Starting phenix.real_space_refine on Sat Mar 2 04:13:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m5d_23673/03_2024/7m5d_23673_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m5d_23673/03_2024/7m5d_23673.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m5d_23673/03_2024/7m5d_23673_ligands.cif 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 { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m5d_23673/03_2024/7m5d_23673_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m5d_23673/03_2024/7m5d_23673_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m5d_23673/03_2024/7m5d_23673.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m5d_23673/03_2024/7m5d_23673.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m5d_23673/03_2024/7m5d_23673_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m5d_23673/03_2024/7m5d_23673_updated.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 4648 5.49 5 S 198 5.16 5 C 78130 2.51 5 N 28535 2.21 5 O 41948 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 52": "NH1" <-> "NH2" Residue "B ARG 63": "NH1" <-> "NH2" Residue "B ARG 80": "NH1" <-> "NH2" Residue "B TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 167": "NH1" <-> "NH2" Residue "B TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 177": "NH1" <-> "NH2" Residue "B ARG 182": "NH1" <-> "NH2" Residue "B GLU 185": "OE1" <-> "OE2" Residue "B ARG 212": "NH1" <-> "NH2" Residue "B GLU 236": "OE1" <-> "OE2" Residue "B ARG 269": "NH1" <-> "NH2" Residue "C ARG 13": "NH1" <-> "NH2" Residue "C GLU 28": "OE1" <-> "OE2" Residue "C ARG 33": "NH1" <-> "NH2" Residue "C ASP 43": "OD1" <-> "OD2" Residue "C ARG 59": "NH1" <-> "NH2" Residue "C GLU 74": "OE1" <-> "OE2" Residue "C ARG 77": "NH1" <-> "NH2" Residue "C ARG 83": "NH1" <-> "NH2" Residue "C GLU 89": "OE1" <-> "OE2" Residue "C ASP 108": "OD1" <-> "OD2" Residue "C PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 169": "NH1" <-> "NH2" Residue "C GLU 183": "OE1" <-> "OE2" Residue "C ARG 184": "NH1" <-> "NH2" Residue "D PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 21": "NH1" <-> "NH2" Residue "D TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 44": "NH1" <-> "NH2" Residue "D ARG 49": "NH1" <-> "NH2" Residue "D ARG 102": "NH1" <-> "NH2" Residue "D GLU 122": "OE1" <-> "OE2" Residue "D PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 144": "OE1" <-> "OE2" Residue "D GLU 152": "OE1" <-> "OE2" Residue "D ARG 162": "NH1" <-> "NH2" Residue "D ARG 170": "NH1" <-> "NH2" Residue "D PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 184": "OD1" <-> "OD2" Residue "E ARG 30": "NH1" <-> "NH2" Residue "E ARG 71": "NH1" <-> "NH2" Residue "E ARG 92": "NH1" <-> "NH2" Residue "E ARG 102": "NH1" <-> "NH2" Residue "E ARG 110": "NH1" <-> "NH2" Residue "E ARG 112": "NH1" <-> "NH2" Residue "E ARG 115": "NH1" <-> "NH2" Residue "E ASP 142": "OD1" <-> "OD2" Residue "E ARG 148": "NH1" <-> "NH2" Residue "E PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 3": "NH1" <-> "NH2" Residue "F GLU 42": "OE1" <-> "OE2" Residue "F PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 56": "OD1" <-> "OD2" Residue "F ASP 60": "OD1" <-> "OD2" Residue "F PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 147": "OD1" <-> "OD2" Residue "F ARG 152": "NH1" <-> "NH2" Residue "F ARG 153": "NH1" <-> "NH2" Residue "F ARG 163": "NH1" <-> "NH2" Residue "F ASP 166": "OD1" <-> "OD2" Residue "F ARG 170": "NH1" <-> "NH2" Residue "G GLU 48": "OE1" <-> "OE2" Residue "G ARG 50": "NH1" <-> "NH2" Residue "G ARG 51": "NH1" <-> "NH2" Residue "G GLU 55": "OE1" <-> "OE2" Residue "G ARG 68": "NH1" <-> "NH2" Residue "G GLU 70": "OE1" <-> "OE2" Residue "G GLU 87": "OE1" <-> "OE2" Residue "G ASP 98": "OD1" <-> "OD2" Residue "G ASP 101": "OD1" <-> "OD2" Residue "G GLU 127": "OE1" <-> "OE2" Residue "G GLU 129": "OE1" <-> "OE2" Residue "G PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 13": "NH1" <-> "NH2" Residue "J ARG 34": "NH1" <-> "NH2" Residue "J ARG 37": "NH1" <-> "NH2" Residue "J GLU 43": "OE1" <-> "OE2" Residue "J TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 95": "NH1" <-> "NH2" Residue "J ARG 96": "NH1" <-> "NH2" Residue "J ARG 120": "NH1" <-> "NH2" Residue "K GLU 4": "OE1" <-> "OE2" Residue "K ARG 17": "NH1" <-> "NH2" Residue "K ARG 18": "NH1" <-> "NH2" Residue "K ASP 56": "OD1" <-> "OD2" Residue "L GLU 10": "OE1" <-> "OE2" Residue "L ARG 21": "NH1" <-> "NH2" Residue "L ARG 33": "NH1" <-> "NH2" Residue "L ARG 41": "NH1" <-> "NH2" Residue "L ARG 47": "NH1" <-> "NH2" Residue "L ARG 60": "NH1" <-> "NH2" Residue "L PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 78": "NH1" <-> "NH2" Residue "L ASP 81": "OD1" <-> "OD2" Residue "L ARG 123": "NH1" <-> "NH2" Residue "L ARG 126": "NH1" <-> "NH2" Residue "M ARG 10": "NH1" <-> "NH2" Residue "M ARG 18": "NH1" <-> "NH2" Residue "M ASP 25": "OD1" <-> "OD2" Residue "M ARG 40": "NH1" <-> "NH2" Residue "M ARG 50": "NH1" <-> "NH2" Residue "M ARG 55": "NH1" <-> "NH2" Residue "M GLU 75": "OE1" <-> "OE2" Residue "M TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 111": "OE1" <-> "OE2" Residue "M ARG 114": "NH1" <-> "NH2" Residue "M PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 8": "NH1" <-> "NH2" Residue "N ARG 12": "NH1" <-> "NH2" Residue "N ARG 17": "NH1" <-> "NH2" Residue "N ARG 22": "NH1" <-> "NH2" Residue "N ARG 46": "NH1" <-> "NH2" Residue "N ARG 63": "NH1" <-> "NH2" Residue "N ARG 64": "NH1" <-> "NH2" Residue "N ARG 69": "NH1" <-> "NH2" Residue "N ASP 72": "OD1" <-> "OD2" Residue "N PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 96": "NH1" <-> "NH2" Residue "N PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 118": "NH1" <-> "NH2" Residue "O ARG 10": "NH1" <-> "NH2" Residue "O ARG 13": "NH1" <-> "NH2" Residue "O ARG 16": "NH1" <-> "NH2" Residue "O ARG 25": "NH1" <-> "NH2" Residue "O TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 81": "NH1" <-> "NH2" Residue "O ARG 94": "NH1" <-> "NH2" Residue "O ARG 102": "NH1" <-> "NH2" Residue "O ARG 111": "NH1" <-> "NH2" Residue "O PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 21": "NH1" <-> "NH2" Residue "P PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 62": "NH1" <-> "NH2" Residue "P ARG 89": "NH1" <-> "NH2" Residue "P TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 101": "NH1" <-> "NH2" Residue "P ARG 109": "NH1" <-> "NH2" Residue "Q ARG 3": "NH1" <-> "NH2" Residue "Q ARG 6": "NH1" <-> "NH2" Residue "Q ARG 13": "NH1" <-> "NH2" Residue "Q ARG 33": "NH1" <-> "NH2" Residue "Q ARG 48": "NH1" <-> "NH2" Residue "Q ARG 70": "NH1" <-> "NH2" Residue "Q TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 21": "NH1" <-> "NH2" Residue "R ARG 68": "NH1" <-> "NH2" Residue "R ARG 78": "NH1" <-> "NH2" Residue "R ARG 79": "NH1" <-> "NH2" Residue "R ARG 84": "NH1" <-> "NH2" Residue "R PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 52": "OE1" <-> "OE2" Residue "S ASP 68": "OD1" <-> "OD2" Residue "S PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 77": "OD1" <-> "OD2" Residue "S GLU 78": "OE1" <-> "OE2" Residue "S ARG 84": "NH1" <-> "NH2" Residue "S ARG 88": "NH1" <-> "NH2" Residue "S ARG 92": "NH1" <-> "NH2" Residue "S ASP 94": "OD1" <-> "OD2" Residue "S ARG 110": "NH1" <-> "NH2" Residue "T ARG 3": "NH1" <-> "NH2" Residue "T ARG 6": "NH1" <-> "NH2" Residue "T GLU 52": "OE1" <-> "OE2" Residue "T GLU 56": "OE1" <-> "OE2" Residue "T TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 6": "NH1" <-> "NH2" Residue "U ARG 82": "NH1" <-> "NH2" Residue "U ARG 86": "NH1" <-> "NH2" Residue "U PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 94": "NH1" <-> "NH2" Residue "V ARG 19": "NH1" <-> "NH2" Residue "V TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 43": "OD1" <-> "OD2" Residue "V GLU 55": "OE1" <-> "OE2" Residue "V PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 66": "OD1" <-> "OD2" Residue "V GLU 69": "OE1" <-> "OE2" Residue "V TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 3": "NH1" <-> "NH2" Residue "X ARG 18": "NH1" <-> "NH2" Residue "X PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 37": "NH1" <-> "NH2" Residue "X ARG 45": "NH1" <-> "NH2" Residue "X ARG 50": "NH1" <-> "NH2" Residue "X ARG 57": "NH1" <-> "NH2" Residue "X GLU 70": "OE1" <-> "OE2" Residue "X ARG 74": "NH1" <-> "NH2" Residue "X TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 13": "OE1" <-> "OE2" Residue "Y ARG 29": "NH1" <-> "NH2" Residue "Y ARG 47": "NH1" <-> "NH2" Residue "Y ASP 49": "OD1" <-> "OD2" Residue "Y ARG 52": "NH1" <-> "NH2" Residue "Z ARG 11": "NH1" <-> "NH2" Residue "Z ARG 30": "NH1" <-> "NH2" Residue "Z ARG 45": "NH1" <-> "NH2" Residue "Z PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 4": "OD1" <-> "OD2" Residue "a ASP 35": "OD1" <-> "OD2" Residue "a ARG 56": "NH1" <-> "NH2" Residue "a ARG 63": "NH1" <-> "NH2" Residue "b ARG 10": "NH1" <-> "NH2" Residue "b ARG 16": "NH1" <-> "NH2" Residue "b TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 52": "NH1" <-> "NH2" Residue "c GLU 7": "OE1" <-> "OE2" Residue "c PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 28": "NH1" <-> "NH2" Residue "c ARG 44": "NH1" <-> "NH2" Residue "d ARG 3": "NH1" <-> "NH2" Residue "d ARG 14": "NH1" <-> "NH2" Residue "d ARG 19": "NH1" <-> "NH2" Residue "d ARG 21": "NH1" <-> "NH2" Residue "d ARG 33": "NH1" <-> "NH2" Residue "d ARG 41": "NH1" <-> "NH2" Residue "e ARG 13": "NH1" <-> "NH2" Residue "e ARG 30": "NH1" <-> "NH2" Residue "e ARG 40": "NH1" <-> "NH2" Residue "e ARG 42": "NH1" <-> "NH2" Residue "f ASP 20": "OD1" <-> "OD2" Residue "f ARG 24": "NH1" <-> "NH2" Residue "g GLU 52": "OE1" <-> "OE2" Residue "g ARG 63": "NH1" <-> "NH2" Residue "g ARG 74": "NH1" <-> "NH2" Residue "g GLU 78": "OE1" <-> "OE2" Residue "g ASP 88": "OD1" <-> "OD2" Residue "g GLU 133": "OE1" <-> "OE2" Residue "g PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 192": "OD1" <-> "OD2" Residue "g PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ARG 208": "NH1" <-> "NH2" Residue "g ARG 225": "NH1" <-> "NH2" Residue "h PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 46": "OE1" <-> "OE2" Residue "h ARG 54": "NH1" <-> "NH2" Residue "h ARG 72": "NH1" <-> "NH2" Residue "h ARG 88": "NH1" <-> "NH2" Residue "h ASP 112": "OD1" <-> "OD2" Residue "h ASP 118": "OD1" <-> "OD2" Residue "h GLU 125": "OE1" <-> "OE2" Residue "h ARG 127": "NH1" <-> "NH2" Residue "h ARG 131": "NH1" <-> "NH2" Residue "h ARG 132": "NH1" <-> "NH2" Residue "h GLU 152": "OE1" <-> "OE2" Residue "h ARG 164": "NH1" <-> "NH2" Residue "h GLU 166": "OE1" <-> "OE2" Residue "h GLU 170": "OE1" <-> "OE2" Residue "h GLU 188": "OE1" <-> "OE2" Residue "i ASP 50": "OD1" <-> "OD2" Residue "i ARG 73": "NH1" <-> "NH2" Residue "i ARG 81": "NH1" <-> "NH2" Residue "i TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ASP 141": "OD1" <-> "OD2" Residue "i GLU 147": "OE1" <-> "OE2" Residue "i ASP 174": "OD1" <-> "OD2" Residue "i PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ASP 190": "OD1" <-> "OD2" Residue "j ARG 45": "NH1" <-> "NH2" Residue "j GLU 65": "OE1" <-> "OE2" Residue "j ARG 68": "NH1" <-> "NH2" Residue "j ARG 69": "NH1" <-> "NH2" Residue "j ARG 93": "NH1" <-> "NH2" Residue "j GLU 116": "OE1" <-> "OE2" Residue "j ARG 157": "NH1" <-> "NH2" Residue "j GLU 162": "OE1" <-> "OE2" Residue "k ASP 13": "OD1" <-> "OD2" Residue "k GLU 33": "OE1" <-> "OE2" Residue "k ARG 45": "NH1" <-> "NH2" Residue "k GLU 75": "OE1" <-> "OE2" Residue "k ARG 79": "NH1" <-> "NH2" Residue "k ASP 82": "OD1" <-> "OD2" Residue "l ARG 4": "NH1" <-> "NH2" Residue "l GLU 21": "OE1" <-> "OE2" Residue "l ARG 53": "NH1" <-> "NH2" Residue "l ARG 78": "NH1" <-> "NH2" Residue "l ARG 79": "NH1" <-> "NH2" Residue "l GLU 90": "OE1" <-> "OE2" Residue "l ARG 92": "NH1" <-> "NH2" Residue "l GLU 139": "OE1" <-> "OE2" Residue "l GLU 146": "OE1" <-> "OE2" Residue "m ASP 48": "OD1" <-> "OD2" Residue "m GLU 52": "OE1" <-> "OE2" Residue "m ASP 54": "OD1" <-> "OD2" Residue "m TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m GLU 91": "OE1" <-> "OE2" Residue "n ARG 11": "NH1" <-> "NH2" Residue "n PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ARG 41": "NH1" <-> "NH2" Residue "n GLU 42": "OE1" <-> "OE2" Residue "n ASP 91": "OD1" <-> "OD2" Residue "n ARG 130": "NH1" <-> "NH2" Residue "o ARG 5": "NH1" <-> "NH2" Residue "o GLU 24": "OE1" <-> "OE2" Residue "o GLU 27": "OE1" <-> "OE2" Residue "o ARG 45": "NH1" <-> "NH2" Residue "o PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o GLU 81": "OE1" <-> "OE2" Residue "o ARG 89": "NH1" <-> "NH2" Residue "o ASP 91": "OD1" <-> "OD2" Residue "o ASP 97": "OD1" <-> "OD2" Residue "p ARG 37": "NH1" <-> "NH2" Residue "p ARG 69": "NH1" <-> "NH2" Residue "p ARG 93": "NH1" <-> "NH2" Residue "p ARG 106": "NH1" <-> "NH2" Residue "q ARG 9": "NH1" <-> "NH2" Residue "q ARG 14": "NH1" <-> "NH2" Residue "q ARG 50": "NH1" <-> "NH2" Residue "q GLU 62": "OE1" <-> "OE2" Residue "q ARG 83": "NH1" <-> "NH2" Residue "q TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ARG 29": "NH1" <-> "NH2" Residue "r ARG 70": "NH1" <-> "NH2" Residue "r ARG 87": "NH1" <-> "NH2" Residue "r ARG 109": "NH1" <-> "NH2" Residue "s ARG 59": "NH1" <-> "NH2" Residue "s ARG 63": "NH1" <-> "NH2" Residue "s ARG 65": "NH1" <-> "NH2" Residue "s ARG 69": "NH1" <-> "NH2" Residue "s ARG 85": "NH1" <-> "NH2" Residue "s GLU 86": "OE1" <-> "OE2" Residue "t GLU 6": "OE1" <-> "OE2" Residue "t PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t ARG 72": "NH1" <-> "NH2" Residue "t ASP 74": "OD1" <-> "OD2" Residue "t GLU 83": "OE1" <-> "OE2" Residue "t ARG 89": "NH1" <-> "NH2" Residue "u PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ASP 23": "OD1" <-> "OD2" Residue "u ARG 28": "NH1" <-> "NH2" Residue "u PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u GLU 45": "OE1" <-> "OE2" Residue "u ARG 51": "NH1" <-> "NH2" Residue "u ASP 69": "OD1" <-> "OD2" Residue "v ARG 11": "NH1" <-> "NH2" Residue "v ASP 15": "OD1" <-> "OD2" Residue "v GLU 26": "OE1" <-> "OE2" Residue "v ARG 27": "NH1" <-> "NH2" Residue "v PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v ASP 48": "OD1" <-> "OD2" Residue "v ASP 57": "OD1" <-> "OD2" Residue "v ARG 65": "NH1" <-> "NH2" Residue "v ARG 77": "NH1" <-> "NH2" Residue "w ARG 61": "NH1" <-> "NH2" Residue "w TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x ASP 12": "OD1" <-> "OD2" Residue "x GLU 20": "OE1" <-> "OE2" Residue "x GLU 24": "OE1" <-> "OE2" Residue "x ARG 32": "NH1" <-> "NH2" Residue "x ASP 64": "OD1" <-> "OD2" Residue "y GLU 15": "OE1" <-> "OE2" Residue "y ASP 43": "OD1" <-> "OD2" Residue "y PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y GLU 53": "OE1" <-> "OE2" Residue "y ARG 60": "NH1" <-> "NH2" Residue "y ARG 74": "NH1" <-> "NH2" Residue "z GLU 8": "OE1" <-> "OE2" Residue "z GLU 31": "OE1" <-> "OE2" Residue "z ARG 33": "NH1" <-> "NH2" Residue "z GLU 44": "OE1" <-> "OE2" Residue "z ARG 45": "NH1" <-> "NH2" Residue "z ARG 55": "NH1" <-> "NH2" Residue "z ARG 62": "NH1" <-> "NH2" Residue "z ARG 67": "NH1" <-> "NH2" Residue "z ARG 69": "NH1" <-> "NH2" Residue "7 PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ARG 49": "NH1" <-> "NH2" Residue "7 GLU 63": "OE1" <-> "OE2" Residue "7 PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ASP 88": "OD1" <-> "OD2" Residue "7 GLU 97": "OE1" <-> "OE2" Residue "7 ARG 122": "NH1" <-> "NH2" Residue "7 ARG 124": "NH1" <-> "NH2" Residue "7 PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ASP 150": "OD1" <-> "OD2" Residue "7 TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ARG 205": "NH1" <-> "NH2" Residue "7 GLU 230": "OE1" <-> "OE2" Residue "7 PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ASP 266": "OD1" <-> "OD2" Residue "7 GLU 274": "OE1" <-> "OE2" Residue "7 ARG 282": "NH1" <-> "NH2" Residue "7 ARG 312": "NH1" <-> "NH2" Residue "7 PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 383": "OE1" <-> "OE2" Residue "7 PHE 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ASP 447": "OD1" <-> "OD2" Residue "7 ARG 452": "NH1" <-> "NH2" Residue "7 GLU 460": "OE1" <-> "OE2" Residue "7 ARG 472": "NH1" <-> "NH2" Residue "7 GLU 490": "OE1" <-> "OE2" Residue "7 ASP 496": "OD1" <-> "OD2" Residue "7 TYR 518": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ARG 527": "NH1" <-> "NH2" Residue "I TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 40": "OE1" <-> "OE2" Residue "H ARG 56": "NH1" <-> "NH2" Residue "H PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 87": "OE1" <-> "OE2" Residue "H GLU 107": "OE1" <-> "OE2" Residue "H PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 31": "OD1" <-> "OD2" Residue "A ARG 34": "NH1" <-> "NH2" Residue "A PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 41": "OE1" <-> "OE2" Residue "A ARG 50": "NH1" <-> "NH2" Residue "A ASP 70": "OD1" <-> "OD2" Residue "A PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 142": "NH1" <-> "NH2" Residue "A GLU 153": "OE1" <-> "OE2" Residue "A ARG 183": "NH1" <-> "NH2" Residue "A ASP 211": "OD1" <-> "OD2" Residue "A PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 328": "NH1" <-> "NH2" Residue "A ASP 338": "OD1" <-> "OD2" Residue "6 PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 153460 Number of models: 1 Model: "" Number of chains: 60 Chain: "1" Number of atoms: 62336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2903, 62336 Classifications: {'RNA': 2903} Modifications used: {'rna2p': 6, 'rna2p_pur': 287, 'rna2p_pyr': 165, 'rna3p': 16, 'rna3p_pur': 1380, 'rna3p_pyr': 1049} Link IDs: {'rna2p': 457, 'rna3p': 2445} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 9 Chain: "2" Number of atoms: 32929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1534, 32929 Classifications: {'RNA': 1534} Modifications used: {'rna2p': 1, 'rna2p_pur': 118, 'rna2p_pyr': 89, 'rna3p': 10, 'rna3p_pur': 751, 'rna3p_pyr': 564} Link IDs: {'rna2p': 207, 'rna3p': 1326} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 2 Chain: "3" Number of atoms: 2569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2569 Classifications: {'RNA': 120} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 8, 'rna3p_pur': 57, 'rna3p_pyr': 48} Link IDs: {'rna2p': 14, 'rna3p': 105} Chain: "4" Number of atoms: 316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 316 Classifications: {'RNA': 15} Modifications used: {'rna2p_pur': 4, 'rna3p_pur': 4, 'rna3p_pyr': 7} Link IDs: {'rna2p': 4, 'rna3p': 10} Chain: "5" Number of atoms: 1627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1627 Classifications: {'RNA': 76} Modifications used: {'rna2p': 2, 'rna2p_pur': 6, 'rna2p_pyr': 6, 'rna3p': 3, 'rna3p_pur': 34, 'rna3p_pyr': 25} Link IDs: {'rna2p': 13, 'rna3p': 62} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 2082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2082 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "C" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1565 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 202} Chain: "D" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "E" Number of atoms: 1410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1410 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "F" Number of atoms: 1313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1313 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 8, 'TRANS': 166} Chain: "G" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1111 Classifications: {'peptide': 149} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 145} Chain: "J" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "K" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 946 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 5, 'TRANS': 117} Chain: "L" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1053 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain: "M" Number of atoms: 1074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1074 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "N" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 951 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "O" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 892 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "P" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 917 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "Q" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "R" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "S" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 857 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "T" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 746 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 1, 'TRANS': 92} Chain: "U" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 788 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 3, 'TRANS': 99} Chain: "V" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 753 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "W" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 582 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 74} Chain: "X" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "Y" Number of atoms: 501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 501 Classifications: {'peptide': 62} Modifications used: {'COO': 1} Link IDs: {'TRANS': 61} Chain: "Z" Number of atoms: 448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 448 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "a" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 522 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "b" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 444 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "c" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 426 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 2, 'TRANS': 49} Chain: "d" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "e" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 504 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "f" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 302 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "g" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1760 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 7, 'TRANS': 217} Chain: "h" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1636 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 7, 'TRANS': 200} Chain: "i" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "j" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1152 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 5, 'TRANS': 150} Chain: "k" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 848 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "l" Number of atoms: 1181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1181 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain: "m" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "n" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1022 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "o" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 790 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 5, 'TRANS': 93} Chain: "p" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 877 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "q" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 957 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 115} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'0TD:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "r" Number of atoms: 900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 900 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "s" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 805 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "t" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 714 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'TRANS': 87} Chain: "u" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 649 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "v" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 648 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "w" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 544 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "x" Number of atoms: 663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 663 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 5, 'TRANS': 77} Chain: "y" Number of atoms: 669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 669 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "z" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 589 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "7" Number of atoms: 4132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 4132 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 19, 'TRANS': 505} Chain: "I" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1032 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 131} Chain: "H" Number of atoms: 988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 988 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain: "A" Number of atoms: 2839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2839 Classifications: {'peptide': 360} Link IDs: {'PTRANS': 11, 'TRANS': 348} Chain: "6" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "a" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM A0HPX SG CYS a 16 66.375 131.589 45.637 1.00 34.28 S ATOM A0HQ9 SG CYS a 18 63.114 130.379 44.502 1.00 39.57 S ATOM A0HU7 SG CYS a 37 63.231 132.160 47.745 1.00 34.65 S ATOM A0HUS SG CYS a 40 64.844 128.847 47.769 1.00 36.81 S Time building chain proxies: 58.15, per 1000 atoms: 0.38 Number of scatterers: 153460 At special positions: 0 Unit cell: (230.214, 272.731, 243.695, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 198 16.00 P 4648 15.00 O 41948 8.00 N 28535 7.00 C 78130 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: 58.90 Conformation dependent library (CDL) restraints added in 8.