Starting phenix.real_space_refine on Fri Feb 23 10:40:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6om6_20121/02_2024/6om6_20121_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6om6_20121/02_2024/6om6_20121.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6om6_20121/02_2024/6om6_20121_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6om6_20121/02_2024/6om6_20121_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6om6_20121/02_2024/6om6_20121_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6om6_20121/02_2024/6om6_20121.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6om6_20121/02_2024/6om6_20121.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6om6_20121/02_2024/6om6_20121_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6om6_20121/02_2024/6om6_20121_updated.pdb" } resolution = 3.1 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4638 5.49 5 S 148 5.16 5 C 72435 2.51 5 N 26902 2.21 5 O 40172 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 GLU 79": "OE1" <-> "OE2" Residue "B ARG 80": "NH1" <-> "NH2" Residue "B TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 121": "OD1" <-> "OD2" Residue "B GLU 145": "OE1" <-> "OE2" Residue "B ARG 167": "NH1" <-> "NH2" Residue "B ARG 177": "NH1" <-> "NH2" Residue "B ARG 182": "NH1" <-> "NH2" Residue "B GLU 199": "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 ARG 59": "NH1" <-> "NH2" Residue "C GLU 64": "OE1" <-> "OE2" Residue "C ARG 77": "NH1" <-> "NH2" Residue "C ARG 83": "NH1" <-> "NH2" Residue "C GLU 86": "OE1" <-> "OE2" Residue "C GLU 88": "OE1" <-> "OE2" Residue "C GLU 89": "OE1" <-> "OE2" Residue "C PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 168": "OE1" <-> "OE2" Residue "C ARG 169": "NH1" <-> "NH2" Residue "C GLU 183": "OE1" <-> "OE2" Residue "C ARG 184": "NH1" <-> "NH2" Residue "D GLU 2": "OE1" <-> "OE2" Residue "D GLU 16": "OE1" <-> "OE2" Residue "D PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 21": "NH1" <-> "NH2" Residue "D ASP 22": "OD1" <-> "OD2" Residue "D GLU 25": "OE1" <-> "OE2" Residue "D ARG 44": "NH1" <-> "NH2" Residue "D ARG 49": "NH1" <-> "NH2" Residue "D ARG 102": "NH1" <-> "NH2" Residue "D PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 140": "OD1" <-> "OD2" Residue "D ARG 162": "NH1" <-> "NH2" Residue "D ARG 170": "NH1" <-> "NH2" Residue "E ARG 30": "NH1" <-> "NH2" Residue "E ASP 46": "OD1" <-> "OD2" Residue "E ASP 51": "OD1" <-> "OD2" Residue "E ASP 56": "OD1" <-> "OD2" Residue "E ARG 71": "NH1" <-> "NH2" Residue "E ARG 92": "NH1" <-> "NH2" Residue "E GLU 98": "OE1" <-> "OE2" Residue "E PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 101": "OE1" <-> "OE2" Residue "E ARG 102": "NH1" <-> "NH2" Residue "E ARG 110": "NH1" <-> "NH2" Residue "E ARG 112": "NH1" <-> "NH2" Residue "E ASP 113": "OD1" <-> "OD2" Residue "E PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 115": "NH1" <-> "NH2" Residue "E TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 144": "OD1" <-> "OD2" Residue "E ARG 148": "NH1" <-> "NH2" Residue "E ASP 153": "OD1" <-> "OD2" Residue "E GLU 165": "OE1" <-> "OE2" Residue "E ASP 174": "OD1" <-> "OD2" Residue "F ARG 3": "NH1" <-> "NH2" Residue "F GLU 42": "OE1" <-> "OE2" Residue "F ASP 47": "OD1" <-> "OD2" Residue "F PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 56": "OD1" <-> "OD2" Residue "F GLU 124": "OE1" <-> "OE2" Residue "F GLU 130": "OE1" <-> "OE2" 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 GLU 167": "OE1" <-> "OE2" Residue "F ARG 170": "NH1" <-> "NH2" Residue "F GLU 173": "OE1" <-> "OE2" Residue "G ASP 7": "OD1" <-> "OD2" Residue "G ASP 17": "OD1" <-> "OD2" Residue "G PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 50": "NH1" <-> "NH2" Residue "G ARG 51": "NH1" <-> "NH2" Residue "G GLU 53": "OE1" <-> "OE2" Residue "G GLU 60": "OE1" <-> "OE2" Residue "G ARG 68": "NH1" <-> "NH2" Residue "G ASP 86": "OD1" <-> "OD2" Residue "G PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 98": "OD1" <-> "OD2" Residue "G GLU 109": "OE1" <-> "OE2" Residue "G GLU 127": "OE1" <-> "OE2" Residue "G PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 149": "OE1" <-> "OE2" Residue "J PHE 4": "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 ASP 49": "OD1" <-> "OD2" Residue "J TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 91": "OE1" <-> "OE2" Residue "J ARG 95": "NH1" <-> "NH2" Residue "J ARG 96": "NH1" <-> "NH2" Residue "J ARG 120": "NH1" <-> "NH2" Residue "K ARG 17": "NH1" <-> "NH2" Residue "K ARG 18": "NH1" <-> "NH2" 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 GLU 76": "OE1" <-> "OE2" Residue "L ARG 78": "NH1" <-> "NH2" 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 PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 40": "NH1" <-> "NH2" Residue "M GLU 47": "OE1" <-> "OE2" Residue "M ARG 50": "NH1" <-> "NH2" Residue "M ARG 55": "NH1" <-> "NH2" Residue "M GLU 75": "OE1" <-> "OE2" Residue "M TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 104": "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 GLU 43": "OE1" <-> "OE2" 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 GLU 74": "OE1" <-> "OE2" Residue "N PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 96": "NH1" <-> "NH2" Residue "N PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 117": "OD1" <-> "OD2" Residue "N ARG 118": "NH1" <-> "NH2" Residue "O ASP 2": "OD1" <-> "OD2" Residue "O ARG 10": "NH1" <-> "NH2" Residue "O ARG 13": "NH1" <-> "NH2" Residue "O ARG 16": "NH1" <-> "NH2" Residue "O GLU 20": "OE1" <-> "OE2" Residue "O ARG 25": "NH1" <-> "NH2" Residue "O ARG 81": "NH1" <-> "NH2" Residue "O ASP 93": "OD1" <-> "OD2" Residue "O ARG 94": "NH1" <-> "NH2" Residue "O ARG 102": "NH1" <-> "NH2" Residue "O ARG 111": "NH1" <-> "NH2" Residue "P GLU 11": "OE1" <-> "OE2" Residue "P ARG 21": "NH1" <-> "NH2" Residue "P GLU 34": "OE1" <-> "OE2" Residue "P GLU 44": "OE1" <-> "OE2" Residue "P ARG 62": "NH1" <-> "NH2" Residue "P GLU 71": "OE1" <-> "OE2" Residue "P ARG 89": "NH1" <-> "NH2" Residue "P TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 101": "NH1" <-> "NH2" Residue "P GLU 102": "OE1" <-> "OE2" 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 TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 33": "NH1" <-> "NH2" Residue "Q PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 48": "NH1" <-> "NH2" Residue "Q ARG 70": "NH1" <-> "NH2" Residue "Q GLU 89": "OE1" <-> "OE2" Residue "Q ASP 91": "OD1" <-> "OD2" Residue "Q ASP 97": "OD1" <-> "OD2" Residue "Q GLU 111": "OE1" <-> "OE2" Residue "R TYR 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 16": "OE1" <-> "OE2" Residue "R ARG 21": "NH1" <-> "NH2" Residue "R GLU 23": "OE1" <-> "OE2" Residue "R PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 45": "OE1" <-> "OE2" Residue "R PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 ASP 22": "OD1" <-> "OD2" Residue "S GLU 52": "OE1" <-> "OE2" Residue "S GLU 59": "OE1" <-> "OE2" Residue "S ASP 67": "OD1" <-> "OD2" Residue "S ASP 68": "OD1" <-> "OD2" 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 GLU 4": "OE1" <-> "OE2" Residue "T ARG 6": "NH1" <-> "NH2" Residue "T GLU 18": "OE1" <-> "OE2" Residue "T PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 52": "OE1" <-> "OE2" Residue "T GLU 54": "OE1" <-> "OE2" Residue "T TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 6": "NH1" <-> "NH2" Residue "U ASP 8": "OD1" <-> "OD2" Residue "U GLU 10": "OE1" <-> "OE2" Residue "U GLU 37": "OE1" <-> "OE2" Residue "U ASP 81": "OD1" <-> "OD2" Residue "U ARG 82": "NH1" <-> "NH2" Residue "U ARG 86": "NH1" <-> "NH2" Residue "U GLU 88": "OE1" <-> "OE2" Residue "U ARG 94": "NH1" <-> "NH2" Residue "U PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 19": "NH1" <-> "NH2" Residue "V TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 76": "OD1" <-> "OD2" Residue "V TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 3": "NH1" <-> "NH2" Residue "X ARG 18": "NH1" <-> "NH2" Residue "X ARG 37": "NH1" <-> "NH2" Residue "X GLU 43": "OE1" <-> "OE2" Residue "X ARG 45": "NH1" <-> "NH2" Residue "X ARG 50": "NH1" <-> "NH2" Residue "X ARG 57": "NH1" <-> "NH2" Residue "X ARG 74": "NH1" <-> "NH2" Residue "X GLU 76": "OE1" <-> "OE2" Residue "X TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 5": "OE1" <-> "OE2" Residue "Y GLU 13": "OE1" <-> "OE2" Residue "Y GLU 17": "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 "Y GLU 59": "OE1" <-> "OE2" Residue "Z ARG 11": "NH1" <-> "NH2" Residue "Z ARG 30": "NH1" <-> "NH2" Residue "Z GLU 37": "OE1" <-> "OE2" Residue "Z ASP 40": "OD1" <-> "OD2" Residue "Z ARG 45": "NH1" <-> "NH2" Residue "Z PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 4": "OD1" <-> "OD2" Residue "a GLU 10": "OE1" <-> "OE2" Residue "a ASP 31": "OD1" <-> "OD2" Residue "a PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 50": "OD1" <-> "OD2" Residue "a ARG 56": "NH1" <-> "NH2" Residue "a ASP 58": "OD1" <-> "OD2" Residue "a PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 63": "NH1" <-> "NH2" Residue "a PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 10": "NH1" <-> "NH2" Residue "b ARG 