Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 28 08:18:44 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jil_22345/04_2023/7jil_22345_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jil_22345/04_2023/7jil_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_22345/04_2023/7jil_22345.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jil_22345/04_2023/7jil_22345.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jil_22345/04_2023/7jil_22345_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jil_22345/04_2023/7jil_22345_neut.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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-1.21rc1-4938/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: 49.49, per 1000 atoms: 0.37 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: 51.13 Conformation dependent library (CDL) restraints added in 5.1 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: 40.85 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: 221.06 Time building geometry restraints manager: 55.79 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: 74046 35.99 - 71.97: 2420 71.97 - 107.96: 181 107.96 - 143.95: 22 143.95 - 179.93: 60 Dihedral angle restraints: 76729 sinusoidal: 61528 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 76726 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: 2.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.120 Extract box with map and model: 18.190 Check model and map are aligned: 1.410 Set scattering table: 0.840 Process input model: 449.630 Find NCS groups from input model: 2.430 Set up NCS constraints: 0.280 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:10.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 486.000 ------------------------------------------------------------------------------- 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 : 14.707 179.933 66917 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 % 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 *********************** 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 : 5.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 85 outliers final: 23 residues processed: 1187 average time/residue: 1.9462 time to fit residues: 3332.4697 Evaluate side-chains 889 residues out of total 4485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 866 time to evaluate : 5.486 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 16 residues processed: 8 average time/residue: 0.9661 time to fit residues: 20.4031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 9.9990 overall best weight: 6.9190 ------------------------------------------------------------------------------- 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 ** B 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 E 27 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 104 ASN L 130 HIS M 22 GLN M 38 HIS M 125 GLN N 102 ASN N 119 ASN 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 Z 52 HIS b 3 HIS b 19 HIS b 26 GLN c 36 ASN ** c 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 56 HIS 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 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 14 HIS s 37 GLN s 50 ASN s 78 ASN u 62 GLN u 83 HIS v 54 ASN w 74 GLN w 86 HIS x 28 ASN y 24 GLN y 25 HIS y 67 ASN y 79 HIS Total number of N/Q/H flips: 94 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.097 144444 Z= 0.421 Angle : 0.680 12.118 216495 Z= 0.348 Chirality : 0.041 0.339 27962 Planarity : 0.005 0.063 11174 Dihedral : 14.728 179.950 57667 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.10 % Allowed : 11.56 % Favored : 88.34 % Rotamer Outliers : 7.64 % 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: -3.33 (0.10), residues: 5180 helix: -1.23 (0.13), residues: 1515 sheet: -2.07 (0.15), residues: 976 loop : -2.90 (0.10), residues: 2689 *********************** 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 1179 residues out of total 4485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 302 poor density : 877 time to evaluate : 5.656 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 302 outliers final: 144 residues processed: 1047 average time/residue: 1.7763 time to fit residues: 2765.9666 Evaluate side-chains 949 residues out of total 4485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 805 time to evaluate : 5.677 Switching outliers to nearest non-outliers outliers start: 144 outliers final: 95 residues processed: 50 average time/residue: 1.0445 time to fit residues: 102.2316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 942 random chunks: chunk 475 optimal weight: 7.9990 chunk 265 optimal weight: 6.9990 chunk 711 optimal weight: 10.0000 chunk 582 optimal weight: 10.0000 chunk 235 optimal weight: 2.9990 chunk 856 optimal weight: 20.0000 chunk 925 optimal weight: 1.9990 chunk 763 optimal weight: 30.0000 chunk 849 optimal weight: 1.9990 chunk 292 optimal weight: 7.9990 chunk 687 optimal weight: 20.