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN a 101 " pdb="ZN ZN a 101 " - pdb=" SG CYS a 37 " pdb="ZN ZN a 101 " - pdb=" SG CYS a 16 " pdb="ZN ZN a 101 " - pdb=" SG CYS a 18 " pdb="ZN ZN a 101 " - pdb=" SG CYS a 40 " Number of angles added : 6 13510 Ramachandran restraints generated. 6755 Oldfield, 0 Emsley, 6755 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12634 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 208 helices and 76 sheets defined 39.6% alpha, 18.6% beta 1571 base pairs and 2594 stacking pairs defined. Time for finding SS restraints: 79.89 Creating SS restraints... Processing helix chain 'B' and resid 11 through 17 removed outlier: 7.530A pdb=" N HIS B 15 " --> pdb=" O PRO B 11 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N VAL B 16 " --> pdb=" O GLY B 12 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N VAL B 17 " --> pdb=" O ARG B 13 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 11 through 17' Processing helix chain 'B' and resid 131 through 136 removed outlier: 3.819A pdb=" N ILE B 135 " --> pdb=" O PRO B 131 " (cutoff:3.500A) Proline residue: B 136 - end of helix No H-bonds generated for 'chain 'B' and resid 131 through 136' Processing helix chain 'B' and resid 207 through 215 removed outlier: 3.970A pdb=" N ALA B 211 " --> pdb=" O LYS B 207 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ARG B 214 " --> pdb=" O ALA B 210 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLY B 215 " --> pdb=" O ALA B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 226 removed outlier: 4.134A pdb=" N MET B 225 " --> pdb=" O ARG B 221 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N ASN B 226 " --> pdb=" O GLY B 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 221 through 226' Processing helix chain 'B' and resid 260 through 268 removed outlier: 3.862A pdb=" N ASP B 264 " --> pdb=" O ASN B 260 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N LYS B 265 " --> pdb=" O LYS B 261 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N PHE B 266 " --> pdb=" O ARG B 262 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ILE B 267 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N VAL B 268 " --> pdb=" O ASP B 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 260 through 268' Processing helix chain 'B' and resid 197 through 202 removed outlier: 4.281A pdb=" N MET B 201 " --> pdb=" O ALA B 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 61 removed outlier: 6.209A pdb=" N THR C 61 " --> pdb=" O ALA C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 72 removed outlier: 3.657A pdb=" N ALA C 71 " --> pdb=" O HIS C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 103 removed outlier: 4.573A pdb=" N ALA C 102 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N ASP C 103 " --> pdb=" O GLU C 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 98 through 103' Processing helix chain 'C' and resid 120 through 125 Processing helix chain 'C' and resid 39 through 44 Processing helix chain 'D' and resid 15 through 20 Processing helix chain 'D' and resid 24 through 41 removed outlier: 3.647A pdb=" N ARG D 40 " --> pdb=" O ALA D 36 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N GLN D 41 " --> pdb=" O ALA D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 116 Processing helix chain 'D' and resid 130 through 142 Processing helix chain 'D' and resid 154 through 163 removed outlier: 3.672A pdb=" N ARG D 162 " --> pdb=" O PHE D 158 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ASN D 163 " --> pdb=" O LEU D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 183 removed outlier: 3.832A pdb=" N PHE D 183 " --> pdb=" O SER D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 201 removed outlier: 3.769A pdb=" N LYS D 194 " --> pdb=" O ALA D 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 21 removed outlier: 5.341A pdb=" N VAL E 13 " --> pdb=" O LYS E 9 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 47 removed outlier: 3.833A pdb=" N LYS E 47 " --> pdb=" O ALA E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 62 removed outlier: 4.379A pdb=" N ASN E 52 " --> pdb=" O LYS E 48 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA E 53 " --> pdb=" O LEU E 49 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLY E 62 " --> pdb=" O ALA E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 111 removed outlier: 5.333A pdb=" N VAL E 108 " --> pdb=" O ILE E 104 " (cutoff:3.500A) Proline residue: E 109 - end of helix Processing helix chain 'E' and resid 162 through 174 removed outlier: 4.275A pdb=" N GLY E 166 " --> pdb=" O SER E 162 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N PHE E 173 " --> pdb=" O LEU E 169 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ASP E 174 " --> pdb=" O LEU E 170 " (cutoff:3.500A) Processing helix chain 'E' and resid 134 through 139 removed outlier: 3.823A pdb=" N ILE E 137 " --> pdb=" O GLU E 134 " (cutoff:3.500A) Proline residue: E 139 - end of helix Processing helix chain 'F' and resid 2 through 7 removed outlier: 3.991A pdb=" N ALA F 7 " --> pdb=" O ARG F 3 " (cutoff:3.500A) Processing helix chain 'F' and resid 60 through 81 Processing helix chain 'F' and resid 137 through 153 removed outlier: 3.576A pdb=" N TYR F 151 " --> pdb=" O ASP F 147 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ARG F 152 " --> pdb=" O LEU F 148 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 28 Processing helix chain 'G' and resid 29 through 34 Processing helix chain 'G' and resid 40 through 48 removed outlier: 3.955A pdb=" N GLU G 45 " --> pdb=" O LYS G 41 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 74 removed outlier: 4.050A pdb=" N LEU G 54 " --> pdb=" O ARG G 50 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ALA G 56 " --> pdb=" O ALA G 52 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ALA G 74 " --> pdb=" O GLU G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 107 removed outlier: 3.558A pdb=" N ALA G 105 " --> pdb=" O ASP G 101 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ALA G 106 " --> pdb=" O ALA G 102 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLY G 107 " --> pdb=" O VAL G 103 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 38 removed outlier: 4.193A pdb=" N GLU J 31 " --> pdb=" O ARG J 27 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 96 Processing helix chain 'J' and resid 97 through 110 removed outlier: 4.469A pdb=" N ILE J 101 " --> pdb=" O PRO J 97 " (cutoff:3.500A) Proline residue: J 110 - end of helix Processing helix chain 'J' and resid 112 through 122 removed outlier: 4.031A pdb=" N LYS J 121 " --> pdb=" O ALA J 117 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N LEU J 122 " --> pdb=" O MET J 118 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 119 Processing helix chain 'L' and resid 37 through 42 removed outlier: 4.034A pdb=" N ARG L 41 " --> pdb=" O GLY L 37 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N SER L 42 " --> pdb=" O GLN L 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 37 through 42' Processing helix chain 'L' and resid 56 through 62 Proline residue: L 62 - end of helix Processing helix chain 'L' and resid 68 through 75 removed outlier: 3.944A pdb=" N ALA L 72 " --> pdb=" O SER L 68 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ILE L 73 " --> pdb=" O ARG L 69 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N ALA L 75 " --> pdb=" O ALA L 71 " (cutoff:3.500A) Processing helix chain 'L' and resid 78 through 85 removed outlier: 4.358A pdb=" N LEU L 82 " --> pdb=" O ARG L 78 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ALA L 83 " --> pdb=" O LEU L 79 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LYS L 84 " --> pdb=" O SER L 80 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL L 85 " --> pdb=" O ASP L 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 78 through 85' Processing helix chain 'L' and resid 91 through 99 Processing helix chain 'L' and resid 128 through 139 Processing helix chain 'M' and resid 42 through 58 Processing helix chain 'M' and resid 109 through 125 removed outlier: 4.214A pdb=" N LYS M 123 " --> pdb=" O LEU M 119 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU M 124 " --> pdb=" O ALA M 120 " (cutoff:3.500A) Proline residue: M 125 - end of helix Processing helix chain 'N' and resid 13 through 32 Processing helix chain 'N' and resid 38 through 57 removed outlier: 3.526A pdb=" N ARG N 45 " --> pdb=" O ALA N 41 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ARG N 46 " --> pdb=" O LYS N 42 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N VAL N 47 " --> pdb=" O GLU N 43 " (cutoff:3.500A) Proline residue: N 50 - end of helix removed outlier: 4.683A pdb=" N THR N 57 " --> pdb=" O THR N 53 " (cutoff:3.500A) Processing helix chain 'N' and resid 59 through 71 Processing helix chain 'N' and resid 72 through 88 removed outlier: 4.760A pdb=" N GLY N 84 " --> pdb=" O PHE N 80 " (cutoff:3.500A) Proline residue: N 85 - end of helix Processing helix chain 'O' and resid 2 through 22 removed outlier: 4.699A pdb=" N ARG O 13 " --> pdb=" O ARG O 9 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N ALA O 14 " --> pdb=" O ARG O 10 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ARG O 16 " --> pdb=" O THR O 12 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 63 removed outlier: 4.883A pdb=" N GLN O 61 " --> pdb=" O ALA O 57 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N LEU O 62 " --> pdb=" O ILE O 58 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N LYS O 63 " --> pdb=" O ALA O 59 " (cutoff:3.500A) Processing helix chain 'O' and resid 67 through 86 Processing helix chain 'O' and resid 101 through 114 Processing helix chain 'P' and resid 2 through 13 removed outlier: 4.038A pdb=" N GLN P 12 " --> pdb=" O LEU P 8 " (cutoff:3.500A) Processing helix chain 'P' and resid 99 through 104 removed outlier: 4.201A pdb=" N ARG P 103 " --> pdb=" O TYR P 99 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N THR P 104 " --> pdb=" O LEU P 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 99 through 104' Processing helix chain 'Q' and resid 6 through 22 removed outlier: 3.666A pdb=" N ILE Q 17 " --> pdb=" O ARG Q 13 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLN Q 20 " --> pdb=" O LYS Q 16 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LYS Q 22 " --> pdb=" O LEU Q 18 " (cutoff:3.500A) Processing helix chain 'Q' and resid 26 through 31 removed outlier: 4.134A pdb=" N ARG Q 30 " --> pdb=" O GLY Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 39 through 73 removed outlier: 3.908A pdb=" N ARG Q 51 " --> pdb=" O TYR Q 47 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N LYS Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ARG Q 55 " --> pdb=" O ARG Q 51 " (cutoff:3.500A) Processing helix chain 'Q' and resid 75 through 87 Processing helix chain 'Q' and resid 91 through 102 Processing helix chain 'Q' and resid 103 through 118 Processing helix chain 'S' and resid 13 through 25 removed outlier: 3.880A pdb=" N VAL S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LEU S 23 " --> pdb=" O LEU S 19 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ILE S 24 " --> pdb=" O VAL S 20 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG S 25 " --> pdb=" O ALA S 21 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 39 removed outlier: 3.703A pdb=" N ASP S 34 " --> pdb=" O SER S 30 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 61 removed outlier: 3.843A pdb=" N VAL S 45 " --> pdb=" O LYS S 41 " (cutoff:3.500A) Processing helix chain 'T' and resid 3 through 11 removed outlier: 4.113A pdb=" N LEU T 11 " --> pdb=" O LEU T 7 " (cutoff:3.500A) Processing helix chain 'T' and resid 17 through 26 Processing helix chain 'T' and resid 39 through 50 Processing helix chain 'U' and resid 66 through 71 removed outlier: 4.045A pdb=" N VAL U 70 " --> pdb=" O GLN U 66 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N ALA U 71 " --> pdb=" O VAL U 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 66 through 71' Processing helix chain 'V' and resid 13 through 24 removed outlier: 3.820A pdb=" N ASN V 24 " --> pdb=" O LEU V 20 " (cutoff:3.500A) Processing helix chain 'V' and resid 43 through 53 removed outlier: 4.485A pdb=" N LYS V 53 " --> pdb=" O ASN V 49 " (cutoff:3.500A) Processing helix chain 'V' and resid 54 through 59 removed outlier: 4.384A pdb=" N SER V 58 " --> pdb=" O ALA V 54 " (cutoff:3.500A) Processing helix chain 'X' and resid 52 through 63 Processing helix chain 'X' and resid 64 through 75 Processing helix chain 'Y' and resid 2 through 8 removed outlier: 4.211A pdb=" N GLU Y 8 " --> pdb=" O LYS Y 4 " (cutoff:3.500A) Processing helix chain 'Y' and resid 10 through 35 removed outlier: 3.785A pdb=" N SER Y 34 " --> pdb=" O MET Y 30 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N GLY Y 35 " --> pdb=" O GLN Y 31 " (cutoff:3.500A) Processing helix chain 'Y' and resid 40 through 61 removed outlier: 4.454A pdb=" N LYS Y 44 " --> pdb=" O SER Y 40 " (cutoff:3.500A) Processing helix chain 'Z' and resid 17 through 28 Processing helix chain 'Z' and resid 41 through 52 Processing helix chain 'a' and resid 44 through 51 removed outlier: 5.901A pdb=" N GLN a 48 " --> pdb=" O PHE a 44 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N ARG a 49 " --> pdb=" O THR a 45 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASP a 50 " --> pdb=" O GLY a 46 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N VAL a 51 " --> pdb=" O LYS a 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 44 through 51' Processing helix chain 'a' and resid 55 through 64 removed outlier: 4.162A pdb=" N ARG a 59 " --> pdb=" O GLY a 55 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N PHE a 64 " --> pdb=" O PHE a 60 " (cutoff:3.500A) Processing helix chain 'b' and resid 9 through 19 removed outlier: 4.944A pdb=" N HIS b 19 " --> pdb=" O MET b 15 " (cutoff:3.500A) Processing helix chain 'd' and resid 8 through 16 Processing helix chain 'd' and resid 17 through 25 removed outlier: 4.285A pdb=" N THR d 24 " --> pdb=" O ALA d 20 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N LYS d 25 " --> pdb=" O ARG d 21 " (cutoff:3.500A) Processing helix chain 'd' and resid 26 through 38 Processing helix chain 'e' and resid 7 through 14 removed outlier: 3.617A pdb=" N ARG e 13 " --> pdb=" O GLY e 9 " (cutoff:3.500A) Processing helix chain 'e' and resid 37 through 46 Proline residue: e 46 - end of helix Processing helix chain 'e' and resid 54 through 63 removed outlier: 3.635A pdb=" N VAL e 58 " --> pdb=" O ASP e 54 " (cutoff:3.500A) Proline residue: e 63 - end of helix Processing helix chain 'g' and resid 5 through 13 removed outlier: 4.562A pdb=" N MET g 9 " --> pdb=" O SER g 5 " (cutoff:3.500A) Processing helix chain 'g' and resid 27 through 32 removed outlier: 3.983A pdb=" N ILE g 31 " --> pdb=" O MET g 27 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N PHE g 32 " --> pdb=" O LYS g 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 27 through 32' Processing helix chain 'g' and resid 42 through 64 Proline residue: g 48 - end of helix removed outlier: 4.032A pdb=" N GLU g 52 " --> pdb=" O PRO g 48 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ARG g 63 " --> pdb=" O LYS g 59 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LYS g 64 " --> pdb=" O ILE g 60 " (cutoff:3.500A) Processing helix chain 'g' and resid 73 through 88 removed outlier: 6.515A pdb=" N SER g 77 " --> pdb=" O LYS g 73 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N GLU g 78 " --> pdb=" O ARG g 74 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N ALA g 79 " --> pdb=" O ALA g 75 " (cutoff:3.500A) Processing helix chain 'g' and resid 103 through 123 removed outlier: 4.263A pdb=" N GLN g 109 " --> pdb=" O LYS g 105 " (cutoff:3.500A) Processing helix chain 'g' and resid 130 through 148 Processing helix chain 'g' and resid 165 through 170 removed outlier: 3.814A pdb=" N HIS g 170 " --> pdb=" O ALA g 166 " (cutoff:3.500A) Processing helix chain 'g' and resid 171 through 180 Processing helix chain 'g' and resid 206 through 227 Processing helix chain 'h' and resid 6 through 12 Processing helix chain 'h' and resid 28 through 48 removed outlier: 3.828A pdb=" N ALA h 48 " --> pdb=" O THR h 44 " (cutoff:3.500A) Processing helix chain 'h' and resid 72 through 78 Processing helix chain 'h' and resid 81 through 96 removed outlier: 5.416A pdb=" N GLU h 85 " --> pdb=" O GLY h 81 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LYS h 86 " --> pdb=" O GLU h 82 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL h 90 " --> pdb=" O LYS h 86 " (cutoff:3.500A) Processing helix chain 'h' and resid 108 through 113 removed outlier: 4.402A pdb=" N ASP h 112 " --> pdb=" O LYS h 108 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N ALA h 113 " --> pdb=" O PRO h 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 108 through 113' Processing helix chain 'h' and resid 114 through 127 Processing helix chain 'h' and resid 129 through 145 removed outlier: 3.715A pdb=" N GLY h 145 " --> pdb=" O ALA h 141 " (cutoff:3.500A) Processing helix chain 'i' and resid 7 through 16 removed outlier: 4.329A pdb=" N LEU i 11 " --> pdb=" O PRO i 7 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER i 12 " --> pdb=" O LYS i 8 " (cutoff:3.500A) Processing helix chain 'i' and resid 27 through 32 removed outlier: 3.863A pdb=" N LYS i 31 " --> pdb=" O ALA i 27 " (cutoff:3.500A) Processing helix chain 'i' and resid 49 through 66 Processing helix chain 'i' and resid 68 through 83 removed outlier: 5.207A pdb=" N LYS i 83 " --> pdb=" O ALA i 79 " (cutoff:3.500A) Processing helix chain 'i' and resid 85 through 97 removed outlier: 4.001A pdb=" N ARG i 97 " --> pdb=" O LEU i 93 " (cutoff:3.500A) Processing helix chain 'i' and resid 98 through 106 Processing helix chain 'i' and resid 110 through 121 removed outlier: 4.002A pdb=" N LYS i 121 " --> pdb=" O LEU i 117 " (cutoff:3.500A) Processing helix chain 'i' and resid 146 through 151 removed outlier: 4.860A pdb=" N LYS i 151 " --> pdb=" O GLU i 147 " (cutoff:3.500A) Processing helix chain 'i' and resid 152 through 166 removed outlier: 3.966A pdb=" N LYS i 156 " --> pdb=" O GLN i 152 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU i 161 " --> pdb=" O ALA i 157 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU i 163 " --> pdb=" O LEU i 159 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLN i 164 " --> pdb=" O GLU i 160 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ARG i 165 " --> pdb=" O LEU i 161 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N GLU i 166 " --> pdb=" O ALA i 162 " (cutoff:3.500A) Processing helix chain 'i' and resid 187 through 192 removed outlier: 4.854A pdb=" N SER i 192 " --> pdb=" O ARG i 188 " (cutoff:3.500A) Processing helix chain 'i' and resid 196 through 206 removed outlier: 4.202A pdb=" N ILE i 200 " --> pdb=" O ASN i 196 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N SER i 205 " --> pdb=" O VAL i 201 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N LYS i 206 " --> pdb=" O GLU i 202 " (cutoff:3.500A) Processing helix chain 'j' and resid 55 through 71 removed outlier: 3.613A pdb=" N ARG j 69 " --> pdb=" O GLU j 65 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ASN j 70 " --> pdb=" O LYS j 66 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N MET j 71 " --> pdb=" O ALA j 67 " (cutoff:3.500A) Processing helix chain 'j' and resid 109 through 119 removed outlier: 3.903A pdb=" N ALA j 113 " --> pdb=" O GLY j 109 " (cutoff:3.500A) Processing helix chain 'j' and resid 132 through 147 Processing helix chain 'j' and resid 149 through 158 Processing helix chain 'j' and resid 160 through 165 Processing helix chain 'k' and resid 11 through 16 removed outlier: 4.077A pdb=" N SER k 15 " --> pdb=" O HIS k 11 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N GLU k 16 " --> pdb=" O PRO k 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 11 through 16' Processing helix chain 'k' and resid 17 through 33 removed outlier: 3.504A pdb=" N GLU k 33 " --> pdb=" O ILE k 29 " (cutoff:3.500A) Processing helix chain 'k' and resid 67 through 81 removed outlier: 4.576A pdb=" N GLU k 73 " --> pdb=" O GLU k 69 " (cutoff:3.500A) Processing helix chain 'l' and resid 20 through 31 removed outlier: 3.593A pdb=" N ALA l 24 " --> pdb=" O SER l 20 " (cutoff:3.500A) Processing helix chain 'l' and resid 35 through 55 removed outlier: 3.738A pdb=" N GLN l 52 " --> pdb=" O GLU l 48 " (cutoff:3.500A) Processing helix chain 'l' and resid 57 through 70 removed outlier: 3.691A pdb=" N ASN l 68 " --> pdb=" O VAL l 64 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N VAL l 69 " --> pdb=" O ALA l 65 " (cutoff:3.500A) Processing helix chain 'l' and resid 92 through 112 removed outlier: 3.547A pdb=" N LYS l 110 " --> pdb=" O GLU l 106 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N GLY l 112 " --> pdb=" O ALA l 108 " (cutoff:3.500A) Processing helix chain 'l' and resid 115 through 130 Processing helix chain 'l' and resid 132 through 149 Processing helix chain 'm' and resid 5 through 21 Processing helix chain 'm' and resid 30 through 44 Processing helix chain 'm' and resid 112 through 120 Processing helix chain 'n' and resid 34 through 39 Processing helix chain 'n' and resid 41 through 56 Proline residue: n 51 - end of helix removed outlier: 4.833A pdb=" N ASP n 56 " --> pdb=" O LEU n 52 " (cutoff:3.500A) Processing helix chain 'n' and resid 71 through 92 removed outlier: 3.697A pdb=" N GLU n 89 " --> pdb=" O ARG n 85 " (cutoff:3.500A) Processing helix chain 'n' and resid 94 through 102 removed outlier: 3.974A pdb=" N LYS n 100 " --> pdb=" O SER n 96 " (cutoff:3.500A) Processing helix chain 'o' and resid 14 through 33 removed outlier: 3.778A pdb=" N THR o 32 " --> pdb=" O THR o 28 " (cutoff:3.500A) Processing helix chain 'o' and resid 80 through 90 removed outlier: 3.943A pdb=" N ALA o 86 " --> pdb=" O LYS o 82 " (cutoff:3.500A) Processing helix chain 'p' and resid 46 through 51 removed outlier: 4.302A pdb=" N GLY p 51 " --> pdb=" O ALA p 47 " (cutoff:3.500A) Processing helix chain 'p' and resid 54 through 59 removed outlier: 3.935A pdb=" N SER p 58 " --> pdb=" O GLY p 54 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N THR p 59 " --> pdb=" O SER p 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 54 through 59' Processing helix chain 'p' and resid 60 through 76 removed outlier: 3.746A pdb=" N LYS p 75 " --> pdb=" O ALA p 71 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N GLU p 76 " --> pdb=" O ASP p 72 " (cutoff:3.500A) Processing helix chain 'p' and resid 94 through 104 removed outlier: 3.865A pdb=" N GLY p 104 " --> pdb=" O LEU p 100 " (cutoff:3.500A) Processing helix chain 'q' and resid 3 through 11 Proline residue: q 11 - end of helix Processing helix chain 'q' and resid 113 through 118 removed outlier: 3.997A pdb=" N TYR q 117 " --> pdb=" O ALA q 113 " (cutoff:3.500A) Processing helix chain 'r' and resid 14 through 22 removed outlier: 4.166A pdb=" N THR r 20 " --> pdb=" O VAL r 16 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N SER r 21 " --> pdb=" O ILE r 17 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ILE r 22 " --> pdb=" O ALA r 18 " (cutoff:3.500A) Processing helix chain 'r' and resid 26 through 38 Processing helix chain 'r' and resid 49 through 64 removed outlier: 3.923A pdb=" N LYS r 62 " --> pdb=" O ASP r 58 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N PHE r 63 " --> pdb=" O GLU r 59 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N VAL r 64 " --> pdb=" O VAL r 60 " (cutoff:3.500A) Processing helix chain 'r' and resid 66 through 84 removed outlier: 3.768A pdb=" N ARG r 71 " --> pdb=" O GLY r 67 " (cutoff:3.500A) 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 21 Processing helix chain 's' and resid 22 through 33 Processing helix chain 's' and resid 37 through 51 removed outlier: 3.955A pdb=" N GLN s 49 " --> pdb=" O VAL s 45 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N THR s 50 " --> pdb=" O LEU s 46 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU s 51 " --> pdb=" O LYS s 47 " (cutoff:3.500A) Processing helix chain 's' and resid 80 through 91 Processing helix chain 't' and resid 4 through 16 Processing helix chain 't' and resid 24 through 43 removed outlier: 4.410A pdb=" N GLY t 41 " --> pdb=" O ASN t 37 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N HIS t 42 " --> pdb=" O HIS t 38 " (cutoff:3.500A) Processing helix chain 't' and resid 49 through 74 removed outlier: 3.986A pdb=" N GLY t 55 " --> pdb=" O HIS t 51 " (cutoff:3.500A) Processing helix chain 't' and resid 75 through 86 Processing helix chain 'u' and resid 53 through 64 Processing helix chain 'u' and resid 68 through 82 Processing helix chain 'w' and resid 11 through 17 Processing helix chain 'w' and resid 25 through 34 removed outlier: 4.382A pdb=" N ASN w 31 " --> pdb=" O ALA w 27 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N TYR w 32 " --> pdb=" O THR w 28 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ILE w 33 " --> pdb=" O LEU w 29 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N THR w 34 " --> pdb=" O LYS w 30 " (cutoff:3.500A) Processing helix chain 'w' and resid 41 through 46 Processing helix chain 'w' and resid 48 through 66 Processing helix chain 'x' and resid 12 through 26 Processing helix chain 'x' and resid 70 through 76 removed outlier: 4.809A pdb=" N PHE x 74 " --> pdb=" O LYS x 70 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ALA x 75 " --> pdb=" O LEU x 71 " (cutoff:3.500A) Proline residue: x 76 - end of helix No H-bonds generated for 'chain 'x' and resid 70 through 76' Processing helix chain 'y' and resid 4 through 41 Processing helix chain 'y' and resid 43 through 65 Proline