16": "NH1" <-> "NH2" Residue "b ASP 46": "OD1" <-> "OD2" Residue "b TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 52": "NH1" <-> "NH2" Residue "c ARG 28": "NH1" <-> "NH2" Residue "c ASP 40": "OD1" <-> "OD2" Residue "c ARG 44": "NH1" <-> "NH2" Residue "c GLU 51": "OE1" <-> "OE2" 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 ARG 24": "NH1" <-> "NH2" Residue "g ASP 8": "OD1" <-> "OD2" Residue "g PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 52": "OE1" <-> "OE2" Residue "g GLU 56": "OE1" <-> "OE2" Residue "g ARG 63": "NH1" <-> "NH2" Residue "g ARG 74": "NH1" <-> "NH2" Residue "g ASP 88": "OD1" <-> "OD2" Residue "g PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 118": "OE1" <-> "OE2" Residue "g PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 127": "OD1" <-> "OD2" Residue "g GLU 142": "OE1" <-> "OE2" Residue "g ASP 153": "OD1" <-> "OD2" Residue "g ASP 159": "OD1" <-> "OD2" Residue "g ASP 165": "OD1" <-> "OD2" Residue "g ASP 167": "OD1" <-> "OD2" Residue "g GLU 169": "OE1" <-> "OE2" Residue "g ASP 194": "OD1" <-> "OD2" Residue "g ASP 204": "OD1" <-> "OD2" Residue "g ARG 208": "NH1" <-> "NH2" Residue "g GLU 223": "OE1" <-> "OE2" Residue "g ARG 225": "NH1" <-> "NH2" Residue "h ASP 34": "OD1" <-> "OD2" Residue "h ASP 36": "OD1" <-> "OD2" Residue "h GLU 46": "OE1" <-> "OE2" Residue "h ARG 54": "NH1" <-> "NH2" Residue "h ARG 72": "NH1" <-> "NH2" Residue "h GLU 82": "OE1" <-> "OE2" Residue "h ARG 88": "NH1" <-> "NH2" Residue "h ASP 93": "OD1" <-> "OD2" Residue "h GLU 105": "OE1" <-> "OE2" Residue "h ASP 112": "OD1" <-> "OD2" Residue "h ARG 127": "NH1" <-> "NH2" Residue "h PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ARG 131": "NH1" <-> "NH2" Residue "h ARG 132": "NH1" <-> "NH2" Residue "h ARG 164": "NH1" <-> "NH2" Residue "h GLU 170": "OE1" <-> "OE2" Residue "i TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i GLU 15": "OE1" <-> "OE2" Residue "i ASP 29": "OD1" <-> "OD2" Residue "i GLU 35": "OE1" <-> "OE2" Residue "i TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 73": "NH1" <-> "NH2" Residue "i ARG 81": "NH1" <-> "NH2" Residue "i GLU 88": "OE1" <-> "OE2" Residue "i GLU 147": "OE1" <-> "OE2" Residue "i GLU 163": "OE1" <-> "OE2" Residue "i GLU 172": "OE1" <-> "OE2" Residue "i ASP 174": "OD1" <-> "OD2" Residue "i ASP 194": "OD1" <-> "OD2" Residue "i GLU 202": "OE1" <-> "OE2" Residue "j PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ARG 45": "NH1" <-> "NH2" Residue "j ARG 68": "NH1" <-> "NH2" Residue "j ARG 69": "NH1" <-> "NH2" Residue "j ARG 93": "NH1" <-> "NH2" Residue "j GLU 145": "OE1" <-> "OE2" Residue "j GLU 151": "OE1" <-> "OE2" Residue "j ARG 157": "NH1" <-> "NH2" Residue "j GLU 162": "OE1" <-> "OE2" Residue "k TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ASP 13": "OD1" <-> "OD2" Residue "k GLU 16": "OE1" <-> "OE2" Residue "k ASP 41": "OD1" <-> "OD2" Residue "k ARG 45": "NH1" <-> "NH2" Residue "k TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k GLU 65": "OE1" <-> "OE2" Residue "k ASP 72": "OD1" <-> "OD2" Residue "k GLU 75": "OE1" <-> "OE2" Residue "k ARG 79": "NH1" <-> "NH2" Residue "k ASP 82": "OD1" <-> "OD2" Residue "k GLU 98": "OE1" <-> "OE2" Residue "l ARG 4": "NH1" <-> "NH2" Residue "l ASP 33": "OD1" <-> "OD2" Residue "l GLU 48": "OE1" <-> "OE2" Residue "l ARG 53": "NH1" <-> "NH2" Residue "l ARG 78": "NH1" <-> "NH2" Residue "l ARG 79": "NH1" <-> "NH2" Residue "l ARG 92": "NH1" <-> "NH2" Residue "l GLU 106": "OE1" <-> "OE2" Residue "l ASP 140": "OD1" <-> "OD2" Residue "m ASP 9": "OD1" <-> "OD2" Residue "m GLU 47": "OE1" <-> "OE2" Residue "m GLU 73": "OE1" <-> "OE2" Residue "m ASP 113": "OD1" <-> "OD2" Residue "m TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ARG 11": "NH1" <-> "NH2" Residue "n PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n GLU 36": "OE1" <-> "OE2" Residue "n ARG 41": "NH1" <-> "NH2" Residue "n ASP 56": "OD1" <-> "OD2" Residue "n GLU 59": "OE1" <-> "OE2" Residue "n TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ARG 130": "NH1" <-> "NH2" Residue "o ARG 5": "NH1" <-> "NH2" Residue "o ARG 45": "NH1" <-> "NH2" Residue "o ASP 60": "OD1" <-> "OD2" Residue "o ASP 75": "OD1" <-> "OD2" 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 PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p GLU 68": "OE1" <-> "OE2" Residue "p ARG 69": "NH1" <-> "NH2" Residue "p TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 70": "OE1" <-> "OE2" Residue "q GLU 76": "OE1" <-> "OE2" Residue "q ARG 83": "NH1" <-> "NH2" Residue "q ASP 109": "OD1" <-> "OD2" Residue "r ARG 29": "NH1" <-> "NH2" Residue "r GLU 50": "OE1" <-> "OE2" Residue "r ARG 70": "NH1" <-> "NH2" Residue "r ARG 87": "NH1" <-> "NH2" Residue "r ARG 109": "NH1" <-> "NH2" Residue "s ASP 18": "OD1" <-> "OD2" Residue "s ASP 54": "OD1" <-> "OD2" 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 PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ARG 85": "NH1" <-> "NH2" Residue "s GLU 86": "OE1" <-> "OE2" Residue "t PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t ASP 68": "OD1" <-> "OD2" Residue "t ARG 72": "NH1" <-> "NH2" Residue "t ARG 89": "NH1" <-> "NH2" Residue "u ARG 28": "NH1" <-> "NH2" Residue "u PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u GLU 34": "OE1" <-> "OE2" Residue "u PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u GLU 45": "OE1" <-> "OE2" Residue "u ARG 51": "NH1" <-> "NH2" Residue "u ASP 55": "OD1" <-> "OD2" Residue "u GLU 77": "OE1" <-> "OE2" Residue "v ARG 11": "NH1" <-> "NH2" Residue "v ARG 27": "NH1" <-> "NH2" Residue "v PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v GLU 49": "OE1" <-> "OE2" Residue "v ASP 57": "OD1" <-> "OD2" Residue "v GLU 60": "OE1" <-> "OE2" Residue "v GLU 63": "OE1" <-> "OE2" Residue "v ARG 65": "NH1" <-> "NH2" Residue "v ARG 77": "NH1" <-> "NH2" Residue "w ASP 22": "OD1" <-> "OD2" Residue "w TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w ARG 61": "NH1" <-> "NH2" Residue "w TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x GLU 20": "OE1" <-> "OE2" Residue "x ARG 32": "NH1" <-> "NH2" Residue "x PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x ASP 64": "OD1" <-> "OD2" Residue "x GLU 65": "OE1" <-> "OE2" Residue "y PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y ARG 60": "NH1" <-> "NH2" Residue "y ARG 74": "NH1" <-> "NH2" Residue "z GLU 10": "OE1" <-> "OE2" Residue "z GLU 24": "OE1" <-> "OE2" Residue "z GLU 31": "OE1" <-> "OE2" Residue "z ARG 33": "NH1" <-> "NH2" 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 "W ARG 14": "NH1" <-> "NH2" Residue "W GLU 17": "OE1" <-> "OE2" Residue "W PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 144295 Number of models: 1 Model: "" Number of chains: 55 Chain: "1" Number of atoms: 62334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2903, 62334 Classifications: {'RNA': 2903} Modifications used: {'rna2p': 5, 'rna2p_pur': 287, 'rna2p_pyr': 165, 'rna3p': 15, 'rna3p_pur': 1381, 'rna3p_pyr': 1050} Link IDs: {'rna2p': 456, 'rna3p': 2446} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 8 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': 116, 'rna2p_pyr': 87, 'rna3p': 10, 'rna3p_pur': 753, 'rna3p_pyr': 566} Link IDs: {'rna2p': 203, 'rna3p': 1330} 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: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 110 Classifications: {'RNA': 5} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 4} Link IDs: {'rna3p': 4} Chain: "5" Number of atoms: 1619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1619 Classifications: {'RNA': 76} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 7, 'rna3p': 2, 'rna3p_pur': 31, 'rna3p_pyr': 30} Link IDs: {'rna2p': 13, 'rna3p': 62} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 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: {'PCIS': 1, 'PTRANS': 5, '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: {'PCIS': 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: "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: "W" Number of atoms: 634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 634 Classifications: {'peptide': 84} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 82} Chain: "1" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'KKL': 1} Classifications: {'undetermined': 1} Time building chain proxies: 54.25, per 1000 atoms: 0.38 Number of scatterers: 144295 At special positions: 0 Unit cell: (227.481, 246.537, 267.975, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 148 16.00 P 4638 15.00 O 40172 8.00 N 26902 7.00 C 72435 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 66.40 Conformation dependent library (CDL) restraints added in 6.5 seconds 11228 Ramachandran restraints generated. 