LYS cc_start: 0.8689 (OUTLIER) cc_final: 0.8325 (mttt) REVERT: W 71 LYS cc_start: 0.8344 (ttmm) cc_final: 0.8125 (ttmm) REVERT: X 6 ASP cc_start: 0.7457 (OUTLIER) cc_final: 0.6852 (m-30) REVERT: X 70 LYS cc_start: 0.8427 (OUTLIER) cc_final: 0.7947 (ttpt) REVERT: a 50 ILE cc_start: 0.8113 (OUTLIER) cc_final: 0.7828 (pp) REVERT: c 20 SER cc_start: 0.8052 (OUTLIER) cc_final: 0.7605 (t) REVERT: e 61 GLN cc_start: 0.8306 (OUTLIER) cc_final: 0.7970 (mt0) REVERT: h 129 TYR cc_start: 0.5220 (OUTLIER) cc_final: 0.2599 (t80) REVERT: h 156 LEU cc_start: 0.7327 (OUTLIER) cc_final: 0.6412 (mt) REVERT: h 165 GLU cc_start: 0.7411 (OUTLIER) cc_final: 0.6881 (mt-10) REVERT: h 202 MET cc_start: 0.7545 (tmm) cc_final: 0.7281 (tpt) REVERT: i 66 GLU cc_start: 0.7194 (OUTLIER) cc_final: 0.6789 (tt0) REVERT: i 67 LYS cc_start: 0.8150 (OUTLIER) cc_final: 0.7577 (ttmt) REVERT: j 56 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8468 (tp) REVERT: j 153 MET cc_start: 0.7769 (OUTLIER) cc_final: 0.7302 (mtt) REVERT: l 30 MET cc_start: 0.8170 (mtp) cc_final: 0.7941 (mtt) REVERT: l 122 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.8037 (tp) REVERT: l 153 PHE cc_start: 0.7749 (m-10) cc_final: 0.7482 (m-10) REVERT: m 71 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.7066 (tm-30) REVERT: n 7 ILE cc_start: 0.7874 (mp) cc_final: 0.7517 (mt) REVERT: n 102 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8178 (pp) REVERT: o 47 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7859 (tt) REVERT: r 17 ILE cc_start: 0.6662 (mt) cc_final: 0.6291 (mm) REVERT: r 45 ILE cc_start: 0.6972 (tp) cc_final: 0.6605 (tt) REVERT: r 81 MET cc_start: 0.7618 (OUTLIER) cc_final: 0.7258 (ttp) REVERT: s 19 LYS cc_start: 0.6600 (ptpt) cc_final: 0.6330 (ptpt) REVERT: w 83 ARG cc_start: 0.8742 (OUTLIER) cc_final: 0.6945 (mtp180) REVERT: y 67 ASN cc_start: 0.7804 (m-40) cc_final: 0.7353 (m110) REVERT: y 71 ASN cc_start: 0.7702 (m-40) cc_final: 0.7490 (m110) outliers start: 240 outliers final: 144 residues processed: 961 average time/residue: 1.7987 time to fit residues: 2552.9648 Evaluate side-chains 962 residues out of total 4485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 795 time to evaluate : 5.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 103 TYR Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain C residue 56 ASN Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 153 SER Chi-restraints excluded: chain C residue 157 LYS Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain E residue 23 PHE Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 130 ASN Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 79 SER Chi-restraints excluded: chain F residue 133 ILE Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 35 SER Chi-restraints excluded: chain J residue 58 ASN Chi-restraints excluded: chain J residue 64 SER Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 75 SER Chi-restraints excluded: chain K residue 93 MET Chi-restraints excluded: chain K residue 115 VAL Chi-restraints excluded: chain L residue 46 SER Chi-restraints excluded: chain L residue 82 THR Chi-restraints excluded: chain L residue 148 VAL Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 134 VAL Chi-restraints excluded: chain N residue 55 SER Chi-restraints excluded: chain N residue 60 THR Chi-restraints excluded: chain N residue 114 GLU Chi-restraints excluded: chain O residue 19 THR Chi-restraints excluded: chain O residue 55 SER Chi-restraints excluded: chain O residue 65 THR Chi-restraints excluded: chain P residue 33 ILE Chi-restraints excluded: chain P residue 111 ILE Chi-restraints excluded: chain Q residue 113 VAL Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 48 THR Chi-restraints excluded: chain R residue 67 LEU Chi-restraints excluded: chain S residue 7 GLU Chi-restraints excluded: chain S residue 34 MET Chi-restraints excluded: chain S residue 46 VAL Chi-restraints excluded: chain S residue 94 ILE Chi-restraints excluded: chain T residue 49 VAL Chi-restraints excluded: chain T residue 89 THR Chi-restraints excluded: chain U residue 2 ILE Chi-restraints excluded: chain U residue 44 VAL Chi-restraints excluded: chain U residue 71 ILE Chi-restraints excluded: chain V residue 20 LYS Chi-restraints excluded: chain V residue 95 PHE Chi-restraints excluded: chain V residue 102 MET Chi-restraints excluded: chain W residue 55 LYS Chi-restraints excluded: chain W residue 81 ILE Chi-restraints excluded: chain X residue 4 VAL Chi-restraints excluded: chain X residue 6 ASP Chi-restraints excluded: chain X residue 55 THR Chi-restraints excluded: chain X residue 68 LEU Chi-restraints excluded: chain X residue 70 LYS Chi-restraints excluded: chain Y residue 41 LEU Chi-restraints excluded: chain Y residue 45 SER Chi-restraints excluded: chain Z residue 6 VAL Chi-restraints excluded: chain 4 residue 34 VAL Chi-restraints excluded: chain 4 residue 42 LEU Chi-restraints excluded: chain a residue 29 THR Chi-restraints excluded: chain a residue 50 ILE Chi-restraints excluded: chain a residue 51 SER Chi-restraints excluded: chain b residue 27 ILE Chi-restraints excluded: chain c residue 20 SER Chi-restraints excluded: chain c residue 31 THR Chi-restraints excluded: chain d residue 2 SER Chi-restraints excluded: chain d residue 25 SER Chi-restraints excluded: chain d residue 43 LEU Chi-restraints excluded: chain e residue 8 SER Chi-restraints excluded: chain e residue 9 SER Chi-restraints excluded: chain e residue 30 SER Chi-restraints excluded: chain e residue 32 ILE Chi-restraints excluded: chain e residue 42 LEU Chi-restraints excluded: chain e residue 61 GLN Chi-restraints excluded: chain f residue 29 LYS Chi-restraints excluded: chain h residue 5 THR Chi-restraints excluded: chain h residue 46 LEU Chi-restraints excluded: chain h residue 69 THR Chi-restraints excluded: chain h residue 84 ASP Chi-restraints excluded: chain h residue 129 TYR Chi-restraints excluded: chain h residue 156 LEU Chi-restraints excluded: chain h residue 165 GLU Chi-restraints excluded: chain i residue 66 GLU Chi-restraints excluded: chain i residue 67 LYS Chi-restraints excluded: chain i residue 126 VAL Chi-restraints excluded: chain i residue 167 THR Chi-restraints excluded: chain j residue 24 VAL Chi-restraints excluded: chain j residue 56 LEU Chi-restraints excluded: chain j residue 78 VAL Chi-restraints excluded: chain j residue 111 VAL Chi-restraints excluded: chain j residue 134 GLN Chi-restraints excluded: chain j residue 153 MET Chi-restraints excluded: chain j residue 165 VAL Chi-restraints excluded: chain k residue 3 HIS Chi-restraints excluded: chain k residue 7 VAL Chi-restraints excluded: chain k residue 31 THR Chi-restraints excluded: chain k residue 39 SER Chi-restraints excluded: chain k residue 45 LEU Chi-restraints excluded: chain k residue 72 LEU Chi-restraints excluded: chain l residue 8 LYS Chi-restraints excluded: chain l residue 29 LEU Chi-restraints excluded: chain l residue 31 TRP Chi-restraints excluded: chain l residue 41 VAL Chi-restraints excluded: chain l residue 71 VAL Chi-restraints excluded: chain l residue 122 LEU Chi-restraints excluded: chain m residue 63 LEU Chi-restraints excluded: chain m residue 71 GLU Chi-restraints excluded: chain m residue 107 SER Chi-restraints excluded: chain n residue 4 ILE Chi-restraints excluded: chain n residue 39 THR Chi-restraints excluded: chain n residue 47 LEU Chi-restraints excluded: chain n residue 102 LEU Chi-restraints excluded: chain o residue 47 LEU Chi-restraints excluded: chain p residue 22 SER Chi-restraints excluded: chain p residue 24 THR Chi-restraints excluded: chain p residue 31 SER Chi-restraints excluded: chain p residue 95 ILE Chi-restraints excluded: chain q residue 19 SER Chi-restraints excluded: chain q residue 73 ASN Chi-restraints excluded: chain q residue 104 THR Chi-restraints excluded: chain r residue 19 LEU Chi-restraints excluded: chain r residue 25 VAL Chi-restraints excluded: chain r residue 81 MET Chi-restraints excluded: chain r residue 97 VAL Chi-restraints excluded: chain r residue 108 THR Chi-restraints excluded: chain u residue 51 LEU Chi-restraints excluded: chain v residue 27 SER Chi-restraints excluded: chain v residue 32 VAL Chi-restraints excluded: chain v residue 53 THR Chi-restraints excluded: chain v residue 71 SER Chi-restraints excluded: chain w residue 55 VAL Chi-restraints excluded: chain w residue 83 ARG Chi-restraints excluded: chain w residue 87 LEU Chi-restraints excluded: chain w residue 89 LEU Chi-restraints excluded: chain x residue 5 LEU Chi-restraints excluded: chain x residue 45 VAL Chi-restraints excluded: chain y residue 50 THR Chi-restraints excluded: chain y residue 70 SER Chi-restraints excluded: chain y residue 77 THR Chi-restraints excluded: chain z residue 58 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 942 random chunks: chunk 878 optimal weight: 6.9990 chunk 102 optimal weight: 30.0000 chunk 519 optimal weight: 10.0000 chunk 665 optimal weight: 30.0000 chunk 515 optimal weight: 10.0000 chunk 767 optimal weight: 0.7980 chunk 508 optimal weight: 10.0000 chunk 907 optimal weight: 9.9990 chunk 568 optimal weight: 20.0000 chunk 553 optimal weight: 10.0000 chunk 419 optimal weight: 10.0000 overall best weight: 7.