residue: y 56 - end of helix Processing helix chain 'y' and resid 68 through 87 removed outlier: 5.367A pdb=" N ALA y 87 " --> pdb=" O ILE y 83 " (cutoff:3.500A) Processing helix chain 'z' and resid 11 through 27 Processing helix chain 'z' and resid 28 through 37 removed outlier: 4.920A pdb=" N PHE z 37 " --> pdb=" O ARG z 33 " (cutoff:3.500A) Processing helix chain 'z' and resid 40 through 69 removed outlier: 4.242A pdb=" N LYS z 59 " --> pdb=" O ARG z 55 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ARG z 67 " --> pdb=" O GLU z 63 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N THR z 68 " --> pdb=" O ASN z 64 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N ARG z 69 " --> pdb=" O ALA z 65 " (cutoff:3.500A) Processing helix chain '7' and resid 4 through 14 removed outlier: 5.629A pdb=" N ARG 7 14 " --> pdb=" O VAL 7 10 " (cutoff:3.500A) Processing helix chain '7' and resid 25 through 38 Processing helix chain '7' and resid 61 through 66 Processing helix chain '7' and resid 95 through 107 removed outlier: 6.103A pdb=" N THR 7 99 " --> pdb=" O PHE 7 95 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N ASP 7 107 " --> pdb=" O LEU 7 103 " (cutoff:3.500A) Processing helix chain '7' and resid 122 through 134 Processing helix chain '7' and resid 150 through 163 Processing helix chain '7' and resid 194 through 199 removed outlier: 4.706A pdb=" N GLY 7 198 " --> pdb=" O GLN 7 194 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N HIS 7 199 " --> pdb=" O SER 7 195 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 194 through 199' Processing helix chain '7' and resid 212 through 220 removed outlier: 4.729A pdb=" N GLY 7 220 " --> pdb=" O ASP 7 216 " (cutoff:3.500A) Processing helix chain '7' and resid 221 through 238 Processing helix chain '7' and resid 242 through 249 Processing helix chain '7' and resid 264 through 276 Processing helix chain '7' and resid 408 through 423 removed outlier: 4.376A pdb=" N GLY 7 423 " --> pdb=" O LEU 7 419 " (cutoff:3.500A) Processing helix chain '7' and resid 442 through 457 Processing helix chain '7' and resid 478 through 490 removed outlier: 4.170A pdb=" N PHE 7 482 " --> pdb=" O ASP 7 478 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N GLU 7 483 " --> pdb=" O ALA 7 479 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N GLU 7 484 " --> pdb=" O LYS 7 480 " (cutoff:3.500A) Processing helix chain '7' and resid 507 through 519 removed outlier: 4.846A pdb=" N TYR 7 518 " --> pdb=" O ALA 7 514 " (cutoff:3.500A) Proline residue: 7 519 - end of helix Processing helix chain 'I' and resid 19 through 24 removed outlier: 4.258A pdb=" N VAL I 23 " --> pdb=" O PRO I 19 " (cutoff:3.500A) Processing helix chain 'I' and resid 33 through 49 removed outlier: 4.225A pdb=" N PHE I 37 " --> pdb=" O ASN I 33 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N CYS I 38 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N PHE I 41 " --> pdb=" O PHE I 37 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA I 43 " --> pdb=" O LYS I 39 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N LYS I 44 " --> pdb=" O ALA I 40 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP I 46 " --> pdb=" O ASN I 42 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N SER I 47 " --> pdb=" O ALA I 43 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N ILE I 48 " --> pdb=" O LYS I 44 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N GLU I 49 " --> pdb=" O THR I 45 " (cutoff:3.500A) Processing helix chain 'I' and resid 74 through 83 removed outlier: 4.449A pdb=" N LYS I 80 " --> pdb=" O ALA I 76 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LYS I 81 " --> pdb=" O VAL I 77 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ALA I 83 " --> pdb=" O LEU I 79 " (cutoff:3.500A) Processing helix chain 'I' and resid 101 through 112 removed outlier: 4.309A pdb=" N LEU I 105 " --> pdb=" O SER I 101 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ILE I 108 " --> pdb=" O GLN I 104 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ALA I 109 " --> pdb=" O LEU I 105 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N GLN I 110 " --> pdb=" O GLN I 106 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N THR I 111 " --> pdb=" O GLU I 107 " (cutoff:3.500A) Processing helix chain 'I' and resid 120 through 136 removed outlier: 3.788A pdb=" N SER I 127 " --> pdb=" O ALA I 123 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ALA I 132 " --> pdb=" O ILE I 128 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ARG I 133 " --> pdb=" O GLU I 129 " (cutoff:3.500A) Processing helix chain 'H' and resid 3 through 21 removed outlier: 3.978A pdb=" N GLU H 17 " --> pdb=" O ALA H 13 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N VAL H 18 " --> pdb=" O GLU H 14 " (cutoff:3.500A) Processing helix chain 'H' and resid 33 through 46 removed outlier: 4.206A pdb=" N ARG H 42 " --> pdb=" O MET H 38 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ARG H 46 " --> pdb=" O ARG H 42 " (cutoff:3.500A) Processing helix chain 'H' and resid 63 through 71 removed outlier: 4.384A pdb=" N THR H 67 " --> pdb=" O ALA H 63 " (cutoff:3.500A) Proline residue: H 68 - end of helix removed outlier: 3.968A pdb=" N CYS H 71 " --> pdb=" O THR H 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 63 through 71' Processing helix chain 'H' and resid 94 through 106 removed outlier: 4.784A pdb=" N GLU H 98 " --> pdb=" O ARG H 94 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N PHE H 99 " --> pdb=" O LEU H 95 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N ALA H 100 " --> pdb=" O PHE H 96 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ALA H 104 " --> pdb=" O ALA H 100 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N PHE H 106 " --> pdb=" O ALA H 102 " (cutoff:3.500A) Processing helix chain 'H' and resid 72 through 78 removed outlier: 3.759A pdb=" N ALA H 75 " --> pdb=" O LEU H 72 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N PHE H 76 " --> pdb=" O LYS H 73 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL H 77 " --> pdb=" O ASP H 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 1 through 26 removed outlier: 4.076A pdb=" N ALA A 26 " --> pdb=" O LEU A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 32 Processing helix chain 'A' and resid 36 through 71 removed outlier: 4.206A pdb=" N ASP A 47 " --> pdb=" O ALA A 43 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N VAL A 48 " --> pdb=" O GLN A 44 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASP A 71 " --> pdb=" O MET A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 101 Processing helix chain 'A' and resid 104 through 109 removed outlier: 4.227A pdb=" N GLU A 108 " --> pdb=" O ASP A 104 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ARG A 109 " --> pdb=" O PRO A 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 104 through 109' Processing helix chain 'A' and resid 121 through 143 Processing helix chain 'A' and resid 170 through 176 Processing helix chain 'A' and resid 218 through 223 removed outlier: 5.112A pdb=" N ARG A 223 " --> pdb=" O PRO A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 240 Processing helix chain 'A' and resid 262 through 299 removed outlier: 5.305A pdb=" N GLY A 299 " --> pdb=" O ARG A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 335 removed outlier: 6.630A pdb=" N VAL A 332 " --> pdb=" O ARG A 328 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N MET A 333 " --> pdb=" O LEU A 329 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLY A 335 " --> pdb=" O GLU A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 359 Proline residue: A 343 - end of helix Processing sheet with id= 1, first strand: chain 'B' and resid 80 through 83 removed outlier: 6.857A pdb=" N LEU B 93 " --> pdb=" O GLU B 79 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N ILE B 74 " --> pdb=" O SER B 118 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N SER B 118 " --> pdb=" O ILE B 74 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N ASP B 114 " --> pdb=" O VAL B 78 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N GLY B 127 " --> pdb=" O GLN B 115 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N GLN B 117 " --> pdb=" O GLY B 127 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'B' and resid 138 through 142 removed outlier: 4.320A pdb=" N SER B 139 " --> pdb=" O ILE B 164 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N THR B 173 " --> pdb=" O VAL B 165 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLU B 180 " --> pdb=" O LEU B 176 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'B' and resid 91 through 96 removed outlier: 4.199A pdb=" N GLU B 100 " --> pdb=" O TYR B 96 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'C' and resid 3 through 7 removed outlier: 7.041A pdb=" N ASP C 200 " --> pdb=" O THR C 112 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N THR C 112 " --> pdb=" O ASP C 200 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N GLU C 168 " --> pdb=" O SER C 113 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'C' and resid 10 through 16 removed outlier: 3.685A pdb=" N GLY C 10 " --> pdb=" O VAL C 26 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL C 20 " --> pdb=" O THR C 16 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'C' and resid 79 through 84 removed outlier: 5.868A pdb=" N ARG C 46 " --> pdb=" O LEU C 84 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N GLN C 49 " --> pdb=" O THR C 35 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N GLN C 94 " --> pdb=" O VAL C 34 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'C' and resid 105 through 108 removed outlier: 6.600A pdb=" N LYS C 105 " --> pdb=" O VAL C 177 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'D' and resid 1 through 5 removed outlier: 3.991A pdb=" N MET D 1 " --> pdb=" O VAL D 14 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N SER D 10 " --> pdb=" O LEU D 5 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'D' and resid 117 through 120 removed outlier: 5.863A pdb=" N ARG D 117 " --> pdb=" O ASP D 184 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'E' and resid 65 through 69 removed outlier: 3.730A pdb=" N GLY E 86 " --> pdb=" O THR E 68 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N ILE E 85 " --> pdb=" O VAL E 40 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N GLY E 39 " --> pdb=" O GLY E 151 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N GLY E 151 " --> pdb=" O GLY E 39 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU E 152 " --> pdb=" O VAL E 132 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'F' and resid 16 through 19 Processing sheet with id= 12, first strand: chain 'F' and resid 41 through 45 Processing sheet with id= 13, first strand: chain 'F' and resid 94 through 98 Processing sheet with id= 14, first strand: chain 'F' and resid 121 through 125 removed outlier: 6.042A pdb=" N THR F 129 " --> pdb=" O LEU F 89 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'G' and resid 2 through 5 removed outlier: 4.353A pdb=" N ASP G 17 " --> pdb=" O LEU G 5 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'G' and resid 76 through 82 removed outlier: 5.943A pdb=" N GLU G 76 " --> pdb=" O LYS G 141 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ILE G 143 " --> pdb=" O GLU G 76 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'J' and resid 14 through 19 Processing sheet with id= 18, first strand: chain 'K' and resid 18 through 21 removed outlier: 4.084A pdb=" N THR K 6 " --> pdb=" O CYS K 21 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N ASN K 82 " --> pdb=" O MET K 7 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'M' and resid 37 through 40 No H-bonds generated for sheet with id= 19 Processing sheet with id= 20, first strand: chain 'M' and resid 62 through 65 removed outlier: 3.851A pdb=" N TYR M 103 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LEU M 33 " --> pdb=" O LEU M 102 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LYS M 100 " --> pdb=" O ALA M 35 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'M' and resid 30 through 36 removed outlier: 7.652A pdb=" N SER M 30 " --> pdb=" O LYS M 133 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LYS M 127 " --> pdb=" O VAL M 36 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'N' and resid 33 through 37 removed outlier: 5.216A pdb=" N ARG N 103 " --> pdb=" O ASN N 107 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N GLY N 101 " --> pdb=" O PRO N 109 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ALA N 111 " --> pdb=" O LYS N 99 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LYS N 99 " --> pdb=" O ALA N 111 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ILE N 113 " --> pdb=" O ILE N 97 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ILE N 97 " --> pdb=" O ILE N 113 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LEU N 115 " --> pdb=" O THR N 95 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N THR N 95 " --> pdb=" O LEU N 115 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'O' and resid 49 through 53 removed outlier: 3.624A pdb=" N VAL O 49 " --> pdb=" O VAL O 39 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ILE O 35 " --> pdb=" O THR O 53 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL O 28 " --> pdb=" O ASP O 93 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'P' and resid 38 through 44 removed outlier: 6.849A pdb=" N THR P 25 " --> pdb=" O LYS P 87 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N SER P 83 " --> pdb=" O LYS P 29 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'P' and resid 49 through 52 removed outlier: 3.632A pdb=" N ALA P 49 " --> pdb=" O THR P 60 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N SER P 57 " --> pdb=" O THR P 76 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'R' and resid 11 through 15 removed outlier: 6.823A pdb=" N LEU R 39 " --> pdb=" O GLY R 50 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ASN R 43 " --> pdb=" O GLU R 46 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N GLU R 46 " --> pdb=" O ASN R 43 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'R' and resid 18 through 23 removed outlier: 4.663A pdb=" N GLN R 18 " --> pdb=" O ILE R 98 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ASP R 95 " --> pdb=" O VAL R 64 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N LYS R 60 " --> pdb=" O THR R 99 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N GLU R 31 " --> pdb=" O VAL R 63 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'R' and resid 57 through 60 Processing sheet with id= 29, first strand: chain 'R' and resid 68 through 78 No H-bonds generated for sheet with id= 29 Processing sheet with id= 30, first strand: chain 'S' and resid 2 through 8 Processing sheet with id= 31, first strand: chain 'T' and resid 28 through 33 removed outlier: 5.956A pdb=" N ASN T 28 " --> pdb=" O LEU T 87 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N LYS T 66 " --> pdb=" O ARG T 77 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ASP T 79 " --> pdb=" O LYS T 64 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N LYS T 64 " --> pdb=" O ASP T 79 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N LYS T 81 " --> pdb=" O VAL T 62 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N VAL T 62 " --> pdb=" O LYS T 81 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ALA T 83 " --> pdb=" O THR T 60 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N THR T 60 " --> pdb=" O ALA T 83 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N VAL T 85 " --> pdb=" O VAL T 58 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N VAL T 58 " --> pdb=" O VAL T 85 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'U' and resid 40 through 45 removed outlier: 5.080A pdb=" N ASN U 40 " --> pdb=" O ALA U 63 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'U' and resid 83 through 86 Processing sheet with id= 34, first strand: chain 'V' and resid 69 through 72 removed outlier: 6.610A pdb=" N ALA V 39 " --> pdb=" O ARG V 9 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE V 89 " --> pdb=" O PRO V 27 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'W' and resid 45 through 48 removed outlier: 6.505A pdb=" N ILE W 82 " --> pdb=" O GLY W 48 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'W' and resid 50 through 54 removed outlier: 7.913A pdb=" N ASN W 50 " --> pdb=" O LYS W 62 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N THR W 58 " --> pdb=" O GLY W 54 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'X' and resid 12 through 19 removed outlier: 3.813A pdb=" N THR X 25 " --> pdb=" O ASN X 17 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ASN X 23 " --> pdb=" O SER X 19 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'X' and resid 35 through 41 Processing sheet with id= 39, first strand: chain 'Z' and resid 33 through 39 removed outlier: 4.156A pdb=" N HIS Z 34 " --> pdb=" O GLN Z 9 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N MET Z 54 " --> pdb=" O THR Z 10 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'a' and resid 20 through 25 removed outlier: 4.477A pdb=" N ASN a 20 " --> pdb=" O CYS a 16 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'c' and resid 19 through 25 removed outlier: 6.476A pdb=" N HIS c 19 " --> pdb=" O SER c 13 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ILE c 48 " --> pdb=" O SER c 14 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N LEU c 34 " --> pdb=" O GLU c 51 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'e' and resid 22 through 25 No H-bonds generated for sheet with id= 42 Processing sheet with id= 43, first strand: chain 'f' and resid 14 through 19 Processing sheet with id= 44, first strand: chain 'g' and resid 15 through 18 removed outlier: 5.240A pdb=" N HIS g 15 " --> pdb=" O ILE g 41 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N HIS g 39 " --> pdb=" O GLY g 17 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'g' and resid 67 through 71 Processing sheet with id= 46, first strand: chain 'h' and resid 54 through 59 Processing sheet with id= 47, first strand: chain 'h' and resid 164 through 169 removed outlier: 5.886A pdb=" N ARG h 164 " --> pdb=" O GLY h 155 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'i' and resid 141 through 144 Processing sheet with id= 49, first strand: chain 'j' and resid 11 through 16 removed outlier: 7.074A pdb=" N LEU j 36 " --> pdb=" O ILE j 16 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'j' and resid 84 through 88 removed outlier: 5.717A pdb=" N ASN j 122 " --> pdb=" O ALA j 99 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'j' and resid 33 through 41 removed outlier: 6.426A pdb=" N ARG j 45 " --> pdb=" O ASP j 41 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'k' and resid 38 through 42 removed outlier: 5.469A pdb=" N TYR k 59 " --> pdb=" O TRP k 42 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N HIS k 3 " --> pdb=" O THR k 92 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'k' and resid 43 through 47 removed outlier: 6.932A pdb=" N HIS k 55 " --> pdb=" O LEU k 47 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'l' and resid 72 through 79 removed outlier: 6.288A pdb=" N THR l 72 " --> pdb=" O VAL l 91 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N TYR l 85 " --> pdb=" O ARG l 78 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'm' and resid 23 through 29 removed outlier: 6.730A pdb=" N ALA m 23 " --> pdb=" O LEU m 63 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASP m 48 " --> pdb=" O THR m 62 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'm' and resid 74 through 77 removed outlier: 6.864A pdb=" N VAL m 103 " --> pdb=" O ILE m 126 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'n' and resid 5 through 11 Processing sheet with id= 58, first strand: chain 'o' and resid 42 through 52 removed outlier: 4.757A pdb=" N LEU o 71 " --> pdb=" O PRO o 43 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N ARG o 5 " --> pdb=" O GLY o 103 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'p' and resid 29 through 36 removed outlier: 4.048A pdb=" N ASN p 29 " --> pdb=" O SER p 26 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'q' and resid 29 through 32 removed outlier: 5.053A pdb=" N LEU q 81 " --> pdb=" O VAL q 98 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N HIS q 96 " --> pdb=" O ARG q 83 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'q' and resid 36 through 41 removed outlier: 5.238A pdb=" N LYS q 51 " --> pdb=" O ILE q 67 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'u' and resid 4 through 10 removed outlier: 4.435A pdb=" N PHE u 16 " --> pdb=" O HIS u 9 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'v' and resid 7 through 12 removed outlier: 4.588A pdb=" N ASP v 57 " --> pdb=" O VAL v 12 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'v' and resid 19 through 30 No H-bonds generated for sheet with id= 64 Processing sheet with id= 65, first strand: chain 'x' and resid 30 through 33 removed outlier: 4.396A pdb=" N LEU x 47 " --> pdb=" O VAL x 62 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain '7' and resid 72 through 78 removed outlier: 3.882A pdb=" N THR 7 89 " --> pdb=" O ILE 7 18 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N SER 7 20 " --> pdb=" O THR 7 89 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N ILE 7 137 " --> pdb=" O ILE 7 251 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N PHE 7 256 " --> pdb=" O ILE 7 169 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain '7' and resid 170 through 173 removed outlier: 5.859A pdb=" N LYS 7 180 " --> pdb=" O ILE 7 173 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY 7 181 " --> pdb=" O GLU 7 189 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N LYS 7 187 " --> pdb=" O TYR 7 183 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N TYR 7 186 " --> pdb=" O GLY 7 209 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain '7' and resid 297 through 301 removed outlier: 4.495A pdb=" N ASP 7 377 " --> pdb=" O VAL 7 300 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain '7' and resid 302 through 305 Processing sheet with id= 70, first strand: chain '7' and resid 329 through 334 removed outlier: 4.348A pdb=" N MET 7 329 " --> pdb=" O ILE 7 342 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain '7' and resid 398 through 401 removed outlier: 4.947A pdb=" N LEU 7 436 " --> pdb=" O ILE 7 401 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain '7' and resid 492 through 496 removed outlier: 5.387A pdb=" N ALA 7 492 " --> pdb=" O ILE 7 504 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N LEU 7 501 " --> pdb=" O VAL 7 474 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'H' and resid 24 through 28 removed outlier: 3.599A pdb=" N ALA H 25 " --> pdb=" O SER H 85 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'A' and resid 144 through 149 removed outlier: 6.794A pdb=" N ILE A 163 " --> pdb=" O MET A 149 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N LYS A 160 " --> pdb=" O ALA A 117 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N ALA A 200 " --> pdb=" O GLY A 118 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ARG A 308 " --> pdb=" O GLY A 181 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N VAL A 187 " --> pdb=" O PHE A 312 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU A 324 " --> pdb=" O ASP A 319 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'A' and resid 224 through 228 Processing sheet with id= 76, first strand: chain 'A' and resid 150 through 153 2309 hydrogen bonds defined for protein. 6813 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3954 hydrogen bonds 6184 hydrogen bond angles 0 basepair planarities 1571 basepair parallelities 2594 stacking parallelities Total time for adding SS restraints: 261.96 Time building geometry restraints manager: 64.