5614 Oldfield, 0 Emsley, 5614 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10496 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: 178 helices and 71 sheets defined 39.3% alpha, 19.4% beta 1551 base pairs and 2639 stacking pairs defined. Time for finding SS restraints: 71.44 Creating SS restraints... Processing helix chain 'B' and resid 10 through 16 removed outlier: 3.614A pdb=" N ARG B 14 " --> pdb=" O SER B 10 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N HIS B 15 " --> pdb=" O PRO B 11 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N VAL B 16 " --> pdb=" O GLY B 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 10 through 16' Processing helix chain 'B' and resid 131 through 136 Proline residue: B 136 - end of helix Processing helix chain 'B' and resid 207 through 215 removed outlier: 4.003A pdb=" N ALA B 211 " --> pdb=" O LYS B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 268 removed outlier: 4.181A pdb=" N ASP B 264 " --> pdb=" O ASN B 260 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N LYS B 265 " --> pdb=" O LYS B 261 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N PHE B 266 " --> pdb=" O ARG B 262 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ILE B 267 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 5.685A 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 'C' and resid 56 through 61 removed outlier: 5.491A pdb=" N THR C 61 " --> pdb=" O ALA C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 72 Processing helix chain 'C' and resid 98 through 103 removed outlier: 4.565A pdb=" N ALA C 102 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 5.065A 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 'D' and resid 15 through 20 Processing helix chain 'D' and resid 24 through 41 removed outlier: 5.635A 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: 4.686A pdb=" N ASN D 163 " --> pdb=" O LEU D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 183 Processing helix chain 'D' and resid 189 through 201 Processing helix chain 'E' and resid 2 through 21 removed outlier: 5.650A pdb=" N VAL E 13 " --> pdb=" O LYS E 9 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LYS E 14 " --> pdb=" O ASP E 10 " (cutoff:3.500A) Processing helix chain 'E' and resid 41 through 46 removed outlier: 4.652A pdb=" N ALA E 45 " --> pdb=" O GLY E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 62 Processing helix chain 'E' and resid 93 through 111 removed outlier: 5.330A 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 134 through 139 removed outlier: 4.872A pdb=" N PHE E 138 " --> pdb=" O GLU E 134 " (cutoff:3.500A) Proline residue: E 139 - end of helix No H-bonds generated for 'chain 'E' and resid 134 through 139' Processing helix chain 'E' and resid 142 through 147 removed outlier: 5.902A pdb=" N ASP E 147 " --> pdb=" O TYR E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 162 through 174 removed outlier: 3.596A pdb=" N GLY E 166 " --> pdb=" O SER E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 29 Proline residue: E 29 - end of helix Processing helix chain 'F' and resid 2 through 8 Proline residue: F 8 - end of helix Processing helix chain 'F' and resid 60 through 81 Processing helix chain 'F' and resid 137 through 153 removed outlier: 4.237A 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 50 Processing helix chain 'G' and resid 51 through 73 removed outlier: 4.336A pdb=" N ALA G 56 " --> pdb=" O ALA G 52 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ASN G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 107 Processing helix chain 'J' and resid 24 through 38 removed outlier: 3.549A pdb=" N ARG J 34 " --> pdb=" O THR J 30 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 96 Processing helix chain 'J' and resid 97 through 110 removed outlier: 4.616A 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 123 removed outlier: 3.603A pdb=" N LEU J 122 " --> pdb=" O MET J 118 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N LYS J 123 " --> pdb=" O PHE J 119 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 72 removed outlier: 4.656A pdb=" N LYS J 72 " --> pdb=" O ASN J 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 67 through 72' Processing helix chain 'K' and resid 104 through 109 removed outlier: 4.067A pdb=" N ARG K 108 " --> pdb=" O THR K 104 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N SER K 109 " --> pdb=" O ARG K 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 104 through 109' Processing helix chain 'K' and resid 112 through 119 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: 3.726A pdb=" N ALA L 72 " --> pdb=" O SER L 68 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ILE L 73 " --> pdb=" O ARG L 69 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR L 74 " --> pdb=" O LYS L 70 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N ALA L 75 " --> pdb=" O ALA L 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 68 through 75' Processing helix chain 'L' and resid 78 through 85 removed outlier: 3.606A pdb=" N LEU L 82 " --> pdb=" O ARG L 78 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ALA L 83 " --> pdb=" O LEU L 79 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N LYS L 84 " --> pdb=" O SER L 80 " (cutoff:3.500A) removed outlier: 3.979A 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: 4.288A pdb=" N LYS M 123 " --> pdb=" O LEU M 119 " (cutoff:3.500A) removed outlier: 3.811A 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: 4.617A pdb=" N ARG N 46 " --> pdb=" O LYS N 42 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL N 47 " --> pdb=" O GLU N 43 " (cutoff:3.500A) Proline residue: N 50 - end of helix removed outlier: 4.620A 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: 5.325A 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: 4.765A pdb=" N ARG O 13 " --> pdb=" O ARG O 9 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N ALA O 14 " --> pdb=" O ARG O 10 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 62 removed outlier: 4.782A pdb=" N GLN O 61 " --> pdb=" O ALA O 57 " (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: 3.885A pdb=" N LYS P 6 " --> pdb=" O SER P 2 " (cutoff:3.500A) Processing helix chain 'P' and resid 97 through 104 removed outlier: 4.818A pdb=" N ARG P 101 " --> pdb=" O LEU P 97 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N GLU P 102 " --> pdb=" O TYR P 98 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ARG P 103 " --> pdb=" O TYR P 99 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N THR P 104 " --> pdb=" O LEU P 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 97 through 104' Processing helix chain 'P' and resid 105 through 110 removed outlier: 3.776A pdb=" N ARG P 109 " --> pdb=" O GLY P 105 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N ILE P 110 " --> pdb=" O LYS P 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 105 through 110' Processing helix chain 'Q' and resid 6 through 22 Processing helix chain 'Q' and resid 26 through 31 removed outlier: 4.154A pdb=" N ARG Q 30 " --> pdb=" O GLY Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 32 through 37 removed outlier: 3.984A pdb=" N GLN Q 37 " --> pdb=" O ARG Q 33 " (cutoff:3.500A) Processing helix chain 'Q' and resid 39 through 73 removed outlier: 3.859A pdb=" N ARG Q 51 " --> pdb=" O TYR Q 47 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N LYS Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) removed outlier: 3.803A 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: 3.711A pdb=" N LEU S 19 " --> pdb=" O GLN S 15 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N VAL S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 39 Processing helix chain 'S' and resid 41 through 61 Processing helix chain 'S' and resid 65 through 70 removed outlier: 3.554A pdb=" N LEU S 69 " --> pdb=" O ASP S 65 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N LYS S 70 " --> pdb=" O ILE S 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 65 through 70' Processing helix chain 'T' and resid 3 through 11 removed outlier: 4.458A pdb=" N LEU T 11 " --> pdb=" O LEU T 7 " (cutoff:3.500A) Processing helix chain 'T' and resid 17 through 27 Processing helix chain 'T' and resid 39 through 51 Processing helix chain 'U' and resid 66 through 71 removed outlier: 3.597A pdb=" N VAL U 70 " --> pdb=" O GLN U 66 " (cutoff:3.500A) removed outlier: 4.873A 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 Processing helix chain 'V' and resid 43 through 53 removed outlier: 4.330A pdb=" N LYS V 53 " --> pdb=" O ASN V 49 " (cutoff:3.500A) Processing helix chain 'V' and resid 54 through 59 removed outlier: 3.861A 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 9 removed outlier: 3.636A pdb=" N GLU Y 8 " --> pdb=" O LYS Y 4 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N LYS Y 9 " --> pdb=" O GLU Y 5 " (cutoff:3.500A) Processing helix chain 'Y' and resid 10 through 35 removed outlier: 4.109A pdb=" N GLY Y 35 " --> pdb=" O GLN Y 31 " (cutoff:3.500A) Processing helix chain 'Y' and resid 40 through 62 removed outlier: 4.211A pdb=" N LYS Y 44 " --> pdb=" O SER Y 40 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLY Y 62 " --> pdb=" O ASN Y 58 " (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 45 through 52 removed outlier: 4.354A pdb=" N ARG a 49 " --> pdb=" O THR a 45 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL a 51 " --> pdb=" O LYS a 47 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ALA