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 40 ASN C 83 GLN C 174 ASN E 30 GLN ** F 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 137 HIS K 4 GLN ** L 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 38 HIS O 47 ASN P 10 ASN W 29 GLN X 20 HIS i 89 GLN k 18 GLN p 100 ASN ** p 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 78 ASN u 62 GLN y 24 GLN y 65 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.096 144444 Z= 0.454 Angle : 0.689 12.129 216495 Z= 0.353 Chirality : 0.043 0.355 27962 Planarity : 0.005 0.062 11174 Dihedral : 23.148 179.605 72706 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.10 % Allowed : 12.22 % Favored : 87.68 % Rotamer: Outliers : 7.89 % Allowed : 26.30 % Favored : 65.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.56 (0.11), residues: 5180 helix: -0.63 (0.13), residues: 1531 sheet: -1.51 (0.16), residues: 990 loop : -2.47 (0.11), residues: 2659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP l 64 HIS 0.011 0.001 HIS y 65 PHE 0.030 0.002 PHE 4 46 TYR 0.034 0.002 TYR h 183 ARG 0.014 0.001 ARG E 128 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10360 Ramachandran restraints generated. 5180 Oldfield, 0 Emsley, 5180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10360 Ramachandran restraints generated. 5180 Oldfield, 0 Emsley, 5180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1119 residues out of total 4485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 312 poor density : 807 time to evaluate : 5.719 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 229 ASP cc_start: 0.7134 (m-30) cc_final: 0.6874 (m-30) REVERT: C 157 LYS cc_start: 0.8818 (OUTLIER) cc_final: 0.8503 (mttp) REVERT: E 23 PHE cc_start: 0.8195 (OUTLIER) cc_final: 0.7495 (t80) REVERT: L 74 GLU cc_start: 0.7298 (OUTLIER) cc_final: 0.7019 (mt-10) REVERT: L 104 ASN cc_start: 0.9073 (m-40) cc_final: 0.8836 (m110) REVERT: M 69 LYS cc_start: 0.8704 (OUTLIER) cc_final: 0.7901 (mmpt) REVERT: V 20 LYS cc_start: 0.8737 (OUTLIER) cc_final: 0.8369 (mttt) REVERT: V 131 LYS cc_start: 0.8839 (ttmm) cc_final: 0.7641 (pmtt) REVERT: W 68 LYS cc_start: 0.8442 (OUTLIER) cc_final: 0.8160 (ttmm) REVERT: W 71 LYS cc_start: 0.8464 (ttmm) cc_final: 0.8150 (ttmm) REVERT: X 6 ASP cc_start: 0.7579 (OUTLIER) cc_final: 0.6957 (m-30) REVERT: X 70 LYS cc_start: 0.8488 (OUTLIER) cc_final: 0.8038 (ttpt) REVERT: a 3 LYS cc_start: 0.7739 (OUTLIER) cc_final: 0.7385 (ptpt) REVERT: c 20 SER cc_start: 0.8154 (OUTLIER) cc_final: 0.7615 (t) REVERT: c 51 LYS cc_start: 0.8312 (OUTLIER) cc_final: 0.7744 (mmtt) REVERT: d 23 MET cc_start: 0.8148 (mmm) cc_final: 0.7854 (mtt) REVERT: e 61 GLN cc_start: 0.8443 (OUTLIER) cc_final: 0.8053 (mt0) REVERT: h 129 TYR cc_start: 0.5462 (OUTLIER) cc_final: 0.2980 (t80) REVERT: h 156 LEU cc_start: 0.7361 (mp) cc_final: 0.6552 (mp) REVERT: h 202 MET cc_start: 0.7634 (tmm) cc_final: 0.7290 (tpt) REVERT: i 66 GLU cc_start: 0.7281 (OUTLIER) cc_final: 0.7071 (tt0) REVERT: i 67 LYS cc_start: 0.8257 (OUTLIER) cc_final: 0.7590 (ttmt) REVERT: i 74 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.7117 (mp0) REVERT: j 56 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8505 (tp) REVERT: j 153 MET cc_start: 0.7884 (OUTLIER) cc_final: 0.7371 (mtt) REVERT: l 30 MET cc_start: 0.8245 (mtp) cc_final: 0.8008 (mtt) REVERT: l 122 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8188 (tp) REVERT: l 153 PHE cc_start: 0.7793 (m-10) cc_final: 0.7570 (m-10) REVERT: m 71 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.7198 (tm-30) REVERT: n 7 ILE cc_start: 0.8003 (mp) cc_final: 0.7672 (mt) REVERT: n 102 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8196 (pp) REVERT: n 111 ARG cc_start: 0.8398 (OUTLIER) cc_final: 0.6787 (ttm170) REVERT: o 47 LEU cc_start: 0.8232 (OUTLIER) cc_final: 0.7927 (tt) REVERT: r 45 ILE cc_start: 0.6972 (tp) cc_final: 0.6604 (tt) REVERT: s 3 LYS cc_start: 0.7482 (OUTLIER) cc_final: 0.7111 (mttt) REVERT: v 6 ASN cc_start: 0.8166 (m-40) cc_final: 0.7776 (OUTLIER) REVERT: w 83 ARG cc_start: 0.8817 (OUTLIER) cc_final: 0.7968 (mtp180) REVERT: x 36 ARG cc_start: 0.8544 (OUTLIER) cc_final: 0.8190 (ptm160) REVERT: y 67 ASN cc_start: 0.8086 (m-40) cc_final: 0.7629 (m-40) REVERT: y 71 ASN cc_start: 0.7903 (m-40) cc_final: 0.7595 (m110) REVERT: y 79 HIS cc_start: 0.7899 (OUTLIER) cc_final: 0.7302 (p-80) outliers start: 312 outliers final: 204 residues processed: 999 average time/residue: 1.7595 time to fit residues: 2601.6555 Evaluate side-chains 1025 residues out of total 4485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 230 poor density : 795 time to evaluate : 5.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 103 TYR Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 56 ASN Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 153 SER Chi-restraints excluded: chain C residue 157 LYS Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain E residue 23 PHE Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 130 ASN Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain F residue 4 ILE Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 39 ASP Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 79 SER Chi-restraints excluded: chain F residue 109 SER Chi-restraints excluded: chain F residue 133 ILE Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 35 SER Chi-restraints excluded: chain J residue 58 ASN Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 133 SER Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 75 SER Chi-restraints excluded: chain K residue 115 VAL Chi-restraints excluded: chain L residue 46 SER Chi-restraints excluded: chain L residue 74 GLU Chi-restraints excluded: chain L residue 82 THR Chi-restraints excluded: chain L residue 121 LEU Chi-restraints excluded: chain L residue 148 VAL Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 31 MET Chi-restraints excluded: chain M residue 58 ARG Chi-restraints excluded: chain M residue 69 LYS Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain M residue 122 LEU Chi-restraints excluded: chain M residue 129 VAL Chi-restraints excluded: chain M residue 134 VAL Chi-restraints excluded: chain N residue 14 THR Chi-restraints excluded: chain N residue 55 SER Chi-restraints excluded: chain N residue 60 THR Chi-restraints excluded: chain N residue 114 GLU Chi-restraints excluded: chain O residue 19 THR Chi-restraints excluded: chain O residue 30 SER Chi-restraints excluded: chain O residue 43 ILE Chi-restraints excluded: chain O residue 55 SER Chi-restraints excluded: chain O residue 65 THR Chi-restraints excluded: chain P residue 61 THR Chi-restraints excluded: chain P residue 78 ASN Chi-restraints excluded: chain P residue 85 ILE Chi-restraints excluded: chain P residue 111 ILE Chi-restraints excluded: chain Q residue 77 SER Chi-restraints excluded: chain Q residue 83 VAL Chi-restraints excluded: chain Q residue 113 VAL Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 48 THR Chi-restraints excluded: chain R residue 67 LEU Chi-restraints excluded: chain S residue 7 GLU Chi-restraints excluded: chain S residue 34 MET Chi-restraints excluded: chain S residue 94 ILE Chi-restraints excluded: chain S residue 124 THR Chi-restraints excluded: chain S residue 126 VAL Chi-restraints excluded: chain T residue 13 VAL Chi-restraints excluded: chain T residue 49 VAL Chi-restraints excluded: chain T residue 77 ILE Chi-restraints excluded: chain T residue 89 THR Chi-restraints excluded: chain U residue 2 ILE Chi-restraints excluded: chain U residue 44 VAL Chi-restraints excluded: chain U residue 65 SER Chi-restraints excluded: chain U residue 71 ILE Chi-restraints excluded: chain V residue 3 SER Chi-restraints excluded: chain V residue 18 SER Chi-restraints excluded: chain V residue 20 LYS Chi-restraints excluded: chain V residue 30 CYS Chi-restraints excluded: chain V residue 95 PHE Chi-restraints excluded: chain V residue 102 MET Chi-restraints excluded: chain W residue 55 LYS Chi-restraints