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.29: 13255 1.29 - 1.43: 70296 1.43 - 1.56: 72874 1.56 - 1.70: 9400 1.70 - 1.83: 350 Bond restraints: 166175 Sorted by residual: bond pdb=" C5 5MU 11939 " pdb=" C6 5MU 11939 " ideal model delta sigma weight residual 1.155 1.453 -0.298 2.00e-02 2.50e+03 2.22e+02 bond pdb=" C5 5MU 1 747 " pdb=" C6 5MU 1 747 " ideal model delta sigma weight residual 1.155 1.450 -0.295 2.00e-02 2.50e+03 2.18e+02 bond pdb=" C5 5MU 5 54 " pdb=" C6 5MU 5 54 " ideal model delta sigma weight residual 1.155 1.449 -0.294 2.00e-02 2.50e+03 2.16e+02 bond pdb=" C4 5MU 1 747 " pdb=" C5 5MU 1 747 " ideal model delta sigma weight residual 1.802 1.609 0.193 2.00e-02 2.50e+03 9.31e+01 bond pdb=" C4 5MU 5 54 " pdb=" C5 5MU 5 54 " ideal model delta sigma weight residual 1.802 1.611 0.191 2.00e-02 2.50e+03 9.15e+01 ... (remaining 166170 not shown) Histogram of bond angle deviations from ideal: 91.28 - 102.39: 8442 102.39 - 113.51: 114384 113.51 - 124.63: 104364 124.63 - 135.74: 20151 135.74 - 146.86: 15 Bond angle restraints: 247356 Sorted by residual: angle pdb=" CA TRP g 23 " pdb=" CB TRP g 23 " pdb=" CG TRP g 23 " ideal model delta sigma weight residual 113.60 130.43 -16.83 1.90e+00 2.77e-01 7.85e+01 angle pdb=" C1' G7M 12069 " pdb=" N9 G7M 12069 " pdb=" C8 G7M 12069 " ideal model delta sigma weight residual 94.96 119.07 -24.11 3.00e+00 1.11e-01 6.46e+01 angle pdb=" C1' 2MG 2 966 " pdb=" N9 2MG 2 966 " pdb=" C8 2MG 2 966 " ideal model delta sigma weight residual 110.07 132.77 -22.70 3.00e+00 1.11e-01 5.72e+01 angle pdb=" C1' 2MG 12445 " pdb=" N9 2MG 12445 " pdb=" C8 2MG 12445 " ideal model delta sigma weight residual 110.07 132.76 -22.69 3.00e+00 1.11e-01 5.72e+01 angle pdb=" C1' 2MG 21516 " pdb=" N9 2MG 21516 " pdb=" C8 2MG 21516 " ideal model delta sigma weight residual 110.07 132.58 -22.51 3.00e+00 1.11e-01 5.63e+01 ... (remaining 247351 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 94140 35.98 - 71.96: 10686 71.96 - 107.94: 1197 107.94 - 143.92: 15 143.92 - 179.91: 33 Dihedral angle restraints: 106071 sinusoidal: 86490 harmonic: 19581 Sorted by residual: dihedral pdb=" CA VAL R 51 " pdb=" C VAL R 51 " pdb=" N PRO R 52 " pdb=" CA PRO R 52 " ideal model delta harmonic sigma weight residual 180.00 131.44 48.56 0 5.00e+00 4.00e-02 9.43e+01 dihedral pdb=" O4' U 1 138 " pdb=" C1' U 1 138 " pdb=" N1 U 1 138 " pdb=" C2 U 1 138 " ideal model delta sinusoidal sigma weight residual 200.00 21.56 178.44 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U 2 467 " pdb=" C1' U 2 467 " pdb=" N1 U 2 467 " pdb=" C2 U 2 467 " ideal model delta sinusoidal sigma weight residual 200.00 38.48 161.52 1 1.50e+01 4.44e-03 8.31e+01 ... (remaining 106068 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.168: 30631 0.168 - 0.335: 645 0.335 - 0.503: 43 0.503 - 0.670: 6 0.670 - 0.838: 1 Chirality restraints: 31326 Sorted by residual: chirality pdb=" CB ILE 7 164 " pdb=" CA ILE 7 164 " pdb=" CG1 ILE 7 164 " pdb=" CG2 ILE 7 164 " both_signs ideal model delta sigma weight residual False 2.64 1.81 0.84 2.00e-01 2.50e+01 1.75e+01 chirality pdb=" CB VAL 7 438 " pdb=" CA VAL 7 438 " pdb=" CG1 VAL 7 438 " pdb=" CG2 VAL 7 438 " both_signs ideal model delta sigma weight residual False -2.63 -1.99 -0.64 2.00e-01 2.50e+01 1.02e+01 chirality pdb=" C1' A 11085 " pdb=" O4' A 11085 " pdb=" C2' A 11085 " pdb=" N9 A 11085 " both_signs ideal model delta sigma weight residual False 2.46 1.92 0.54 2.00e-01 2.50e+01 7.18e+00 ... (remaining 31323 not shown) Planarity restraints: 14137 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 5MC 21407 " 0.074 2.00e-02 2.50e+03 6.22e-01 8.71e+03 pdb=" C4' 5MC 21407 " 0.470 2.00e-02 2.50e+03 pdb=" O4' 5MC 21407 " 0.584 2.00e-02 2.50e+03 pdb=" C3' 5MC 21407 " -0.562 2.00e-02 2.50e+03 pdb=" O3' 5MC 21407 " -0.731 2.00e-02 2.50e+03 pdb=" C2' 5MC 21407 " -0.137 2.00e-02 2.50e+03 pdb=" O2' 5MC 21407 " 1.046 2.00e-02 2.50e+03 pdb=" C1' 5MC 21407 " 0.208 2.00e-02 2.50e+03 pdb=" N1 5MC 21407 " -0.953 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG 21516 " -0.049 2.00e-02 2.50e+03 6.20e-01 8.66e+03 pdb=" C4' 2MG 21516 " -0.468 2.00e-02 2.50e+03 pdb=" O4' 2MG 21516 " -0.686 2.00e-02 2.50e+03 pdb=" C3' 2MG 21516 " 0.589 2.00e-02 2.50e+03 pdb=" O3' 2MG 21516 " 0.671 2.00e-02 2.50e+03 pdb=" C2' 2MG 21516 " 0.175 2.00e-02 2.50e+03 pdb=" O2' 2MG 21516 " -0.986 2.00e-02 2.50e+03 pdb=" C1' 2MG 21516 " -0.210 2.00e-02 2.50e+03 pdb=" N9 2MG 21516 " 0.963 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMG 12251 " 0.065 2.00e-02 2.50e+03 6.18e-01 8.61e+03 pdb=" C4' OMG 12251 " 0.458 2.00e-02 2.50e+03 pdb=" O4' OMG 12251 " 0.664 2.00e-02 2.50e+03 pdb=" C3' OMG 12251 " -0.587 2.00e-02 2.50e+03 pdb=" O3' OMG 12251 " -0.678 2.00e-02 2.50e+03 pdb=" C2' OMG 12251 " -0.170 2.00e-02 2.50e+03 pdb=" O2' OMG 12251 " 1.002 2.00e-02 2.50e+03 pdb=" C1' OMG 12251 " 0.200 2.00e-02 2.50e+03 pdb=" N9 OMG 12251 " -0.955 2.00e-02 2.50e+03 ... (remaining 14134 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 26686 2.78 - 3.31: 125226 3.31 - 3.84: 327059 3.84 - 4.37: 380745 4.37 - 4.90: 523041 Nonbonded interactions: 1382757 Sorted by model distance: nonbonded pdb=" O6 G 12107 " pdb=" O2 U 12182 " model vdw 2.254 3.040 nonbonded pdb=" OP2 G 1 411 " pdb=" O2' A 12406 " model vdw 2.264 2.440 nonbonded pdb=" OG SER G 93 " pdb=" O VAL G 121 " model vdw 2.271 2.440 nonbonded pdb=" OG1 THR g 72 " pdb=" OE2 GLU g 169 " model vdw 2.272 2.440 nonbonded pdb=" O2' C 21147 " pdb=" OH TYR n 7 " model vdw 2.275 2.440 ... (remaining 1382752 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: 2.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.140 Extract box with map and model: 16.040 Check model and map are aligned: 1.740 Set scattering table: 1.090 Process input model: 592.260 Find NCS groups from input model: 3.120 Set up NCS constraints: 0.350 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:11.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 629.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.298 166175 Z= 0.415 Angle : 1.274 24.106 247356 Z= 0.679 Chirality : 0.065 0.838 31326 Planarity : 0.020 0.622 14137 Dihedral : 22.739 179.906 93437 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.19 % Favored : 97.69 % Rotamer: Outliers : 0.02 % Allowed : 0.75 % Favored : 99.24 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.44 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.10), residues: 6755 helix: 0.85 (0.10), residues: 2352 sheet: -0.98 (0.14), residues: 1265 loop : -1.13 (0.10), residues: 3138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.118 0.004 TRP g 23 HIS 0.034 0.003 HIS g 39 PHE 0.069 0.005 PHE w 10 TYR 0.040 0.004 TYR i 135 ARG 0.024 0.001 ARG J 120 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13510 Ramachandran restraints generated. 6755 Oldfield, 0 Emsley, 6755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13510 Ramachandran restraints generated. 6755 Oldfield, 0 Emsley, 6755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1495 residues out of total 5623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1494 time to evaluate : 6.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 173 GLN cc_start: 0.8630 (mt0) cc_final: 0.8384 (mt0) REVERT: E 96 MET cc_start: 0.8380 (ttp) cc_final: 0.8058 (ttp) REVERT: E 153 ASP cc_start: 0.7532 (p0) cc_final: 0.7324 (p0) REVERT: E 161 LYS cc_start: 0.7110 (mttt) cc_final: 0.6821 (ptmm) REVERT: M 82 MET cc_start: 0.8658 (mmp) cc_final: 0.8439 (mmp) REVERT: S 66 ILE cc_start: 0.7032 (mm) cc_final: 0.5961 (mp) REVERT: S 97 LEU cc_start: 0.8338 (mt) cc_final: 0.8098 (mt) REVERT: W 25 ARG cc_start: 0.8209 (mmt90) cc_final: 0.7949 (mpt180) REVERT: W 39 ARG cc_start: 0.8631 (mtp-110) cc_final: 0.7862 (mtp180) REVERT: W 44 LYS cc_start: 0.7710 (ttmt) cc_final: 0.7430 (tttm) REVERT: Z 19 LYS cc_start: 0.8523 (ttmm) cc_final: 0.8175 (ttpp) REVERT: b 15 MET cc_start: 0.8793 (mtt) cc_final: 0.8568 (mtm) REVERT: f 2 LYS cc_start: 0.7992 (mttp) cc_final: 0.7778 (mmtt) REVERT: g 8 ASP cc_start: 0.5084 (p0) cc_final: 0.4843 (p0) REVERT: g 56 GLU cc_start: 0.6165 (tp30) cc_final: 0.5849 (mm-30) REVERT: g 136 MET cc_start: 0.6986 (ttp) cc_final: 0.6758 (tmm) REVERT: h 166 GLU cc_start: 0.7148 (mm-30) cc_final: 0.6630 (mm-30) REVERT: i 148 LYS cc_start: 0.7038 (ttpp) cc_final: 0.6582 (tppp) REVERT: k 93 LYS cc_start: 0.7206 (ttmm) cc_final: 0.6682 (ptmm) REVERT: m 27 MET cc_start: 0.8652 (ptp) cc_final: 0.8073 (ptp) REVERT: p 68 GLU cc_start: 0.7666 (mt-10) cc_final: 0.7435 (mt-10) REVERT: q 75 GLN cc_start: 0.7330 (pt0) cc_final: 0.7095 (mt0) REVERT: s 24 ARG cc_start: 0.7508 (mtp85) cc_final: 0.7231 (ttm110) REVERT: u 26 ASN cc_start: 0.8195 (m110) cc_final: 0.7970 (m110) REVERT: 7 384 MET cc_start: 0.2945 (mmm) cc_final: 0.2524 (mmm) REVERT: 7 454 LYS cc_start: 0.5618 (tptm) cc_final: 0.5018 (mttm) REVERT: 7 459 VAL cc_start: 0.5200 (m) cc_final: 0.4685 (t) REVERT: 7 472 ARG cc_start: 0.5839 (mmp80) cc_final: 0.4986 (mmp80) REVERT: 7 501 LEU cc_start: 0.6754 (tp) cc_final: 0.6338 (mt) REVERT: 7 516 GLU cc_start: 0.5453 (pp20) cc_final: 0.4934 (mp0) REVERT: H 1 MET cc_start: 0.3692 (tpp) cc_final: 0.2496 (mtp) REVERT: A 44 GLN cc_start: 0.6181 (mt0) cc_final: 0.4858 (mm-40) REVERT: A 68 MET cc_start: 0.2983 (mtp) cc_final: 0.2691 (tmm) REVERT: A 208 GLU cc_start: 0.7109 (tt0) cc_final: 0.6863 (tt0) REVERT: A 258 GLN cc_start: 0.8571 (mt0) cc_final: 0.8263 (mt0) REVERT: A 263 GLN cc_start: 0.7908 (tt0) cc_final: 0.6674 (tt0) outliers start: 1 outliers final: 5 residues processed: 1494 average time/residue: 2.4316 time to fit residues: 5077.2292 Evaluate side-chains 1032 residues out of total 5623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1027 time to evaluate : 6.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain g residue 164 ILE Chi-restraints excluded: chain v residue 57 ASP Chi-restraints excluded: chain 7 residue 478 ASP Chi-restraints excluded: chain A residue 185 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1125 random chunks: chunk 949 optimal weight: 0.6980 chunk 852 optimal weight: 4.9990 chunk 473 optimal weight: 2.9990 chunk 291 optimal weight: 10.0000 chunk 575 optimal weight: 6.9990 chunk 455 optimal weight: 10.0000 chunk 881 optimal weight: 10.0000 chunk 341 optimal weight: 10.0000 chunk 536 optimal weight: 2.9990 chunk 656 optimal weight: 0.9980 chunk 1021 optimal weight: 0.0570 overall best weight: 1.5502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 46 ASN B 153 GLN C 49 GLN C 67 HIS D 30 GLN D 115 GLN D 136 GLN E 27 GLN F 104 ASN J 58 ASN ** J 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 138 GLN K 88 ASN M 97 GLN N 9 GLN N 18 GLN ** O 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 12 GLN P 15 GLN P 66 ASN ** R 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 86 GLN S 60 HIS Y 58 ASN b 42 HIS c 45 GLN e 28 ASN ** g 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 177 ASN h 69 HIS h 100 GLN i 41 HIS k 3 HIS n 126 GLN o 64 GLN q 46 ASN s 62 ASN t 35 GLN t 37 ASN 7 53 GLN 7 199 HIS 7 333 GLN ** 7 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 433 ASN 7 458 ASN I 106 GLN A 287 GLN A 288 GLN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 166175 Z= 0.171 Angle : 0.644 16.295 247356 Z= 0.340 Chirality : 0.034 0.404 31326 Planarity : 0.006 0.136 14137 Dihedral : 23.120 179.854 79983 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.52 % Favored : 97.44 % Rotamer: Outliers : 2.93 % Allowed : 13.78 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.44 % 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: -0.10 (0.10), residues: 6755 helix: 1.28 (0.11), residues: 2329 sheet: -0.64 (0.14), residues: 1294 loop : -0.80 (0.10), residues: 3132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP h 201 HIS 0.011 0.001 HIS g 168 PHE 0.022 0.001 PHE H 113 TYR 0.019 0.001 TYR 7 360 ARG 0.007 0.001 ARG i 184 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13510 Ramachandran restraints generated. 6755 Oldfield, 0 Emsley, 6755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13510 Ramachandran restraints generated. 6755 Oldfield, 0 Emsley, 6755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1309 residues out of total 5623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 1144 time to evaluate : 6.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1 MET cc_start: 0.7299 (OUTLIER) cc_final: 0.5712 (tmt) REVERT: C 11 MET cc_start: 0.8770 (mtp) cc_final: 0.8531 (mtp) REVERT: C 173 GLN cc_start: 0.8794 (mt0) cc_final: 0.8554 (mt0) REVERT: D 144 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7162 (tm-30) REVERT: E 15 LYS cc_start: 0.8295 (tttm) cc_final: 0.7820 (tttm) REVERT: E 134 GLU cc_start: 0.7292 (OUTLIER) cc_final: 0.7072 (pm20) REVERT: F 27 LYS cc_start: 0.6055 (OUTLIER) cc_final: 0.5844 (tptm) REVERT: L 143 GLU cc_start: 0.6930 (pt0) cc_final: 0.6690 (pt0) REVERT: M 6 ARG cc_start: 0.7330 (OUTLIER) cc_final: 0.6817 (ptm160) REVERT: M 60 GLN cc_start: 0.7605 (OUTLIER) cc_final: 0.7250 (mp10) REVERT: M 82 MET cc_start: 0.8725 (mmp) cc_final: 0.8504 (mmp) REVERT: N 12 ARG cc_start: 0.8856 (OUTLIER) cc_final: 0.8079 (mtp85) REVERT: N 13 ASN cc_start: 0.7977 (p0) cc_final: 0.7547 (p0) REVERT: P 27 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7615 (tm-30) REVERT: P 46 VAL cc_start: 0.8695 (p) cc_final: 0.8491 (t) REVERT: R 70 GLU cc_start: 0.7402 (OUTLIER) cc_final: 0.7002 (tm-30) REVERT: R 86 GLN cc_start: 0.7732 (OUTLIER) cc_final: 0.6699 (mp-120) REVERT: S 65 ASP cc_start: 0.7510 (t0) cc_final: 0.7303 (t0) REVERT: U 19 LYS cc_start: 0.7809 (ttmt) cc_final: 0.7570 (ttpt) REVERT: W 39 ARG cc_start: 0.8652 (mtp-110) cc_final: 0.7845 (mtp85) REVERT: Z 19 LYS cc_start: 0.8571 (ttmm) cc_final: 0.8147 (ttpp) REVERT: b 20 ASP cc_start: 0.7380 (m-30) cc_final: 0.7160 (m-30) REVERT: b 23 THR cc_start: 0.8483 (p) cc_final: 0.8252 (m) REVERT: f 2 LYS cc_start: 0.8158 (mttp) cc_final: 0.7836 (mmtt) REVERT: g 66 LYS cc_start: 0.7386 (OUTLIER) cc_final: 0.6880 (mtpt) REVERT: g 73 LYS cc_start: 0.7274 (mtpp) cc_final: 0.6881 (mttm) REVERT: g 113 ARG cc_start: 0.6814 (tpt170) cc_final: 0.6574 (tpt170) REVERT: g 135 LEU cc_start: 0.5954 (mm) cc_final: 0.5713 (pp) REVERT: g 136 MET cc_start: 0.6986 (ttp) cc_final: 0.6517 (ttp) REVERT: g 169 GLU cc_start: 0.7124 (OUTLIER) cc_final: 0.6783 (mp0) REVERT: i 45 LYS cc_start: 0.7313 (tptp) cc_final: 0.6745 (tppt) REVERT: i 148 LYS cc_start: 0.7057 (ttpp) cc_final: 0.6588 (tppp) REVERT: i 156 LYS cc_start: 0.6826 (tppp) cc_final: 0.6562 (pttt) REVERT: k 93 LYS cc_start: 0.7295 (ttmm) cc_final: 0.6829 (ptmm) REVERT: m 27 MET cc_start: 0.8675 (ptp) cc_final: 0.8060 (ptp) REVERT: m 89 LYS cc_start: 0.7696 (OUTLIER) cc_final: 0.7429 (ttpp) REVERT: r 93 ARG cc_start: 0.7035 (OUTLIER) cc_final: 0.6310 (tpt-90) REVERT: y 18 ARG cc_start: 0.8439 (ttp-110) cc_final: 0.8097 (ttp80) REVERT: 7 62 MET cc_start: 0.0592 (mpp) cc_final: -0.0252 (tmm) REVERT: 7 97 GLU cc_start: 0.5914 (tp30) cc_final: 0.5609 (tp30) REVERT: 7 127 MET cc_start: 0.3208 (tpt) cc_final: 0.2607 (tpp) REVERT: 7 206 ILE cc_start: 0.0860 (OUTLIER) cc_final: 0.0377 (pt) REVERT: 7 378 THR cc_start: 0.6468 (OUTLIER) cc_final: 0.6058 (t) REVERT: 7 472 ARG cc_start: 0.6023 (mmp80) cc_final: 0.5321 (mmp80) REVERT: 7 487 ARG cc_start: 0.5392 (mtm110) cc_final: 0.4919 (tmm160) REVERT: H 1 MET cc_start: 0.3637 (tpp) cc_final: 0.2361 (mtp) REVERT: A 17 GLU cc_start: 0.6380 (mp0) cc_final: 0.6176 (mp0) REVERT: A 68 MET cc_start: 0.3088 (mtp) cc_final: 0.2685 (tmm) REVERT: A 288 GLN cc_start: 0.7935 (OUTLIER) cc_final: 0.7613 (mm-40) REVERT: A 338 ASP cc_start: 0.7813 (m-30) cc_final: 0.7417 (m-30) REVERT: A 347 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.7334 (mt-10) outliers start: 165 outliers final: 37 residues processed: 1210 average time/residue: 2.3250 time to fit residues: 4001.7027 Evaluate side-chains 1054 residues out of total 5623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 999 time to evaluate : 7.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 144 GLU Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 134 GLU Chi-restraints excluded: chain E residue 153 ASP Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 27 LYS Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain M residue 6 ARG Chi-restraints excluded: chain M residue 60 GLN Chi-restraints excluded: chain M residue 119 LEU Chi-restraints excluded: chain N residue 12 ARG Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain O residue 45 SER Chi-restraints excluded: chain P residue 27 GLU Chi-restraints excluded: chain P residue 80 VAL Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 70 GLU Chi-restraints excluded: chain R residue 86 GLN Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 101 SER Chi-restraints excluded: chain T residue 21 SER Chi-restraints excluded: chain X residue 66 THR Chi-restraints excluded: chain Y residue 16 THR Chi-restraints excluded: chain Y residue 40 SER Chi-restraints excluded: chain g residue 10 LEU Chi-restraints excluded: chain g residue 66 LYS Chi-restraints excluded: chain g residue 169 GLU Chi-restraints excluded: chain j residue 32 SER Chi-restraints excluded: chain j residue 120 VAL Chi-restraints excluded: chain k residue 7 VAL Chi-restraints excluded: chain l residue 94 VAL Chi-restraints excluded: chain m residue 89 LYS Chi-restraints excluded: chain m residue 129 VAL Chi-restraints excluded: chain n residue 111 VAL Chi-restraints excluded: chain q residue 64 THR Chi-restraints excluded: chain q residue 119 VAL Chi-restraints excluded: chain r residue 93 ARG Chi-restraints excluded: chain t residue 75 VAL Chi-restraints excluded: chain u residue 24 SER Chi-restraints excluded: chain x residue 58 VAL Chi-restraints excluded: chain y residue 14 SER Chi-restraints excluded: chain 7 residue 206 ILE Chi-restraints excluded: chain 7 residue 378 THR Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 193 GLN Chi-restraints excluded: chain A residue 288 GLN Chi-restraints excluded: chain A residue 347 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1125 random chunks: chunk 567 optimal weight: 0.7980 chunk 317 optimal weight: 10.0000 chunk 850 optimal weight: 8.9990 chunk 695 optimal weight: 9.9990 chunk 281 optimal weight: 10.0000 chunk 1023 optimal weight: 10.0000 chunk 1105 optimal weight: 9.9990 chunk 911 optimal weight: 1.9990 chunk 1014 optimal weight: 30.0000 chunk 348 optimal weight: 10.0000 chunk 821 optimal weight: 10.0000 overall best weight: 6.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 38 ASN F 104 ASN J 138 GLN K 3 GLN K 88 ASN N 18 GLN ** O 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 15 GLN Q 44 GLN S 61 ASN Y 20 ASN Y 58 ASN c 45 GLN g 51 ASN ** g 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 59 GLN i 126 ASN i 198 HIS j 82 GLN k 3 HIS ** k 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 50 GLN o 64 GLN p 15 GLN ** q 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 112 GLN t 80 GLN y 3 ASN y 21 ASN 7 21 HIS 7 53 GLN 7 80 HIS 7 333 GLN A 59 GLN A 95 GLN A 288 GLN A 296 ASN ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.3595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.091 166175 Z= 0.452 Angle : 0.808 16.493 247356 Z= 0.419 Chirality : 0.047 0.526 31326 Planarity : 0.008 0.152 14137 Dihedral : 23.412 179.330 79973 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.61 % Favored : 96.36 % Rotamer: Outliers : 4.82 % Allowed : 16.09 % Favored : 79.09 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.44 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.10), residues: 6755 helix: 0.55 (0.10), residues: 2342 sheet: -0.59 (0.14), residues: 1313 loop : -0.92 (0.10), residues: 3100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.003 TRP 7 59 HIS 0.016 0.002 HIS k 37 PHE 0.025 0.003 PHE Q 57 TYR 0.022 0.003 TYR S 38 ARG 0.018 0.001 ARG n 95 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13510 Ramachandran restraints generated. 6755 Oldfield, 0 Emsley, 6755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13510 Ramachandran restraints generated. 6755 Oldfield, 0 Emsley, 6755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1376 residues out of total 5623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 271 poor density : 1105 time to evaluate : 7.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 35 GLU cc_start: 0.8029 (pt0) cc_final: 0.7636 (pt0) REVERT: B 132 MET cc_start: 0.8944 (mtm) cc_final: 0.8664 (mtm) REVERT: B 167 ARG cc_start: 0.7721 (ttp-110) cc_final: 0.7275 (ttt-90) REVERT: C 131 ASP cc_start: 0.7505 (m-30) cc_final: 0.7296 (m-30) REVERT: D 21 ARG cc_start: 0.7591 (ptp-170) cc_final: 0.7351 (ptm160) REVERT: D 67 ARG cc_start: 0.8700 (mtp180) cc_final: 0.8425 (mmm160) REVERT: D 144 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7020 (tm-30) REVERT: D 155 GLU cc_start: 0.7377 (OUTLIER) cc_final: 0.6887 (tp30) REVERT: D 197 GLU cc_start: 0.7023 (OUTLIER) cc_final: 0.6428 (tm-30) REVERT: E 30 ARG cc_start: 0.7907 (OUTLIER) cc_final: 0.6394 (ptt90) REVERT: E 144 ASP cc_start: 0.6571 (OUTLIER) cc_final: 0.6230 (m-30) REVERT: F 44 LYS cc_start: 0.6668 (OUTLIER) cc_final: 0.5741 (mmtp) REVERT: F 172 LYS cc_start: 0.8606 (OUTLIER) cc_final: 0.7997 (ttmt) REVERT: L 143 GLU cc_start: 0.7311 (pt0) cc_final: 0.7017 (pt0) REVERT: M 6 ARG cc_start: 0.7619 (OUTLIER) cc_final: 0.6849 (ptm160) REVERT: M 60 GLN cc_start: 0.7600 (OUTLIER) cc_final: 0.7205 (mp10) REVERT: N 57 THR cc_start: 0.8415 (p) cc_final: 0.7887 (m) REVERT: N 65 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.7992 (tp) REVERT: N 95 THR cc_start: 0.8723 (p) cc_final: 0.8505 (p) REVERT: P 27 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7716 (tm-30) REVERT: Q 85 LYS cc_start: 0.8958 (OUTLIER) cc_final: 0.8592 (mttt) REVERT: R 6 GLN cc_start: 0.8262 (OUTLIER) cc_final: 0.7519 (tp40) REVERT: R 16 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.6479 (mp0) REVERT: R 40 MET cc_start: 0.8462 (ttm) cc_final: 0.8250 (ttm) REVERT: R 70 GLU cc_start: 0.7545 (OUTLIER) cc_final: 0.7112 (tm-30) REVERT: T 76 ARG cc_start: 0.8286 (OUTLIER) cc_final: 0.8005 (ttt-90) REVERT: U 79 LYS cc_start: 0.8802 (OUTLIER) cc_final: 0.8541 (mttt) REVERT: V 59 GLU cc_start: 0.7678 (mt-10) cc_final: 0.7411 (mt-10) REVERT: W 17 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.7203 (mp0) REVERT: Y 5 GLU cc_start: 0.7561 (mp0) cc_final: 0.7181 (mp0) REVERT: Z 19 LYS cc_start: 0.8568 (ttmm) cc_final: 0.8222 (ttpp) REVERT: f 1 MET cc_start: 0.8683 (tpp) cc_final: 0.8398 (ttm) REVERT: f 2 LYS cc_start: 0.8217 (mttp) cc_final: 0.7951 (mmtt) REVERT: f 18 LYS cc_start: 0.8897 (tttt) cc_final: 0.8621 (tttt) REVERT: g 10 LEU cc_start: 0.7304 (OUTLIER) cc_final: 0.7101 (tt) REVERT: g 58 ASN cc_start: 0.7513 (t0) cc_final: 0.7122 (t0) REVERT: g 87 CYS cc_start: 0.7458 (p) cc_final: 0.7117 (p) REVERT: g 113 ARG cc_start: 0.7315 (tpt170) cc_final: 0.6946 (tpt170) REVERT: g 136 MET cc_start: 0.6901 (ttp) cc_final: 0.6593 (ttp) REVERT: g 161 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8356 (mp) REVERT: h 14 ILE cc_start: 0.8391 (mp) cc_final: 0.8187 (mt) REVERT: i 44 ARG cc_start: 0.6500 (ptm160) cc_final: 0.6299 (ptt180) REVERT: i 47 ARG cc_start: 0.6286 (ttm-80) cc_final: 0.5701 (ttm110) REVERT: i 128 ARG cc_start: 0.7411 (mtt180) cc_final: 0.7041 (tmt-80) REVERT: i 148 LYS cc_start: 0.7393 (ttpp) cc_final: 0.6843 (tppp) REVERT: j 68 ARG cc_start: 0.7688 (OUTLIER) cc_final: 0.6706 (mpp-170) REVERT: j 159 LYS cc_start: 0.8798 (OUTLIER) cc_final: 0.8437 (mttp) REVERT: k 93 LYS cc_start: 0.7444 (ttmm) cc_final: 0.6998 (ptmm) REVERT: l 118 LEU cc_start: 0.7987 (tp) cc_final: 0.7684 (tp) REVERT: m 124 GLU cc_start: 0.8468 (tt0) cc_final: 0.8150 (tt0) REVERT: n 85 ARG cc_start: 0.7879 (ttm-80) cc_final: 0.7598 (mtm180) REVERT: n 99 ARG cc_start: 0.8043 (tpp-160) cc_final: 0.7725 (mtp85) REVERT: q 9 ARG cc_start: 0.7806 (ttp-110) cc_final: 0.7444 (mtm110) REVERT: r 31 LYS cc_start: 0.8112 (mtmm) cc_final: 0.7778 (mtpp) REVERT: r 93 ARG cc_start: 0.7408 (OUTLIER) cc_final: 0.6627 (tpt170) REVERT: w 50 LYS cc_start: 0.8290 (tttt) cc_final: 0.7968 (ttpt) REVERT: x 6 LYS cc_start: 0.8267 (pttt) cc_final: 0.8048 (pttm) REVERT: x 44 MET cc_start: 0.7381 (mtp) cc_final: 0.7094 (mtt) REVERT: y 57 ILE cc_start: 0.8012 (OUTLIER) cc_final: 0.7795 (tt) REVERT: 7 206 ILE cc_start: 0.0958 (OUTLIER) cc_final: 0.0660 (mt) REVERT: 7 280 MET cc_start: 0.3060 (OUTLIER) cc_final: 0.1768 (pmm) REVERT: 7 378 THR cc_start: 0.6305 (OUTLIER) cc_final: 0.5937 (t) REVERT: 7 472 ARG cc_start: 0.6343 (mmp80) cc_final: 0.5485 (mmp80) REVERT: 7 516 GLU cc_start: 0.5537 (pp20) cc_final: 0.5216 (mm-30) REVERT: H 1 MET cc_start: 0.3507 (tpp) cc_final: 0.2788 (mtp) REVERT: H 38 MET cc_start: 0.3590 (OUTLIER) cc_final: 0.3295 (ttm) REVERT: A 17 GLU cc_start: 0.6519 (OUTLIER) cc_final: 0.6173 (mp0) REVERT: A 90 GLU cc_start: 0.5786 (OUTLIER) cc_final: 0.5451 (tm-30) REVERT: A 169 ASP cc_start: 0.6777 (m-30) cc_final: 0.6577 (p0) REVERT: A 279 HIS cc_start: 0.6594 (t70) cc_final: 0.6293 (t-90) outliers start: 271 outliers final: 121 residues processed: 1242 average time/residue: 2.3253 time to fit residues: 4094.7360 Evaluate side-chains 1144 residues out of total 5623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 993 time to evaluate : 6.