a 52 " --> pdb=" O GLN a 48 " (cutoff:3.500A) Processing helix chain 'a' and resid 55 through 64 Processing helix chain 'b' and resid 9 through 18 Processing helix chain 'd' and resid 8 through 16 Processing helix chain 'd' and resid 17 through 25 removed outlier: 4.304A pdb=" N THR d 24 " --> pdb=" O ALA d 20 " (cutoff:3.500A) removed outlier: 5.452A 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 Processing helix chain 'e' and resid 32 through 37 removed outlier: 4.919A pdb=" N LYS e 36 " --> pdb=" O ILE e 32 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N ALA e 37 " --> pdb=" O LEU e 33 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 32 through 37' Processing helix chain 'e' and resid 38 through 46 Proline residue: e 46 - end of helix Processing helix chain 'e' and resid 51 through 63 removed outlier: 3.519A pdb=" N LEU e 55 " --> pdb=" O SER e 51 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N GLY e 56 " --> pdb=" O LYS e 52 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N LEU e 57 " --> pdb=" O GLY e 53 " (cutoff:3.500A) Proline residue: e 63 - end of helix Processing helix chain 'g' and resid 5 through 13 Processing helix chain 'g' and resid 24 through 29 Proline residue: g 29 - end of helix Processing helix chain 'g' and resid 43 through 64 Proline residue: g 48 - end of helix Processing helix chain 'g' and resid 76 through 88 Processing helix chain 'g' and resid 103 through 122 removed outlier: 4.197A pdb=" N GLN g 109 " --> pdb=" O LYS g 105 " (cutoff:3.500A) Processing helix chain 'g' and resid 130 through 149 Processing helix chain 'g' and resid 165 through 170 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 Processing helix chain 'h' and resid 72 through 78 Processing helix chain 'h' and resid 81 through 96 removed outlier: 4.480A pdb=" N GLU h 85 " --> pdb=" O GLY h 81 " (cutoff:3.500A) Processing helix chain 'h' and resid 108 through 113 removed outlier: 3.876A pdb=" N ASP h 112 " --> pdb=" O LYS h 108 " (cutoff:3.500A) removed outlier: 5.534A 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 removed outlier: 3.830A pdb=" N SER h 119 " --> pdb=" O LEU h 115 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ARG h 126 " --> pdb=" O SER h 122 " (cutoff:3.500A) Processing helix chain 'h' and resid 129 through 145 Processing helix chain 'i' and resid 7 through 16 Processing helix chain 'i' and resid 27 through 32 Processing helix chain 'i' and resid 49 through 66 Processing helix chain 'i' and resid 68 through 83 removed outlier: 4.969A pdb=" N LYS i 83 " --> pdb=" O ALA i 79 " (cutoff:3.500A) Processing helix chain 'i' and resid 85 through 97 Processing helix chain 'i' and resid 98 through 106 Processing helix chain 'i' and resid 110 through 121 removed outlier: 3.521A pdb=" N LYS i 121 " --> pdb=" O LEU i 117 " (cutoff:3.500A) Processing helix chain 'i' and resid 146 through 151 removed outlier: 4.852A pdb=" N LYS i 151 " --> pdb=" O GLU i 147 " (cutoff:3.500A) Processing helix chain 'i' and resid 152 through 166 removed outlier: 4.218A pdb=" N LYS i 156 " --> pdb=" O GLN i 152 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N GLU i 166 " --> pdb=" O ALA i 162 " (cutoff:3.500A) Processing helix chain 'i' and resid 187 through 192 removed outlier: 3.927A pdb=" N LEU i 191 " --> pdb=" O GLU i 187 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N SER i 192 " --> pdb=" O ARG i 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 187 through 192' Processing helix chain 'i' and resid 196 through 206 Processing helix chain 'j' and resid 55 through 71 removed outlier: 4.037A pdb=" N ASN j 70 " --> pdb=" O LYS j 66 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N MET j 71 " --> pdb=" O ALA j 67 " (cutoff:3.500A) Processing helix chain 'j' and resid 109 through 119 Processing helix chain 'j' and resid 132 through 148 removed outlier: 5.840A pdb=" N ASN j 148 " --> pdb=" O LEU j 144 " (cutoff:3.500A) 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: 4.486A pdb=" N SER k 15 " --> pdb=" O HIS k 11 " (cutoff:3.500A) removed outlier: 5.774A 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: 3.632A pdb=" N MET k 21 " --> pdb=" O GLN k 17 " (cutoff:3.500A) Processing helix chain 'k' and resid 67 through 81 Processing helix chain 'l' and resid 20 through 31 Processing helix chain 'l' and resid 35 through 55 Processing helix chain 'l' and resid 57 through 70 Processing helix chain 'l' and resid 92 through 112 removed outlier: 6.111A 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: 3.888A pdb=" N ASP n 56 " --> pdb=" O LEU n 52 " (cutoff:3.500A) Processing helix chain 'n' and resid 71 through 92 Processing helix chain 'n' and resid 94 through 102 Processing helix chain 'o' and resid 14 through 33 Processing helix chain 'o' and resid 80 through 91 removed outlier: 3.693A pdb=" N VAL o 84 " --> pdb=" O THR o 80 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ASP o 85 " --> pdb=" O GLU o 81 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N ASP o 91 " --> pdb=" O LEU o 87 " (cutoff:3.500A) Processing helix chain 'p' and resid 46 through 51 removed outlier: 3.780A pdb=" N GLY p 51 " --> pdb=" O ALA p 47 " (cutoff:3.500A) Processing helix chain 'p' and resid 54 through 59 removed outlier: 4.259A pdb=" N SER p 58 " --> pdb=" O GLY p 54 " (cutoff:3.500A) removed outlier: 4.314A 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: 5.794A pdb=" N GLU p 76 " --> pdb=" O ASP p 72 " (cutoff:3.500A) Processing helix chain 'p' and resid 93 through 104 removed outlier: 5.082A pdb=" N ILE p 97 " --> pdb=" O ARG p 93 " (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 Processing helix chain 'r' and resid 14 through 22 removed outlier: 4.129A 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 44 through 49 removed outlier: 4.205A pdb=" N LEU r 48 " --> pdb=" O LYS r 44 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N SER r 49 " --> pdb=" O ILE r 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 44 through 49' Processing helix chain 'r' and resid 50 through 64 removed outlier: 4.578A pdb=" N VAL r 64 " --> pdb=" O VAL r 60 " (cutoff:3.500A) Processing helix chain 'r' and resid 66 through 84 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 52 Proline residue: s 52 - end of helix 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 44 removed outlier: 4.329A pdb=" N GLY t 41 " --> pdb=" O ASN t 37 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N HIS t 42 " --> pdb=" O HIS t 38 " (cutoff:3.500A) Processing helix chain 't' and resid 49 through 74 removed outlier: 3.939A 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 removed outlier: 3.718A pdb=" N ALA w 15 " --> pdb=" O CYS w 11 " (cutoff:3.500A) Processing helix chain 'w' and resid 25 through 34 removed outlier: 5.362A 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 41 through 46 removed outlier: 4.142A pdb=" N ILE x 45 " --> pdb=" O PHE x 41 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N GLY x 46 " --> pdb=" O PRO x 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'x' and resid 41 through 46' Processing helix chain 'x' and resid 70 through 76 removed outlier: 4.093A pdb=" N PHE x 74 " --> pdb=" O LYS x 70 " (cutoff:3.500A) Proline residue: x 76 - end of helix Processing helix chain 'x' and resid 64 through 69 removed outlier: 3.840A pdb=" N VAL x 67 " --> pdb=" O ASP x 64 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N GLY x 68 " --> pdb=" O GLU x 65 " (cutoff:3.500A) Processing helix chain 'y' and resid 4 through 41 Processing helix chain 'y' and resid 44 through 65 Proline residue: y 56 - end of helix Processing helix chain 'y' and resid 68 through 87 removed outlier: 4.824A 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: 5.471A pdb=" N PHE z 37 " --> pdb=" O ARG z 33 " (cutoff:3.500A) Processing helix chain 'z' and resid 40 through 69 removed outlier: 5.011A pdb=" N ARG z 62 " --> pdb=" O LYS z 58 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLU z 63 " --> pdb=" O LYS z 59 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N THR z 68 " --> pdb=" O ASN z 64 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N ARG z 69 " --> pdb=" O ALA z 65 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'B' and resid 2 through 5 Processing sheet with id= 2, first strand: chain 'B' and resid 33 through 36 No H-bonds generated for sheet with id= 2 Processing sheet with id= 3, first strand: chain 'B' and resid 80 through 83 removed outlier: 6.746A pdb=" N LEU B 93 " --> pdb=" O GLU B 79 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ASP B 114 " --> pdb=" O VAL B 78 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'B' and resid 138 through 141 removed outlier: 4.487A pdb=" N SER B 139 " --> pdb=" O ILE B 164 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N THR B 173 " --> pdb=" O VAL B 165 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N GLU B 180 " --> pdb=" O LEU B 176 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'B' and resid 91 through 96 removed outlier: 4.725A pdb=" N GLU B 100 " --> pdb=" O TYR B 96 