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 40 ASN C 67 HIS C 136 GLN D 206 ASN E 27 ASN E 30 GLN G 33 GLN J 89 GLN K 4 GLN M 38 HIS N 119 ASN P 78 ASN Q 56 ASN S 26 ASN T 55 ASN V 58 HIS W 29 GLN X 20 HIS Z 19 GLN ** c 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 68 GLN ** i 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 128 ASN j 25 ASN k 18 GLN l 120 GLN n 5 HIS n 25 ASN p 34 ASN p 100 ASN ** p 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 78 ASN u 62 GLN v 6 ASN v 57 ASN y 24 GLN y 65 HIS y 71 ASN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.073 144444 Z= 0.271 Angle : 0.570 11.277 216495 Z= 0.297 Chirality : 0.036 0.301 27962 Planarity : 0.004 0.065 11174 Dihedral : 14.638 179.172 57667 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.54 % Favored : 89.38 % Rotamer Outliers : 7.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.91 (0.11), residues: 5180 helix: -0.84 (0.13), residues: 1514 sheet: -1.73 (0.16), residues: 924 loop : -2.71 (0.10), residues: 2742 *********************** 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 1119 residues out of total 4485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 284 poor density : 835 time to evaluate : 5.552 Fit side-chains revert: symmetry clash outliers start: 284 outliers final: 175 residues processed: 1005 average time/residue: 1.7644 time to fit residues: 2656.4093 Evaluate side-chains 969 residues out of total 4485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 794 time to evaluate : 5.325 Switching outliers to nearest non-outliers outliers start: 175 outliers final: 118 residues processed: 60 average time/residue: 1.0412 time to fit residues: 120.3469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 942 random chunks: chunk 846 optimal weight: 20.0000 chunk 644 optimal weight: 10.0000 chunk 444 optimal weight: 10.0000 chunk 94 optimal weight: 10.0000 chunk 408 optimal weight: 10.0000 chunk 575 optimal weight: 10.0000 chunk 860 optimal weight: 8.9990 chunk 910 optimal weight: 9.9990 chunk 449 optimal weight: 10.0000 chunk 815 optimal weight: 8.9990 chunk 245 optimal weight: 20.0000 overall best weight: 9.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 ASN B 58 HIS ** B 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 40 ASN C 136 GLN C 174 ASN D 206 ASN J 117 ASN J 137 HIS K 4 GLN ** L 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 104 ASN M 38 HIS N 119 ASN O 47 ASN Q 56 ASN S 26 ASN W 29 GLN X 20 HIS c 47 ASN d 41 HIS e 31 HIS ** i 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 128 ASN j 25 ASN k 11 ASN k 18 GLN l 120 GLN n 5 HIS n 25 ASN p 34 ASN p 100 ASN r 91 HIS s 78 ASN u 62 GLN v 6 ASN ** v 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 24 GLN y 67 ASN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.010 0.107 144444 Z= 0.576 Angle : 0.775 12.217 216495 Z= 0.395 Chirality : 0.047 0.404 27962 Planarity : 0.006 0.073 11174 Dihedral : 15.105 179.994 57667 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.14 % Allowed : 12.63 % Favored : 87.24 % Rotamer Outliers : 9.03 % 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: -2.95 (0.11), residues: 5180 helix: -1.01 (0.13), residues: 1528 sheet: -1.64 (0.16), residues: 980 loop : -2.71 (0.10), residues: 2672 *********************** 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 1173 residues out of total 4485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 357 poor density : 816 time to evaluate : 5.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 357 outliers final: 210 residues processed: 1032 average time/residue: 1.7566 time to fit residues: 2719.6333 Evaluate side-chains 1007 residues out of total 4485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 210 poor density : 797 time to evaluate : 5.483 Switching outliers to nearest non-outliers outliers start: 210 outliers final: 135 residues processed: 75 average time/residue: 1.0742 time to fit residues: 152.1036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 942 random chunks: chunk 758 optimal weight: 5.9990 chunk 516 optimal weight: 7.9990 chunk 13 optimal weight: 2.9990 chunk 677 optimal weight: 20.0000 chunk 375 optimal weight: 2.9990 chunk 777 optimal weight: 6.9990 chunk 629 optimal weight: 8.9990 chunk 1 optimal