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain C residue 46 ARG Chi-restraints excluded: chain C residue 56 LYS Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain D residue 6 LYS Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain D residue 144 GLU Chi-restraints excluded: chain D residue 155 GLU Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain E residue 30 ARG Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 144 ASP Chi-restraints excluded: chain E residue 153 ASP Chi-restraints excluded: chain E residue 161 LYS Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain F residue 172 LYS Chi-restraints excluded: chain G residue 130 VAL Chi-restraints excluded: chain G residue 147 VAL Chi-restraints excluded: chain J residue 34 ARG Chi-restraints excluded: chain J residue 60 ASP Chi-restraints excluded: chain J residue 98 GLU Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain M residue 6 ARG Chi-restraints excluded: chain M residue 60 GLN Chi-restraints excluded: chain N residue 12 ARG Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 29 VAL Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain O residue 45 SER Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 91 SER Chi-restraints excluded: chain P residue 27 GLU Chi-restraints excluded: chain P residue 70 VAL Chi-restraints excluded: chain Q residue 85 LYS Chi-restraints excluded: chain R residue 6 GLN Chi-restraints excluded: chain R residue 16 GLU Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 70 GLU Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 73 LYS Chi-restraints excluded: chain R residue 86 GLN Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 45 VAL Chi-restraints excluded: chain S residue 101 SER Chi-restraints excluded: chain T residue 76 ARG Chi-restraints excluded: chain U residue 59 VAL Chi-restraints excluded: chain U residue 67 VAL Chi-restraints excluded: chain U residue 79 LYS Chi-restraints excluded: chain V residue 1 MET Chi-restraints excluded: chain W residue 17 GLU Chi-restraints excluded: chain W residue 62 LYS Chi-restraints excluded: chain W residue 78 LYS Chi-restraints excluded: chain X residue 66 THR Chi-restraints excluded: chain Y residue 16 THR Chi-restraints excluded: chain Z residue 57 VAL Chi-restraints excluded: chain c residue 22 THR Chi-restraints excluded: chain d residue 22 MET Chi-restraints excluded: chain d residue 25 LYS Chi-restraints excluded: chain f residue 6 SER Chi-restraints excluded: chain f residue 36 ARG Chi-restraints excluded: chain g residue 10 LEU Chi-restraints excluded: chain g residue 111 ILE Chi-restraints excluded: chain g residue 130 THR Chi-restraints excluded: chain g residue 161 LEU Chi-restraints excluded: chain g residue 211 THR Chi-restraints excluded: chain h residue 21 THR Chi-restraints excluded: chain h residue 26 THR Chi-restraints excluded: chain h residue 44 THR Chi-restraints excluded: chain h residue 53 SER Chi-restraints excluded: chain h residue 59 ARG Chi-restraints excluded: chain h residue 66 VAL Chi-restraints excluded: chain h residue 67 THR Chi-restraints excluded: chain h residue 94 ILE Chi-restraints excluded: chain h residue 101 ILE Chi-restraints excluded: chain h residue 128 VAL Chi-restraints excluded: chain i residue 25 VAL Chi-restraints excluded: chain i residue 143 VAL Chi-restraints excluded: chain i residue 166 GLU Chi-restraints excluded: chain j residue 15 LEU Chi-restraints excluded: chain j residue 32 SER Chi-restraints excluded: chain j residue 68 ARG Chi-restraints excluded: chain j residue 120 VAL Chi-restraints excluded: chain j residue 156 LYS Chi-restraints excluded: chain j residue 159 LYS Chi-restraints excluded: chain k residue 7 VAL Chi-restraints excluded: chain l residue 23 LEU Chi-restraints excluded: chain l residue 56 LYS Chi-restraints excluded: chain l residue 90 GLU Chi-restraints excluded: chain l residue 94 VAL Chi-restraints excluded: chain m residue 72 VAL Chi-restraints excluded: chain m residue 79 SER Chi-restraints excluded: chain m residue 129 VAL Chi-restraints excluded: chain n residue 29 VAL Chi-restraints excluded: chain n residue 63 LEU Chi-restraints excluded: chain p residue 30 THR Chi-restraints excluded: chain p residue 34 ILE Chi-restraints excluded: chain p residue 108 THR Chi-restraints excluded: chain p residue 116 ILE Chi-restraints excluded: chain q residue 4 VAL Chi-restraints excluded: chain q residue 64 THR Chi-restraints excluded: chain q residue 86 ARG Chi-restraints excluded: chain q residue 119 VAL Chi-restraints excluded: chain r residue 28 THR Chi-restraints excluded: chain r residue 68 ASP Chi-restraints excluded: chain r residue 93 ARG Chi-restraints excluded: chain s residue 11 VAL Chi-restraints excluded: chain s residue 67 THR Chi-restraints excluded: chain s residue 90 ARG Chi-restraints excluded: chain t residue 57 LEU Chi-restraints excluded: chain t residue 75 VAL Chi-restraints excluded: chain u residue 24 SER Chi-restraints excluded: chain v residue 57 ASP Chi-restraints excluded: chain v residue 67 LEU Chi-restraints excluded: chain x residue 58 VAL Chi-restraints excluded: chain y residue 57 ILE Chi-restraints excluded: chain 7 residue 206 ILE Chi-restraints excluded: chain 7 residue 280 MET Chi-restraints excluded: chain 7 residue 320 VAL Chi-restraints excluded: chain 7 residue 378 THR Chi-restraints excluded: chain 7 residue 408 LYS Chi-restraints excluded: chain 7 residue 419 LEU Chi-restraints excluded: chain 7 residue 425 VAL Chi-restraints excluded: chain 7 residue 478 ASP Chi-restraints excluded: chain 7 residue 513 LEU Chi-restraints excluded: chain H residue 38 MET Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 160 LYS Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 292 SER Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 347 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1125 random chunks: chunk 1011 optimal weight: 9.9990 chunk 769 optimal weight: 0.7980 chunk 531 optimal weight: 2.9990 chunk 113 optimal weight: 6.9990 chunk 488 optimal weight: 0.0770 chunk 687 optimal weight: 2.9990 chunk 1027 optimal weight: 0.3980 chunk 1087 optimal weight: 20.0000 chunk 536 optimal weight: 9.9990 chunk 973 optimal weight: 10.0000 chunk 293 optimal weight: 10.0000 overall best weight: 1.4542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 150 GLN ** D 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 195 GLN F 38 ASN F 104 ASN ** J 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 138 GLN K 29 HIS K 88 ASN K 89 ASN N 18 GLN O 19 GLN O 100 HIS P 10 GLN P 12 GLN P 15 GLN R 86 GLN S 9 HIS S 61 ASN U 27 ASN Y 20 ASN Y 39 GLN Y 58 ASN ** g 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 139 GLN i 131 ASN k 3 HIS ** k 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 15 GLN t 62 GLN u 40 ASN x 69 HIS y 3 ASN y 21 ASN 7 267 HIS ** 7 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 238 ASN A 296 ASN A 346 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.3449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 166175 Z= 0.148 Angle : 0.591 14.014 247356 Z= 0.322 Chirality : 0.034 0.505 31326 Planarity : 0.006 0.126 14137 Dihedral : 23.286 178.778 79973 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.98 % Favored : 96.99 % Rotamer: Outliers : 3.68 % Allowed : 19.97 % Favored : 76.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.44 % 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: -0.14 (0.10), residues: 6755 helix: 0.99 (0.11), residues: 2344 sheet: -0.40 (0.14), residues: 1280 loop : -0.72 (0.11), residues: 3131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP 7 59 HIS 0.012 0.001 HIS k 37 PHE 0.016 0.001 PHE A 177 TYR 0.016 0.001 TYR S 38 ARG 0.009 0.000 ARG h 72 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13510 Ramachandran restraints generated. 6755 Oldfield, 0 Emsley, 6755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13510 Ramachandran restraints generated. 6755 Oldfield, 0 Emsley, 6755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1243 residues out of total 5623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 207 poor density : 1036 time to evaluate : 7.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 35 GLU cc_start: 0.7979 (pt0) cc_final: 0.7615 (pt0) REVERT: B 128 ASN cc_start: 0.9037 (m-40) cc_final: 0.8642 (m110) REVERT: B 132 MET cc_start: 0.8822 (mtm) cc_final: 0.8606 (mtm) REVERT: B 167 ARG cc_start: 0.7750 (ttp-110) cc_final: 0.7309 (ttt-90) REVERT: D 21 ARG cc_start: 0.7556 (ptp-170) cc_final: 0.7302 (ptm160) REVERT: D 88 ARG cc_start: 0.8257 (OUTLIER) cc_final: 0.7892 (mmp80) REVERT: D 144 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7057 (tm-30) REVERT: F 44 LYS cc_start: 0.6715 (mmtm) cc_final: 0.5803 (mmtp) REVERT: K 117 SER cc_start: 0.8663 (p) cc_final: 0.8333 (m) REVERT: M 6 ARG cc_start: 0.7479 (OUTLIER) cc_final: 0.6795 (ptm160) REVERT: M 88 ASN cc_start: 0.9040 (OUTLIER) cc_final: 0.8763 (m-40) REVERT: N 57 THR cc_start: 0.8158 (p) cc_final: 0.7914 (m) REVERT: N 74 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.7999 (tt0) REVERT: N 95 THR cc_start: 0.8556 (p) cc_final: 0.8232 (p) REVERT: P 27 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7723 (tm-30) REVERT: R 70 GLU cc_start: 0.7484 (OUTLIER) cc_final: 0.7011 (tm-30) REVERT: R 86 GLN cc_start: 0.7823 (OUTLIER) cc_final: 0.6825 (mp-120) REVERT: V 59 GLU cc_start: 0.7627 (mt-10) cc_final: 0.7368 (mt-10) REVERT: W 17 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7083 (mp0) REVERT: Y 4 LYS cc_start: 0.8084 (ttmm) cc_final: 0.7786 (ttmt) REVERT: Z 19 LYS cc_start: 0.8565 (ttmm) cc_final: 0.8189 (ttpp) REVERT: b 23 THR cc_start: 0.8877 (p) cc_final: 0.8576 (m) REVERT: c 7 GLU cc_start: 0.6786 (OUTLIER) cc_final: 0.6219 (pt0) REVERT: d 22 MET cc_start: 0.9049 (mmm) cc_final: 0.8670 (mmm) REVERT: f 2 LYS cc_start: 0.8234 (mttp) cc_final: 0.7966 (mmtt) REVERT: g 10 LEU cc_start: 0.7245 (OUTLIER) cc_final: 0.7043 (tt) REVERT: g 66 LYS cc_start: 0.7613 (OUTLIER) cc_final: 0.7144 (mtpt) REVERT: g 82 ASP cc_start: 0.6541 (p0) cc_final: 0.5489 (m-30) REVERT: g 136 MET cc_start: 0.6821 (ttp) cc_final: 0.6614 (ttp) REVERT: g 169 GLU cc_start: 0.7418 (OUTLIER) cc_final: 0.7046 (mp0) REVERT: h 72 ARG cc_start: 0.7171 (mtm110) cc_final: 0.6330 (mtm110) REVERT: h 86 LYS cc_start: 0.6371 (pttt) cc_final: 0.5883 (ptpt) REVERT: i 47 ARG cc_start: 0.6181 (ttm-80) cc_final: 0.5612 (ttm110) REVERT: i 128 ARG cc_start: 0.7378 (mtt180) cc_final: 0.6982 (tmt-80) REVERT: i 131 ASN cc_start: 0.7303 (t0) cc_final: 0.6857 (t0) REVERT: i 148 LYS cc_start: 0.7388 (ttpp) cc_final: 0.6901 (tppp) REVERT: i 179 GLU cc_start: 0.6769 (tt0) cc_final: 0.6071 (pp20) REVERT: j 13 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.7099 (pt0) REVERT: j 68 ARG cc_start: 0.7666 (OUTLIER) cc_final: 0.6643 (mpp-170) REVERT: j 147 MET cc_start: 0.7650 (ttp) cc_final: 0.7246 (ttp) REVERT: k 93 LYS cc_start: 0.7360 (ttmm) cc_final: 0.6862 (ptmm) REVERT: l 118 LEU cc_start: 0.7920 (tp) cc_final: 0.7629 (tp) REVERT: n 99 ARG cc_start: 0.8028 (tpp-160) cc_final: 0.7809 (mtp85) REVERT: o 46 LYS cc_start: 0.8326 (mtpm) cc_final: 0.7809 (mtpt) REVERT: o 48 ARG cc_start: 0.8154 (mtt90) cc_final: 0.7902 (mtm-85) REVERT: p 53 ARG cc_start: 0.8736 (mmp-170) cc_final: 0.8534 (mtp180) REVERT: q 9 ARG cc_start: 0.7769 (ttp-110) cc_final: 0.7520 (mtm110) REVERT: q 40 THR cc_start: 0.8853 (OUTLIER) cc_final: 0.8543 (m) REVERT: q 78 SER cc_start: 0.8510 (m) cc_final: 0.8192 (m) REVERT: q 86 ARG cc_start: 0.8325 (OUTLIER) cc_final: 0.7672 (ptt-90) REVERT: r 31 LYS cc_start: 0.8088 (mtmm) cc_final: 0.7731 (mtpp) REVERT: x 59 PRO cc_start: 0.8603 (Cg_endo) cc_final: 0.8378 (Cg_exo) REVERT: 7 60 MET cc_start: 0.1346 (mmm) cc_final: 0.0846 (mmm) REVERT: 7 62 MET cc_start: 0.2164 (mtm) cc_final: 0.1859 (mtm) REVERT: 7 97 GLU cc_start: 0.5567 (tp30) cc_final: 0.4881 (tp30) REVERT: 7 206 ILE cc_start: 0.0861 (OUTLIER) cc_final: 0.0228 (pt) REVERT: 7 378 THR cc_start: 0.6195 (OUTLIER) cc_final: 0.5858 (t) REVERT: 7 400 ARG cc_start: 0.6024 (ttp-110) cc_final: 0.5744 (ttp80) REVERT: 7 472 ARG cc_start: 0.6062 (mmp80) cc_final: 0.5338 (mmp80) REVERT: 7 487 ARG cc_start: 0.5505 (mtm110) cc_final: 0.4864 (tmm160) REVERT: 7 516 GLU cc_start: 0.5439 (pp20) cc_final: 0.5095 (mm-30) REVERT: H 1 MET cc_start: 0.3382 (tpp) cc_final: 0.2721 (mtp) REVERT: A 68 MET cc_start: 0.3942 (tpt) cc_final: 0.3383 (tmm) REVERT: A 77 MET cc_start: 0.5458 (ttp) cc_final: 0.5235 (mtp) REVERT: A 279 HIS cc_start: 0.6582 (t70) cc_final: 0.6304 (t-90) outliers start: 207 outliers final: 81 residues processed: 1141 average time/residue: 2.2812 time to fit residues: 3730.7418 Evaluate side-chains 1075 residues out of total 5623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 975 time to evaluate : 6.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain C residue 46 ARG Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 88 ARG Chi-restraints excluded: chain D residue 144 GLU Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 161 LYS Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 147 VAL Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain M residue 6 ARG Chi-restraints excluded: chain M residue 88 ASN Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 74 GLU Chi-restraints excluded: chain O residue 91 SER Chi-restraints excluded: chain P residue 27 GLU Chi-restraints excluded: chain R residue 16 GLU Chi-restraints excluded: chain R residue 70 GLU Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 73 LYS Chi-restraints excluded: chain R residue 86 GLN Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 101 SER Chi-restraints excluded: chain T residue 21 SER Chi-restraints excluded: chain U residue 59 VAL Chi-restraints excluded: chain U residue 60 GLU Chi-restraints excluded: chain W residue 17 GLU Chi-restraints excluded: chain W residue 62 LYS Chi-restraints excluded: chain W residue 78 LYS Chi-restraints excluded: chain Y residue 16 THR Chi-restraints excluded: chain c residue 7 GLU Chi-restraints excluded: chain c residue 22 THR Chi-restraints excluded: chain f residue 6 SER Chi-restraints excluded: chain g residue 10 LEU Chi-restraints excluded: chain g residue 23 TRP Chi-restraints excluded: chain g residue 66 LYS Chi-restraints excluded: chain g residue 135 LEU Chi-restraints excluded: chain g residue 164 ILE Chi-restraints excluded: chain g residue 169 GLU Chi-restraints excluded: chain h residue 20 SER Chi-restraints excluded: chain h residue 66 VAL Chi-restraints excluded: chain h residue 101 ILE Chi-restraints excluded: chain h residue 121 THR Chi-restraints excluded: chain h residue 128 VAL Chi-restraints excluded: chain i residue 25 VAL Chi-restraints excluded: chain i residue 101 VAL Chi-restraints excluded: chain i residue 166 GLU Chi-restraints excluded: chain j residue 13 GLU Chi-restraints excluded: chain j residue 32 SER Chi-restraints excluded: chain j residue 68 ARG Chi-restraints excluded: chain j residue 120 VAL Chi-restraints excluded: chain j residue 156 LYS Chi-restraints excluded: chain l residue 6 VAL Chi-restraints excluded: chain l residue 69 VAL Chi-restraints excluded: chain l residue 94 VAL Chi-restraints excluded: chain m residue 72 VAL Chi-restraints excluded: chain m residue 129 VAL Chi-restraints excluded: chain n residue 29 VAL Chi-restraints excluded: chain n residue 63 LEU Chi-restraints excluded: chain n residue 111 VAL Chi-restraints excluded: chain p residue 30 THR Chi-restraints excluded: chain p residue 34 ILE Chi-restraints excluded: chain q residue 40 THR Chi-restraints excluded: chain q residue 64 THR Chi-restraints excluded: chain q residue 86 ARG Chi-restraints excluded: chain q residue 119 VAL Chi-restraints excluded: chain s residue 90 ARG Chi-restraints excluded: chain v residue 42 THR Chi-restraints excluded: chain v residue 57 ASP Chi-restraints excluded: chain v residue 67 LEU Chi-restraints excluded: chain y residue 14 SER Chi-restraints excluded: chain z residue 42 THR Chi-restraints excluded: chain 7 residue 59 TRP Chi-restraints excluded: chain 7 residue 206 ILE Chi-restraints excluded: chain 7 residue 320 VAL Chi-restraints excluded: chain 7 residue 378 THR Chi-restraints excluded: chain 7 residue 408 LYS Chi-restraints excluded: chain 7 residue 425 VAL Chi-restraints excluded: chain 7 residue 466 VAL Chi-restraints excluded: chain 7 residue 478 ASP Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 330 ASP Chi-restraints excluded: chain A residue 347 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1125 random chunks: chunk 905 optimal weight: 7.9990 chunk 617 optimal weight: 2.9990 chunk 15 optimal weight: 10.0000 chunk 809 optimal weight: 7.9990 chunk 448 optimal weight: 10.0000 chunk 927 optimal weight: 30.0000 chunk 751 optimal weight: 7.9990 chunk 1 optimal weight: 10.0000 chunk 555 optimal weight: 5.9990 chunk 976 optimal weight: 7.9990 chunk 274 optimal weight: 10.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 150 GLN ** D 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 156 ASN D 195 GLN ** F 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 138 GLN ** K 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 88 ASN N 18 GLN O 19 GLN P 10 GLN P 15 GLN R 86 GLN S 61 ASN V 49 ASN Y 20 ASN c 45 GLN g 42 ASN ** h 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 139 GLN k 3 HIS ** k 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 62 GLN u 40 ASN y 3 ASN 7 467 ASN ** 7 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 238 ASN A 296 ASN ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.3897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.097 166175 Z= 0.448 Angle : 0.777 15.361 247356 Z= 0.403 Chirality : 0.047 0.517 31326 Planarity : 0.008 0.149 14137 Dihedral : 23.378 179.607 79973 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.04 % Favored : 95.94 % Rotamer: Outliers : 5.10 % Allowed : 20.40 % Favored : 74.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.44 % 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: -0.46 (0.10), residues: 6755 helix: 0.60 (0.11), residues: 2342 sheet: -0.45 (0.14), residues: 1295 loop : -0.87 (0.10), residues: 3118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP 7 59 HIS 0.013 0.002 HIS k 37 PHE 0.022 0.003 PHE Q 57 TYR 0.023 0.003 TYR S 38 ARG 0.009 0.001 ARG S 11 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13510 Ramachandran restraints generated. 6755 Oldfield, 0 Emsley, 6755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13510 Ramachandran restraints generated. 6755 Oldfield, 0 Emsley, 6755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1274 residues out of total 5623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 287 poor density : 987 time to evaluate : 7.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 23 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7101 (mp0) REVERT: B 128 ASN cc_start: 0.9106 (m-40) cc_final: 0.8783 (m110) REVERT: B 132 MET cc_start: 0.9076 (mtm) cc_final: 0.8790 (mtm) REVERT: B 167 ARG cc_start: 0.7862 (ttp-110) cc_final: 0.7343 (ttt-90) REVERT: C 89 GLU cc_start: 0.7364 (OUTLIER) cc_final: 0.6954 (mt-10) REVERT: D 21 ARG cc_start: 0.7734 (ptp-170) cc_final: 0.7436 (ptm160) REVERT: D 67 ARG cc_start: 0.8755 (mtp180) cc_final: 0.8477 (mmm160) REVERT: D 144 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7018 (tm-30) REVERT: D 197 GLU cc_start: 0.7039 (OUTLIER) cc_final: 0.6712 (tm-30) REVERT: F 44 LYS cc_start: 0.6848 (mmtm) cc_final: 0.6006 (mttp) REVERT: F 172 LYS cc_start: 0.8512 (OUTLIER) cc_final: 0.7953 (ttmt) REVERT: K 117 SER cc_start: 0.8671 (OUTLIER) cc_final: 0.8432 (m) REVERT: M 6 ARG cc_start: 0.7681 (OUTLIER) cc_final: 0.6946 (ptm160) REVERT: N 57 THR cc_start: 0.8367 (p) cc_final: 0.7934 (m) REVERT: N 65 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.7963 (tp) REVERT: N 74 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.8059 (tt0) REVERT: N 95 THR cc_start: 0.8624 (p) cc_final: 0.8354 (p) REVERT: P 13 MET cc_start: 0.8763 (mmm) cc_final: 0.8456 (mtt) REVERT: R 2 TYR cc_start: 0.8882 (p90) cc_final: 0.8663 (p90) REVERT: R 6 GLN cc_start: 0.8263 (OUTLIER) cc_final: 0.7544 (tp40) REVERT: R 27 ILE cc_start: 0.8823 (mm) cc_final: 0.8540 (mp) REVERT: R 70 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.7044 (tm-30) REVERT: R 86 GLN cc_start: 0.8131 (OUTLIER) cc_final: 0.7604 (pt0) REVERT: S 92 ARG cc_start: 0.8344 (OUTLIER) cc_final: 0.7581 (ttm-80) REVERT: U 29 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8754 (mm) REVERT: U 79 LYS cc_start: 0.8846 (OUTLIER) cc_final: 0.8572 (mttt) REVERT: W 17 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7292 (mp0) REVERT: W 83 GLU cc_start: 0.7206 (OUTLIER) cc_final: 0.6886 (mt-10) REVERT: Z 19 LYS cc_start: 0.8559 (ttmm) cc_final: 0.8246 (ttpp) REVERT: f 2 LYS cc_start: 0.8237 (mttp) cc_final: 0.7944 (mmtt) REVERT: f 34 LYS cc_start: 0.8979 (OUTLIER) cc_final: 0.7622 (ptpt) REVERT: g 10 LEU cc_start: 0.7414 (OUTLIER) cc_final: 0.7202 (tt) REVERT: g 66 LYS cc_start: 0.7769 (OUTLIER) cc_final: 0.7401 (mtpt) REVERT: g 161 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8430 (mp) REVERT: g 169 GLU cc_start: 0.7352 (OUTLIER) cc_final: 0.7045 (mp0) REVERT: h 72 ARG cc_start: 0.7366 (mtm110) cc_final: 0.6641 (mtm110) REVERT: h 121 THR cc_start: 0.8567 (OUTLIER) cc_final: 0.8354 (t) REVERT: h 185 ASN cc_start: 0.8697 (OUTLIER) cc_final: 0.8419 (m-40) REVERT: i 47 ARG cc_start: 0.6309 (ttm-80) cc_final: 0.6078 (ttm-80) REVERT: i 128 ARG cc_start: 0.7475 (mtt180) cc_final: 0.7108 (tmt-80) REVERT: i 148 LYS cc_start: 0.7437 (ttpp) cc_final: 0.7021 (tppp) REVERT: i 179 GLU cc_start: 0.6976 (tt0) cc_final: 0.6186 (pp20) REVERT: j 13 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7234 (pt0) REVERT: j 68 ARG cc_start: 0.7726 (OUTLIER) cc_final: 0.6694 (mpp-170) REVERT: j 147 MET cc_start: 0.7843 (OUTLIER) cc_final: 0.7373 (ttp) REVERT: j 159 LYS cc_start: 0.8780 (OUTLIER) cc_final: 0.8445 (mttp) REVERT: k 93 LYS cc_start: 0.7567 (ttmm) cc_final: 0.6972 (ptmm) REVERT: l 118 LEU cc_start: 0.8020 (tp) cc_final: 0.7703 (tp) REVERT: n 47 VAL cc_start: 0.8200 (p) cc_final: 0.7861 (t) REVERT: o 46 LYS cc_start: 0.8428 (mtpm) cc_final: 0.7927 (mtpt) REVERT: q 9 ARG cc_start: 0.7809 (ttp-110) cc_final: 0.7524 (mtm110) REVERT: q 40 THR cc_start: 0.8943 (OUTLIER) cc_final: 0.8589 (m) REVERT: q 78 SER cc_start: 0.8718 (OUTLIER) cc_final: 0.8379 (m) REVERT: q 86 ARG cc_start: 0.8324 (OUTLIER) cc_final: 0.8090 (ppp80) REVERT: q 91 PRO cc_start: 0.8584 (Cg_endo) cc_final: 0.8131 (Cg_exo) REVERT: s 61 ARG cc_start: 0.8657 (OUTLIER) cc_final: 0.7686 (ttm170) REVERT: u 34 GLU cc_start: 0.8632 (OUTLIER) cc_final: 0.8324 (tt0) REVERT: w 50 LYS cc_start: 0.8253 (tttt) cc_final: 0.7959 (ttpt) REVERT: x 59 PRO cc_start: 0.8638 (Cg_endo) cc_final: 0.8402 (Cg_exo) REVERT: y 57 ILE cc_start: 0.8085 (OUTLIER) cc_final: 0.7812 (tt) REVERT: z 69 ARG cc_start: 0.6872 (OUTLIER) cc_final: 0.5797 (ppt-90) REVERT: 7 60 MET cc_start: 0.1559 (mmm) cc_final: 0.1003 (mmm) REVERT: 7 62 MET cc_start: 0.1864 (mtm) cc_final: 0.1605 (mtm) REVERT: 7 378 THR cc_start: 0.6327 (OUTLIER) cc_final: 0.5944 (t) REVERT: 7 400 ARG cc_start: 0.6122 (ttp-110) cc_final: 0.5917 (ttp80) REVERT: 7 472 ARG cc_start: 0.6090 (mmp80) cc_final: 0.5024 (mmp80) REVERT: 7 516 GLU cc_start: 0.5962 (pp20) cc_final: 0.5460 (mm-30) REVERT: I 16 MET cc_start: 0.2423 (OUTLIER) cc_final: 0.2130 (tmt) REVERT: H 1 MET cc_start: 0.3300 (tpp) cc_final: 0.2705 (mtp) REVERT: H 38 MET cc_start: 0.5112 (OUTLIER) cc_final: 0.4863 (ttt) REVERT: A 14 GLU cc_start: 0.7207 (OUTLIER) cc_final: 0.6622 (mt-10) REVERT: A 17 GLU cc_start: 0.6466 (OUTLIER) cc_final: 0.6050 (mp0) REVERT: A 77 MET cc_start: 0.5707 (ttp) cc_final: 0.4822 (pmm) REVERT: A 90 GLU cc_start: 0.5612 (OUTLIER) cc_final: 0.5101 (tt0) REVERT: A 94 GLN cc_start: 0.5212 (mm-40) cc_final: 0.4962 (mp10) REVERT: A 279 HIS cc_start: 0.6645 (t70) cc_final: 0.6435 (t70) outliers start: 287 outliers final: 150 residues processed: 1146 average time/residue: 2.2692 time to fit residues: 3733.6198 Evaluate side-chains 1151 residues out of total 5623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 960 time to evaluate : 6.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 23 GLU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain C residue 46 ARG Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain D residue 144 GLU Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 144 ASP Chi-restraints excluded: chain E residue 161 LYS Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain F residue 172 LYS Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 130 VAL Chi-restraints excluded: chain G residue 147 VAL Chi-restraints excluded: chain J residue 60 ASP Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 117 SER Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain L residue 143 GLU Chi-restraints excluded: chain M residue 6 ARG Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 29 VAL Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain N residue 74 GLU Chi-restraints excluded: chain O residue 5 SER Chi-restraints excluded: chain O residue 45 SER Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 91 SER Chi-restraints excluded: chain P residue 70 VAL Chi-restraints excluded: chain Q residue 3 ARG Chi-restraints excluded: chain R residue 6 GLN Chi-restraints excluded: chain R residue 16 GLU Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 70 GLU Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 73 LYS Chi-restraints excluded: chain R residue 86 GLN Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 45 VAL Chi-restraints excluded: chain S residue 92 ARG Chi-restraints excluded: chain S residue 101 SER Chi-restraints excluded: chain U residue 15 THR Chi-restraints excluded: chain U residue 29 LEU Chi-restraints excluded: chain U residue 49 VAL Chi-restraints excluded: chain U residue 67 VAL Chi-restraints excluded: chain U residue 77 THR Chi-restraints excluded: chain U residue 79 LYS Chi-restraints excluded: chain V residue 1 MET Chi-restraints excluded: chain W residue 17 GLU Chi-restraints excluded: chain W residue 44 LYS Chi-restraints excluded: chain W residue 62 LYS Chi-restraints excluded: chain W residue 83 GLU Chi-restraints excluded: chain X residue 66 THR Chi-restraints excluded: chain Y residue 16 THR Chi-restraints excluded: chain Z residue 57 VAL Chi-restraints excluded: chain Z residue 58 GLU Chi-restraints excluded: chain c residue 7 GLU Chi-restraints excluded: chain c residue 22 THR Chi-restraints excluded: chain d residue 25 LYS Chi-restraints excluded: chain f residue 6 SER Chi-restraints excluded: chain f residue 34 LYS Chi-restraints excluded: chain g residue 10 LEU Chi-restraints excluded: chain g residue 56 GLU Chi-restraints excluded: chain g residue 66 LYS Chi-restraints excluded: chain g residue 100 MET Chi-restraints excluded: chain g residue 130 THR Chi-restraints excluded: chain g residue 135 LEU Chi-restraints excluded: chain g residue 161 LEU Chi-restraints excluded: chain g residue 164 ILE Chi-restraints excluded: chain g residue 169 GLU Chi-restraints excluded: chain g residue 211 THR Chi-restraints excluded: chain h residue 21 THR Chi-restraints excluded: chain h residue 44 THR Chi-restraints excluded: chain h residue 53 SER Chi-restraints excluded: chain h residue 59 ARG Chi-restraints excluded: chain h residue 66 VAL Chi-restraints excluded: chain h residue 67 THR Chi-restraints excluded: chain h residue 94 ILE Chi-restraints excluded: chain h residue 101 ILE Chi-restraints excluded: chain h residue 121 THR Chi-restraints excluded: chain h residue 128 VAL Chi-restraints excluded: chain h residue 185 ASN Chi-restraints excluded: chain i residue 25 VAL Chi-restraints excluded: chain i residue 101 VAL Chi-restraints excluded: chain i residue 143 VAL Chi-restraints excluded: chain i residue 166 GLU Chi-restraints excluded: chain i residue 191 LEU Chi-restraints excluded: chain j residue 13 GLU Chi-restraints excluded: chain j residue 32 SER Chi-restraints excluded: chain j residue 68 ARG Chi-restraints excluded: chain j residue 120 VAL Chi-restraints excluded: chain j residue 130 SER Chi-restraints excluded: chain j residue 147 MET Chi-restraints excluded: chain j residue 156 LYS Chi-restraints excluded: chain j residue 159 LYS Chi-restraints excluded: chain k residue 96 VAL Chi-restraints excluded: chain k residue 102 MET Chi-restraints excluded: chain l residue 6 VAL Chi-restraints excluded: chain l residue 13 LEU Chi-restraints excluded: chain l residue 22 LEU Chi-restraints excluded: chain l residue 23 LEU Chi-restraints excluded: chain l residue 69 VAL Chi-restraints excluded: chain l residue 94 VAL Chi-restraints excluded: chain l residue 133 THR Chi-restraints excluded: chain m residue 72 VAL Chi-restraints excluded: chain m residue 79 SER Chi-restraints excluded: chain m residue 89 LYS Chi-restraints excluded: chain m residue 129 VAL Chi-restraints excluded: chain n residue 29 VAL Chi-restraints excluded: chain n residue 111 VAL Chi-restraints excluded: chain o residue 6 ILE Chi-restraints excluded: chain p residue 30 THR Chi-restraints excluded: chain p residue 34 ILE Chi-restraints excluded: chain p residue 108 THR Chi-restraints excluded: chain p residue 116 ILE Chi-restraints excluded: chain q residue 4 VAL Chi-restraints excluded: chain q residue 21 VAL Chi-restraints excluded: chain q residue 40 THR Chi-restraints excluded: chain q residue 58 THR Chi-restraints excluded: chain q residue 64 THR Chi-restraints excluded: chain q residue 78 SER Chi-restraints excluded: chain q residue 86 ARG Chi-restraints excluded: chain q residue 119 VAL Chi-restraints excluded: chain r residue 17 ILE Chi-restraints excluded: chain r residue 28 THR Chi-restraints excluded: chain r residue 68 ASP Chi-restraints excluded: chain r residue 97 VAL Chi-restraints excluded: chain s residue 11 VAL Chi-restraints excluded: chain s residue 61 ARG Chi-restraints excluded: chain s residue 67 THR Chi-restraints excluded: chain s residue 90 ARG Chi-restraints excluded: chain t residue 75 VAL Chi-restraints excluded: chain u residue 34 GLU Chi-restraints excluded: chain v residue 42 THR Chi-restraints excluded: chain v residue 57 ASP Chi-restraints excluded: chain v residue 67 LEU Chi-restraints excluded: chain x residue 58 VAL Chi-restraints excluded: chain y residue 6 SER Chi-restraints excluded: chain y residue 57 ILE Chi-restraints excluded: chain z residue 69 ARG Chi-restraints excluded: chain 7 residue 7 LEU Chi-restraints excluded: chain 7 residue 320 VAL Chi-restraints excluded: chain 7 residue 378 THR Chi-restraints excluded: chain 7 residue 384 MET Chi-restraints excluded: chain 7 residue 408 LYS Chi-restraints excluded: chain 7 residue 419 LEU Chi-restraints excluded: chain 7 residue 425 VAL Chi-restraints excluded: chain 7 residue 466 VAL Chi-restraints excluded: chain 7 residue 499 ASP Chi-restraints excluded: chain I residue 16 MET Chi-restraints excluded: chain H residue 38 MET Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 84 TYR Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 325 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1125 random chunks: chunk 365 optimal weight: 10.0000 chunk 979 optimal weight: 2.9990 chunk 214 optimal weight: 30.0000 chunk 638 optimal weight: 5.9990 chunk 268 optimal weight: 6.9990 chunk 1088 optimal weight: 6.9990 chunk 903 optimal weight: 0.0270 chunk 503 optimal weight: 3.9990 chunk 90 optimal weight: 10.0000 chunk 360 optimal weight: 10.0000 chunk 571 optimal weight: 5.9990 overall best weight: 3.