excluded: chain W residue 68 LYS Chi-restraints excluded: chain W residue 77 SER Chi-restraints excluded: chain W residue 81 ILE Chi-restraints excluded: chain X residue 4 VAL Chi-restraints excluded: chain X residue 6 ASP Chi-restraints excluded: chain X residue 55 THR Chi-restraints excluded: chain X residue 68 LEU Chi-restraints excluded: chain X residue 70 LYS Chi-restraints excluded: chain Y residue 41 LEU Chi-restraints excluded: chain Y residue 45 SER Chi-restraints excluded: chain Z residue 6 VAL Chi-restraints excluded: chain 4 residue 34 VAL Chi-restraints excluded: chain 5 residue 8 LYS Chi-restraints excluded: chain a residue 3 LYS Chi-restraints excluded: chain a residue 29 THR Chi-restraints excluded: chain a residue 51 SER Chi-restraints excluded: chain b residue 27 ILE Chi-restraints excluded: chain c residue 20 SER Chi-restraints excluded: chain c residue 31 THR Chi-restraints excluded: chain c residue 51 LYS Chi-restraints excluded: chain d residue 2 SER Chi-restraints excluded: chain d residue 25 SER Chi-restraints excluded: chain d residue 43 LEU Chi-restraints excluded: chain d residue 46 SER Chi-restraints excluded: chain e residue 8 SER Chi-restraints excluded: chain e residue 9 SER Chi-restraints excluded: chain e residue 16 VAL Chi-restraints excluded: chain e residue 30 SER Chi-restraints excluded: chain e residue 32 ILE Chi-restraints excluded: chain e residue 42 LEU Chi-restraints excluded: chain e residue 61 GLN Chi-restraints excluded: chain h residue 5 THR Chi-restraints excluded: chain h residue 46 LEU Chi-restraints excluded: chain h residue 69 THR Chi-restraints excluded: chain h residue 84 ASP Chi-restraints excluded: chain h residue 129 TYR Chi-restraints excluded: chain i residue 19 ILE Chi-restraints excluded: chain i residue 66 GLU Chi-restraints excluded: chain i residue 67 LYS Chi-restraints excluded: chain i residue 74 GLU Chi-restraints excluded: chain i residue 121 THR Chi-restraints excluded: chain i residue 126 VAL Chi-restraints excluded: chain i residue 167 THR Chi-restraints excluded: chain j residue 24 VAL Chi-restraints excluded: chain j residue 56 LEU Chi-restraints excluded: chain j residue 78 VAL Chi-restraints excluded: chain j residue 83 ASN Chi-restraints excluded: chain j residue 106 SER Chi-restraints excluded: chain j residue 111 VAL Chi-restraints excluded: chain j residue 133 SER Chi-restraints excluded: chain j residue 134 GLN Chi-restraints excluded: chain j residue 153 MET Chi-restraints excluded: chain j residue 165 VAL Chi-restraints excluded: chain j residue 170 VAL Chi-restraints excluded: chain k residue 3 HIS Chi-restraints excluded: chain k residue 7 VAL Chi-restraints excluded: chain k residue 31 THR Chi-restraints excluded: chain k residue 39 SER Chi-restraints excluded: chain k residue 45 LEU Chi-restraints excluded: chain k residue 72 LEU Chi-restraints excluded: chain k residue 84 ARG Chi-restraints excluded: chain l residue 8 LYS Chi-restraints excluded: chain l residue 23 THR Chi-restraints excluded: chain l residue 29 LEU Chi-restraints excluded: chain l residue 31 TRP Chi-restraints excluded: chain l residue 71 VAL Chi-restraints excluded: chain l residue 122 LEU Chi-restraints excluded: chain m residue 31 LEU Chi-restraints excluded: chain m residue 63 LEU Chi-restraints excluded: chain m residue 71 GLU Chi-restraints excluded: chain m residue 107 SER Chi-restraints excluded: chain m residue 112 LEU Chi-restraints excluded: chain n residue 4 ILE Chi-restraints excluded: chain n residue 39 THR Chi-restraints excluded: chain n residue 47 LEU Chi-restraints excluded: chain n residue 102 LEU Chi-restraints excluded: chain n residue 111 ARG Chi-restraints excluded: chain o residue 14 HIS Chi-restraints excluded: chain o residue 15 MET Chi-restraints excluded: chain o residue 47 LEU Chi-restraints excluded: chain p residue 22 SER Chi-restraints excluded: chain p residue 24 THR Chi-restraints excluded: chain p residue 31 SER Chi-restraints excluded: chain p residue 44 SER Chi-restraints excluded: chain p residue 95 ILE Chi-restraints excluded: chain p residue 106 THR Chi-restraints excluded: chain q residue 22 VAL Chi-restraints excluded: chain q residue 73 ASN Chi-restraints excluded: chain q residue 104 THR Chi-restraints excluded: chain r residue 12 HIS Chi-restraints excluded: chain r residue 19 LEU Chi-restraints excluded: chain r residue 25 VAL Chi-restraints excluded: chain r residue 64 VAL Chi-restraints excluded: chain r residue 97 VAL Chi-restraints excluded: chain r residue 108 THR Chi-restraints excluded: chain s residue 3 LYS Chi-restraints excluded: chain s residue 75 MET Chi-restraints excluded: chain u residue 9 ARG Chi-restraints excluded: chain u residue 27 SER Chi-restraints excluded: chain u residue 30 ASP Chi-restraints excluded: chain u residue 51 LEU Chi-restraints excluded: chain v residue 26 ILE Chi-restraints excluded: chain v residue 27 SER Chi-restraints excluded: chain v residue 32 VAL Chi-restraints excluded: chain v residue 53 THR Chi-restraints excluded: chain v residue 65 SER Chi-restraints excluded: chain v residue 71 SER Chi-restraints excluded: chain w residue 55 VAL Chi-restraints excluded: chain w residue 83 ARG Chi-restraints excluded: chain w residue 87 LEU Chi-restraints excluded: chain w residue 89 LEU Chi-restraints excluded: chain w residue 90 MET Chi-restraints excluded: chain x residue 5 LEU Chi-restraints excluded: chain x residue 36 ARG Chi-restraints excluded: chain x residue 45 VAL Chi-restraints excluded: chain y residue 50 THR Chi-restraints excluded: chain y residue 70 SER Chi-restraints excluded: chain y residue 77 THR Chi-restraints excluded: chain y residue 79 HIS Chi-restraints excluded: chain z residue 58 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 942 random chunks: chunk 561 optimal weight: 10.0000 chunk 362 optimal weight: 4.9990 chunk 542 optimal weight: 10.0000 chunk 273 optimal weight: 8.9990 chunk 178 optimal weight: 9.9990 chunk 175 optimal weight: 9.9990 chunk 577 optimal weight: 20.0000 chunk 618 optimal weight: 10.0000 chunk 448 optimal weight: 8.9990 chunk 84 optimal weight: 0.0370 chunk 713 optimal weight: 6.9990 overall best weight: 6.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 40 ASN C 83 GLN C 136 GLN E 30 GLN ** F 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 33 GLN K 4 GLN ** L 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 38 HIS P 10 ASN W 29 GLN X 20 HIS ** k 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 18 GLN o 57 ASN p 100 ASN ** p 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 78 ASN u 62 GLN y 24 GLN y 30 ASN y 65 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 144444 Z= 0.362 Angle : 0.646 11.861 216495 Z= 0.335 Chirality : 0.040 0.363 27962 Planarity : 0.005 0.070 11174 Dihedral : 23.155 179.786 72706 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.08 % Allowed : 11.70 % Favored : 88.22 % Rotamer: Outliers : 7.16 % Allowed : 27.48 % Favored : 65.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -2.53 (0.11), residues: 5180 helix: -0.59 (0.13), residues: 1523 sheet: -1.50 (0.16), residues: 997 loop : -2.45 (0.11), residues: 2660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP l 64 HIS 0.011 0.001 HIS M 38 PHE 0.040 0.002 PHE 4 46 TYR 0.037 0.002 TYR h 183 ARG 0.012 0.001 ARG p 96 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10360 Ramachandran restraints generated. 5180 Oldfield, 0 Emsley, 5180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10360 Ramachandran restraints generated. 5180 Oldfield, 0 Emsley, 5180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1079 residues out of total 4485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 283 poor density : 796 time to evaluate : 5.