weight: 3.9990 chunk 464 optimal weight: 10.0000 chunk 817 optimal weight: 6.9990 chunk 229 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 E 30 GLN K 4 GLN ** L 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 38 HIS N 61 HIS N 119 ASN O 47 ASN Q 56 ASN S 73 ASN V 58 HIS W 29 GLN X 20 HIS ** c 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 41 HIS ** i 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 138 ASN k 18 GLN l 70 ASN n 5 HIS n 25 ASN p 34 ASN p 100 ASN ** p 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 112 GLN r 14 HIS s 78 ASN u 41 ASN u 62 GLN v 57 ASN x 65 ASN x 69 HIS y 24 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.067 144444 Z= 0.267 Angle : 0.592 11.662 216495 Z= 0.309 Chirality : 0.037 0.310 27962 Planarity : 0.005 0.057 11174 Dihedral : 14.844 179.736 57667 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.81 % Favored : 89.13 % Rotamer Outliers : 7.33 % 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: -2.65 (0.11), residues: 5180 helix: -0.66 (0.13), residues: 1514 sheet: -1.54 (0.16), residues: 971 loop : -2.55 (0.10), residues: 2695 *********************** 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 1140 residues out of total 4485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 290 poor density : 850 time to evaluate : 5.658 Fit side-chains revert: symmetry clash outliers start: 290 outliers final: 191 residues processed: 1036 average time/residue: 1.7983 time to fit residues: 2796.4360 Evaluate side-chains 1007 residues out of total 4485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 816 time to evaluate : 5.554 Switching outliers to nearest non-outliers outliers start: 191 outliers final: 132 residues processed: 60 average time/residue: 1.1166 time to fit residues: 125.4576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 179 optimal weight: 0.9990 chunk 534 optimal weight: 10.0000 chunk 224 optimal weight: 0.6980 chunk 911 optimal weight: 6.9990 chunk 756 optimal weight: 0.9980 chunk 421 optimal weight: 10.0000 chunk 75 optimal weight: 2.9990 chunk 301 optimal weight: 10.0000 chunk 478 optimal weight: 8.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 83 GLN C 136 GLN C 174 ASN G 33 GLN K 4 GLN ** L 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 38 HIS N 119 ASN Q 56 ASN W 29 GLN X 20 HIS ** c 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 41 HIS ** i 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 11 ASN k 18 GLN l 70 ASN n 5 HIS p 34 ASN p 100 ASN ** p 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 78 ASN u 62 GLN y 24 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 144444 Z= 0.170 Angle : 0.557 12.010 216495 Z= 0.293 Chirality : 0.034 0.290 27962 Planarity : 0.004 0.062 11174 Dihedral : 14.809 179.824 57667 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.02 % Favored : 88.92 % Rotamer Outliers : 6.88 % 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: -2.48 (0.11), residues: 5180 helix: -0.47 (0.13), residues: 1516 sheet: -1.44 (0.16), residues: 962 loop : -2.48 (0.11), residues: 2702 *********************** 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 1104 residues out of total 4485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 272 poor density : 832 time to evaluate : 7.325 Fit side-chains revert: symmetry clash outliers start: 272 outliers final: 185 residues processed: 1023 average time/residue: 1.7423 time to fit residues: 2681.2737 Evaluate side-chains 984 residues out of total 4485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 799 time to evaluate : 5.491 Switching outliers to nearest non-outliers outliers start: 185 outliers final: 142 residues processed: 44 average time/residue: 1.1145 time to fit residues: 93.7277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 942 random chunks: chunk 878 optimal weight: 0.0980 chunk 102 optimal weight: 40.0000 chunk 519 optimal weight: 10.0000 chunk 665 optimal weight: 30.0000 chunk 515 optimal weight: 10.0000 chunk 767 optimal weight: 8.9990 chunk 508 optimal weight: 10.0000 chunk 907 optimal weight: 0.7980 chunk 568 optimal weight: 20.0000 chunk 553 optimal weight: 10.0000 chunk 419 optimal weight: 10.0000 overall best weight: 5.9790 ------------------------------------------------------------------------------- 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 E 30 GLN G 33 GLN K 4 GLN ** L 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 38 HIS O 47 ASN P 10 ASN Q 56 ASN W 29 GLN X 20 HIS ** c 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 41 HIS ** i 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 18 GLN l 70 