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 156 ASN F 104 ASN ** J 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 88 ASN N 18 GLN O 98 GLN P 10 GLN P 12 GLN P 15 GLN R 86 GLN T 59 ASN U 27 ASN V 49 ASN Y 20 ASN c 45 GLN g 42 ASN ** h 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 139 GLN i 131 ASN k 3 HIS ** k 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 62 GLN u 40 ASN y 3 ASN y 21 ASN 7 65 GLN 7 267 HIS ** 7 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 445 GLN ** 7 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 296 ASN ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.3908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 166175 Z= 0.275 Angle : 0.654 14.648 247356 Z= 0.351 Chirality : 0.039 0.517 31326 Planarity : 0.006 0.138 14137 Dihedral : 23.360 179.362 79973 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.80 % Favored : 96.18 % Rotamer: Outliers : 4.64 % Allowed : 21.27 % Favored : 74.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.44 % 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: -0.35 (0.10), residues: 6755 helix: 0.74 (0.11), residues: 2350 sheet: -0.45 (0.14), residues: 1295 loop : -0.82 (0.11), residues: 3110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP 7 59 HIS 0.011 0.001 HIS k 37 PHE 0.016 0.002 PHE i 182 TYR 0.020 0.002 TYR w 32 ARG 0.008 0.001 ARG v 6 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13510 Ramachandran restraints generated. 6755 Oldfield, 0 Emsley, 6755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13510 Ramachandran restraints generated. 6755 Oldfield, 0 Emsley, 6755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1235 residues out of total 5623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 261 poor density : 974 time to evaluate : 7.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 69 ARG cc_start: 0.9180 (OUTLIER) cc_final: 0.8912 (mmm160) REVERT: B 128 ASN cc_start: 0.9087 (m-40) cc_final: 0.8741 (m110) REVERT: B 132 MET cc_start: 0.9024 (mtm) cc_final: 0.8657 (mtm) REVERT: B 167 ARG cc_start: 0.7905 (ttp-110) cc_final: 0.7348 (ttt-90) REVERT: C 1 MET cc_start: 0.7319 (OUTLIER) cc_final: 0.6345 (ttm) REVERT: C 89 GLU cc_start: 0.7387 (OUTLIER) cc_final: 0.7154 (mm-30) REVERT: D 21 ARG cc_start: 0.7701 (ptp-170) cc_final: 0.7468 (ptm160) REVERT: D 144 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.6909 (tm-30) REVERT: D 155 GLU cc_start: 0.7350 (OUTLIER) cc_final: 0.6809 (tp30) REVERT: D 197 GLU cc_start: 0.6892 (OUTLIER) cc_final: 0.6662 (tm-30) REVERT: F 27 LYS cc_start: 0.6838 (tptm) cc_final: 0.6634 (tptt) REVERT: F 44 LYS cc_start: 0.6866 (mmtm) cc_final: 0.6108 (mttp) REVERT: F 172 LYS cc_start: 0.8459 (OUTLIER) cc_final: 0.7944 (ttmt) REVERT: K 117 SER cc_start: 0.8574 (p) cc_final: 0.8341 (m) REVERT: L 48 ARG cc_start: 0.8819 (OUTLIER) cc_final: 0.7702 (mpp80) REVERT: M 6 ARG cc_start: 0.7583 (OUTLIER) cc_final: 0.6847 (ptm160) REVERT: M 88 ASN cc_start: 0.9083 (OUTLIER) cc_final: 0.8809 (m-40) REVERT: N 49 GLU cc_start: 0.8567 (mt-10) cc_final: 0.8308 (mt-10) REVERT: N 57 THR cc_start: 0.8276 (p) cc_final: 0.7997 (m) REVERT: N 65 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.7923 (tp) REVERT: N 74 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.8045 (tt0) REVERT: R 6 GLN cc_start: 0.8235 (OUTLIER) cc_final: 0.7506 (tp40) REVERT: R 27 ILE cc_start: 0.8782 (mm) cc_final: 0.8490 (mp) REVERT: R 70 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.7082 (tm-30) REVERT: S 92 ARG cc_start: 0.8327 (OUTLIER) cc_final: 0.7563 (ttm-80) REVERT: W 17 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7245 (mp0) REVERT: W 83 GLU cc_start: 0.7142 (OUTLIER) cc_final: 0.6879 (mt-10) REVERT: Y 4 LYS cc_start: 0.8166 (ttmm) cc_final: 0.7858 (ttmt) REVERT: Z 19 LYS cc_start: 0.8570 (ttmm) cc_final: 0.8219 (ttpp) REVERT: a 10 GLU cc_start: 0.7360 (OUTLIER) cc_final: 0.7072 (pm20) REVERT: f 2 LYS cc_start: 0.8210 (mttp) cc_final: 0.7900 (mmtt) REVERT: f 6 SER cc_start: 0.9124 (OUTLIER) cc_final: 0.8850 (t) REVERT: g 161 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8422 (mp) REVERT: g 169 GLU cc_start: 0.7307 (OUTLIER) cc_final: 0.6990 (mp0) REVERT: h 72 ARG cc_start: 0.7449 (mtm110) cc_final: 0.6770 (mmm160) REVERT: h 179 ARG cc_start: 0.8264 (OUTLIER) cc_final: 0.7510 (ptt90) REVERT: i 47 ARG cc_start: 0.6457 (ttm-80) cc_final: 0.6222 (ttm-80) REVERT: i 128 ARG cc_start: 0.7394 (mtt180) cc_final: 0.7072 (tmt-80) REVERT: i 148 LYS cc_start: 0.7508 (ttpp) cc_final: 0.7073 (tppp) REVERT: i 179 GLU cc_start: 0.6953 (tt0) cc_final: 0.6163 (pp20) REVERT: j 68 ARG cc_start: 0.7717 (OUTLIER) cc_final: 0.6710 (mpp-170) REVERT: j 147 MET cc_start: 0.7761 (ttp) cc_final: 0.7293 (ttp) REVERT: k 93 LYS cc_start: 0.7513 (ttmm) cc_final: 0.6965 (ptmm) REVERT: l 48 GLU cc_start: 0.6300 (mm-30) cc_final: 0.6045 (mm-30) REVERT: l 118 LEU cc_start: 0.7988 (tp) cc_final: 0.7730 (tp) REVERT: o 6 ILE cc_start: 0.7099 (OUTLIER) cc_final: 0.6638 (mt) REVERT: o 46 LYS cc_start: 0.8397 (mtpm) cc_final: 0.7901 (mtpt) REVERT: q 9 ARG cc_start: 0.7781 (ttp-110) cc_final: 0.7516 (mtm110) REVERT: q 40 THR cc_start: 0.8880 (OUTLIER) cc_final: 0.8583 (m) REVERT: q 78 SER cc_start: 0.8739 (OUTLIER) cc_final: 0.8442 (m) REVERT: q 86 ARG cc_start: 0.8361 (OUTLIER) cc_final: 0.7697 (ptt-90) REVERT: q 91 PRO cc_start: 0.8601 (Cg_endo) cc_final: 0.8156 (Cg_exo) REVERT: r 93 ARG cc_start: 0.7397 (OUTLIER) cc_final: 0.6574 (tpt170) REVERT: u 1 MET cc_start: 0.8127 (pmm) cc_final: 0.7775 (pmm) REVERT: u 34 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.8320 (tt0) REVERT: x 59 PRO cc_start: 0.8626 (Cg_endo) cc_final: 0.8417 (Cg_exo) REVERT: y 57 ILE cc_start: 0.8107 (OUTLIER) cc_final: 0.7830 (tt) REVERT: 7 60 MET cc_start: 0.1341 (mmm) cc_final: 0.0621 (mmm) REVERT: 7 62 MET cc_start: 0.1891 (mtm) cc_final: 0.1663 (mtm) REVERT: 7 222 ASP cc_start: 0.3127 (OUTLIER) cc_final: 0.1250 (t0) REVERT: 7 227 LEU cc_start: 0.1807 (OUTLIER) cc_final: 0.1555 (tp) REVERT: 7 378 THR cc_start: 0.6263 (OUTLIER) cc_final: 0.5882 (t) REVERT: 7 472 ARG cc_start: 0.6025 (mmp80) cc_final: 0.5012 (mmp80) REVERT: 7 516 GLU cc_start: 0.6083 (pp20) cc_final: 0.5545 (mm-30) REVERT: I 16 MET cc_start: 0.2230 (OUTLIER) cc_final: 0.1895 (tmt) REVERT: H 1 MET cc_start: 0.3132 (tpp) cc_final: 0.2589 (mtp) REVERT: A 14 GLU cc_start: 0.7185 (OUTLIER) cc_final: 0.6643 (mt-10) REVERT: A 17 GLU cc_start: 0.6386 (OUTLIER) cc_final: 0.6000 (mp0) REVERT: A 68 MET cc_start: 0.4060 (tpp) cc_final: 0.3789 (tpp) REVERT: A 77 MET cc_start: 0.5616 (ttp) cc_final: 0.4787 (pmm) REVERT: A 94 GLN cc_start: 0.5177 (mm-40) cc_final: 0.4953 (mp10) REVERT: A 279 HIS cc_start: 0.6631 (t70) cc_final: 0.6314 (t-90) outliers start: 261 outliers final: 148 residues processed: 1116 average time/residue: 2.2619 time to fit residues: 3633.3209 Evaluate side-chains 1140 residues out of total 5623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 956 time to evaluate : 6.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 69 ARG Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 46 ARG Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain D residue 144 GLU Chi-restraints excluded: chain D residue 155 GLU Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 153 ASP Chi-restraints excluded: chain E residue 161 LYS Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain F residue 172 LYS Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 45 GLU Chi-restraints excluded: chain G residue 147 VAL Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 60 ASP Chi-restraints excluded: chain J residue 95 ARG Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain L residue 48 ARG Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain L residue 143 GLU Chi-restraints excluded: chain M residue 6 ARG Chi-restraints excluded: chain M residue 88 ASN Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 29 VAL Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain N residue 74 GLU Chi-restraints excluded: chain O residue 91 SER Chi-restraints excluded: chain P residue 104 THR Chi-restraints excluded: chain Q residue 3 ARG Chi-restraints excluded: chain R residue 6 GLN Chi-restraints excluded: chain R residue 16 GLU Chi-restraints excluded: chain R residue 70 GLU Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 73 LYS Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 45 VAL Chi-restraints excluded: chain S residue 82 MET Chi-restraints excluded: chain S residue 92 ARG Chi-restraints excluded: chain S residue 101 SER Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain U residue 5 ILE Chi-restraints excluded: chain U residue 15 THR Chi-restraints excluded: chain U residue 49 VAL Chi-restraints excluded: chain U residue 60 GLU Chi-restraints excluded: chain U residue 67 VAL Chi-restraints excluded: chain V residue 1 MET Chi-restraints excluded: chain W residue 17 GLU Chi-restraints excluded: chain W residue 44 LYS Chi-restraints excluded: chain W residue 62 LYS Chi-restraints excluded: chain W residue 78 LYS Chi-restraints excluded: chain W residue 83 GLU Chi-restraints excluded: chain X residue 66 THR Chi-restraints excluded: chain Z residue 57 VAL Chi-restraints excluded: chain Z residue 58 GLU Chi-restraints excluded: chain a residue 10 GLU Chi-restraints excluded: chain c residue 7 GLU Chi-restraints excluded: chain c residue 22 THR Chi-restraints excluded: chain d residue 25 LYS Chi-restraints excluded: chain e residue 32 ILE Chi-restraints excluded: chain f residue 6 SER Chi-restraints excluded: chain g residue 23 TRP Chi-restraints excluded: chain g residue 56 GLU Chi-restraints excluded: chain g residue 100 MET Chi-restraints excluded: chain g residue 130 THR Chi-restraints excluded: chain g residue 135 LEU Chi-restraints excluded: chain g residue 161 LEU Chi-restraints excluded: chain g residue 164 ILE Chi-restraints excluded: chain g residue 169 GLU Chi-restraints excluded: chain h residue 53 SER Chi-restraints excluded: chain h residue 59 ARG Chi-restraints excluded: chain h residue 66 VAL Chi-restraints excluded: chain h residue 67 THR Chi-restraints excluded: chain h residue 75 ILE Chi-restraints excluded: chain h residue 101 ILE Chi-restraints excluded: chain h residue 128 VAL Chi-restraints excluded: chain h residue 179 ARG Chi-restraints excluded: chain i residue 101 VAL Chi-restraints excluded: chain i residue 143 VAL Chi-restraints excluded: chain i residue 166 GLU Chi-restraints excluded: chain i residue 191 LEU Chi-restraints excluded: chain j residue 13 GLU Chi-restraints excluded: chain j residue 32 SER Chi-restraints excluded: chain j residue 68 ARG Chi-restraints excluded: chain j residue 120 VAL Chi-restraints excluded: chain j residue 130 SER Chi-restraints excluded: chain j residue 156 LYS Chi-restraints excluded: chain k residue 102 MET Chi-restraints excluded: chain l residue 6 VAL Chi-restraints excluded: chain l residue 56 LYS Chi-restraints excluded: chain l residue 69 VAL Chi-restraints excluded: chain l residue 94 VAL Chi-restraints excluded: chain l residue 133 THR Chi-restraints excluded: chain m residue 72 VAL Chi-restraints excluded: chain m residue 79 SER Chi-restraints excluded: chain m residue 89 LYS Chi-restraints excluded: chain m residue 129 VAL Chi-restraints excluded: chain n residue 29 VAL Chi-restraints excluded: chain n residue 63 LEU Chi-restraints excluded: chain n residue 111 VAL Chi-restraints excluded: chain o residue 6 ILE Chi-restraints excluded: chain p residue 30 THR Chi-restraints excluded: chain p residue 34 ILE Chi-restraints excluded: chain p residue 116 ILE Chi-restraints excluded: chain q residue 21 VAL Chi-restraints excluded: chain q residue 40 THR Chi-restraints excluded: chain q residue 41 THR Chi-restraints excluded: chain q residue 58 THR Chi-restraints excluded: chain q residue 64 THR Chi-restraints excluded: chain q residue 78 SER Chi-restraints excluded: chain q residue 86 ARG Chi-restraints excluded: chain q residue 97 THR Chi-restraints excluded: chain q residue 119 VAL Chi-restraints excluded: chain r residue 68 ASP Chi-restraints excluded: chain r residue 93 ARG Chi-restraints excluded: chain r residue 97 VAL Chi-restraints excluded: chain s residue 11 VAL Chi-restraints excluded: chain s residue 67 THR Chi-restraints excluded: chain s residue 90 ARG Chi-restraints excluded: chain t residue 40 GLN Chi-restraints excluded: chain t residue 75 VAL Chi-restraints excluded: chain u residue 24 SER Chi-restraints excluded: chain u residue 34 GLU Chi-restraints excluded: chain v residue 42 THR Chi-restraints excluded: chain v residue 57 ASP Chi-restraints excluded: chain v residue 67 LEU Chi-restraints excluded: chain x residue 39 THR Chi-restraints excluded: chain x residue 58 VAL Chi-restraints excluded: chain y residue 6 SER Chi-restraints excluded: chain y residue 14 SER Chi-restraints excluded: chain y residue 57 ILE Chi-restraints excluded: chain z residue 42 THR Chi-restraints excluded: chain z residue 69 ARG Chi-restraints excluded: chain 7 residue 7 LEU Chi-restraints excluded: chain 7 residue 137 ILE Chi-restraints excluded: chain 7 residue 222 ASP Chi-restraints excluded: chain 7 residue 227 LEU Chi-restraints excluded: chain 7 residue 320 VAL Chi-restraints excluded: chain 7 residue 378 THR Chi-restraints excluded: chain 7 residue 408 LYS Chi-restraints excluded: chain 7 residue 419 LEU Chi-restraints excluded: chain 7 residue 425 VAL Chi-restraints excluded: chain 7 residue 466 VAL Chi-restraints excluded: chain I residue 8 VAL Chi-restraints excluded: chain I residue 16 MET Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 84 TYR Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 347 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1125 random chunks: chunk 1049 optimal weight: 9.9990 chunk 122 optimal weight: 8.9990 chunk 620 optimal weight: 10.0000 chunk 794 optimal weight: 8.9990 chunk 615 optimal weight: 1.9990 chunk 916 optimal weight: 3.9990 chunk 607 optimal weight: 5.9990 chunk 1084 optimal weight: 30.0000 chunk 678 optimal weight: 5.9990 chunk 661 optimal weight: 0.0970 chunk 500 optimal weight: 0.9980 overall best weight: 2.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 70 ASN ** D 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 156 ASN ** J 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 29 HIS K 88 ASN N 18 GLN O 19 GLN P 10 GLN P 12 GLN P 15 GLN R 86 GLN T 59 ASN U 27 ASN V 49 ASN Y 20 ASN Y 58 ASN c 45 GLN g 177 ASN ** h 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 139 GLN k 3 HIS k 37 HIS ** l 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 50 GLN n 75 GLN ** p 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 40 ASN y 3 ASN y 21 ASN ** 7 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 296 ASN ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.3898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 166175 Z= 0.210 Angle : 0.614 14.342 247356 Z= 0.333 Chirality : 0.036 0.511 31326 Planarity : 0.006 0.133 14137 Dihedral : 23.311 179.840 79973 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.76 % Favored : 96.23 % Rotamer: Outliers : 4.27 % Allowed : 22.19 % Favored : 73.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.44 % 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: -0.22 (0.10), residues: 6755 helix: 0.87 (0.11), residues: 2350 sheet: -0.40 (0.14), residues: 1297 loop : -0.76 (0.11), residues: 3108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 248 HIS 0.009 0.001 HIS k 37 PHE 0.015 0.002 PHE k 8 TYR 0.018 0.002 TYR w 32 ARG 0.009 0.000 ARG v 6 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13510 Ramachandran restraints generated. 6755 Oldfield, 0 Emsley, 6755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13510 Ramachandran restraints generated. 6755 Oldfield, 0 Emsley, 6755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1213 residues out of total 5623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 240 poor density : 973 time to evaluate : 7.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 128 ASN cc_start: 0.9061 (m-40) cc_final: 0.8708 (m110) REVERT: B 132 MET cc_start: 0.8995 (mtm) cc_final: 0.8734 (mtm) REVERT: B 167 ARG cc_start: 0.7872 (ttp-110) cc_final: 0.7337 (ttt-90) REVERT: B 189 ARG cc_start: 0.8894 (mtt-85) cc_final: 0.8684 (mtt-85) REVERT: C 89 GLU cc_start: 0.7373 (OUTLIER) cc_final: 0.7138 (mm-30) REVERT: C 183 GLU cc_start: 0.7326 (OUTLIER) cc_final: 0.7085 (pt0) REVERT: D 21 ARG cc_start: 0.7706 (ptp-170) cc_final: 0.7476 (ptm160) REVERT: D 144 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7092 (tm-30) REVERT: D 155 GLU cc_start: 0.7349 (OUTLIER) cc_final: 0.6800 (tp30) REVERT: F 44 LYS cc_start: 0.6720 (mmtm) cc_final: 0.5977 (mttp) REVERT: K 117 SER cc_start: 0.8551 (p) cc_final: 0.8313 (m) REVERT: L 48 ARG cc_start: 0.8789 (OUTLIER) cc_final: 0.7694 (mpp80) REVERT: L 84 LYS cc_start: 0.8208 (OUTLIER) cc_final: 0.7602 (mttt) REVERT: M 6 ARG cc_start: 0.7523 (OUTLIER) cc_final: 0.6831 (ptm160) REVERT: M 88 ASN cc_start: 0.9071 (OUTLIER) cc_final: 0.8791 (m-40) REVERT: N 57 THR cc_start: 0.8209 (p) cc_final: 0.7986 (m) REVERT: N 65 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.7925 (tp) REVERT: N 74 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.8026 (tt0) REVERT: R 2 TYR cc_start: 0.8734 (p90) cc_final: 0.8487 (p90) REVERT: R 6 GLN cc_start: 0.8191 (OUTLIER) cc_final: 0.7489 (tp40) REVERT: R 27 ILE cc_start: 0.8784 (mm) cc_final: 0.8489 (mp) REVERT: R 70 GLU cc_start: 0.7493 (OUTLIER) cc_final: 0.7001 (tm-30) REVERT: R 86 GLN cc_start: 0.8109 (OUTLIER) cc_final: 0.7640 (pt0) REVERT: S 92 ARG cc_start: 0.8318 (OUTLIER) cc_final: 0.7513 (ttm-80) REVERT: U 26 LYS cc_start: 0.8070 (mmpt) cc_final: 0.7741 (mmpt) REVERT: W 17 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7220 (mp0) REVERT: W 83 GLU cc_start: 0.7143 (OUTLIER) cc_final: 0.6845 (mt-10) REVERT: Y 4 LYS cc_start: 0.8111 (ttmm) cc_final: 0.7807 (ttmt) REVERT: Z 19 LYS cc_start: 0.8558 (ttmm) cc_final: 0.8208 (ttpp) REVERT: a 10 GLU cc_start: 0.7369 (OUTLIER) cc_final: 0.7143 (pm20) REVERT: c 7 GLU cc_start: 0.6943 (OUTLIER) cc_final: 0.6405 (pt0) REVERT: f 2 LYS cc_start: 0.8246 (mttp) cc_final: 0.7920 (mmtt) REVERT: f 6 SER cc_start: 0.9133 (p) cc_final: 0.8835 (t) REVERT: f 34 LYS cc_start: 0.8976 (OUTLIER) cc_final: 0.7739 (ptpt) REVERT: g 169 GLU cc_start: 0.7321 (OUTLIER) cc_final: 0.7098 (mp0) REVERT: h 72 ARG cc_start: 0.7528 (mtm110) cc_final: 0.6856 (mmm160) REVERT: h 86 LYS cc_start: 0.6606 (pttt) cc_final: 0.6143 (ptpt) REVERT: h 88 ARG cc_start: 0.7357 (ttp-110) cc_final: 0.7050 (ttp-110) REVERT: i 128 ARG cc_start: 0.7356 (mtt180) cc_final: 0.7029 (tmt-80) REVERT: i 131 ASN cc_start: 0.7285 (t0) cc_final: 0.6841 (t0) REVERT: i 148 LYS cc_start: 0.7444 (ttpp) cc_final: 0.7068 (tppp) REVERT: i 160 GLU cc_start: 0.5961 (OUTLIER) cc_final: 0.5743 (pp20) REVERT: i 179 GLU cc_start: 0.6960 (tt0) cc_final: 0.6169 (pp20) REVERT: j 68 ARG cc_start: 0.7720 (OUTLIER) cc_final: 0.6732 (mpp-170) REVERT: j 147 MET cc_start: 0.7677 (ttp) cc_final: 0.7232 (ttp) REVERT: j 159 LYS cc_start: 0.8666 (OUTLIER) cc_final: 0.8377 (mttp) REVERT: k 93 LYS cc_start: 0.7481 (ttmm) cc_final: 0.6943 (ptmm) REVERT: l 116 MET cc_start: 0.8504 (tpt) cc_final: 0.8258 (tpt) REVERT: l 118 LEU cc_start: 0.7970 (tp) cc_final: 0.7719 (tp) REVERT: o 46 LYS cc_start: 0.8409 (mtpm) cc_final: 0.7918 (mtpt) REVERT: q 40 THR cc_start: 0.8860 (OUTLIER) cc_final: 0.8635 (m) REVERT: q 78 SER cc_start: 0.8683 (m) cc_final: 0.8408 (m) REVERT: q 86 ARG cc_start: 0.8353 (OUTLIER) cc_final: 0.7696 (ptt-90) REVERT: q 91 PRO cc_start: 0.8583 (Cg_endo) cc_final: 0.8140 (Cg_exo) REVERT: r 93 ARG cc_start: 0.7365 (OUTLIER) cc_final: 0.6554 (tpt170) REVERT: u 1 MET cc_start: 0.8052 (OUTLIER) cc_final: 0.7667 (pmm) REVERT: u 34 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.8307 (tt0) REVERT: y 57 ILE cc_start: 0.8056 (OUTLIER) cc_final: 0.7797 (tt) REVERT: 7 60 MET cc_start: 0.1336 (mmm) cc_final: 0.0584 (mmm) REVERT: 7 222 ASP cc_start: 0.3167 (OUTLIER) cc_final: 0.1302 (t0) REVERT: 7 227 LEU cc_start: 0.1795 (OUTLIER) cc_final: 0.1528 (tp) REVERT: 7 378 THR cc_start: 0.6340 (OUTLIER) cc_final: 0.5920 (t) REVERT: 7 472 ARG cc_start: 0.5940 (mmp80) cc_final: 0.4936 (mmp80) REVERT: 7 516 GLU cc_start: 0.6175 (pp20) cc_final: 0.5629 (mm-30) REVERT: I 16 MET cc_start: 0.2266 (OUTLIER) cc_final: 0.1935 (tmt) REVERT: H 1 MET cc_start: 0.3235 (tpp) cc_final: 0.2659 (mtp) REVERT: A 14 GLU cc_start: 0.7164 (OUTLIER) cc_final: 0.6635 (mt-10) REVERT: A 17 GLU cc_start: 0.6345 (OUTLIER) cc_final: 0.6002 (mp0) REVERT: A 77 MET cc_start: 0.5592 (ttp) cc_final: 0.4911 (pmm) REVERT: A 279 HIS cc_start: 0.6601 (t70) cc_final: 0.6275 (t-90) outliers start: 240 outliers final: 144 residues processed: 1104 average time/residue: 2.2774 time to fit residues: 3642.3193 Evaluate side-chains 1126 residues out of total 5623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 947 time to evaluate : 7.