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 229 ASP cc_start: 0.7126 (m-30) cc_final: 0.6875 (m-30) REVERT: C 157 LYS cc_start: 0.8816 (OUTLIER) cc_final: 0.8506 (mttp) REVERT: E 23 PHE cc_start: 0.8185 (OUTLIER) cc_final: 0.7491 (t80) REVERT: F 160 TYR cc_start: 0.8299 (m-80) cc_final: 0.8025 (m-80) REVERT: L 74 GLU cc_start: 0.7260 (OUTLIER) cc_final: 0.6994 (mt-10) REVERT: L 104 ASN cc_start: 0.9073 (m-40) cc_final: 0.8832 (m110) REVERT: M 69 LYS cc_start: 0.8686 (OUTLIER) cc_final: 0.7897 (mmpt) REVERT: V 20 LYS cc_start: 0.8742 (OUTLIER) cc_final: 0.8367 (mttt) REVERT: V 131 LYS cc_start: 0.8819 (ttmm) cc_final: 0.7672 (pmtt) REVERT: W 68 LYS cc_start: 0.8448 (OUTLIER) cc_final: 0.8229 (ttmm) REVERT: X 6 ASP cc_start: 0.7591 (OUTLIER) cc_final: 0.6973 (m-30) REVERT: X 70 LYS cc_start: 0.8483 (OUTLIER) cc_final: 0.8034 (ttpt) REVERT: a 3 LYS cc_start: 0.7691 (OUTLIER) cc_final: 0.7334 (ptpt) REVERT: c 20 SER cc_start: 0.8129 (OUTLIER) cc_final: 0.7608 (t) REVERT: c 51 LYS cc_start: 0.8338 (OUTLIER) cc_final: 0.7780 (mmtt) REVERT: e 61 GLN cc_start: 0.8418 (OUTLIER) cc_final: 0.8043 (mt0) REVERT: h 129 TYR cc_start: 0.5570 (OUTLIER) cc_final: 0.3129 (t80) REVERT: h 156 LEU cc_start: 0.7377 (mp) cc_final: 0.6589 (mt) REVERT: h 202 MET cc_start: 0.7722 (tmm) cc_final: 0.7400 (tpt) REVERT: i 66 GLU cc_start: 0.7225 (OUTLIER) cc_final: 0.6947 (tt0) REVERT: i 67 LYS cc_start: 0.8205 (OUTLIER) cc_final: 0.7547 (ttmt) REVERT: i 74 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.7158 (mp0) REVERT: j 56 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8517 (tp) REVERT: j 153 MET cc_start: 0.7869 (OUTLIER) cc_final: 0.7381 (mtt) REVERT: l 30 MET cc_start: 0.8230 (mtp) cc_final: 0.7997 (mtt) REVERT: l 122 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.8164 (tp) REVERT: l 153 PHE cc_start: 0.7804 (m-10) cc_final: 0.7568 (m-10) REVERT: m 71 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7195 (tm-30) REVERT: n 7 ILE cc_start: 0.8001 (mp) cc_final: 0.7666 (mt) REVERT: n 102 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8190 (pp) REVERT: n 111 ARG cc_start: 0.8400 (OUTLIER) cc_final: 0.6807 (ttm170) REVERT: o 47 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7923 (tt) REVERT: r 45 ILE cc_start: 0.6927 (tp) cc_final: 0.6571 (tt) REVERT: s 3 LYS cc_start: 0.7474 (OUTLIER) cc_final: 0.7125 (mttt) REVERT: w 83 ARG cc_start: 0.8809 (OUTLIER) cc_final: 0.7955 (mtp180) REVERT: x 36 ARG cc_start: 0.8528 (OUTLIER) cc_final: 0.8167 (ptm160) REVERT: y 67 ASN cc_start: 0.8005 (m-40) cc_final: 0.7564 (m-40) REVERT: y 71 ASN cc_start: 0.7876 (m-40) cc_final: 0.7595 (m110) REVERT: y 79 HIS cc_start: 0.7870 (OUTLIER) cc_final: 0.7292 (p-80) outliers start: 283 outliers final: 211 residues processed: 974 average time/residue: 1.7807 time to fit residues: 2563.5521 Evaluate side-chains 1030 residues out of total 4485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 238 poor density : 792 time to evaluate : 5.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 103 TYR Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 56 ASN Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 153 SER Chi-restraints excluded: chain C residue 157 LYS Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain E residue 23 PHE Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 130 ASN Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain F residue 4 ILE Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 39 ASP Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 79 SER Chi-restraints excluded: chain F residue 133 ILE Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 15 THR Chi-restraints excluded: chain J residue 17 THR Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 35 SER Chi-restraints excluded: chain J residue 58 ASN Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 117 ASN Chi-restraints excluded: chain J residue 133 SER Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 75 SER Chi-restraints excluded: chain K residue 115 VAL Chi-restraints excluded: chain L residue 46 SER Chi-restraints excluded: chain L residue 74 GLU Chi-restraints excluded: chain L residue 82 THR Chi-restraints excluded: chain L residue 121 LEU Chi-restraints excluded: chain L residue 148 VAL Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 31 MET Chi-restraints excluded: chain M residue 69 LYS Chi-restraints excluded: chain M residue 84 ARG Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain M residue 129 VAL Chi-restraints excluded: chain M residue 134 VAL Chi-restraints excluded: chain N residue 55 SER Chi-restraints excluded: chain N residue 60 THR Chi-restraints excluded: chain N residue 114 GLU Chi-restraints excluded: chain O residue 19 THR Chi-restraints excluded: chain O residue 30 SER Chi-restraints excluded: chain O residue 55 SER Chi-restraints excluded: chain O residue 65 THR Chi-restraints excluded: chain P residue 59 THR Chi-restraints excluded: chain P residue 61 THR Chi-restraints excluded: chain P residue 78 ASN Chi-restraints excluded: chain P residue 85 ILE Chi-restraints excluded: chain P residue 111 ILE Chi-restraints excluded: chain Q residue 77 SER Chi-restraints excluded: chain Q residue 83 VAL Chi-restraints excluded: chain Q residue 113 VAL Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 48 THR Chi-restraints excluded: chain R residue 67 LEU Chi-restraints excluded: chain S residue 7 GLU Chi-restraints excluded: chain S residue 34 MET Chi-restraints excluded: chain S residue 94 ILE Chi-restraints excluded: chain S residue 124 THR Chi-restraints excluded: chain S residue 126 VAL Chi-restraints excluded: chain T residue 13 VAL Chi-restraints excluded: chain T residue 49 VAL Chi-restraints excluded: chain T residue 77 ILE Chi-restraints excluded: chain T residue 89 THR Chi-restraints excluded: chain U residue 2 ILE Chi-restraints excluded: chain U residue 44 VAL Chi-restraints excluded: chain U residue 65 SER Chi-restraints excluded: chain U residue 69 SER Chi-restraints excluded: chain U residue 71 ILE Chi-restraints excluded: chain U residue 97 SER Chi-restraints excluded: chain V residue 3 SER Chi-restraints excluded: chain V residue 18 SER Chi-restraints excluded: chain V residue 20 LYS Chi-restraints excluded: chain V residue 30 CYS Chi-restraints excluded: chain V residue 77 ILE Chi-restraints excluded: chain V residue 95 PHE Chi-restraints excluded: chain V residue 102 MET Chi-restraints excluded: chain W residue 55 LYS Chi-restraints excluded: chain W residue 68 LYS Chi-restraints excluded: chain W residue 81 ILE Chi-restraints excluded: chain X residue 4 VAL Chi-restraints excluded: chain X residue 6 ASP Chi-restraints excluded: chain X residue 55 THR Chi-restraints excluded: chain X residue 68 LEU Chi-restraints excluded: chain X residue 70 LYS Chi-restraints excluded: chain Y residue 41 LEU Chi-restraints excluded: chain Y residue 45 SER Chi-restraints excluded: chain Z residue 6 VAL Chi-restraints excluded: chain 4 residue 34 VAL Chi-restraints excluded: chain 5 residue 8 LYS Chi-restraints excluded: chain a residue 3 LYS Chi-restraints excluded: chain a residue 29 THR Chi-restraints excluded: chain a residue 47 LYS Chi-restraints excluded: chain a residue 51 SER Chi-restraints excluded: chain b residue 27 ILE Chi-restraints excluded: chain c residue 20 SER Chi-restraints excluded: chain c residue 31 THR Chi-restraints excluded: chain c residue 51 LYS Chi-restraints excluded: chain d residue 2 SER Chi-restraints excluded: chain d residue 25 SER Chi-restraints excluded: chain d residue 41 HIS Chi-restraints excluded: chain d residue 43 LEU Chi-restraints excluded: chain e residue 8 SER Chi-restraints excluded: chain e residue 9 SER Chi-restraints excluded: chain e residue 16 VAL Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 30 SER Chi-restraints excluded: chain e residue 32 ILE Chi-restraints excluded: chain e residue 42 LEU Chi-restraints excluded: chain e residue 61 GLN Chi-restraints excluded: chain f residue 16 ILE Chi-restraints excluded: chain h residue 5 THR Chi-restraints excluded: chain h residue 46 LEU Chi-restraints excluded: chain h residue 69 THR Chi-restraints excluded: chain h residue 84 ASP Chi-restraints excluded: chain h residue 129 TYR Chi-restraints excluded: chain h residue 206 VAL Chi-restraints excluded: chain i residue 19 ILE Chi-restraints excluded: chain i residue 66 GLU Chi-restraints excluded: chain i residue 67 LYS Chi-restraints excluded: chain i residue 74 GLU Chi-restraints excluded: chain i residue 121 THR Chi-restraints excluded: chain i residue 126 VAL Chi-restraints excluded: chain i residue 167 THR Chi-restraints excluded: chain j residue 24 VAL Chi-restraints excluded: chain j residue 56 LEU Chi-restraints excluded: chain j residue 78 VAL Chi-restraints excluded: chain j residue 83 ASN Chi-restraints excluded: chain j residue 106 SER Chi-restraints excluded: chain j residue 111 VAL Chi-restraints excluded: chain j residue 133 SER Chi-restraints excluded: chain j residue 134 GLN Chi-restraints excluded: chain j residue 153 MET Chi-restraints excluded: chain j residue 165 VAL Chi-restraints excluded: chain k residue 3 HIS Chi-restraints excluded: chain k residue 7 VAL Chi-restraints excluded: chain k residue 31 THR Chi-restraints excluded: chain k residue 39 SER Chi-restraints excluded: chain k residue 72 LEU Chi-restraints excluded: chain k residue 84 ARG Chi-restraints excluded: chain l