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'C' and resid 3 through 7 removed outlier: 6.717A pdb=" N LYS C 105 " --> pdb=" O VAL C 177 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'C' and resid 10 through 16 removed outlier: 3.633A pdb=" N GLY C 10 " --> pdb=" O VAL C 26 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N VAL C 20 " --> pdb=" O THR C 16 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'C' and resid 36 through 40 removed outlier: 4.210A pdb=" N LEU C 40 " --> pdb=" O TYR C 45 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N TYR C 45 " --> pdb=" O LEU C 40 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N GLN C 49 " --> pdb=" O THR C 35 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N GLN C 94 " --> pdb=" O VAL C 34 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'C' and resid 46 through 51 removed outlier: 6.086A pdb=" N ARG C 46 " --> pdb=" O LEU C 84 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'D' and resid 1 through 6 removed outlier: 4.624A pdb=" N SER D 10 " --> pdb=" O LEU D 5 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'D' and resid 117 through 120 removed outlier: 3.661A pdb=" N LYS D 185 " --> pdb=" O ASP D 145 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'E' and resid 65 through 69 removed outlier: 5.362A pdb=" N ILE E 85 " --> pdb=" O VAL E 40 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N GLY E 39 " --> pdb=" O GLY E 151 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N GLY E 151 " --> pdb=" O GLY E 39 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'F' and resid 16 through 19 Processing sheet with id= 14, first strand: chain 'F' and resid 41 through 45 Processing sheet with id= 15, first strand: chain 'F' and resid 82 through 89 removed outlier: 6.255A pdb=" N THR F 129 " --> pdb=" O LEU F 89 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'F' and resid 94 through 98 Processing sheet with id= 17, first strand: chain 'G' and resid 17 through 20 removed outlier: 4.494A pdb=" N ASP G 17 " --> pdb=" O LEU G 5 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N LYS G 35 " --> pdb=" O LEU G 6 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'G' and resid 76 through 82 removed outlier: 6.232A pdb=" N GLU G 76 " --> pdb=" O LYS G 141 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA G 140 " --> pdb=" O PHE G 132 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL G 142 " --> pdb=" O VAL G 130 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL G 130 " --> pdb=" O VAL G 142 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'J' and resid 52 through 57 removed outlier: 5.103A pdb=" N ASP J 19 " --> pdb=" O LEU J 140 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'J' and resid 74 through 78 removed outlier: 8.400A pdb=" N GLY J 83 " --> pdb=" O THR J 78 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'K' and resid 18 through 21 removed outlier: 4.191A pdb=" N THR K 6 " --> pdb=" O CYS K 21 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N ASN K 82 " --> pdb=" O MET K 7 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'L' and resid 119 through 123 No H-bonds generated for sheet with id= 22 Processing sheet with id= 23, first strand: chain 'M' and resid 30 through 36 removed outlier: 7.680A pdb=" N SER M 30 " --> pdb=" O LYS M 133 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N LYS M 127 " --> pdb=" O VAL M 36 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'M' and resid 73 through 76 removed outlier: 6.851A pdb=" N ILE M 73 " --> pdb=" O GLU M 90 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'N' and resid 33 through 37 removed outlier: 5.897A pdb=" N ALA N 108 " --> pdb=" O PHE N 102 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N PHE N 102 " --> pdb=" O ALA N 108 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N MET N 110 " --> pdb=" O CYS N 100 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'O' and resid 49 through 52 Processing sheet with id= 27, first strand: chain 'P' and resid 38 through 46 removed outlier: 6.572A pdb=" N THR P 25 " --> pdb=" O LYS P 87 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'P' and resid 49 through 53 removed outlier: 3.794A pdb=" N ALA P 49 " --> pdb=" O THR P 60 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ARG P 53 " --> pdb=" O HIS P 56 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'R' and resid 11 through 14 removed outlier: 3.951A pdb=" N ASN R 43 " --> pdb=" O GLU R 46 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N GLU R 46 " --> pdb=" O ASN R 43 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'R' and resid 18 through 22 removed outlier: 5.210A pdb=" N GLN R 18 " --> pdb=" O ILE R 98 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ASP R 95 " --> pdb=" O VAL R 64 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N LYS R 60 " --> pdb=" O THR R 99 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N GLU R 31 " --> pdb=" O VAL R 63 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'R' and resid 57 through 60 Processing sheet with id= 32, first strand: chain 'R' and resid 65 through 68 Processing sheet with id= 33, first strand: chain 'R' and resid 69 through 78 removed outlier: 5.522A pdb=" N GLU R 70 " --> pdb=" O GLN R 91 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N GLN R 91 " --> pdb=" O GLU R 70 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N TYR R 83 " --> pdb=" O ARG R 78 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'S' and resid 2 through 8 removed outlier: 5.167A pdb=" N THR S 100 " --> pdb=" O GLY S 79 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LYS S 73 " --> pdb=" O VAL S 106 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'S' and resid 81 through 88 removed outlier: 3.630A pdb=" N ARG S 92 " --> pdb=" O ARG S 88 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'T' and resid 29 through 33 removed outlier: 4.777A pdb=" N LYS T 66 " --> pdb=" O ARG T 77 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N ASP T 79 " --> pdb=" O LYS T 64 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LYS T 64 " --> pdb=" O ASP T 79 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N LYS T 81 " --> pdb=" O VAL T 62 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL T 62 " --> pdb=" O LYS T 81 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ALA T 83 " --> pdb=" O THR T 60 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N THR T 60 " --> pdb=" O ALA T 83 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N VAL T 85 " --> pdb=" O VAL T 58 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N VAL T 58 " --> pdb=" O VAL T 85 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'U' and resid 40 through 45 removed outlier: 4.667A pdb=" N ASN U 40 " --> pdb=" O ALA U 63 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'U' and resid 82 through 87 removed outlier: 7.380A pdb=" N ARG U 82 " --> pdb=" O LYS U 97 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N ARG U 94 " --> pdb=" O ILE U 103 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'V' and resid 69 through 72 removed outlier: 6.349A pdb=" N ALA V 39 " --> pdb=" O ARG V 9 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE V 89 " --> pdb=" O PRO V 27 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'X' and resid 12 through 19 removed outlier: 6.560A pdb=" N VAL X 13 " --> pdb=" O ARG X 28 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ARG X 28 " --> pdb=" O VAL X 13 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N GLY X 15 " --> pdb=" O LYS X 26 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LYS X 26 " --> pdb=" O GLY X 15 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ASN X 17 " --> pdb=" O ALA X 24 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ALA X 24 " --> pdb=" O ASN X 17 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N SER X 19 " --> pdb=" O LEU X 22 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'X' and resid 35 through 41 Processing sheet with id= 42, first strand: chain 'Z' and resid 33 through 39 removed outlier: 4.581A pdb=" N HIS Z 34 " --> pdb=" O GLN Z 9 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N MET Z 54 " --> pdb=" O THR Z 10 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'a' and resid 20 through 25 removed outlier: 4.773A pdb=" N ASN a 20 " --> pdb=" O CYS a 16 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'c' and resid 19 through 24 removed outlier: 6.164A pdb=" N HIS c 19 " --> pdb=" O SER c 13 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N ILE c 48 " --> pdb=" O SER c 14 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N LEU c 34 " --> pdb=" O GLU c 51 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'e' and resid 22 through 25 removed outlier: 5.227A pdb=" N PHE e 22 " --> pdb=" O VAL e 50 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'f' and resid 13 through 19 removed outlier: 8.436A pdb=" N ASN f 13 " --> pdb=" O SER f 28 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N SER f 28 " --> pdb=" O ASN f 13 