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain C residue 46 ARG Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 183 GLU Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain D residue 144 GLU Chi-restraints excluded: chain D residue 155 GLU Chi-restraints excluded: chain E residue 51 ASP Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 144 ASP Chi-restraints excluded: chain E residue 153 ASP Chi-restraints excluded: chain E residue 161 LYS Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 45 GLU Chi-restraints excluded: chain G residue 147 VAL Chi-restraints excluded: chain J residue 60 ASP Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 48 ARG Chi-restraints excluded: chain L residue 84 LYS Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain L residue 143 GLU Chi-restraints excluded: chain M residue 6 ARG Chi-restraints excluded: chain M residue 88 ASN Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain N residue 74 GLU Chi-restraints excluded: chain O residue 5 SER Chi-restraints excluded: chain O residue 26 LEU Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 76 LYS Chi-restraints excluded: chain O residue 91 SER Chi-restraints excluded: chain Q residue 3 ARG Chi-restraints excluded: chain R residue 6 GLN Chi-restraints excluded: chain R residue 16 GLU Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 70 GLU Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 73 LYS Chi-restraints excluded: chain R residue 86 GLN Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 45 VAL Chi-restraints excluded: chain S residue 82 MET Chi-restraints excluded: chain S residue 92 ARG Chi-restraints excluded: chain S residue 101 SER Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain U residue 5 ILE Chi-restraints excluded: chain U residue 15 THR Chi-restraints excluded: chain U residue 49 VAL Chi-restraints excluded: chain U residue 67 VAL Chi-restraints excluded: chain U residue 77 THR Chi-restraints excluded: chain V residue 1 MET Chi-restraints excluded: chain W residue 17 GLU Chi-restraints excluded: chain W residue 44 LYS Chi-restraints excluded: chain W residue 62 LYS Chi-restraints excluded: chain W residue 78 LYS Chi-restraints excluded: chain W residue 83 GLU Chi-restraints excluded: chain X residue 66 THR Chi-restraints excluded: chain Z residue 57 VAL Chi-restraints excluded: chain Z residue 58 GLU Chi-restraints excluded: chain a residue 10 GLU Chi-restraints excluded: chain c residue 7 GLU Chi-restraints excluded: chain c residue 22 THR Chi-restraints excluded: chain d residue 25 LYS Chi-restraints excluded: chain e residue 32 ILE Chi-restraints excluded: chain f residue 34 LYS Chi-restraints excluded: chain g residue 56 GLU Chi-restraints excluded: chain g residue 116 ASP Chi-restraints excluded: chain g residue 130 THR Chi-restraints excluded: chain g residue 135 LEU Chi-restraints excluded: chain g residue 164 ILE Chi-restraints excluded: chain g residue 169 GLU Chi-restraints excluded: chain g residue 199 VAL Chi-restraints excluded: chain h residue 47 LEU Chi-restraints excluded: chain h residue 53 SER Chi-restraints excluded: chain h residue 59 ARG Chi-restraints excluded: chain h residue 66 VAL Chi-restraints excluded: chain h residue 67 THR Chi-restraints excluded: chain h residue 101 ILE Chi-restraints excluded: chain h residue 121 THR Chi-restraints excluded: chain h residue 128 VAL Chi-restraints excluded: chain i residue 25 VAL Chi-restraints excluded: chain i residue 143 VAL Chi-restraints excluded: chain i residue 160 GLU Chi-restraints excluded: chain i residue 166 GLU Chi-restraints excluded: chain i residue 191 LEU Chi-restraints excluded: chain j residue 13 GLU Chi-restraints excluded: chain j residue 32 SER Chi-restraints excluded: chain j residue 68 ARG Chi-restraints excluded: chain j residue 120 VAL Chi-restraints excluded: chain j residue 130 SER Chi-restraints excluded: chain j residue 156 LYS Chi-restraints excluded: chain j residue 159 LYS Chi-restraints excluded: chain k residue 85 ILE Chi-restraints excluded: chain k residue 96 VAL Chi-restraints excluded: chain l residue 6 VAL Chi-restraints excluded: chain l residue 56 LYS Chi-restraints excluded: chain l residue 69 VAL Chi-restraints excluded: chain l residue 94 VAL Chi-restraints excluded: chain l residue 133 THR Chi-restraints excluded: chain m residue 72 VAL Chi-restraints excluded: chain m residue 79 SER Chi-restraints excluded: chain m residue 89 LYS Chi-restraints excluded: chain m residue 129 VAL Chi-restraints excluded: chain n residue 29 VAL Chi-restraints excluded: chain n residue 63 LEU Chi-restraints excluded: chain n residue 111 VAL Chi-restraints excluded: chain p residue 30 THR Chi-restraints excluded: chain p residue 34 ILE Chi-restraints excluded: chain q residue 4 VAL Chi-restraints excluded: chain q residue 21 VAL Chi-restraints excluded: chain q residue 40 THR Chi-restraints excluded: chain q residue 41 THR Chi-restraints excluded: chain q residue 58 THR Chi-restraints excluded: chain q residue 64 THR Chi-restraints excluded: chain q residue 86 ARG Chi-restraints excluded: chain q residue 119 VAL Chi-restraints excluded: chain r residue 93 ARG Chi-restraints excluded: chain r residue 97 VAL Chi-restraints excluded: chain s residue 11 VAL Chi-restraints excluded: chain s residue 67 THR Chi-restraints excluded: chain s residue 90 ARG Chi-restraints excluded: chain t residue 40 GLN Chi-restraints excluded: chain t residue 75 VAL Chi-restraints excluded: chain u residue 1 MET Chi-restraints excluded: chain u residue 24 SER Chi-restraints excluded: chain u residue 34 GLU Chi-restraints excluded: chain v residue 42 THR Chi-restraints excluded: chain v residue 57 ASP Chi-restraints excluded: chain v residue 67 LEU Chi-restraints excluded: chain x residue 39 THR Chi-restraints excluded: chain x residue 58 VAL Chi-restraints excluded: chain y residue 57 ILE Chi-restraints excluded: chain z residue 69 ARG Chi-restraints excluded: chain 7 residue 33 VAL Chi-restraints excluded: chain 7 residue 130 THR Chi-restraints excluded: chain 7 residue 137 ILE Chi-restraints excluded: chain 7 residue 222 ASP Chi-restraints excluded: chain 7 residue 227 LEU Chi-restraints excluded: chain 7 residue 320 VAL Chi-restraints excluded: chain 7 residue 378 THR Chi-restraints excluded: chain 7 residue 408 LYS Chi-restraints excluded: chain 7 residue 419 LEU Chi-restraints excluded: chain 7 residue 425 VAL Chi-restraints excluded: chain 7 residue 466 VAL Chi-restraints excluded: chain I residue 8 VAL Chi-restraints excluded: chain I residue 16 MET Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 347 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1125 random chunks: chunk 670 optimal weight: 0.8980 chunk 433 optimal weight: 10.0000 chunk 647 optimal weight: 6.9990 chunk 326 optimal weight: 10.0000 chunk 213 optimal weight: 40.0000 chunk 210 optimal weight: 40.0000 chunk 689 optimal weight: 3.9990 chunk 738 optimal weight: 4.9990 chunk 536 optimal weight: 9.9990 chunk 101 optimal weight: 10.0000 chunk 852 optimal weight: 5.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 70 ASN C 150 GLN ** D 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 156 ASN F 38 ASN ** K 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 88 ASN N 18 GLN O 19 GLN P 10 GLN P 12 GLN P 15 GLN T 59 ASN U 27 ASN V 49 ASN Y 20 ASN c 45 GLN ** h 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 139 GLN k 3 HIS ** l 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 40 ASN y 3 ASN ** 7 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 296 ASN ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.4057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 166175 Z= 0.327 Angle : 0.680 14.702 247356 Z= 0.362 Chirality : 0.041 0.511 31326 Planarity : 0.007 0.143 14137 Dihedral : 23.337 179.838 79973 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.03 % Favored : 95.96 % Rotamer: Outliers : 4.78 % Allowed : 22.16 % Favored : 73.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.44 % 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: -0.37 (0.10), residues: 6755 helix: 0.68 (0.11), residues: 2364 sheet: -0.44 (0.14), residues: 1298 loop : -0.81 (0.11), residues: 3093 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP 7 59 HIS 0.008 0.001 HIS k 11 PHE 0.024 0.002 PHE y 51 TYR 0.022 0.002 TYR w 32 ARG 0.009 0.001 ARG Y 23 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13510 Ramachandran restraints generated. 6755 Oldfield, 0 Emsley, 6755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13510 Ramachandran restraints generated. 6755 Oldfield, 0 Emsley, 6755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1226 residues out of total 5623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 269 poor density : 957 time to evaluate : 7.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 128 ASN cc_start: 0.9063 (m-40) cc_final: 0.8753 (m110) REVERT: B 132 MET cc_start: 0.9048 (mtm) cc_final: 0.8702 (mtm) REVERT: B 167 ARG cc_start: 0.7912 (ttp-110) cc_final: 0.7355 (ttt-90) REVERT: B 182 ARG cc_start: 0.9044 (OUTLIER) cc_final: 0.8754 (ttt180) REVERT: C 89 GLU cc_start: 0.7354 (OUTLIER) cc_final: 0.7120 (mm-30) REVERT: C 183 GLU cc_start: 0.7360 (OUTLIER) cc_final: 0.7068 (pt0) REVERT: D 144 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7112 (tm-30) REVERT: D 155 GLU cc_start: 0.7369 (OUTLIER) cc_final: 0.6815 (tp30) REVERT: F 44 LYS cc_start: 0.6622 (mmtm) cc_final: 0.5930 (mttp) REVERT: F 172 LYS cc_start: 0.8437 (OUTLIER) cc_final: 0.7934 (ttmt) REVERT: J 13 ARG cc_start: 0.8009 (OUTLIER) cc_final: 0.7317 (mtt90) REVERT: L 48 ARG cc_start: 0.8833 (OUTLIER) cc_final: 0.7738 (mpp80) REVERT: M 6 ARG cc_start: 0.7567 (OUTLIER) cc_final: 0.6859 (ptm160) REVERT: M 88 ASN cc_start: 0.9093 (OUTLIER) cc_final: 0.8804 (m-40) REVERT: N 57 THR cc_start: 0.8271 (p) cc_final: 0.7935 (m) REVERT: N 65 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.7921 (tp) REVERT: N 74 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.8065 (tt0) REVERT: R 6 GLN cc_start: 0.8226 (OUTLIER) cc_final: 0.7496 (tp40) REVERT: R 27 ILE cc_start: 0.8758 (mm) cc_final: 0.8461 (mp) REVERT: R 70 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.7102 (tm-30) REVERT: S 92 ARG cc_start: 0.8348 (OUTLIER) cc_final: 0.7584 (ttm-80) REVERT: U 29 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8662 (mm) REVERT: W 17 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7305 (mp0) REVERT: W 83 GLU cc_start: 0.7137 (OUTLIER) cc_final: 0.6890 (mt-10) REVERT: Z 19 LYS cc_start: 0.8570 (ttmm) cc_final: 0.8240 (ttpp) REVERT: a 10 GLU cc_start: 0.7413 (OUTLIER) cc_final: 0.7119 (pm20) REVERT: a 22 MET cc_start: 0.7700 (mtm) cc_final: 0.7306 (mtp) REVERT: f 2 LYS cc_start: 0.8212 (mttp) cc_final: 0.7883 (mmtt) REVERT: f 6 SER cc_start: 0.9156 (OUTLIER) cc_final: 0.8865 (t) REVERT: f 34 LYS cc_start: 0.8970 (OUTLIER) cc_final: 0.7638 (ptpt) REVERT: g 9 MET cc_start: 0.6814 (OUTLIER) cc_final: 0.6459 (mtm) REVERT: g 169 GLU cc_start: 0.7256 (OUTLIER) cc_final: 0.7025 (mp0) REVERT: h 72 ARG cc_start: 0.7586 (mtm110) cc_final: 0.6973 (mmm160) REVERT: h 161 GLU cc_start: 0.7166 (OUTLIER) cc_final: 0.6885 (tt0) REVERT: i 47 ARG cc_start: 0.6514 (ttm-80) cc_final: 0.6297 (ttm-80) REVERT: i 128 ARG cc_start: 0.7336 (mtt180) cc_final: 0.7006 (tmt-80) REVERT: i 148 LYS cc_start: 0.7444 (ttpp) cc_final: 0.7024 (tppp) REVERT: i 150 LYS cc_start: 0.7362 (ttmt) cc_final: 0.7107 (mttm) REVERT: i 153 SER cc_start: 0.5714 (p) cc_final: 0.5446 (m) REVERT: i 160 GLU cc_start: 0.6018 (OUTLIER) cc_final: 0.5756 (pp20) REVERT: i 179 GLU cc_start: 0.7038 (tt0) cc_final: 0.6214 (pp20) REVERT: j 68 ARG cc_start: 0.7733 (OUTLIER) cc_final: 0.6681 (mpp-170) REVERT: j 111 MET cc_start: 0.8423 (mtp) cc_final: 0.8028 (mtt) REVERT: j 147 MET cc_start: 0.7737 (ttp) cc_final: 0.7294 (ttp) REVERT: j 159 LYS cc_start: 0.8702 (OUTLIER) cc_final: 0.8389 (mttp) REVERT: k 93 LYS cc_start: 0.7591 (ttmm) cc_final: 0.7015 (ptmm) REVERT: k 102 MET cc_start: 0.5821 (OUTLIER) cc_final: 0.5336 (ptp) REVERT: l 118 LEU cc_start: 0.7987 (tp) cc_final: 0.7693 (tp) REVERT: n 47 VAL cc_start: 0.8008 (p) cc_final: 0.7778 (t) REVERT: o 6 ILE cc_start: 0.7135 (OUTLIER) cc_final: 0.6694 (mt) REVERT: o 46 LYS cc_start: 0.8362 (mtpm) cc_final: 0.7919 (mtpt) REVERT: q 40 THR cc_start: 0.8870 (OUTLIER) cc_final: 0.8626 (m) REVERT: q 78 SER cc_start: 0.8737 (m) cc_final: 0.8424 (m) REVERT: q 86 ARG cc_start: 0.8375 (OUTLIER) cc_final: 0.7705 (ptt-90) REVERT: q 91 PRO cc_start: 0.8609 (Cg_endo) cc_final: 0.8152 (Cg_exo) REVERT: r 7 ILE cc_start: 0.8046 (pt) cc_final: 0.7515 (pt) REVERT: r 93 ARG cc_start: 0.7405 (OUTLIER) cc_final: 0.7054 (tpt170) REVERT: u 34 GLU cc_start: 0.8630 (OUTLIER) cc_final: 0.8339 (tt0) REVERT: y 57 ILE cc_start: 0.8075 (OUTLIER) cc_final: 0.7809 (tt) REVERT: z 69 ARG cc_start: 0.6865 (OUTLIER) cc_final: 0.5762 (ppt-90) REVERT: 7 60 MET cc_start: 0.1399 (mmm) cc_final: 0.0585 (mmm) REVERT: 7 378 THR cc_start: 0.6367 (OUTLIER) cc_final: 0.5937 (t) REVERT: 7 472 ARG cc_start: 0.6058 (mmp80) cc_final: 0.4961 (mmp80) REVERT: 7 516 GLU cc_start: 0.6335 (pp20) cc_final: 0.5870 (mm-30) REVERT: I 16 MET cc_start: 0.2312 (OUTLIER) cc_final: 0.1978 (tmt) REVERT: H 1 MET cc_start: 0.3138 (tpp) cc_final: 0.2615 (mtp) REVERT: A 14 GLU cc_start: 0.7187 (OUTLIER) cc_final: 0.6644 (mt-10) REVERT: A 17 GLU cc_start: 0.6504 (OUTLIER) cc_final: 0.6102 (mp0) REVERT: A 77 MET cc_start: 0.5585 (ttp) cc_final: 0.4947 (pmm) REVERT: A 279 HIS cc_start: 0.6636 (t70) cc_final: 0.6312 (t-90) outliers start: 269 outliers final: 159 residues processed: 1106 average time/residue: 2.2615 time to fit residues: 3580.9170 Evaluate side-chains 1136 residues out of total 5623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 938 time to evaluate : 7.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 182 ARG Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain C residue 46 ARG Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 183 GLU Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain D residue 144 GLU Chi-restraints excluded: chain D residue 155 GLU Chi-restraints excluded: chain D residue 199 MET Chi-restraints excluded: chain E residue 51 ASP Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 153 ASP Chi-restraints excluded: chain E residue 161 LYS Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain F residue 172 LYS Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 45 GLU Chi-restraints excluded: chain G residue 130 VAL Chi-restraints excluded: chain G residue 147 VAL Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 13 ARG Chi-restraints excluded: chain J residue 60 ASP Chi-restraints excluded: chain J residue 95 ARG Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 48 ARG Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain L residue 143 GLU Chi-restraints excluded: chain M residue 6 ARG Chi-restraints excluded: chain M residue 88 ASN Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 29 VAL Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain N residue 74 GLU Chi-restraints excluded: chain O residue 5 SER Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 76 LYS Chi-restraints excluded: chain O residue 91 SER Chi-restraints excluded: chain P residue 104 THR Chi-restraints excluded: chain Q residue 3 ARG Chi-restraints excluded: chain R residue 6 GLN Chi-restraints excluded: chain R residue 16 GLU Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 70 GLU Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 73 LYS Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 45 VAL Chi-restraints excluded: chain S residue 82 MET Chi-restraints excluded: chain S residue 92 ARG Chi-restraints excluded: chain S residue 101 SER Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain U residue 5 ILE Chi-restraints excluded: chain U residue 15 THR Chi-restraints excluded: chain U residue 29 LEU Chi-restraints excluded: chain U residue 49 VAL Chi-restraints excluded: chain U residue 67 VAL Chi-restraints excluded: chain U residue 77 THR Chi-restraints excluded: chain V residue 1 MET Chi-restraints excluded: chain W residue 17 GLU Chi-restraints excluded: chain W residue 44 LYS Chi-restraints excluded: chain W residue 62 LYS Chi-restraints excluded: chain W residue 83 GLU Chi-restraints excluded: chain X residue 66 THR Chi-restraints excluded: chain Z residue 57 VAL Chi-restraints excluded: chain Z residue 58 GLU Chi-restraints excluded: chain a residue 10 GLU Chi-restraints excluded: chain c residue 7 GLU Chi-restraints excluded: chain c residue 22 THR Chi-restraints excluded: chain d residue 25 LYS Chi-restraints excluded: chain e residue 32 ILE Chi-restraints excluded: chain f residue 4 ARG Chi-restraints excluded: chain f residue 6 SER Chi-restraints excluded: chain f residue 34 LYS Chi-restraints excluded: chain g residue 9 MET Chi-restraints excluded: chain g residue 10 LEU Chi-restraints excluded: chain g residue 23 TRP Chi-restraints excluded: chain g residue 56 GLU Chi-restraints excluded: chain g residue 116 ASP Chi-restraints excluded: chain g residue 130 THR Chi-restraints excluded: chain g residue 135 LEU Chi-restraints excluded: chain g residue 164 ILE Chi-restraints excluded: chain g residue 169 GLU Chi-restraints excluded: chain g residue 199 VAL Chi-restraints excluded: chain h residue 53 SER Chi-restraints excluded: chain h residue 59 ARG Chi-restraints excluded: chain h residue 66 VAL Chi-restraints excluded: chain h residue 67 THR Chi-restraints excluded: chain h residue 101 ILE Chi-restraints excluded: chain h residue 121 THR Chi-restraints excluded: chain h residue 128 VAL Chi-restraints excluded: chain h residue 161 GLU Chi-restraints excluded: chain i residue 25 VAL Chi-restraints excluded: chain i residue 143 VAL Chi-restraints excluded: chain i residue 160 GLU Chi-restraints excluded: chain i residue 166 GLU Chi-restraints excluded: chain i residue 191 LEU Chi-restraints excluded: chain j residue 13 GLU Chi-restraints excluded: chain j residue 32 SER Chi-restraints excluded: chain j residue 68 ARG Chi-restraints excluded: chain j residue 120 VAL Chi-restraints excluded: chain j residue 130 SER Chi-restraints excluded: chain j residue 156 LYS Chi-restraints excluded: chain j residue 159 LYS Chi-restraints excluded: chain k residue 85 ILE Chi-restraints excluded: chain k residue 102 MET Chi-restraints excluded: chain l residue 6 VAL Chi-restraints excluded: chain l residue 56 LYS Chi-restraints excluded: chain l residue 69 VAL Chi-restraints excluded: chain l residue 94 VAL Chi-restraints excluded: chain l residue 133 THR Chi-restraints excluded: chain m residue 72 VAL Chi-restraints excluded: chain m residue 79 SER Chi-restraints excluded: chain m residue 89 LYS Chi-restraints excluded: chain m residue 90 ASP Chi-restraints excluded: chain m residue 129 VAL Chi-restraints excluded: chain n residue 29 VAL Chi-restraints excluded: chain n residue 63 LEU Chi-restraints excluded: chain n residue 111 VAL Chi-restraints excluded: chain o residue 6 ILE Chi-restraints excluded: chain p residue 30 THR Chi-restraints excluded: chain p residue 34 ILE Chi-restraints excluded: chain p residue 116 ILE Chi-restraints excluded: chain q residue 4 VAL Chi-restraints excluded: chain q residue 21 VAL Chi-restraints excluded: chain q residue 40 THR Chi-restraints excluded: chain q residue 41 THR Chi-restraints excluded: chain q residue 58 THR Chi-restraints excluded: chain q residue 64 THR Chi-restraints excluded: chain q residue 86 ARG Chi-restraints excluded: chain q residue 119 VAL Chi-restraints excluded: chain r residue 93 ARG Chi-restraints excluded: chain r residue 97 VAL Chi-restraints excluded: chain s residue 11 VAL Chi-restraints excluded: chain s residue 67 THR Chi-restraints excluded: chain s residue 90 ARG Chi-restraints excluded: chain t residue 40 GLN Chi-restraints excluded: chain t residue 75 VAL Chi-restraints excluded: chain u residue 24 SER Chi-restraints excluded: chain u residue 34 GLU Chi-restraints excluded: chain v residue 42 THR Chi-restraints excluded: chain v residue 57 ASP Chi-restraints excluded: chain v residue 67 LEU Chi-restraints excluded: chain x residue 39 THR Chi-restraints excluded: chain x residue 44 MET Chi-restraints excluded: chain x residue 58 VAL Chi-restraints excluded: chain y residue 6 SER Chi-restraints excluded: chain y residue 14 SER Chi-restraints excluded: chain y residue 57 ILE Chi-restraints excluded: chain z residue 69 ARG Chi-restraints excluded: chain 7 residue 33 VAL Chi-restraints excluded: chain 7 residue 130 THR Chi-restraints excluded: chain 7 residue 137 ILE Chi-restraints excluded: chain 7 residue 222 ASP Chi-restraints excluded: chain 7 residue 320 VAL Chi-restraints excluded: chain 7 residue 378 THR Chi-restraints excluded: chain 7 residue 408 LYS Chi-restraints excluded: chain 7 residue 419 LEU Chi-restraints excluded: chain 7 residue 425 VAL Chi-restraints excluded: chain 7 residue 466 VAL Chi-restraints excluded: chain I residue 8 VAL Chi-restraints excluded: chain I residue 16 MET Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 319 ASP Chi-restraints excluded: chain A residue 325 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1125 random chunks: chunk 986 optimal weight: 9.9990 chunk 1038 optimal weight: 9.9990 chunk 947 optimal weight: 10.0000 chunk 1010 optimal weight: 0.5980 chunk 608 optimal weight: 0.6980 chunk 440 optimal weight: 10.0000 chunk 793 optimal weight: 9.9990 chunk 310 optimal weight: 30.0000 chunk 913 optimal weight: 10.0000 chunk 955 optimal weight: 9.9990 chunk 1006 optimal weight: 6.9990 overall best weight: 5.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 70 ASN C 150 GLN ** D 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 156 ASN G 66 ASN ** K 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 88 ASN N 18 GLN O 19 GLN P 10 GLN P 12 GLN P 15 GLN R 86 GLN T 59 ASN U 27 ASN V 49 ASN Y 20 ASN c 45 GLN ** h 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 139 GLN k 3 HIS ** m 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 50 GLN ** p 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 62 GLN u 40 ASN y 3 ASN ** 7 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 296 ASN ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.4277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 166175 Z= 0.390 Angle : 0.733 15.214 247356 Z= 0.387 Chirality : 0.044 0.536 31326 Planarity : 0.007 0.146 14137 Dihedral : 23.433 179.322 79973 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.41 % Favored : 95.57 % Rotamer: Outliers : 4.66 % Allowed : 22.46 % Favored : 72.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.44 % 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: -0.57 (0.10), residues: 6755 helix: 0.44 (0.10), residues: 2371 sheet: -0.46 (0.14), residues: 1285 loop : -0.90 (0.11), residues: 3099 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP g 23 HIS 0.009 0.002 HIS k 11 PHE 0.027 0.002 PHE G 139 TYR 0.023 0.002 TYR S 38 ARG 0.010 0.001 ARG z 55 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13510 Ramachandran restraints generated. 6755 Oldfield, 0 Emsley, 6755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13510 Ramachandran restraints generated. 6755 Oldfield, 0 Emsley, 6755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1200 residues out of total 5623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 262 poor density : 938 time to evaluate : 7.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 132 MET cc_start: 0.9077 (mtm) cc_final: 0.8832 (mtm) REVERT: B 167 ARG cc_start: 0.7834 (ttp-110) cc_final: 0.7313 (ttt-90) REVERT: B 182 ARG cc_start: 0.9069 (OUTLIER) cc_final: 0.8786 (ttt180) REVERT: C 1 MET cc_start: 0.7447 (tmm) cc_final: 0.7179 (ttm) REVERT: C 89 GLU cc_start: 0.7328 (OUTLIER) cc_final: 0.7099 (mm-30) REVERT: C 131 ASP cc_start: 0.7546 (m-30) cc_final: 0.7334 (m-30) REVERT: D 144 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7142 (tm-30) REVERT: D 155 GLU cc_start: 0.7462 (OUTLIER) cc_final: 0.6924 (tp30) REVERT: E 80 ARG cc_start: 0.8055 (OUTLIER) cc_final: 0.7314 (mtp180) REVERT: F 44 LYS cc_start: 0.6750 (mmtm) cc_final: 0.6021 (mttp) REVERT: F 172 LYS cc_start: 0.8499 (OUTLIER) cc_final: 0.8002 (ttmt) REVERT: J 13 ARG cc_start: 0.8024 (OUTLIER) cc_final: 0.7369 (mtt90) REVERT: L 48 ARG cc_start: 0.8857 (OUTLIER) cc_final: 0.7786 (mpp80) REVERT: M 6 ARG cc_start: 0.7642 (OUTLIER) cc_final: 0.6907 (ptm160) REVERT: M 88 ASN cc_start: 0.9083 (OUTLIER) cc_final: 0.8802 (m-40) REVERT: N 57 THR cc_start: 0.8315 (p) cc_final: 0.7953 (m) REVERT: N 65 LEU cc_start: 0.8350 (OUTLIER) cc_final: 0.7923 (tp) REVERT: N 74 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.8117 (tt0) REVERT: R 2 TYR cc_start: 0.8931 (p90) cc_final: 0.8731 (p90) REVERT: R 6 GLN cc_start: 0.8266 (OUTLIER) cc_final: 0.7525 (tp40) REVERT: R 27 ILE cc_start: 0.8705 (mm) cc_final: 0.8414 (mp) REVERT: R 70 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.7103 (tm-30) REVERT: R 86 GLN cc_start: 0.8078 (OUTLIER) cc_final: 0.7662 (pt0) REVERT: S 92 ARG cc_start: 0.8360 (OUTLIER) cc_final: 0.7613 (ttm-80) REVERT: U 29 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8715 (mm) REVERT: W 17 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7269 (mp0) REVERT: W 83 GLU cc_start: 0.7162 (OUTLIER) cc_final: 0.6888 (mt-10) REVERT: Y 23 ARG cc_start: 0.8441 (mtt90) cc_final: 0.7972 (mtt180) REVERT: Z 19 LYS cc_start: 0.8552 (ttmm) cc_final: 0.8238 (ttpp) REVERT: a 10 GLU cc_start: 0.7451 (OUTLIER) cc_final: 0.7135 (pm20) REVERT: a 22 MET cc_start: 0.7720 (mtm) cc_final: 0.7344 (mtp) REVERT: f 2 LYS cc_start: 0.8277 (mttp) cc_final: 0.7930 (mmtt) REVERT: f 6 SER cc_start: 0.9140 (OUTLIER) cc_final: 0.8882 (t) REVERT: f 34 LYS cc_start: 0.8976 (OUTLIER) cc_final: 0.7602 (ptpt) REVERT: g 9 MET cc_start: 0.6840 (OUTLIER) cc_final: 0.6518 (mtm) REVERT: g 169 GLU cc_start: 0.7306 (OUTLIER) cc_final: 0.7036 (mp0) REVERT: h 72 ARG cc_start: 0.7630 (mtm110) cc_final: 0.7000 (ttt-90) REVERT: h 179 ARG cc_start: 0.8297 (OUTLIER) cc_final: 0.7447 (ptt90) REVERT: h 185 ASN cc_start: 0.8681 (OUTLIER) cc_final: 0.8418 (m-40) REVERT: h 188 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.7310 (mt-10) REVERT: i 128 ARG cc_start: 0.7288 (mtt180) cc_final: 0.6988 (tmt-80) REVERT: i 148 LYS cc_start: 0.7439 (ttpp) cc_final: 0.7003 (tppp) REVERT: i 150 LYS cc_start: 0.7385 (ttmt) cc_final: 0.7034 (mttm) REVERT: i 153 SER cc_start: 0.5965 (p) cc_final: 0.5680 (m) REVERT: i 160 GLU cc_start: 0.6106 (OUTLIER) cc_final: 0.5874 (pp20) REVERT: i 179 GLU cc_start: 0.7020 (tt0) cc_final: 0.6228 (pp20) REVERT: j 68 ARG cc_start: 0.7752 (OUTLIER) cc_final: 0.6708 (mpp-170) REVERT: j 111 MET cc_start: 0.8564 (mtp) cc_final: 0.8161 (mtt) REVERT: j 147 MET cc_start: 0.7786 (ttp) cc_final: 0.7312 (ttp) REVERT: j 159 LYS cc_start: 0.8735 (OUTLIER) cc_final: 0.8373 (mttp) REVERT: k 56 LYS cc_start: 0.7931 (ttmm) cc_final: 0.7537 (ttmt) REVERT: k 93 LYS cc_start: 0.7665 (ttmm) cc_final: 0.7016 (ptmm) REVERT: l 118 LEU cc_start: 0.7990 (tp) cc_final: 0.7660 (tp) REVERT: n 47 VAL cc_start: 0.8190 (p) cc_final: 0.7853 (t) REVERT: o 46 LYS cc_start: 0.8385 (mtpm) cc_final: 0.7945 (mtpt) REVERT: q 40 THR cc_start: 0.8902 (OUTLIER) cc_final: 0.8630 (m) REVERT: q 78 SER cc_start: 0.8735 (OUTLIER) cc_final: 0.8427 (m) REVERT: q 86 ARG cc_start: 0.8378 (OUTLIER) cc_final: 0.7715 (ptt-90) REVERT: q 91 PRO cc_start: 0.8656 (Cg_endo) cc_final: 0.8199 (Cg_exo) REVERT: r 31 LYS cc_start: 0.7906 (mtpp) cc_final: 0.7657 (mtmm) REVERT: r 93 ARG cc_start: 0.7381 (OUTLIER) cc_final: 0.7013 (tpt170) REVERT: u 34 GLU cc_start: 0.8643 (OUTLIER) cc_final: 0.8341 (tt0) REVERT: y 57 ILE cc_start: 0.7989 (OUTLIER) cc_final: 0.7768 (tt) REVERT: z 69 ARG cc_start: 0.6870 (OUTLIER) cc_final: 0.5772 (ppt-90) REVERT: 7 60 MET cc_start: 0.1495 (mmm) cc_final: 0.0676 (mmm) REVERT: 7 306 ASN cc_start: 0.4510 (m110) cc_final: 0.4013 (m110) REVERT: 7 329 MET cc_start: 0.3478 (tpt) cc_final: 0.2952 (mpm) REVERT: 7 378 THR cc_start: 0.6288 (OUTLIER) cc_final: 0.5833 (t) REVERT: 7 437 ILE cc_start: 0.6595 (mp) cc_final: 0.6339 (pp) REVERT: 7 472 ARG cc_start: 0.6350 (mmp80) cc_final: 0.5211 (mmp80) REVERT: 7 516 GLU cc_start: 0.6359 (pp20) cc_final: 0.5923 (mm-30) REVERT: I 16 MET cc_start: 0.2260 (OUTLIER) cc_final: 0.1924 (tmt) REVERT: H 1 MET cc_start: 0.3375 (tpp) cc_final: 0.3013 (mtp) REVERT: H 52 MET cc_start: 0.4232 (OUTLIER) cc_final: 0.1554 (mtp) REVERT: H 123 ILE cc_start: 0.1493 (OUTLIER) cc_final: 0.1005 (tp) REVERT: A 14 GLU cc_start: 0.7170 (OUTLIER) cc_final: 0.6639 (mt-10) REVERT: A 17 GLU cc_start: 0.6546 (OUTLIER) cc_final: 0.6062 (mp0) REVERT: A 77 MET cc_start: 0.5588 (ttp) cc_final: 0.4925 (pmm) REVERT: A 90 GLU cc_start: 0.5515 (OUTLIER) cc_final: 0.5276 (tm-30) REVERT: A 279 HIS cc_start: 0.6684 (t70) cc_final: 0.6364 (t-90) outliers start: 262 outliers final: 164 residues processed: 1081 average time/residue: 2.2932 time to fit residues: 3555.2607 Evaluate side-chains 1123 residues out of total 5623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 208 poor density : 915 time to evaluate : 7.