residue 8 LYS Chi-restraints excluded: chain l residue 23 THR Chi-restraints excluded: chain l residue 29 LEU Chi-restraints excluded: chain l residue 31 TRP Chi-restraints excluded: chain l residue 41 VAL Chi-restraints excluded: chain l residue 71 VAL Chi-restraints excluded: chain l residue 100 SER Chi-restraints excluded: chain l residue 122 LEU Chi-restraints excluded: chain m residue 31 LEU Chi-restraints excluded: chain m residue 63 LEU Chi-restraints excluded: chain m residue 71 GLU Chi-restraints excluded: chain m residue 107 SER Chi-restraints excluded: chain n residue 4 ILE Chi-restraints excluded: chain n residue 39 THR Chi-restraints excluded: chain n residue 102 LEU Chi-restraints excluded: chain n residue 111 ARG Chi-restraints excluded: chain o residue 15 MET Chi-restraints excluded: chain o residue 47 LEU Chi-restraints excluded: chain p residue 22 SER Chi-restraints excluded: chain p residue 24 THR Chi-restraints excluded: chain p residue 31 SER Chi-restraints excluded: chain p residue 44 SER Chi-restraints excluded: chain p residue 95 ILE Chi-restraints excluded: chain p residue 103 ILE Chi-restraints excluded: chain p residue 106 THR Chi-restraints excluded: chain q residue 22 VAL Chi-restraints excluded: chain q residue 73 ASN Chi-restraints excluded: chain q residue 104 THR Chi-restraints excluded: chain r residue 12 HIS Chi-restraints excluded: chain r residue 19 LEU Chi-restraints excluded: chain r residue 25 VAL Chi-restraints excluded: chain r residue 64 VAL Chi-restraints excluded: chain r residue 97 VAL Chi-restraints excluded: chain r residue 108 THR Chi-restraints excluded: chain s residue 3 LYS Chi-restraints excluded: chain s residue 46 VAL Chi-restraints excluded: chain t residue 36 SER Chi-restraints excluded: chain u residue 9 ARG Chi-restraints excluded: chain u residue 27 SER Chi-restraints excluded: chain u residue 30 ASP Chi-restraints excluded: chain u residue 44 THR Chi-restraints excluded: chain u residue 51 LEU Chi-restraints excluded: chain u residue 85 LEU Chi-restraints excluded: chain v residue 27 SER Chi-restraints excluded: chain v residue 32 VAL Chi-restraints excluded: chain v residue 53 THR Chi-restraints excluded: chain v residue 71 SER Chi-restraints excluded: chain w residue 55 VAL Chi-restraints excluded: chain w residue 83 ARG Chi-restraints excluded: chain w residue 87 LEU Chi-restraints excluded: chain w residue 89 LEU Chi-restraints excluded: chain w residue 90 MET Chi-restraints excluded: chain x residue 5 LEU Chi-restraints excluded: chain x residue 36 ARG Chi-restraints excluded: chain x residue 45 VAL Chi-restraints excluded: chain y residue 50 THR Chi-restraints excluded: chain y residue 70 SER Chi-restraints excluded: chain y residue 77 THR Chi-restraints excluded: chain y residue 79 HIS Chi-restraints excluded: chain z residue 21 ARG Chi-restraints excluded: chain z residue 58 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 942 random chunks: chunk 825 optimal weight: 10.0000 chunk 869 optimal weight: 8.9990 chunk 793 optimal weight: 5.9990 chunk 846 optimal weight: 30.0000 chunk 509 optimal weight: 10.0000 chunk 368 optimal weight: 40.0000 chunk 664 optimal weight: 20.0000 chunk 259 optimal weight: 1.9990 chunk 764 optimal weight: 20.0000 chunk 800 optimal weight: 0.9980 chunk 843 optimal weight: 20.0000 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 40 ASN C 83 GLN C 136 GLN E 30 GLN ** F 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 33 GLN K 4 GLN ** L 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 10 ASN W 29 GLN X 20 HIS i 89 GLN k 18 GLN o 57 ASN p 100 ASN ** p 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 78 ASN u 62 GLN y 24 GLN y 30 ASN y 65 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 144444 Z= 0.345 Angle : 0.634 11.766 216495 Z= 0.329 Chirality : 0.039 0.331 27962 Planarity : 0.005 0.076 11174 Dihedral : 23.145 179.827 72706 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.08 % Allowed : 11.76 % Favored : 88.17 % Rotamer: Outliers : 6.95 % Allowed : 27.48 % Favored : 65.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.51 (0.11), residues: 5180 helix: -0.58 (0.13), residues: 1533 sheet: -1.47 (0.16), residues: 988 loop : -2.45 (0.11), residues: 2659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP l 64 HIS 0.010 0.001 HIS y 65 PHE 0.039 0.002 PHE 4 46 TYR 0.032 0.002 TYR h 183 ARG 0.013 0.001 ARG h 163 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10360 Ramachandran restraints generated. 5180 Oldfield, 0 Emsley, 5180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10360 Ramachandran restraints generated. 5180 Oldfield, 0 Emsley, 5180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1068 residues out of total 4485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 275 poor density : 793 time to evaluate : 5.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 229 ASP cc_start: 0.7126 (m-30) cc_final: 0.6881 (m-30) REVERT: C 157 LYS cc_start: 0.8807 (OUTLIER) cc_final: 0.8502 (mttp) REVERT: E 23 PHE cc_start: 0.8180 (OUTLIER) cc_final: 0.7482 (t80) REVERT: E 113 ARG cc_start: 0.8201 (ptp-170) cc_final: 0.7970 (ptp-170) REVERT: F 160 TYR cc_start: 0.8301 (m-80) cc_final: 0.8012 (m-80) REVERT: J 42 ARG cc_start: 0.8572 (OUTLIER) cc_final: 0.8283 (tpt170) REVERT: L 74 GLU cc_start: 0.7258 (OUTLIER) cc_final: 0.6992 (mt-10) REVERT: L 104 ASN cc_start: 0.9069 (m-40) cc_final: 0.8825 (m110) REVERT: M 58 ARG cc_start: 0.7770 (OUTLIER) cc_final: 0.7546 (ttp-170) REVERT: M 69 LYS cc_start: 0.8687 (OUTLIER) cc_final: 0.7905 (mmpt) REVERT: V 20 LYS cc_start: 0.8741 (OUTLIER) cc_final: 0.8369 (mttt) REVERT: V 131 LYS cc_start: 0.8825 (ttmm) cc_final: 0.7654 (pmtt) REVERT: W 68 LYS cc_start: 0.8409 (OUTLIER) cc_final: 0.8147 (ttmm) REVERT: X 6 ASP cc_start: 0.7589 (OUTLIER) cc_final: 0.6979 (m-30) REVERT: X 70 LYS cc_start: 0.8453 (OUTLIER) cc_final: 0.8015 (ttpt) REVERT: a 3 LYS cc_start: 0.7675 (OUTLIER) cc_final: 0.7318 (ptpt) REVERT: b 13 ARG cc_start: 0.8651 (OUTLIER) cc_final: 0.8230 (ptt90) REVERT: c 20 SER cc_start: 0.8194 (OUTLIER) cc_final: 0.7687 (t) REVERT: e 61 GLN cc_start: 0.8416 (OUTLIER) cc_final: 0.8044 (mt0) REVERT: h 10 ASN cc_start: 0.7490 (OUTLIER) cc_final: 0.7007 (p0) REVERT: h 129 TYR cc_start: 0.5538 (OUTLIER) cc_final: 0.3122 (t80) REVERT: h 141 MET cc_start: 0.6867 (tpp) cc_final: 0.6419 (tpt) REVERT: h 156 LEU cc_start: 0.7308 (OUTLIER) cc_final: 0.6782 (mp) REVERT: h 202 MET cc_start: 0.7737 (tmm) cc_final: 0.7409 (tpt) REVERT: i 66 GLU cc_start: 0.7268 (OUTLIER) cc_final: 0.6990 (tt0) REVERT: i 67 LYS cc_start: 0.8200 (OUTLIER) cc_final: 0.7555 (ttmt) REVERT: i 74 GLU cc_start: 0.7593 (OUTLIER) cc_final: 0.7267 (mp0) REVERT: j 56 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8516 (tp) REVERT: j 153 MET cc_start: 0.7901 (OUTLIER) cc_final: 0.7406 (mtt) REVERT: l 30 MET cc_start: 0.8244 (mtp) cc_final: 0.8026 (mtt) REVERT: l 122 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.8164 (tp) REVERT: l 153 PHE cc_start: 0.7781 (m-10) cc_final: 0.7562 (m-10) REVERT: m 2 TYR cc_start: 0.6830 (m-80) cc_final: 0.6062 (t80) REVERT: m 71 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7201 (tm-30) REVERT: n 7 ILE cc_start: 0.7998 (mp) cc_final: 0.7665 (mt) REVERT: n 102 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8179 (pp) REVERT: n 111 ARG cc_start: 0.8386 (OUTLIER) cc_final: 0.6776 (ttm170) REVERT: o 47 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7925 (tt) REVERT: q 86 ARG cc_start: 0.7322 (ppp80) cc_final: 0.7118 (ppt-90) REVERT: r 45 ILE cc_start: 0.6928 (tp) cc_final: 0.6571 (tt) REVERT: s 3 LYS cc_start: 0.7474 (OUTLIER) cc_final: 0.7098 (mttt) REVERT: w 83 ARG cc_start: 0.8792 (OUTLIER) cc_final: 0.7312 (mtp180) REVERT: x 36 ARG cc_start: 0.8518 (OUTLIER) cc_final: 0.8152 (ptm160) REVERT: y 67 ASN cc_start: 0.7972 (m-40) cc_final: 0.7510 (m-40) REVERT: y 71 ASN cc_start: 0.7860 (m-40) cc_final: 0.7551 (m110) REVERT: y 79 HIS cc_start: 0.7877 (OUTLIER) cc_final: 0.7291 (p-80) outliers start: 275 outliers final: 212 residues processed: 963 average time/residue: 1.7828 time to fit residues: 2538.4937 Evaluate side-chains 1024 residues out of total 4485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 243 poor density : 781 time to evaluate : 5.