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'g' and resid 15 through 18 removed outlier: 5.806A pdb=" N HIS g 15 " --> pdb=" O ILE g 41 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N HIS g 39 " --> pdb=" O GLY g 17 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'g' and resid 89 through 93 Processing sheet with id= 49, first strand: chain 'h' and resid 54 through 59 Processing sheet with id= 50, first strand: chain 'h' and resid 164 through 169 removed outlier: 5.392A pdb=" N ARG h 164 " --> pdb=" O GLY h 155 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N ASP h 181 " --> pdb=" O LYS h 204 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'i' and resid 141 through 145 removed outlier: 6.532A pdb=" N MET i 178 " --> pdb=" O ILE i 145 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'j' and resid 11 through 16 removed outlier: 6.735A pdb=" N LEU j 36 " --> pdb=" O ILE j 16 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'j' and resid 84 through 88 removed outlier: 6.271A pdb=" N ASN j 122 " --> pdb=" O ALA j 99 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'j' and resid 33 through 41 removed outlier: 6.800A pdb=" N ARG j 45 " --> pdb=" O ASP j 41 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'k' and resid 38 through 41 removed outlier: 4.435A pdb=" N HIS k 3 " --> pdb=" O THR k 92 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'k' and resid 43 through 47 removed outlier: 7.221A pdb=" N HIS k 55 " --> pdb=" O LEU k 47 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'l' and resid 72 through 79 removed outlier: 6.688A pdb=" N THR l 72 " --> pdb=" O VAL l 91 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N TYR l 85 " --> pdb=" O ARG l 78 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'm' and resid 23 through 28 removed outlier: 6.461A pdb=" N ALA m 23 " --> pdb=" O LEU m 63 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP m 48 " --> pdb=" O THR m 62 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'm' and resid 74 through 77 removed outlier: 3.683A pdb=" N CYS m 127 " --> pdb=" O VAL m 103 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VAL m 103 " --> pdb=" O ILE m 126 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N ILE m 85 " --> pdb=" O ILE m 125 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'n' and resid 5 through 11 Processing sheet with id= 61, first strand: chain 'o' and resid 36 through 40 Processing sheet with id= 62, first strand: chain 'o' and resid 44 through 53 removed outlier: 7.887A pdb=" N ALA o 61 " --> pdb=" O ILE o 53 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'p' and resid 42 through 45 removed outlier: 4.160A pdb=" N ASN p 29 " --> pdb=" O SER p 26 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'q' and resid 29 through 34 removed outlier: 4.543A pdb=" N SER q 78 " --> pdb=" O CYS q 34 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N LEU q 81 " --> pdb=" O VAL q 98 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N HIS q 96 " --> pdb=" O ARG q 83 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'q' and resid 35 through 42 removed outlier: 6.973A pdb=" N ALA q 48 " --> pdb=" O PRO q 42 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N LYS q 51 " --> pdb=" O ILE q 67 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'u' and resid 4 through 10 removed outlier: 6.080A pdb=" N ASN u 40 " --> pdb=" O PRO u 15 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N TYR u 17 " --> pdb=" O PHE u 38 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N PHE u 38 " --> pdb=" O TYR u 17 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N VAL u 19 " --> pdb=" O VAL u 36 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'v' and resid 7 through 11 removed outlier: 7.054A pdb=" N GLU v 60 " --> pdb=" O VAL v 76 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'v' and resid 19 through 30 No H-bonds generated for sheet with id= 68 Processing sheet with id= 69, first strand: chain 'x' and resid 47 through 52 removed outlier: 4.253A pdb=" N LEU x 47 " --> pdb=" O VAL x 62 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'W' and resid 34 through 37 removed outlier: 4.501A pdb=" N SER W 35 " --> pdb=" O ALA W 61 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N LEU W 59 " --> pdb=" O ILE W 37 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N THR W 58 " --> pdb=" O GLY W 54 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N ASN W 50 " --> pdb=" O LYS W 62 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'W' and resid 45 through 48 1985 hydrogen bonds defined for protein. 5862 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3895 hydrogen bonds 6092 hydrogen bond angles 0 basepair planarities 1551 basepair parallelities 2639 stacking parallelities Total time for adding SS restraints: 226.61 Time building geometry restraints manager: 71.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.08 - 1.23: 4292 1.23 - 1.38: 52782 1.38 - 1.54: 89365 1.54 - 1.69: 10139 1.69 - 1.84: 266 Bond restraints: 156844 Sorted by residual: bond pdb=" N13 KKL 13301 " pdb=" N14 KKL 13301 " ideal model delta sigma weight residual 1.370 1.727 -0.357 2.00e-02 2.50e+03 3.19e+02 bond pdb=" N PRO q 42 " pdb=" CA PRO q 42 " ideal model delta sigma weight residual 1.469 1.696 -0.227 1.28e-02 6.10e+03 3.15e+02 bond pdb=" C5 5MU 5 54 " pdb=" C6 5MU 5 54 " ideal model delta sigma weight residual 1.155 1.451 -0.296 2.00e-02 2.50e+03 2.19e+02 bond pdb=" C5 5MU 1 747 " pdb=" C6 5MU 1 747 " ideal model delta sigma weight residual 1.155 1.443 -0.288 2.00e-02 2.50e+03 2.07e+02 bond pdb=" C5 5MU 11939 " pdb=" C6 5MU 11939 " ideal model delta sigma weight residual 1.155 1.442 -0.287 2.00e-02 2.50e+03 2.06e+02 ... (remaining 156839 not shown) Histogram of bond angle deviations from ideal: 93.55 - 110.82: 90154 110.82 - 128.10: 136619 128.10 - 145.38: 7949 145.38 - 162.66: 0 162.66 - 179.94: 1 Bond angle restraints: 234723 Sorted by residual: angle pdb=" O3' C 21383 " pdb=" C3' C 21383 " pdb=" C2' C 21383 " ideal model delta sigma weight residual 113.70 141.78 -28.08 1.50e+00 4.44e-01 3.50e+02 angle pdb=" C THR q 41 " pdb=" N PRO q 42 " pdb=" CA PRO q 42 " ideal model delta sigma weight residual 119.84 139.64 -19.80 1.25e+00 6.40e-01 2.51e+02 angle pdb=" C4' G 21276 " pdb=" C3' G 21276 " pdb=" O3' G 21276 " ideal model delta sigma weight residual 113.00 93.55 19.45 1.50e+00 4.44e-01 1.68e+02 angle pdb=" C3' C 21383 " pdb=" O3' C 21383 " pdb=" P C 21384 " ideal model delta sigma weight residual 120.20 134.55 -14.35 1.50e+00 4.44e-01 9.16e+01 angle pdb=" CA PRO q 42 " pdb=" N PRO q 42 " pdb=" CD PRO q 42 " ideal model delta sigma weight residual 112.00 101.00 11.00 1.40e+00 5.10e-01 6.17e+01 ... (remaining 234718 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 87775 35.97 - 71.95: 11298 71.95 - 107.92: 1250 107.92 - 143.90: 14 143.90 - 179.87: 45 Dihedral angle restraints: 100382 sinusoidal: 84110 harmonic: 16272 Sorted by residual: dihedral pdb=" CA ALA k 95 " pdb=" C ALA k 95 " pdb=" N VAL k 96 " pdb=" CA VAL k 96 " ideal model delta harmonic sigma weight residual 180.00 -91.13 -88.87 0 5.00e+00 4.00e-02 3.16e+02 dihedral pdb=" CA GLY J 82 " pdb=" C GLY J 82 " pdb=" N GLY J 83 " pdb=" CA GLY J 83 " ideal model delta harmonic sigma weight residual -180.00 -93.68 -86.32 0 5.00e+00 4.00e-02 2.98e+02 dihedral pdb=" CA GLY u 10 " pdb=" C GLY u 10 " pdb=" N ALA u 11 " pdb=" CA ALA u 11 " ideal model delta harmonic sigma weight residual 180.00 97.76 82.24 0 5.00e+00 4.00e-02 2.71e+02 ... (remaining 100379 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.326: 29899 0.326 - 0.651: 8 0.651 - 0.977: 0 0.977 - 1.302: 0 1.302 - 1.628: 1 Chirality restraints: 29908 Sorted by residual: chirality pdb=" C3' C 21383 " pdb=" C4' C 21383 " pdb=" O3' C 21383 " pdb=" C2' C 21383 " both_signs ideal model delta sigma weight residual False -2.48 -0.85 -1.63 2.00e-01 2.50e+01 6.62e+01 chirality pdb=" CA PRO q 42 " pdb=" N PRO q 42 " pdb=" C PRO q 42 " pdb=" CB PRO q 42 " both_signs ideal model delta sigma weight residual False 2.72 3.30 -0.59 2.00e-01 2.50e+01 8.57e+00 chirality pdb=" C3' U 11379 " pdb=" C4' U 11379 " pdb=" O3' U 11379 " pdb=" C2' U 11379 " both_signs ideal model delta sigma weight residual False -2.48 -2.10 -0.38 2.00e-01 2.50e+01 3.59e+00 ... (remaining 29905 not shown) Planarity restraints: 12506 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 2MG 21516 " 0.042 2.00e-02 2.50e+03 5.88e-01 7.79e+03 pdb=" C4' 2MG 21516 " 0.443 2.00e-02 2.50e+03 pdb=" O4' 2MG 21516 " 0.652 2.00e-02 2.50e+03 pdb=" C3' 2MG 21516 " -0.597 2.00e-02 2.50e+03 pdb=" O3' 2MG 21516 " -0.603 2.00e-02 2.50e+03 pdb=" C2' 2MG 21516 " -0.201 2.00e-02 2.50e+03 pdb=" O2' 2MG 21516 " 0.938 2.00e-02 2.50e+03 pdb=" C1' 2MG 21516 " 0.222 2.00e-02 2.50e+03 pdb=" N9 2MG 21516 " -0.895 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG 12445 " 0.002 2.00e-02 2.50e+03 5.88e-01 7.77e+03 pdb=" C4' 2MG 12445 " 0.459 2.00e-02 2.50e+03 pdb=" O4' 2MG 12445 " 0.820 2.00e-02 2.50e+03 pdb=" C3' 2MG 12445 " -0.585 2.00e-02 2.50e+03 pdb=" O3' 2MG 12445 " -0.515 2.00e-02 