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 182 ARG Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain C residue 46 ARG Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain D residue 144 GLU Chi-restraints excluded: chain D residue 155 GLU Chi-restraints excluded: chain D residue 199 MET Chi-restraints excluded: chain E residue 80 ARG Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 153 ASP Chi-restraints excluded: chain E residue 161 LYS Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain F residue 172 LYS Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 45 GLU Chi-restraints excluded: chain G residue 130 VAL Chi-restraints excluded: chain G residue 147 VAL Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 13 ARG Chi-restraints excluded: chain J residue 60 ASP Chi-restraints excluded: chain J residue 95 ARG Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain K residue 53 LYS Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 48 ARG Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain L residue 143 GLU Chi-restraints excluded: chain M residue 6 ARG Chi-restraints excluded: chain M residue 88 ASN Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 29 VAL Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain N residue 74 GLU Chi-restraints excluded: chain O residue 5 SER Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 76 LYS Chi-restraints excluded: chain O residue 91 SER Chi-restraints excluded: chain P residue 104 THR Chi-restraints excluded: chain Q residue 3 ARG Chi-restraints excluded: chain R residue 6 GLN Chi-restraints excluded: chain R residue 16 GLU Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 70 GLU Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 73 LYS Chi-restraints excluded: chain R residue 86 GLN Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 45 VAL Chi-restraints excluded: chain S residue 67 ASP Chi-restraints excluded: chain S residue 82 MET Chi-restraints excluded: chain S residue 92 ARG Chi-restraints excluded: chain S residue 101 SER Chi-restraints excluded: chain T residue 37 ASP Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain U residue 15 THR Chi-restraints excluded: chain U residue 29 LEU Chi-restraints excluded: chain U residue 49 VAL Chi-restraints excluded: chain U residue 67 VAL Chi-restraints excluded: chain U residue 77 THR Chi-restraints excluded: chain V residue 1 MET Chi-restraints excluded: chain W residue 17 GLU Chi-restraints excluded: chain W residue 44 LYS Chi-restraints excluded: chain W residue 62 LYS Chi-restraints excluded: chain W residue 78 LYS Chi-restraints excluded: chain W residue 83 GLU Chi-restraints excluded: chain X residue 66 THR Chi-restraints excluded: chain Z residue 57 VAL Chi-restraints excluded: chain Z residue 58 GLU Chi-restraints excluded: chain a residue 10 GLU Chi-restraints excluded: chain c residue 7 GLU Chi-restraints excluded: chain c residue 22 THR Chi-restraints excluded: chain d residue 25 LYS Chi-restraints excluded: chain e residue 32 ILE Chi-restraints excluded: chain f residue 4 ARG Chi-restraints excluded: chain f residue 6 SER Chi-restraints excluded: chain f residue 34 LYS Chi-restraints excluded: chain g residue 9 MET Chi-restraints excluded: chain g residue 23 TRP Chi-restraints excluded: chain g residue 56 GLU Chi-restraints excluded: chain g residue 100 MET Chi-restraints excluded: chain g residue 116 ASP Chi-restraints excluded: chain g residue 130 THR Chi-restraints excluded: chain g residue 135 LEU Chi-restraints excluded: chain g residue 164 ILE Chi-restraints excluded: chain g residue 169 GLU Chi-restraints excluded: chain g residue 199 VAL Chi-restraints excluded: chain h residue 44 THR Chi-restraints excluded: chain h residue 53 SER Chi-restraints excluded: chain h residue 59 ARG Chi-restraints excluded: chain h residue 66 VAL Chi-restraints excluded: chain h residue 67 THR Chi-restraints excluded: chain h residue 101 ILE Chi-restraints excluded: chain h residue 121 THR Chi-restraints excluded: chain h residue 128 VAL Chi-restraints excluded: chain h residue 179 ARG Chi-restraints excluded: chain h residue 185 ASN Chi-restraints excluded: chain h residue 188 GLU Chi-restraints excluded: chain i residue 143 VAL Chi-restraints excluded: chain i residue 160 GLU Chi-restraints excluded: chain i residue 166 GLU Chi-restraints excluded: chain i residue 191 LEU Chi-restraints excluded: chain j residue 13 GLU Chi-restraints excluded: chain j residue 32 SER Chi-restraints excluded: chain j residue 68 ARG Chi-restraints excluded: chain j residue 94 VAL Chi-restraints excluded: chain j residue 120 VAL Chi-restraints excluded: chain j residue 130 SER Chi-restraints excluded: chain j residue 156 LYS Chi-restraints excluded: chain j residue 159 LYS Chi-restraints excluded: chain k residue 88 MET Chi-restraints excluded: chain k residue 96 VAL Chi-restraints excluded: chain l residue 56 LYS Chi-restraints excluded: chain l residue 69 VAL Chi-restraints excluded: chain l residue 94 VAL Chi-restraints excluded: chain l residue 133 THR Chi-restraints excluded: chain m residue 72 VAL Chi-restraints excluded: chain m residue 79 SER Chi-restraints excluded: chain m residue 89 LYS Chi-restraints excluded: chain m residue 129 VAL Chi-restraints excluded: chain n residue 29 VAL Chi-restraints excluded: chain n residue 63 LEU Chi-restraints excluded: chain n residue 111 VAL Chi-restraints excluded: chain p residue 30 THR Chi-restraints excluded: chain p residue 34 ILE Chi-restraints excluded: chain p residue 116 ILE Chi-restraints excluded: chain q residue 4 VAL Chi-restraints excluded: chain q residue 21 VAL Chi-restraints excluded: chain q residue 40 THR Chi-restraints excluded: chain q residue 41 THR Chi-restraints excluded: chain q residue 58 THR Chi-restraints excluded: chain q residue 64 THR Chi-restraints excluded: chain q residue 78 SER Chi-restraints excluded: chain q residue 86 ARG Chi-restraints excluded: chain q residue 119 VAL Chi-restraints excluded: chain r residue 28 THR Chi-restraints excluded: chain r residue 93 ARG Chi-restraints excluded: chain r residue 97 VAL Chi-restraints excluded: chain s residue 11 VAL Chi-restraints excluded: chain s residue 90 ARG Chi-restraints excluded: chain t residue 40 GLN Chi-restraints excluded: chain t residue 71 LYS Chi-restraints excluded: chain t residue 75 VAL Chi-restraints excluded: chain u residue 24 SER Chi-restraints excluded: chain u residue 34 GLU Chi-restraints excluded: chain v residue 42 THR Chi-restraints excluded: chain v residue 57 ASP Chi-restraints excluded: chain v residue 67 LEU Chi-restraints excluded: chain x residue 39 THR Chi-restraints excluded: chain x residue 44 MET Chi-restraints excluded: chain x residue 58 VAL Chi-restraints excluded: chain y residue 6 SER Chi-restraints excluded: chain y residue 14 SER Chi-restraints excluded: chain y residue 57 ILE Chi-restraints excluded: chain z residue 14 VAL Chi-restraints excluded: chain z residue 69 ARG Chi-restraints excluded: chain 7 residue 33 VAL Chi-restraints excluded: chain 7 residue 130 THR Chi-restraints excluded: chain 7 residue 137 ILE Chi-restraints excluded: chain 7 residue 222 ASP Chi-restraints excluded: chain 7 residue 320 VAL Chi-restraints excluded: chain 7 residue 378 THR Chi-restraints excluded: chain 7 residue 408 LYS Chi-restraints excluded: chain 7 residue 419 LEU Chi-restraints excluded: chain 7 residue 425 VAL Chi-restraints excluded: chain 7 residue 466 VAL Chi-restraints excluded: chain I residue 8 VAL Chi-restraints excluded: chain I residue 16 MET Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 52 MET Chi-restraints excluded: chain H residue 123 ILE Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 319 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1125 random chunks: chunk 663 optimal weight: 7.9990 chunk 1068 optimal weight: 9.9990 chunk 652 optimal weight: 0.9990 chunk 506 optimal weight: 2.9990 chunk 742 optimal weight: 0.9980 chunk 1120 optimal weight: 4.9990 chunk 1031 optimal weight: 10.0000 chunk 892 optimal weight: 7.9990 chunk 92 optimal weight: 10.0000 chunk 689 optimal weight: 3.9990 chunk 547 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 70 ASN C 150 GLN ** D 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 156 ASN G 66 ASN K 29 HIS K 88 ASN N 18 GLN P 10 GLN P 12 GLN P 15 GLN T 59 ASN U 27 ASN V 49 ASN Y 20 ASN Y 58 ASN ** h 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 82 GLN k 3 HIS ** m 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 40 ASN y 3 ASN y 21 ASN ** 7 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 194 GLN ** 7 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 296 ASN ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.4215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 166175 Z= 0.203 Angle : 0.635 14.652 247356 Z= 0.345 Chirality : 0.037 0.524 31326 Planarity : 0.006 0.134 14137 Dihedral : 23.437 179.479 79973 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.94 % Favored : 96.05 % Rotamer: Outliers : 3.56 % Allowed : 23.80 % Favored : 72.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.44 % 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: -0.42 (0.10), residues: 6755 helix: 0.62 (0.11), residues: 2366 sheet: -0.49 (0.14), residues: 1290 loop : -0.81 (0.11), residues: 3099 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 248 HIS 0.006 0.001 HIS k 11 PHE 0.023 0.002 PHE y 51 TYR 0.019 0.002 TYR S 38 ARG 0.008 0.000 ARG z 47 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13510 Ramachandran restraints generated. 6755 Oldfield, 0 Emsley, 6755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13510 Ramachandran restraints generated. 6755 Oldfield, 0 Emsley, 6755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1150 residues out of total 5623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 950 time to evaluate : 7.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 35 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.7510 (pt0) REVERT: B 132 MET cc_start: 0.9024 (mtm) cc_final: 0.8720 (mtm) REVERT: B 182 ARG cc_start: 0.9020 (OUTLIER) cc_final: 0.8730 (ttt180) REVERT: C 1 MET cc_start: 0.7335 (tmm) cc_final: 0.7060 (ttm) REVERT: D 88 ARG cc_start: 0.8287 (OUTLIER) cc_final: 0.7914 (mmp80) REVERT: D 144 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7131 (tm-30) REVERT: D 155 GLU cc_start: 0.7447 (OUTLIER) cc_final: 0.6913 (tp30) REVERT: D 170 ARG cc_start: 0.7945 (mtt180) cc_final: 0.7743 (mtt180) REVERT: F 44 LYS cc_start: 0.6684 (mmtm) cc_final: 0.5998 (mttp) REVERT: F 172 LYS cc_start: 0.8454 (OUTLIER) cc_final: 0.7974 (ttmt) REVERT: L 48 ARG cc_start: 0.8793 (OUTLIER) cc_final: 0.7691 (mpp80) REVERT: M 6 ARG cc_start: 0.7607 (OUTLIER) cc_final: 0.6905 (ptm160) REVERT: M 88 ASN cc_start: 0.9072 (OUTLIER) cc_final: 0.8810 (m-40) REVERT: N 57 THR cc_start: 0.8237 (p) cc_final: 0.8024 (m) REVERT: N 65 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.7912 (tp) REVERT: N 74 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.8079 (tt0) REVERT: R 6 GLN cc_start: 0.8221 (OUTLIER) cc_final: 0.7562 (tp40) REVERT: R 27 ILE cc_start: 0.8689 (mm) cc_final: 0.8378 (mp) REVERT: R 70 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.7088 (tm-30) REVERT: T 49 LYS cc_start: 0.8260 (OUTLIER) cc_final: 0.7989 (tttt) REVERT: U 29 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8716 (mm) REVERT: W 17 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7193 (mp0) REVERT: W 72 LYS cc_start: 0.8419 (mmpt) cc_final: 0.8185 (mmtm) REVERT: W 83 GLU cc_start: 0.7124 (OUTLIER) cc_final: 0.6848 (mt-10) REVERT: Z 19 LYS cc_start: 0.8548 (ttmm) cc_final: 0.8221 (ttpp) REVERT: a 10 GLU cc_start: 0.7389 (OUTLIER) cc_final: 0.7090 (pm20) REVERT: a 22 MET cc_start: 0.7617 (mtm) cc_final: 0.7301 (mtp) REVERT: c 7 GLU cc_start: 0.7097 (OUTLIER) cc_final: 0.6554 (pt0) REVERT: f 2 LYS cc_start: 0.8233 (mttp) cc_final: 0.7904 (mmtt) REVERT: f 6 SER cc_start: 0.9117 (OUTLIER) cc_final: 0.8851 (t) REVERT: f 34 LYS cc_start: 0.8956 (OUTLIER) cc_final: 0.7748 (ptpt) REVERT: g 9 MET cc_start: 0.6653 (OUTLIER) cc_final: 0.6441 (mtm) REVERT: g 169 GLU cc_start: 0.7258 (OUTLIER) cc_final: 0.7013 (mp0) REVERT: h 72 ARG cc_start: 0.7570 (mtm110) cc_final: 0.6997 (mmm160) REVERT: h 86 LYS cc_start: 0.6707 (pttt) cc_final: 0.6206 (ptpt) REVERT: h 88 ARG cc_start: 0.7320 (ttp-110) cc_final: 0.6991 (ttp-170) REVERT: h 161 GLU cc_start: 0.7192 (OUTLIER) cc_final: 0.6927 (tt0) REVERT: h 188 GLU cc_start: 0.7463 (OUTLIER) cc_final: 0.7246 (mt-10) REVERT: i 128 ARG cc_start: 0.7260 (mtt180) cc_final: 0.6832 (tmt-80) REVERT: i 148 LYS cc_start: 0.7395 (ttpp) cc_final: 0.6945 (tppp) REVERT: i 153 SER cc_start: 0.5888 (p) cc_final: 0.5612 (m) REVERT: i 179 GLU cc_start: 0.6976 (tt0) cc_final: 0.6226 (pp20) REVERT: j 68 ARG cc_start: 0.7719 (OUTLIER) cc_final: 0.6685 (mpp-170) REVERT: j 111 MET cc_start: 0.8503 (mtp) cc_final: 0.8093 (mtt) REVERT: j 147 MET cc_start: 0.7675 (ttp) cc_final: 0.7259 (ttp) REVERT: j 159 LYS cc_start: 0.8664 (OUTLIER) cc_final: 0.8333 (mttp) REVERT: k 56 LYS cc_start: 0.7883 (ttmm) cc_final: 0.7525 (ttmt) REVERT: k 93 LYS cc_start: 0.7633 (ttmm) cc_final: 0.6979 (ptmm) REVERT: l 118 LEU cc_start: 0.7957 (tp) cc_final: 0.7641 (tp) REVERT: n 47 VAL cc_start: 0.8007 (p) cc_final: 0.7797 (t) REVERT: o 46 LYS cc_start: 0.8352 (mtpm) cc_final: 0.7965 (mtpt) REVERT: q 40 THR cc_start: 0.8850 (OUTLIER) cc_final: 0.8624 (m) REVERT: q 78 SER cc_start: 0.8716 (OUTLIER) cc_final: 0.8446 (m) REVERT: q 86 ARG cc_start: 0.8347 (OUTLIER) cc_final: 0.7691 (ptt-90) REVERT: q 91 PRO cc_start: 0.8628 (Cg_endo) cc_final: 0.8176 (Cg_exo) REVERT: r 31 LYS cc_start: 0.7875 (mtpp) cc_final: 0.7622 (mtmm) REVERT: r 93 ARG cc_start: 0.7382 (OUTLIER) cc_final: 0.6983 (tpt170) REVERT: y 57 ILE cc_start: 0.8094 (OUTLIER) cc_final: 0.7774 (tt) REVERT: 7 60 MET cc_start: 0.1434 (mmm) cc_final: 0.0593 (mmm) REVERT: 7 306 ASN cc_start: 0.4582 (m110) cc_final: 0.4099 (m110) REVERT: 7 329 MET cc_start: 0.3460 (tpt) cc_final: 0.3102 (mpp) REVERT: 7 352 ASP cc_start: 0.5039 (m-30) cc_final: 0.3472 (t0) REVERT: 7 378 THR cc_start: 0.6259 (OUTLIER) cc_final: 0.5812 (t) REVERT: 7 472 ARG cc_start: 0.6243 (mmp80) cc_final: 0.5119 (mmp80) REVERT: 7 516 GLU cc_start: 0.6269 (pp20) cc_final: 0.5881 (mm-30) REVERT: I 16 MET cc_start: 0.2302 (OUTLIER) cc_final: 0.1944 (tmt) REVERT: H 1 MET cc_start: 0.3314 (tpp) cc_final: 0.2852 (mtp) REVERT: A 14 GLU cc_start: 0.7150 (OUTLIER) cc_final: 0.6639 (mt-10) REVERT: A 17 GLU cc_start: 0.6502 (OUTLIER) cc_final: 0.6105 (mp0) REVERT: A 74 MET cc_start: 0.4311 (mtp) cc_final: 0.3756 (mtm) REVERT: A 77 MET cc_start: 0.5435 (ttp) cc_final: 0.4972 (pmm) REVERT: A 90 GLU cc_start: 0.5463 (OUTLIER) cc_final: 0.5262 (tm-30) REVERT: A 279 HIS cc_start: 0.6604 (t70) cc_final: 0.6309 (t-90) outliers start: 200 outliers final: 134 residues processed: 1061 average time/residue: 2.3107 time to fit residues: 3517.7292 Evaluate side-chains 1101 residues out of total 5623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 930 time to evaluate : 7.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 182 ARG Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain C residue 46 ARG Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 88 ARG Chi-restraints excluded: chain D residue 144 GLU Chi-restraints excluded: chain D residue 155 GLU Chi-restraints excluded: chain E residue 51 ASP Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 153 ASP Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain F residue 172 LYS Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 45 GLU Chi-restraints excluded: chain G residue 147 VAL Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 60 ASP Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain L residue 48 ARG Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain L residue 143 GLU Chi-restraints excluded: chain M residue 6 ARG Chi-restraints excluded: chain M residue 88 ASN Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain N residue 74 GLU Chi-restraints excluded: chain O residue 5 SER Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain Q residue 3 ARG Chi-restraints excluded: chain R residue 6 GLN Chi-restraints excluded: chain R residue 16 GLU Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 70 GLU Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 73 LYS Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 45 VAL Chi-restraints excluded: chain S residue 67 ASP Chi-restraints excluded: chain S residue 82 MET Chi-restraints excluded: chain S residue 101 SER Chi-restraints excluded: chain T residue 49 LYS Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain U residue 15 THR Chi-restraints excluded: chain U residue 29 LEU Chi-restraints excluded: chain U residue 49 VAL Chi-restraints excluded: chain U residue 67 VAL Chi-restraints excluded: chain W residue 17 GLU Chi-restraints excluded: chain W residue 44 LYS Chi-restraints excluded: chain W residue 62 LYS Chi-restraints excluded: chain W residue 78 LYS Chi-restraints excluded: chain W residue 83 GLU Chi-restraints excluded: chain X residue 66 THR Chi-restraints excluded: chain Z residue 57 VAL Chi-restraints excluded: chain Z residue 58 GLU Chi-restraints excluded: chain a residue 10 GLU Chi-restraints excluded: chain c residue 7 GLU Chi-restraints excluded: chain c residue 22 THR Chi-restraints excluded: chain d residue 25 LYS Chi-restraints excluded: chain e residue 32 ILE Chi-restraints excluded: chain f residue 4 ARG Chi-restraints excluded: chain f residue 6 SER Chi-restraints excluded: chain f residue 34 LYS Chi-restraints excluded: chain g residue 9 MET Chi-restraints excluded: chain g residue 23 TRP Chi-restraints excluded: chain g residue 56 GLU Chi-restraints excluded: chain g residue 116 ASP Chi-restraints excluded: chain g residue 130 THR Chi-restraints excluded: chain g residue 135 LEU Chi-restraints excluded: chain g residue 164 ILE Chi-restraints excluded: chain g residue 169 GLU Chi-restraints excluded: chain g residue 199 VAL Chi-restraints excluded: chain h residue 53 SER Chi-restraints excluded: chain h residue 59 ARG Chi-restraints excluded: chain h residue 66 VAL Chi-restraints excluded: chain h residue 67 THR Chi-restraints excluded: chain h residue 101 ILE Chi-restraints excluded: chain h residue 128 VAL Chi-restraints excluded: chain h residue 161 GLU Chi-restraints excluded: chain h residue 188 GLU Chi-restraints excluded: chain i residue 143 VAL Chi-restraints excluded: chain i residue 166 GLU Chi-restraints excluded: chain i residue 191 LEU Chi-restraints excluded: chain j residue 13 GLU Chi-restraints excluded: chain j residue 32 SER Chi-restraints excluded: chain j residue 68 ARG Chi-restraints excluded: chain j residue 94 VAL Chi-restraints excluded: chain j residue 120 VAL Chi-restraints excluded: chain j residue 130 SER Chi-restraints excluded: chain j residue 156 LYS Chi-restraints excluded: chain j residue 159 LYS Chi-restraints excluded: chain l residue 23 LEU Chi-restraints excluded: chain l residue 56 LYS Chi-restraints excluded: chain l residue 69 VAL Chi-restraints excluded: chain l residue 94 VAL Chi-restraints excluded: chain l residue 133 THR Chi-restraints excluded: chain m residue 72 VAL Chi-restraints excluded: chain m residue 89 LYS Chi-restraints excluded: chain m residue 129 VAL Chi-restraints excluded: chain n residue 29 VAL Chi-restraints excluded: chain n residue 111 VAL Chi-restraints excluded: chain p residue 30 THR Chi-restraints excluded: chain p residue 34 ILE Chi-restraints excluded: chain q residue 21 VAL Chi-restraints excluded: chain q residue 40 THR Chi-restraints excluded: chain q residue 41 THR Chi-restraints excluded: chain q residue 58 THR Chi-restraints excluded: chain q residue 64 THR Chi-restraints excluded: chain q residue 78 SER Chi-restraints excluded: chain q residue 86 ARG Chi-restraints excluded: chain q residue 119 VAL Chi-restraints excluded: chain r residue 93 ARG Chi-restraints excluded: chain r residue 97 VAL Chi-restraints excluded: chain s residue 11 VAL Chi-restraints excluded: chain s residue 90 ARG Chi-restraints excluded: chain t residue 40 GLN Chi-restraints excluded: chain t residue 75 VAL Chi-restraints excluded: chain u residue 24 SER Chi-restraints excluded: chain v residue 42 THR Chi-restraints excluded: chain v residue 57 ASP Chi-restraints excluded: chain v residue 67 LEU Chi-restraints excluded: chain x residue 39 THR Chi-restraints excluded: chain x residue 58 VAL Chi-restraints excluded: chain y residue 6 SER Chi-restraints excluded: chain y residue 14 SER Chi-restraints excluded: chain y residue 57 ILE Chi-restraints excluded: chain z residue 14 VAL Chi-restraints excluded: chain z residue 69 ARG Chi-restraints excluded: chain 7 residue 33 VAL Chi-restraints excluded: chain 7 residue 137 ILE Chi-restraints excluded: chain 7 residue 222 ASP Chi-restraints excluded: chain 7 residue 320 VAL Chi-restraints excluded: chain 7 residue 378 THR Chi-restraints excluded: chain 7 residue 408 LYS Chi-restraints excluded: chain 7 residue 419 LEU Chi-restraints excluded: chain 7 residue 425 VAL Chi-restraints excluded: chain 7 residue 466 VAL Chi-restraints excluded: chain I residue 8 VAL Chi-restraints excluded: chain I residue 16 MET Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 319 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1125 random chunks: chunk 708 optimal weight: 0.9980 chunk 950 optimal weight: 3.9990 chunk 273 optimal weight: 10.0000 chunk 822 optimal weight: 5.9990 chunk 131 optimal weight: 10.0000 chunk 248 optimal weight: 10.0000 chunk 893 optimal weight: 10.0000 chunk 374 optimal weight: 30.0000 chunk 917 optimal weight: 7.9990 chunk 113 optimal weight: 10.0000 chunk 164 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 70 ASN C 150 GLN ** D 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 156 ASN ** K 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 88 ASN N 18 GLN O 19 GLN P 10 GLN P 12 GLN T 59 ASN U 27 ASN V 49 ASN Y 20 ASN ** h 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 139 GLN j 82 GLN k 3 HIS ** m 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 60 GLN t 62 GLN u 40 ASN y 3 ASN ** 7 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 433 ASN ** 7 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 296 ASN ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.152827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.120835 restraints weight = 154143.893| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 1.79 r_work: 0.2914 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.4323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.095 166175 Z= 0.401 Angle : 0.734 15.131 247356 Z= 0.386 Chirality : 0.044 0.533 31326 Planarity : 0.007 0.146 14137 Dihedral : 23.411 179.741 79973 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.52 % Favored : 95.47 % Rotamer: Outliers : 3.97 % Allowed : 23.56 % Favored : 72.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.44 % 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: -0.57 (0.10), residues: 6755 helix: 0.45 (0.11), residues: 2371 sheet: -0.49 (0.14), residues: 1308 loop : -0.90 (0.11), residues: 3076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP g 23 HIS 0.008 0.002 HIS k 11 PHE 0.020 0.002 PHE Q 57 TYR 0.026 0.002 TYR c 49 ARG 0.007 0.001 ARG S 11 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 51451.32 seconds wall clock time: 893 minutes 24.82 seconds (53604.82 seconds total)