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 103 TYR Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 56 ASN Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 153 SER Chi-restraints excluded: chain C residue 157 LYS Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain E residue 23 PHE Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 130 ASN Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 170 LYS Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain F residue 4 ILE Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 39 ASP Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 56 ASP Chi-restraints excluded: chain F residue 79 SER Chi-restraints excluded: chain F residue 133 ILE Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 15 THR Chi-restraints excluded: chain J residue 17 THR Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 35 SER Chi-restraints excluded: chain J residue 42 ARG Chi-restraints excluded: chain J residue 58 ASN Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 117 ASN Chi-restraints excluded: chain J residue 133 SER Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 75 SER Chi-restraints excluded: chain K residue 115 VAL Chi-restraints excluded: chain L residue 46 SER Chi-restraints excluded: chain L residue 74 GLU Chi-restraints excluded: chain L residue 82 THR Chi-restraints excluded: chain L residue 148 VAL Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 31 MET Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain M residue 58 ARG Chi-restraints excluded: chain M residue 69 LYS Chi-restraints excluded: chain M residue 84 ARG Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain M residue 129 VAL Chi-restraints excluded: chain M residue 134 VAL Chi-restraints excluded: chain N residue 8 ASN Chi-restraints excluded: chain N residue 55 SER Chi-restraints excluded: chain N residue 60 THR Chi-restraints excluded: chain N residue 114 GLU Chi-restraints excluded: chain O residue 19 THR Chi-restraints excluded: chain O residue 30 SER Chi-restraints excluded: chain O residue 43 ILE Chi-restraints excluded: chain O residue 55 SER Chi-restraints excluded: chain O residue 65 THR Chi-restraints excluded: chain P residue 33 ILE Chi-restraints excluded: chain P residue 59 THR Chi-restraints excluded: chain P residue 61 THR Chi-restraints excluded: chain P residue 85 ILE Chi-restraints excluded: chain P residue 111 ILE Chi-restraints excluded: chain Q residue 77 SER Chi-restraints excluded: chain Q residue 113 VAL Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 48 THR Chi-restraints excluded: chain R residue 67 LEU Chi-restraints excluded: chain S residue 7 GLU Chi-restraints excluded: chain S residue 34 MET Chi-restraints excluded: chain S residue 46 VAL Chi-restraints excluded: chain S residue 94 ILE Chi-restraints excluded: chain S residue 124 THR Chi-restraints excluded: chain S residue 126 VAL Chi-restraints excluded: chain T residue 13 VAL Chi-restraints excluded: chain T residue 49 VAL Chi-restraints excluded: chain T residue 77 ILE Chi-restraints excluded: chain T residue 89 THR Chi-restraints excluded: chain U residue 2 ILE Chi-restraints excluded: chain U residue 44 VAL Chi-restraints excluded: chain U residue 65 SER Chi-restraints excluded: chain U residue 69 SER Chi-restraints excluded: chain U residue 71 ILE Chi-restraints excluded: chain U residue 97 SER Chi-restraints excluded: chain V residue 3 SER Chi-restraints excluded: chain V residue 18 SER Chi-restraints excluded: chain V residue 20 LYS Chi-restraints excluded: chain V residue 30 CYS Chi-restraints excluded: chain V residue 77 ILE Chi-restraints excluded: chain V residue 95 PHE Chi-restraints excluded: chain V residue 102 MET Chi-restraints excluded: chain W residue 55 LYS Chi-restraints excluded: chain W residue 68 LYS Chi-restraints excluded: chain W residue 77 SER Chi-restraints excluded: chain W residue 81 ILE Chi-restraints excluded: chain X residue 4 VAL Chi-restraints excluded: chain X residue 6 ASP Chi-restraints excluded: chain X residue 55 THR Chi-restraints excluded: chain X residue 68 LEU Chi-restraints excluded: chain X residue 70 LYS Chi-restraints excluded: chain Y residue 41 LEU Chi-restraints excluded: chain Y residue 45 SER Chi-restraints excluded: chain Z residue 6 VAL Chi-restraints excluded: chain 4 residue 34 VAL Chi-restraints excluded: chain 5 residue 8 LYS Chi-restraints excluded: chain a residue 3 LYS Chi-restraints excluded: chain a residue 29 THR Chi-restraints excluded: chain a residue 51 SER Chi-restraints excluded: chain b residue 13 ARG Chi-restraints excluded: chain b residue 27 ILE Chi-restraints excluded: chain c residue 20 SER Chi-restraints excluded: chain c residue 31 THR Chi-restraints excluded: chain d residue 2 SER Chi-restraints excluded: chain d residue 25 SER Chi-restraints excluded: chain d residue 41 HIS Chi-restraints excluded: chain d residue 43 LEU Chi-restraints excluded: chain d residue 46 SER Chi-restraints excluded: chain e residue 8 SER Chi-restraints excluded: chain e residue 9 SER Chi-restraints excluded: chain e residue 16 VAL Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 30 SER Chi-restraints excluded: chain e residue 32 ILE Chi-restraints excluded: chain e residue 42 LEU Chi-restraints excluded: chain e residue 61 GLN Chi-restraints excluded: chain f residue 16 ILE Chi-restraints excluded: chain h residue 5 THR Chi-restraints excluded: chain h residue 10 ASN Chi-restraints excluded: chain h residue 46 LEU Chi-restraints excluded: chain h residue 69 THR Chi-restraints excluded: chain h residue 129 TYR Chi-restraints excluded: chain h residue 151 LEU Chi-restraints excluded: chain h residue 156 LEU Chi-restraints excluded: chain i residue 19 ILE Chi-restraints excluded: chain i residue 66 GLU Chi-restraints excluded: chain i residue 67 LYS Chi-restraints excluded: chain i residue 74 GLU Chi-restraints excluded: chain i residue 121 THR Chi-restraints excluded: chain i residue 126 VAL Chi-restraints excluded: chain i residue 167 THR Chi-restraints excluded: chain j residue 24 VAL Chi-restraints excluded: chain j residue 56 LEU Chi-restraints excluded: chain j residue 78 VAL Chi-restraints excluded: chain j residue 83 ASN Chi-restraints excluded: chain j residue 106 SER Chi-restraints excluded: chain j residue 111 VAL Chi-restraints excluded: chain j residue 133 SER Chi-restraints excluded: chain j residue 134 GLN Chi-restraints excluded: chain j residue 153 MET Chi-restraints excluded: chain j residue 165 VAL Chi-restraints excluded: chain j residue 170 VAL Chi-restraints excluded: chain k residue 3 HIS Chi-restraints excluded: chain k residue 7 VAL Chi-restraints excluded: chain k residue 31 THR Chi-restraints excluded: chain k residue 39 SER Chi-restraints excluded: chain k residue 45 LEU Chi-restraints excluded: chain k residue 72 LEU Chi-restraints excluded: chain k residue 84 ARG Chi-restraints excluded: chain l residue 8 LYS Chi-restraints excluded: chain l residue 23 THR Chi-restraints excluded: chain l residue 29 LEU Chi-restraints excluded: chain l residue 31 TRP Chi-restraints excluded: chain l residue 41 VAL Chi-restraints excluded: chain l residue 71 VAL Chi-restraints excluded: chain l residue 122 LEU Chi-restraints excluded: chain m residue 31 LEU Chi-restraints excluded: chain m residue 71 GLU Chi-restraints excluded: chain m residue 107 SER Chi-restraints excluded: chain n residue 4 ILE Chi-restraints excluded: chain n residue 60 ASP Chi-restraints excluded: chain n residue 102 LEU Chi-restraints excluded: chain n residue 111 ARG Chi-restraints excluded: chain o residue 15 MET Chi-restraints excluded: chain o residue 47 LEU Chi-restraints excluded: chain p residue 22 SER Chi-restraints excluded: chain p residue 24 THR Chi-restraints excluded: chain p residue 31 SER Chi-restraints excluded: chain p residue 44 SER Chi-restraints excluded: chain p residue 106 THR Chi-restraints excluded: chain q residue 22 VAL Chi-restraints excluded: chain q residue 73 ASN Chi-restraints excluded: chain q residue 74 LEU Chi-restraints excluded: chain q residue 104 THR Chi-restraints excluded: chain r residue 12 HIS Chi-restraints excluded: chain r residue 19 LEU Chi-restraints excluded: chain r residue 25 VAL Chi-restraints excluded: chain r residue 64 VAL Chi-restraints excluded: chain r residue 97 VAL Chi-restraints excluded: chain r residue 108 THR Chi-restraints excluded: chain s residue 3 LYS Chi-restraints excluded: chain s residue 46 VAL Chi-restraints excluded: chain t residue 36 SER Chi-restraints excluded: chain u residue 9 ARG Chi-restraints excluded: chain u residue 27 SER Chi-restraints excluded: chain u residue 30 ASP Chi-restraints excluded: chain u residue 44 THR Chi-restraints excluded: chain u residue 51 LEU Chi-restraints excluded: chain v residue 27 SER Chi-restraints excluded: chain v residue 32 VAL Chi-restraints excluded: chain v residue 53 THR Chi-restraints excluded: chain v residue 71 SER Chi-restraints excluded: chain w residue 55 VAL Chi-restraints excluded: chain w residue 83 ARG Chi-restraints excluded: chain w residue 87 LEU Chi-restraints excluded: chain w residue 89 LEU Chi-restraints excluded: chain w residue 90 MET Chi-restraints excluded: chain x residue 5 LEU Chi-restraints excluded: chain x residue 36 ARG Chi-restraints excluded: chain x residue 45 VAL Chi-restraints excluded: chain y residue 50 THR Chi-restraints excluded: chain y residue 70 SER Chi-restraints excluded: chain y residue 77 THR Chi-restraints excluded: chain y residue 79 HIS Chi-restraints excluded: chain z residue 21 ARG Chi-restraints excluded: chain z residue 58 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 942 random chunks: chunk 555 optimal weight: 20.0000 chunk 894 optimal weight: 8.9990 chunk 546 optimal weight: 10.0000 chunk 424 optimal weight: 10.0000 chunk 621 optimal weight: 10.0000 chunk 938 optimal weight: 8.9990 chunk 863 optimal weight: 5.9990 chunk 747 optimal weight: 10.0000 chunk 77 optimal weight: 5.9990 chunk 577 optimal weight: 20.0000 chunk 458 optimal weight: 6.