ASN n 5 HIS p 100 ASN ** p 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 78 ASN u 62 GLN y 24 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.089 144444 Z= 0.364 Angle : 0.632 12.109 216495 Z= 0.328 Chirality : 0.039 0.328 27962 Planarity : 0.005 0.059 11174 Dihedral : 14.861 179.275 57667 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.08 % Allowed : 11.78 % Favored : 88.15 % Rotamer Outliers : 7.33 % 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: -2.50 (0.11), residues: 5180 helix: -0.56 (0.13), residues: 1533 sheet: -1.44 (0.16), residues: 977 loop : -2.46 (0.11), residues: 2670 *********************** 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 1088 residues out of total 4485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 290 poor density : 798 time to evaluate : 5.630 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 290 outliers final: 203 residues processed: 995 average time/residue: 1.7606 time to fit residues: 2618.5497 Evaluate side-chains 988 residues out of total 4485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 203 poor density : 785 time to evaluate : 5.039 Switching outliers to nearest non-outliers outliers start: 203 outliers final: 149 residues processed: 55 average time/residue: 1.0393 time to fit residues: 110.1173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 6.9990 chunk 542 optimal weight: 10.0000 chunk 273 optimal weight: 9.9990 chunk 178 optimal weight: 9.9990 chunk 175 optimal weight: 7.9990 chunk 577 optimal weight: 20.0000 chunk 618 optimal weight: 10.0000 chunk 448 optimal weight: 10.0000 chunk 84 optimal weight: 0.2980 chunk 713 optimal weight: 7.9990 overall best weight: 6.6588 ------------------------------------------------------------------------------- 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 G 33 GLN K 4 GLN ** L 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 38 HIS P 10 ASN Q 56 ASN R 23 HIS W 29 GLN X 20 HIS ** c 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 41 HIS ** i 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 11 ASN k 18 GLN l 70 ASN n 5 HIS ** p 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 78 ASN u 62 GLN y 24 GLN y 30 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.090 144444 Z= 0.399 Angle : 0.663 12.044 216495 Z= 0.343 Chirality : 0.041 0.343 27962 Planarity : 0.005 0.069 11174 Dihedral : 14.973 179.668 57667 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.10 % Allowed : 12.14 % Favored : 87.76 % Rotamer Outliers : 6.85 % 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: -0.59 (0.13), residues: 1526 sheet: -1.41 (0.16), residues: 996 loop : -2.46 (0.11), residues: 2658 *********************** 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 1067 residues out of total 4485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 271 poor density : 796 time to evaluate : 5.645 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 271 outliers final: 197 residues processed: 987 average time/residue: 1.7395 time to fit residues: 2577.4217 Evaluate side-chains 979 residues out of total 4485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 197 poor density : 782 time to evaluate : 5.498 Switching outliers to nearest non-outliers outliers start: 197 outliers final: 154 residues processed: 43 average time/residue: 1.0285 time to fit residues: 87.9747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 942 random chunks: chunk 825 optimal weight: 8.9990 chunk 869 optimal weight: 20.0000 chunk 793 optimal weight: 7.9990 chunk 846 optimal weight: 20.0000 chunk 509 optimal weight: 8.9990 chunk 368 optimal weight: 30.0000 chunk 664 optimal weight: 20.0000 chunk 259 optimal weight: 0.8980 chunk 764 optimal weight: 0.7980 chunk 800 optimal weight: 0.9990 chunk 843 optimal weight: 7.9990 overall best weight: 3.7386 ------------------------------------------------------------------------------- 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 E 30 GLN K 4 GLN ** L 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 38 HIS O 47 ASN Q 56 ASN W 12 ASN W 29 GLN X 20 HIS ** c 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 41 HIS ** i 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 18 GLN l 70 ASN n 5 HIS n 25 ASN ** p 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 62 GLN y 24 GLN y 30 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.073 144444 Z= 0.243 Angle : 0.600 12.721 216495 Z= 0.315 Chirality : 0.037 0.322 27962 Planarity : 0.005 0.068 11174 Dihedral : 14.923 179.894 57667 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.39 % Favored : 88.55 % Rotamer Outliers : 5.99 % 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: -2.42 (0.11), residues: 5180 helix: -0.50 (0.13), residues: 1533 sheet: -1.37 (0.17), residues: 974 loop : -2.41 (0.11), residues: 2673 *********************** 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 1032 residues out of total 4485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 237 poor density : 795 time to evaluate : 5.626 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 237 outliers final: 187 residues processed: 978 average time/residue: 1.7519 time to fit residues: 2577.6469 Evaluate side-chains 970 residues out of total 4485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 783 time to evaluate : 5.538 Switching outliers to nearest non-outliers outliers start: 187 outliers final: 158 residues processed: 31 average time/residue: 1.1077 time to fit residues: 67.5390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 546 optimal weight: 10.0000 chunk 424 optimal weight: 10.0000 chunk 621 optimal weight: 10.0000 chunk 938 optimal weight: 7.9990 chunk 863 optimal weight: 0.9980 chunk 747 optimal weight: 6.9990 chunk 77 optimal weight: 0.0870 chunk 577 optimal weight: 20.0000 chunk 458 optimal weight: 8.9990 overall best weight: 3.4162 ------------------------------------------------------------------------------- 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 K 4 GLN ** L 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 119 ASN Q 56 ASN W 12 ASN W 29 GLN X 20 HIS ** c 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 30 ASN ** i 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 11 ASN l 70 ASN l 120 GLN n 5 HIS n 25 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 Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.068 144444 Z= 0.224 Angle : 0.574 13.929 216495 Z= 0.300 Chirality : 0.036 0.297 27962 Planarity : 0.004 0.056 11174 Dihedral : 14.824 179.712 57667 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.31 % Favored : 88.63 % Rotamer Outliers : 4.98 % 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: -2.31 (0.11), residues: 5180 helix: -0.37 (0.13), residues: 1528 sheet: -1.32 (0.17), residues: 960 loop : -2.36 (0.11), residues: 2692 ********************** 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 1002 residues out of total 4485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 197 poor density : 805 time to evaluate : 5.624 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 197 outliers final: 167 residues processed: 970 average time/residue: 1.7717 time to fit residues: 2568.6951 Evaluate side-chains 960 residues out of total 4485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 793 time to evaluate : 5.478 Switching outliers to nearest non-outliers outliers start: 167 outliers final: 149 residues processed: 19 average time/residue: 1.2118 time to fit residues: 45.5656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 10.0000 chunk 228 optimal weight: 9.9990 chunk 689 optimal weight: 10.0000 chunk 110 optimal weight: 0.9980 chunk 207 optimal weight: 10.0000 chunk 748 optimal weight: 0.1980 chunk 313 optimal weight: 10.0000 chunk 768 optimal weight: 6.9990 chunk 94 optimal weight: 8.9990 chunk 137 optimal weight: 0.0570 overall best weight: 3.4502 ------------------------------------------------------------------------------- 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 G 33 GLN K 4 GLN ** L 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 56 ASN W 12 ASN W 29 GLN X 20 HIS ** c 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 41 HIS ** i 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 18 GLN l 120 GLN n 5 HIS n 25 ASN 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 67 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.125916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.090233 restraints weight = 204317.954| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 0.84 r_work: 0.2996 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.058 144444 Z= 0.225 Angle : 0.566 12.288 216495 Z= 0.295 Chirality : 0.035 0.287 27962 Planarity : 0.004 0.055 11174 Dihedral : 14.747 179.938 57667 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.16 % Favored : 88.80 % Rotamer Outliers : 4.98 % 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: -2.22 (0.11), residues: 5180 helix: -0.30 (0.13), residues: 1533 sheet: -1.33 (0.16), residues: 969 loop : -2.29 (0.11), residues: 2678 =============================================================================== Job complete usr+sys time: 38621.43 seconds wall clock time: 671 minutes 15.78 seconds (40275.78 seconds total)