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 40 ASN C 83 GLN C 136 GLN D 170 ASN E 30 GLN E 138 GLN ** F 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 33 GLN K 4 GLN ** L 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 38 HIS W 29 GLN X 20 HIS i 89 GLN k 18 GLN p 100 ASN ** p 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 78 ASN u 62 GLN y 24 GLN y 30 ASN y 65 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.091 144444 Z= 0.444 Angle : 0.694 12.134 216495 Z= 0.357 Chirality : 0.043 0.359 27962 Planarity : 0.006 0.076 11174 Dihedral : 23.195 179.815 72706 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.10 % Allowed : 12.39 % Favored : 87.51 % Rotamer: Outliers : 6.85 % Allowed : 27.79 % Favored : 65.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.58 (0.11), residues: 5180 helix: -0.69 (0.13), residues: 1534 sheet: -1.45 (0.16), residues: 1016 loop : -2.49 (0.11), residues: 2630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP l 64 HIS 0.010 0.001 HIS y 65 PHE 0.039 0.002 PHE 4 46 TYR 0.026 0.002 TYR h 183 ARG 0.012 0.001 ARG E 128 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10360 Ramachandran restraints generated. 5180 Oldfield, 0 Emsley, 5180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10360 Ramachandran restraints generated. 5180 Oldfield, 0 Emsley, 5180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1064 residues out of total 4485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 271 poor density : 793 time to evaluate : 5.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 229 ASP cc_start: 0.7140 (m-30) cc_final: 0.6880 (m-30) REVERT: C 157 LYS cc_start: 0.8815 (OUTLIER) cc_final: 0.8494 (mttp) REVERT: E 23 PHE cc_start: 0.8272 (OUTLIER) cc_final: 0.7479 (t80) REVERT: J 42 ARG cc_start: 0.8591 (OUTLIER) cc_final: 0.8206 (tpt170) REVERT: L 74 GLU cc_start: 0.7294 (OUTLIER) cc_final: 0.7021 (mt-10) REVERT: L 104 ASN cc_start: 0.9077 (m-40) cc_final: 0.8840 (m110) REVERT: M 58 ARG cc_start: 0.7793 (OUTLIER) cc_final: 0.7573 (ttp-170) REVERT: M 69 LYS cc_start: 0.8706 (OUTLIER) cc_final: 0.7915 (mmpt) REVERT: V 20 LYS cc_start: 0.8705 (OUTLIER) cc_final: 0.8328 (mttt) REVERT: V 131 LYS cc_start: 0.8832 (ttmm) cc_final: 0.7671 (pmtt) REVERT: W 68 LYS cc_start: 0.8448 (OUTLIER) cc_final: 0.8120 (ttmm) REVERT: X 6 ASP cc_start: 0.7610 (OUTLIER) cc_final: 0.6997 (m-30) REVERT: X 70 LYS cc_start: 0.8491 (OUTLIER) cc_final: 0.8039 (ttpt) REVERT: a 3 LYS cc_start: 0.7827 (OUTLIER) cc_final: 0.7425 (ptpt) REVERT: b 13 ARG cc_start: 0.8721 (OUTLIER) cc_final: 0.8289 (ptt90) REVERT: e 61 GLN cc_start: 0.8440 (OUTLIER) cc_final: 0.8049 (mt0) REVERT: h 10 ASN cc_start: 0.7566 (OUTLIER) cc_final: 0.7050 (p0) REVERT: h 129 TYR cc_start: 0.5387 (OUTLIER) cc_final: 0.3231 (t80) REVERT: h 202 MET cc_start: 0.7813 (tmm) cc_final: 0.7413 (tpt) REVERT: i 67 LYS cc_start: 0.8266 (OUTLIER) cc_final: 0.7573 (ttmt) REVERT: i 74 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.7290 (mp0) REVERT: i 85 GLU cc_start: 0.7822 (tm-30) cc_final: 0.7489 (tm-30) REVERT: j 56 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8526 (tp) REVERT: j 153 MET cc_start: 0.7940 (OUTLIER) cc_final: 0.7429 (mtt) REVERT: l 30 MET cc_start: 0.8296 (mtp) cc_final: 0.8045 (mtt) REVERT: l 66 ASP cc_start: 0.7502 (OUTLIER) cc_final: 0.7252 (m-30) REVERT: l 122 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.8145 (tp) REVERT: l 153 PHE cc_start: 0.7796 (m-10) cc_final: 0.7565 (m-10) REVERT: m 2 TYR cc_start: 0.6614 (m-80) cc_final: 0.5889 (t80) REVERT: m 71 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.7305 (tm-30) REVERT: n 7 ILE cc_start: 0.8075 (mp) cc_final: 0.7755 (mt) REVERT: n 102 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8254 (pp) REVERT: n 111 ARG cc_start: 0.8466 (OUTLIER) cc_final: 0.6847 (ttm170) REVERT: o 47 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.7988 (tt) REVERT: q 86 ARG cc_start: 0.7417 (ppp80) cc_final: 0.7155 (ppt-90) REVERT: r 45 ILE cc_start: 0.6901 (tp) cc_final: 0.6522 (tt) REVERT: s 3 LYS cc_start: 0.7486 (OUTLIER) cc_final: 0.7124 (mttt) REVERT: s 19 LYS cc_start: 0.6731 (ptpt) cc_final: 0.6382 (ptpt) REVERT: v 58 ILE cc_start: 0.9246 (mt) cc_final: 0.9046 (mt) REVERT: w 57 GLU cc_start: 0.7573 (tp30) cc_final: 0.7355 (tp30) REVERT: w 83 ARG cc_start: 0.8805 (OUTLIER) cc_final: 0.8030 (mtp180) REVERT: x 36 ARG cc_start: 0.8565 (OUTLIER) cc_final: 0.8182 (ptm160) REVERT: y 71 ASN cc_start: 0.7732 (m-40) cc_final: 0.7461 (m110) REVERT: y 79 HIS cc_start: 0.7930 (OUTLIER) cc_final: 0.7330 (p-80) outliers start: 271 outliers final: 208 residues processed: 961 average time/residue: 1.7908 time to fit residues: 2538.8023 Evaluate side-chains 1016 residues out of total 4485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 237 poor density : 779 time to evaluate : 5.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 103 TYR Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 56 ASN Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 153 SER Chi-restraints excluded: chain C residue 157 LYS Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain E residue 23 PHE Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 130 ASN Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 170 LYS Chi-restraints excluded: chain F residue 4 ILE Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 39 ASP Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 56 ASP Chi-restraints excluded: chain F residue 79 SER Chi-restraints excluded: chain F residue 109 SER Chi-restraints excluded: chain F residue 133 ILE Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 15 THR Chi-restraints excluded: chain J residue 17 THR Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 35 SER Chi-restraints excluded: chain J residue 42 ARG Chi-restraints excluded: chain J residue 58 ASN Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 117 ASN Chi-restraints excluded: chain J residue 133 SER Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 75 SER Chi-restraints excluded: chain K residue 115 VAL Chi-restraints excluded: chain L residue 46 SER Chi-restraints excluded: chain L residue 74 GLU Chi-restraints excluded: chain L residue 82 THR Chi-restraints excluded: chain L residue 148 VAL Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 31 MET Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain M residue 58 ARG Chi-restraints excluded: chain M residue 69 LYS Chi-restraints excluded: chain M residue 84 ARG Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain M residue 129 VAL Chi-restraints excluded: chain M residue 134 VAL Chi-restraints excluded: chain N residue 55 SER Chi-restraints excluded: chain N residue 60 THR Chi-restraints excluded: chain N residue 114 GLU Chi-restraints excluded: chain O residue 4 THR Chi-restraints excluded: chain O residue 19 THR Chi-restraints excluded: chain O residue 30 SER Chi-restraints excluded: chain O residue 55 SER Chi-restraints excluded: chain O residue 65 THR Chi-restraints excluded: chain P residue 33 ILE Chi-restraints excluded: chain P residue 61 THR Chi-restraints excluded: chain P residue 85 ILE Chi-restraints excluded: chain P residue 111 ILE Chi-restraints excluded: chain Q residue 74 MET Chi-restraints excluded: chain Q residue 77 SER Chi-restraints excluded: chain Q residue 83 VAL Chi-restraints excluded: chain Q residue 113 VAL Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 48 THR Chi-restraints excluded: chain R residue 67 LEU Chi-restraints excluded: chain S residue 7 GLU Chi-restraints excluded: chain S residue 34 MET Chi-restraints excluded: chain S residue 94 ILE Chi-restraints excluded: chain S residue 124 THR Chi-restraints excluded: chain S residue 126 VAL Chi-restraints excluded: chain T residue 13 VAL Chi-restraints excluded: chain T residue 49 VAL Chi-restraints excluded: chain T residue 77 ILE Chi-restraints excluded: chain U residue 2 ILE Chi-restraints excluded: chain U residue 44 VAL Chi-restraints excluded: chain U residue 65 SER Chi-restraints excluded: chain U residue 69 SER Chi-restraints excluded: chain U residue 71 ILE Chi-restraints excluded: chain U residue 97 SER Chi-restraints excluded: chain V residue 3 SER Chi-restraints excluded: chain V residue 18 SER Chi-restraints excluded: chain V residue 20 LYS Chi-restraints excluded: chain V residue 30 CYS Chi-restraints excluded: chain V residue 77 ILE Chi-restraints excluded: chain V residue 95 PHE Chi-restraints excluded: chain V residue 102 MET Chi-restraints excluded: chain W residue 68 LYS Chi-restraints excluded: chain W residue 77 SER Chi-restraints excluded: chain W residue 81 ILE Chi-restraints excluded: chain X residue 4 VAL Chi-restraints excluded: chain X residue 6 ASP Chi-restraints excluded: chain X residue 55 THR Chi-restraints excluded: chain X residue 68 LEU Chi-restraints excluded: chain X residue 70 LYS Chi-restraints excluded: chain Y residue 41 LEU Chi-restraints excluded: chain Y residue 45 SER Chi-restraints excluded: chain Z residue 6 VAL Chi-restraints excluded: chain 4 residue 34 VAL Chi-restraints excluded: chain 5 residue 8 LYS Chi-restraints excluded: chain a residue 3 LYS Chi-restraints excluded: chain a residue 29 THR Chi-restraints excluded: chain a residue 51 SER Chi-restraints excluded: chain b residue 13 ARG Chi-restraints excluded: chain b residue 27 ILE Chi-restraints excluded: chain c residue 20 SER Chi-restraints excluded: chain c residue 31 THR Chi-restraints excluded: chain d residue 2 SER Chi-restraints excluded: chain d residue 25 SER Chi-restraints excluded: chain d residue 41 HIS Chi-restraints excluded: chain d residue 42 LYS Chi-restraints excluded: chain d residue 43 LEU Chi-restraints excluded: chain d residue 46 SER Chi-restraints excluded: chain e residue 8 SER Chi-restraints excluded: chain e residue 9 SER Chi-restraints excluded: chain e residue 16 VAL Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 30 SER Chi-restraints excluded: chain e residue 42 LEU Chi-restraints excluded: chain e residue 61 GLN Chi-restraints excluded: chain f residue 16 ILE Chi-restraints excluded: chain h residue 5 THR Chi-restraints excluded: chain h residue 10 ASN Chi-restraints excluded: chain h residue 46 LEU Chi-restraints excluded: chain h residue 69 THR Chi-restraints excluded: chain h residue 129 TYR Chi-restraints excluded: chain i residue 19 ILE Chi-restraints excluded: chain i residue 67 LYS Chi-restraints excluded: chain i residue 74 GLU Chi-restraints excluded: chain i residue 121 THR Chi-restraints excluded: chain i residue 126 VAL Chi-restraints excluded: chain i residue 167 THR Chi-restraints excluded: chain j residue 24 VAL Chi-restraints excluded: chain j residue 56 LEU Chi-restraints excluded: chain j residue 78 VAL Chi-restraints excluded: chain j residue 83 ASN Chi-restraints excluded: chain j residue 106 SER Chi-restraints excluded: chain j residue 111 VAL Chi-restraints excluded: chain j residue 133 SER Chi-restraints excluded: chain j residue 134 GLN Chi-restraints excluded: chain j residue 153 MET Chi-restraints excluded: chain j residue 165 VAL Chi-restraints excluded: chain j residue 170 VAL Chi-restraints excluded: chain k residue 3 HIS Chi-restraints excluded: chain k residue 7 VAL Chi-restraints excluded: chain k residue 31 THR Chi-restraints excluded: chain k residue 39 SER Chi-restraints excluded: chain k residue 72 LEU Chi-restraints excluded: chain k residue 84 ARG Chi-restraints excluded: chain l residue 8 LYS Chi-restraints excluded: chain l residue 23 THR Chi-restraints excluded: chain l residue 29 LEU Chi-restraints excluded: chain l residue 31 TRP Chi-restraints excluded: chain l residue 66 ASP Chi-restraints excluded: chain l residue 71 VAL Chi-restraints excluded: chain l residue 122 LEU Chi-restraints excluded: chain m residue 31 LEU Chi-restraints excluded: chain m residue 71 GLU Chi-restraints excluded: chain m residue 107 SER Chi-restraints excluded: chain n residue 4 ILE Chi-restraints excluded: chain n residue 60 ASP Chi-restraints excluded: chain n residue 102 LEU Chi-restraints excluded: chain n residue 111 ARG Chi-restraints excluded: chain o residue 15 MET Chi-restraints excluded: chain o residue 47 LEU Chi-restraints excluded: chain p residue 22 SER Chi-restraints excluded: chain p residue 24 THR Chi-restraints excluded: chain p residue 31 SER Chi-restraints excluded: chain p residue 44 SER Chi-restraints excluded: chain p residue 103 ILE Chi-restraints excluded: chain p residue 106 THR Chi-restraints excluded: chain q residue 22 VAL Chi-restraints excluded: chain q residue 73 ASN Chi-restraints excluded: chain q residue 104 THR Chi-restraints excluded: chain r residue 12 HIS Chi-restraints excluded: chain r residue 19 LEU Chi-restraints excluded: chain r residue 25 VAL Chi-restraints excluded: chain r residue 64 VAL Chi-restraints excluded: chain r residue 97 VAL Chi-restraints excluded: chain r residue 108 THR Chi-restraints excluded: chain s residue 3 LYS Chi-restraints excluded: chain s residue 75 MET Chi-restraints excluded: chain t residue 36 SER Chi-restraints excluded: chain u residue 9 ARG Chi-restraints excluded: chain u residue 27 SER Chi-restraints excluded: chain u residue 30 ASP Chi-restraints excluded: chain u residue 44 THR Chi-restraints excluded: chain v residue 26 ILE Chi-restraints excluded: chain v residue 27 SER Chi-restraints excluded: chain v residue 32 VAL Chi-restraints excluded: chain v residue 53 THR Chi-restraints excluded: chain v residue 71 SER Chi-restraints excluded: chain v residue 78 LEU Chi-restraints excluded: chain w residue 55 VAL Chi-restraints excluded: chain w residue 83 ARG Chi-restraints excluded: chain w residue 87 LEU Chi-restraints excluded: chain w residue 89 LEU Chi-restraints excluded: chain w residue 90 MET Chi-restraints excluded: chain x residue 5 LEU Chi-restraints excluded: chain x residue 36 ARG Chi-restraints excluded: chain x residue 45 VAL Chi-restraints excluded: chain y residue 50 THR Chi-restraints excluded: chain y residue 70 SER Chi-restraints excluded: chain y residue 77 THR Chi-restraints excluded: chain y residue 79 HIS Chi-restraints excluded: chain z residue 21 ARG Chi-restraints excluded: chain z residue 58 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 942 random chunks: chunk 593 optimal weight: 20.0000 chunk 796 optimal weight: 8.9990 chunk 228 optimal weight: 6.9990 chunk 689 optimal weight: 10.0000 chunk 110 optimal weight: 0.6980 chunk 207 optimal weight: 1.9990 chunk 748 optimal weight: 0.0040 chunk 313 optimal weight: 10.0000 chunk 768 optimal weight: 10.0000 chunk 94 optimal weight: 3.9990 chunk 137 optimal weight: 0.9990 overall best weight: 1.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 40 ASN C 83 GLN C 136 GLN D 80 ASN E 30 GLN ** F 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 4 GLN O 47 ASN V 58 HIS W 29 GLN X 20 HIS i 89 GLN j 25 ASN k 18 GLN l 120 GLN n 73 GLN o 57 ASN ** p 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 61 HIS u 62 GLN x 69 HIS y 24 GLN y 30 ASN y 65 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.128231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.092872 restraints weight = 205646.424| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 0.83 r_work: 0.3068 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 144444 Z= 0.145 Angle : 0.550 14.639 216495 Z= 0.285 Chirality : 0.033 0.268 27962 Planarity : 0.004 0.054 11174 Dihedral : 23.106 179.754 72706 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.02 % Favored : 89.94 % Rotamer: Outliers : 4.40 % Allowed : 30.57 % Favored : 65.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.21 (0.11), residues: 5180 helix: -0.20 (0.14), residues: 1509 sheet: -1.35 (0.17), residues: 968 loop : -2.30 (0.11), residues: 2703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP l 64 HIS 0.008 0.001 HIS y 65 PHE 0.034 0.001 PHE 4 46 TYR 0.029 0.001 TYR h 183 ARG 0.013 0.000 ARG W 73 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 37644.80 seconds wall clock time: 654 minutes 6.15 seconds (39246.15 seconds total)