2.50e+03 pdb=" C2' 2MG 12445 " -0.273 2.00e-02 2.50e+03 pdb=" O2' 2MG 12445 " 0.819 2.00e-02 2.50e+03 pdb=" C1' 2MG 12445 " 0.191 2.00e-02 2.50e+03 pdb=" N9 2MG 12445 " -0.916 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 5MC 21407 " -0.037 2.00e-02 2.50e+03 5.72e-01 7.36e+03 pdb=" C4' 5MC 21407 " -0.445 2.00e-02 2.50e+03 pdb=" O4' 5MC 21407 " -0.617 2.00e-02 2.50e+03 pdb=" C3' 5MC 21407 " 0.585 2.00e-02 2.50e+03 pdb=" O3' 5MC 21407 " 0.586 2.00e-02 2.50e+03 pdb=" C2' 5MC 21407 " 0.206 2.00e-02 2.50e+03 pdb=" O2' 5MC 21407 " -0.912 2.00e-02 2.50e+03 pdb=" C1' 5MC 21407 " -0.232 2.00e-02 2.50e+03 pdb=" N1 5MC 21407 " 0.866 2.00e-02 2.50e+03 ... (remaining 12503 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.58: 2592 2.58 - 3.16: 106818 3.16 - 3.74: 318342 3.74 - 4.32: 408543 4.32 - 4.90: 536805 Nonbonded interactions: 1373100 Sorted by model distance: nonbonded pdb=" O2' G 12447 " pdb=" OP2 U 12500 " model vdw 2.005 2.440 nonbonded pdb=" O2' C 12452 " pdb=" N23 KKL 13301 " model vdw 2.007 2.520 nonbonded pdb=" O4' U 21126 " pdb=" O2 C 21281 " model vdw 2.126 3.040 nonbonded pdb=" OE1 GLN V 51 " pdb=" OH TYR V 57 " model vdw 2.217 2.440 nonbonded pdb=" O2' G 1 370 " pdb=" OP1 G 1 424 " model vdw 2.225 2.440 ... (remaining 1373095 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: 4.250 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: 0.100 Extract box with map and model: 17.190 Check model and map are aligned: 1.510 Set scattering table: 0.960 Process input model: 521.330 Find NCS groups from input model: 2.780 Set up NCS constraints: 0.330 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 550.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 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 : 0.008 0.357 156844 Z= 0.461 Angle : 0.907 28.077 234723 Z= 0.482 Chirality : 0.048 1.628 29908 Planarity : 0.018 0.588 12506 Dihedral : 23.855 179.871 89886 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 1.12 % Allowed : 4.22 % Favored : 94.66 % Rotamer: Outliers : 0.30 % Allowed : 8.71 % Favored : 90.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % Cis-general : 0.00 % Twisted Proline : 5.41 % Twisted General : 5.40 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.33 (0.09), residues: 5614 helix: -2.25 (0.09), residues: 1966 sheet: -1.97 (0.14), residues: 1057 loop : -2.15 (0.10), residues: 2591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP g 23 HIS 0.014 0.002 HIS p 118 PHE 0.028 0.002 PHE G 47 TYR 0.045 0.002 TYR D 35 ARG 0.017 0.001 ARG o 89 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11228 Ramachandran restraints generated. 5614 Oldfield, 0 Emsley, 5614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11228 Ramachandran restraints generated. 5614 Oldfield, 0 Emsley, 5614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1937 residues out of total 4672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 1923 time to evaluate : 6.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 114 ASP cc_start: 0.8620 (m-30) cc_final: 0.8357 (m-30) REVERT: B 117 GLN cc_start: 0.8690 (tt0) cc_final: 0.8305 (tp-100) REVERT: B 201 MET cc_start: 0.8752 (ptt) cc_final: 0.8433 (ptm) REVERT: B 203 ARG cc_start: 0.8443 (ptp-110) cc_final: 0.8183 (ptp90) REVERT: C 126 ASN cc_start: 0.8876 (m-40) cc_final: 0.8575 (m110) REVERT: C 128 ARG cc_start: 0.8456 (mtt90) cc_final: 0.7449 (mtp180) REVERT: C 137 SER cc_start: 0.9000 (m) cc_final: 0.8652 (p) REVERT: C 181 ASP cc_start: 0.8249 (t70) cc_final: 0.7934 (t0) REVERT: C 199 SER cc_start: 0.9189 (m) cc_final: 0.8971 (m) REVERT: D 123 LYS cc_start: 0.8686 (tptt) cc_final: 0.8472 (tppt) REVERT: D 136 GLN cc_start: 0.9385 (tp-100) cc_final: 0.8774 (tp-100) REVERT: D 140 ASP cc_start: 0.8759 (m-30) cc_final: 0.8399 (m-30) REVERT: D 156 ASN cc_start: 0.8964 (m-40) cc_final: 0.8496 (m-40) REVERT: D 168 ASP cc_start: 0.8307 (t0) cc_final: 0.7896 (t0) REVERT: E 38 MET cc_start: 0.8244 (mtp) cc_final: 0.7750 (mtt) REVERT: E 99 PHE cc_start: 0.9138 (t80) cc_final: 0.8923 (t80) REVERT: E 114 PHE cc_start: 0.8358 (t80) cc_final: 0.8139 (t80) REVERT: E 122 PHE cc_start: 0.7830 (m-80) cc_final: 0.7223 (m-80) REVERT: E 138 PHE cc_start: 0.8914 (m-80) cc_final: 0.8516 (m-80) REVERT: F 26 ILE cc_start: 0.8306 (tt) cc_final: 0.7991 (mp) REVERT: F 58 TYR cc_start: 0.7454 (m-80) cc_final: 0.6910 (m-80) REVERT: F 83 PHE cc_start: 0.8483 (m-80) cc_final: 0.8116 (m-80) REVERT: F 137 ASP cc_start: 0.8781 (t0) cc_final: 0.8515 (t0) REVERT: F 149 ARG cc_start: 0.8476 (ttt-90) cc_final: 0.8263 (ttp80) REVERT: F 151 TYR cc_start: 0.9016 (m-80) cc_final: 0.8646 (m-80) REVERT: G 1 MET cc_start: 0.5839 (ttt) cc_final: 0.5540 (ttt) REVERT: G 27 ARG cc_start: 0.9012 (ttp-110) cc_final: 0.8804 (ttm110) REVERT: J 16 TYR cc_start: 0.8943 (m-80) cc_final: 0.8612 (m-80) REVERT: J 31 GLU cc_start: 0.8751 (tp30) cc_final: 0.8499 (tp30) REVERT: J 96 ARG cc_start: 0.8641 (ttt-90) cc_final: 0.8345 (mmm-85) REVERT: J 106 LYS cc_start: 0.9347 (tttp) cc_final: 0.9017 (ttmm) REVERT: J 118 MET cc_start: 0.8535 (mtt) cc_final: 0.8216 (mtt) REVERT: K 4 GLU cc_start: 0.8590 (mp0) cc_final: 0.8368 (mp0) REVERT: K 12 ASP cc_start: 0.8549 (p0) cc_final: 0.8330 (p0) REVERT: K 53 LYS cc_start: 0.9004 (mttm) cc_final: 0.8368 (mttp) REVERT: K 88 ASN cc_start: 0.8836 (t0) cc_final: 0.8253 (t0) REVERT: L 76 GLU cc_start: 0.7861 (mt-10) cc_final: 0.7150 (mt-10) REVERT: L 81 ASP cc_start: 0.8769 (t0) cc_final: 0.8451 (t0) REVERT: L 105 ILE cc_start: 0.9391 (mm) cc_final: 0.9085 (mm) REVERT: L 143 GLU cc_start: 0.8661 (pt0) cc_final: 0.8288 (pm20) REVERT: M 3 GLN cc_start: 0.9056 (tt0) cc_final: 0.8766 (tt0) REVERT: M 22 GLN cc_start: 0.8543 (mm-40) cc_final: 0.8194 (mm-40) REVERT: M 25 ASP cc_start: 0.8856 (m-30) cc_final: 0.8625 (m-30) REVERT: M 60 GLN cc_start: 0.8589 (mm110) cc_final: 0.7901 (mm-40) REVERT: M 103 TYR cc_start: 0.8947 (m-80) cc_final: 0.8582 (m-80) REVERT: M 105 MET cc_start: 0.8440 (ttm) cc_final: 0.8015 (mtt) REVERT: M 110 GLU cc_start: 0.8966 (tt0) cc_final: 0.8427 (tm-30) REVERT: M 119 LEU cc_start: 0.9644 (mt) cc_final: 0.9190 (mp) REVERT: M 127 LYS cc_start: 0.9166 (ttmm) cc_final: 0.8907 (ttpt) REVERT: N 9 GLN cc_start: 0.8556 (tt0) cc_final: 0.8231 (tt0) REVERT: N 20 MET cc_start: 0.9323 (ttp) cc_final: 0.8987 (ttp) REVERT: N 72 ASP cc_start: 0.8124 (t0) cc_final: 0.7740 (t70) REVERT: N 107 ASN cc_start: 0.9410 (t0) cc_final: 0.9153 (t0) REVERT: O 15 ARG cc_start: 0.8917 (mtt180) cc_final: 0.8498 (mmt90) REVERT: O 38 GLN cc_start: 0.8907 (pm20) cc_final: 0.7982 (pm20) REVERT: O 58 ILE cc_start: 0.8679 (mp) cc_final: 0.8278 (mp) REVERT: O 68 LYS cc_start: 0.8542 (mmtp) cc_final: 0.8314 (mmtp) REVERT: O 80 GLU cc_start: 0.9047 (mt-10) cc_final: 0.8748 (mm-30) REVERT: O 93 ASP cc_start: 0.7989 (t0) cc_final: 0.6583 (t0) REVERT: O 98 GLN cc_start: 0.8402 (mm110) cc_final: 0.8023 (mm110) REVERT: P 6 LYS cc_start: 0.8807 (mtpt) cc_final: 0.8558 (mptt) REVERT: P 29 LYS cc_start: 0.8920 (mttt) cc_final: 0.8629 (mtpp) REVERT: P 37 LYS cc_start: 0.9088 (ttmt) cc_final: 0.8761 (mppt) REVERT: P 82 ASP cc_start: 0.9046 (t70) cc_final: 0.8773 (t0) REVERT: Q 102 ASP cc_start: 0.8411 (t0) cc_final: 0.8078 (t0) REVERT: R 2 TYR cc_start: 0.9332 (p90) cc_final: 0.8993 (p90) REVERT: R 6 GLN cc_start: 0.7823 (tp-100) cc_final: 0.7616 (tm-30) REVERT: R 18 GLN cc_start: 0.8565 (mp10) cc_final: 0.8307 (mp10) REVERT: R 34 GLU cc_start: 0.8531 (mm-30) cc_final: 0.8106 (mm-30) REVERT: R 48 LYS cc_start: 0.9272 (ptpp) cc_final: 0.8909 (ptpp) REVERT: R 62 GLU cc_start: 0.8154 (tp30) cc_final: 0.7556 (tp30) REVERT: R 101 ILE cc_start: 0.8372 (pt) cc_final: 0.7984 (pt) REVERT: S 2 GLU cc_start: 0.8915 (mp0) cc_final: 0.8704 (mp0) REVERT: S 51 LEU cc_start: 0.9323 (tp) cc_final: 0.9073 (tp) REVERT: S 52 GLU cc_start: 0.8816 (mt-10) cc_final: 0.8256 (mt-10) REVERT: S 62 ASP cc_start: 0.8749 (t0) cc_final: 0.8053 (t0) REVERT: S 73 LYS cc_start: 0.8938 (mttt) cc_final: 0.8657 (mttm) REVERT: S 104 THR cc_start: 0.9405 (m) cc_final: 0.8755 (p) REVERT: S 109 ASP cc_start: 0.8806 (p0) cc_final: 0.8246 (p0) REVERT: T 91 GLN cc_start: 0.8927 (mm-40) cc_final: 0.8441 (mm-40) REVERT: U 9 ASP cc_start: 0.8616 (m-30) cc_final: 0.8378 (m-30) REVERT: U 10 GLU cc_start: 0.8408 (tt0) cc_final: 0.7779 (tm-30) REVERT: U 11 VAL cc_start: 0.9597 (m) cc_final: 0.8868 (m) REVERT: U 26 LYS cc_start: 0.9052 (mmmt) cc_final: 0.8631 (mmmm) REVERT: U 29 LEU cc_start: 0.9207 (mm) cc_final: 0.8925 (mm) REVERT: U 40 ASN cc_start: 0.8514 (m-40) cc_final: 0.8205 (m-40) REVERT: U 41 LEU cc_start: 0.8964 (mt) cc_final: 0.8716 (mt) REVERT: U 60 GLU cc_start: 0.8236 (tt0) cc_final: 0.7992 (tt0) REVERT: U 96 PHE cc_start: 0.9236 (m-80) cc_final: 0.8751 (m-10) REVERT: U 103 ILE cc_start: 0.9252 (mt) cc_final: 0.9023 (mt) REVERT: V 50 MET cc_start: 0.9382 (mtt) cc_final: 0.9175 (mtp) REVERT: V 75 GLN cc_start: 0.9235 (tp40) cc_final: 0.8944 (tp40) REVERT: V 82 TYR cc_start: 0.9310 (p90) cc_final: 0.8968 (p90) REVERT: V 83 LYS cc_start: 0.9492 (mttt) cc_final: 0.9223 (mttp) REVERT: V 90 ASP cc_start: 0.8974 (m-30) cc_final: 0.8626 (m-30) REVERT: X 35 SER cc_start: 0.9372 (m) cc_final: 0.9133 (t) REVERT: X 41 GLU cc_start: 0.7398 (tp30) cc_final: 0.7187 (tp30) REVERT: X 60 ASP cc_start: 0.8998 (m-30) cc_final: 0.8759 (m-30) REVERT: X 70 GLU cc_start: 0.8542 (tm-30) cc_final: 0.8061 (tm-30) REVERT: X 77 LYS cc_start: 0.8792 (mmmt) cc_final: 0.8369 (mmmm) REVERT: Y 16 THR cc_start: 0.9550 (p) cc_final: 0.9341 (p) REVERT: Y 29 ARG cc_start: 0.8962 (ttp-110) cc_final: 0.8730 (ttp-170) REVERT: Y 31 GLN cc_start: 0.9342 (mt0) cc_final: 0.9091 (mt0) REVERT: Y 45 GLN cc_start: 0.9000 (mt0) cc_final: 0.8748 (mt0) REVERT: Y 49 ASP cc_start: 0.9002 (m-30) cc_final: 0.8769 (m-30) REVERT: b 12 LYS cc_start: 0.8809 (mmmt) cc_final: 0.8448 (mmmt) REVERT: b 31 ASP cc_start: 0.8576 (t70) cc_final: 0.8343 (t0) REVERT: b 36 GLU cc_start: 0.8373 (pt0) cc_final: 0.8078 (pt0) REVERT: b 46 ASP cc_start: 0.9113 (m-30) cc_final: 0.8894 (m-30) REVERT: b 48 TYR cc_start: 0.8729 (m-80) cc_final: 0.7963 (m-10) REVERT: c 5 ILE cc_start: 0.9105 (tp) cc_final: 0.8675 (mm) REVERT: c 7 GLU cc_start: 0.8240 (tm-30) cc_final: 0.7791 (tm-30) REVERT: c 34 LEU cc_start: 0.8067 (tp) cc_final: 0.7735 (tp) REVERT: c 37 LYS cc_start: 0.9096 (tttt) cc_final: 0.8531 (ttmt) REVERT: c 39 PHE cc_start: 0.8842 (t80) cc_final: 0.8215 (t80) REVERT: d 2 LYS cc_start: 0.9391 (tttt) cc_final: 0.9168 (tttm) REVERT: e 4 ILE cc_start: 0.9381 (mt) cc_final: 0.8984 (mt) REVERT: e 64 TYR cc_start: 0.8203 (m-80) cc_final: 0.7323 (m-80) REVERT: f 35 GLN cc_start: 0.9078 (mt0) cc_final: 0.8830 (mt0) REVERT: g 6 MET cc_start: 0.7741 (mmp) cc_final: 0.7369 (mmm) REVERT: g 23 TRP cc_start: 0.8071 (p-90) cc_final: 0.7392 (p-90) REVERT: g 24 ASN cc_start: 0.5173 (t0) cc_final: 0.4243 (t0) REVERT: g 27 MET cc_start: 0.7920 (mmt) cc_final: 0.7620 (mmt) REVERT: g 93 ASN cc_start: 0.7348 (p0) cc_final: 0.6967 (p0) REVERT: g 100 MET cc_start: 0.7869 (ptp) cc_final: 0.7391 (mtm) REVERT: g 103 ASN cc_start: 0.7161 (t0) cc_final: 0.6864 (t0) REVERT: g 127 ASP cc_start: 0.6910 (m-30) cc_final: 0.5861 (m-30) REVERT: g 132 LYS cc_start: 0.5902 (mttm) cc_final: 0.5606 (mmtm) REVERT: g 157 LEU cc_start: 0.7727 (tt) cc_final: 0.7329 (mm) REVERT: g 165 ASP cc_start: 0.5031 (t0) cc_final: 0.4722 (t0) REVERT: g 174 LYS cc_start: 0.8138 (tttt) cc_final: 0.7913 (tptp) REVERT: g 175 GLU cc_start: 0.7781 (mt-10) cc_final: 0.7566 (mt-10) REVERT: g 179 LEU cc_start: 0.7743 (mm) cc_final: 0.7405 (mm) REVERT: g 204 ASP cc_start: 0.7401 (p0) cc_final: 0.7200 (p0) REVERT: h 25 ASN cc_start: 0.7951 (t0) cc_final: 0.7708 (t0) REVERT: h 110 GLU cc_start: 0.8866 (mt-10) cc_final: 0.8396 (mt-10) REVERT: h 140 ASN cc_start: 0.9265 (m110) cc_final: 0.8832 (m-40) REVERT: h 152 GLU cc_start: 0.8209 (tm-30) cc_final: 0.7618 (tm-30) REVERT: h 168 TYR cc_start: 0.8739 (m-80) cc_final: 0.8438 (m-80) REVERT: h 183 ASP cc_start: 0.8599 (t0) cc_final: 0.7771 (t0) REVERT: h 185 ASN cc_start: 0.8782 (t0) cc_final: 0.8466 (t0) REVERT: h 201 TRP cc_start: 0.8431 (m-10) cc_final: 0.8213 (m-10) REVERT: i 51 TYR cc_start: 0.8972 (t80) cc_final: 0.8723 (t80) REVERT: i 55 LEU cc_start: 0.9306 (tt) cc_final: 0.8998 (tt) REVERT: i 100 ASN cc_start: 0.8457 (t0) cc_final: 0.8197 (t0) REVERT: i 104 ARG cc_start: 0.8869 (mmm-85) cc_final: 0.8655 (mmt90) REVERT: i 141 ASP cc_start: 0.7930 (m-30) cc_final: 0.7454 (m-30) REVERT: j 41 ASP cc_start: 0.8847 (p0) cc_final: 0.8253 (p0) REVERT: j 128 TYR cc_start: 0.9030 (m-80) cc_final: 0.8612 (m-80) REVERT: j 141 ILE cc_start: 0.9392 (mt) cc_final: 0.9095 (mt) REVERT: j 142 ASP cc_start: 0.8437 (t70) cc_final: 0.7539 (t70) REVERT: j 145 GLU cc_start: 0.8257 (pp20) cc_final: 0.7881 (pp20) REVERT: k 3 HIS cc_start: 0.8455 (m90) cc_final: 0.8230 (m90) REVERT: k 24 ARG cc_start: 0.8819 (mtt90) cc_final: 0.8616 (mtt90) REVERT: k 37 HIS cc_start: 0.8432 (m-70) cc_final: 0.7318 (m-70) REVERT: k 46 GLN cc_start: 0.8241 (tp40) cc_final: 0.7969 (tp40) REVERT: k 61 LEU cc_start: 0.8106 (tt) cc_final: 0.7871 (mp) REVERT: l 136 LYS cc_start: 0.8913 (pttp) cc_final: 0.8704 (ptmm) REVERT: l 142 HIS cc_start: 0.8802 (m90) cc_final: 0.7984 (m-70) REVERT: l 148 ASN cc_start: 0.7559 (p0) cc_final: 0.7242 (p0) REVERT: m 5 ASP cc_start: 0.8956 (t0) cc_final: 0.7994 (t0) REVERT: m 43 GLU cc_start: 0.8498 (tp30) cc_final: 0.7808 (mm-30) REVERT: m 114 ARG cc_start: 0.8283 (ttp80) cc_final: 0.8046 (ptm-80) REVERT: m 118 GLN cc_start: 0.8808 (mt0) cc_final: 0.8498 (mt0) REVERT: m 127 CYS cc_start: 0.9152 (p) cc_final: 0.8876 (p) REVERT: n 57 MET cc_start: 0.8314 (mmm) cc_final: 0.7685 (ttm) REVERT: n 84 THR cc_start: 0.9390 (p) cc_final: 0.9157 (p) REVERT: n 90 TYR cc_start: 0.8951 (t80) cc_final: 0.8716 (t80) REVERT: n 99 ARG cc_start: 0.8606 (mmt180) cc_final: 0.8251 (mmt90) REVERT: n 112 GLU cc_start: 0.7656 (tt0) cc_final: 0.7165 (tt0) REVERT: o 10 LEU cc_start: 0.9066 (mm) cc_final: 0.8809 (mm) REVERT: o 49 PHE cc_start: 0.8131 (m-80) cc_final: 0.7840 (m-80) REVERT: p 31 ILE cc_start: 0.9309 (mt) cc_final: 0.9082 (mt) REVERT: p 34 ILE cc_start: 0.9273 (mm) cc_final: 0.9055 (mm) REVERT: p 68 GLU cc_start: 0.8629 (mm-30) cc_final: 0.8260 (mm-30) REVERT: p 101 ASN cc_start: 0.8981 (t0) cc_final: 0.8748 (p0) REVERT: q 7 LEU cc_start: 0.9550 (mt) cc_final: 0.9340 (mt) REVERT: q 24 LEU cc_start: 0.9047 (mt) cc_final: 0.8472 (mt) REVERT: q 29 GLN cc_start: 0.9404 (mp10) cc_final: 0.9145 (mp10) REVERT: q 43 LYS cc_start: 0.6869 (mmtp) cc_final: 0.6108 (mmmm) REVERT: q 57 LEU cc_start: 0.9028 (mt) cc_final: 0.8760 (mp) REVERT: q 59 ASN cc_start: 0.9059 (p0) cc_final: 0.8434 (p0) REVERT: q 75 GLN cc_start: 0.9087 (pt0) cc_final: 0.8745 (pm20) REVERT: r 7 ILE cc_start: 0.9096 (tp) cc_final: 0.8828 (pt) REVERT: r 23 TYR cc_start: 0.8389 (t80) cc_final: 0.7674 (t80) REVERT: r 42 ASP cc_start: 0.8521 (p0) cc_final: 0.7830 (t0) REVERT: r 43 VAL cc_start: 0.8635 (p) cc_final: 0.8433 (m) REVERT: r 70 ARG cc_start: 0.8875 (mmt180) cc_final: 0.8624 (mtt-85) REVERT: r 86 TYR cc_start: 0.8427 (t80) cc_final: 0.8064 (t80) REVERT: s 4 GLN cc_start: 0.8218 (mm110) cc_final: 0.7775 (mm-40) REVERT: s 33 ASP cc_start: 0.8911 (t0) cc_final: 0.8546 (p0) REVERT: s 52 PRO cc_start: 0.6816 (Cg_exo) cc_final: 0.6545 (Cg_endo) REVERT: t 24 SER cc_start: 0.9098 (m) cc_final: 0.8412 (t) REVERT: t 26 GLU cc_start: 0.8476 (pm20) cc_final: 0.7637 (pm20) REVERT: t 45 GLU cc_start: 0.8900 (tt0) cc_final: 0.8602 (tt0) REVERT: t 63 ARG cc_start: 0.9048 (ttp-170) cc_final: 0.8669 (ttp-170) REVERT: t 64 ARG cc_start: 0.8781 (mmm160) cc_final: 0.7947 (tpp-160) REVERT: t 65 LYS cc_start: 0.9320 (mttt) cc_final: 0.9068 (mttm) REVERT: t 68 ASP cc_start: 0.8811 (m-30) cc_final: 0.8273 (m-30) REVERT: t 80 GLN cc_start: 0.8186 (tm-30) cc_final: 0.7929 (tm-30) REVERT: t 84 ARG cc_start: 0.9040 (tpp80) cc_final: 0.8751 (tpp80) REVERT: u 47 GLU cc_start: 0.8310 (pp20) cc_final: 0.8028 (pp20) REVERT: u 63 GLN cc_start: 0.8754 (mm-40) cc_final: 0.8282 (mm-40) REVERT: u 66 THR cc_start: 0.9151 (t) cc_final: 0.8923 (p) REVERT: v 18 GLU cc_start: 0.8137 (pt0) cc_final: 0.7902 (pt0) REVERT: v 55 ILE cc_start: 0.9405 (mp) cc_final: 0.9063 (mm) REVERT: v 57 ASP cc_start: 0.7252 (m-30) cc_final: 0.6836 (m-30) REVERT: v 61 ILE cc_start: 0.8930 (pt) cc_final: 0.8614 (pt) REVERT: v 73 TRP cc_start: 0.9251 (m100) cc_final: 0.8163 (m100) REVERT: v 80 GLU cc_start: 0.8758 (pp20) cc_final: 0.8546 (pp20) REVERT: v 81 LYS cc_start: 0.9001 (tptt) cc_final: 0.8784 (tppt) REVERT: w 35 GLU cc_start: 0.8253 (pp20) cc_final: 0.7911 (pp20) REVERT: w 50 LYS cc_start: 0.8795 (tttt) cc_final: 0.8444 (tttt) REVERT: w 57 ARG cc_start: 0.9286 (ttm110) cc_final: 0.9062 (ttm110) REVERT: w 61 ARG cc_start: 0.8994 (mtm-85) cc_final: 0.8756 (mtt90) REVERT: w 72 ASP cc_start: 0.8340 (p0) cc_final: 0.8065 (p0) REVERT: x 41 PHE cc_start: 0.7894 (m-80) cc_final: 0.7644 (m-10) REVERT: y 27 MET cc_start: 0.9129 (ttp) cc_final: 0.8770 (tmm) REVERT: y 48 GLN cc_start: 0.9072 (tp-100) cc_final: 0.8728 (tp-100) REVERT: y 54 MET cc_start: 0.9202 (tmm) cc_final: 0.8997 (tmm) REVERT: z 33 ARG cc_start: 0.7700 (ptp-110) cc_final: 0.7400 (ptt180) REVERT: W 16 SER cc_start: 0.9002 (m) cc_final: 0.8748 (p) REVERT: W 35 SER cc_start: 0.9318 (m) cc_final: 0.9109 (m) outliers start: 14 outliers final: 4 residues processed: 1936 average time/residue: 1.3051 time to fit residues: 4275.9587 Evaluate side-chains 1541 residues out of total 4672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1537 time to evaluate : 6.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain o residue 84 VAL Chi-restraints excluded: chain q residue 63 VAL Chi-restraints excluded: chain q residue 90 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1010 random chunks: chunk 852 optimal weight: 7.9990 chunk 765 optimal weight: 5.9990 chunk 424 optimal weight: 20.0000 chunk 261 optimal weight: 0.9990 chunk 516 optimal weight: 2.9990 chunk 408 optimal weight: 20.0000 chunk 791 optimal weight: 6.9990 chunk 306 optimal weight: 20.0000 chunk 481 optimal weight: 8.9990 chunk 589 optimal weight: 3.9990 chunk 917 optimal weight: 20.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 86 ASN B 90 ASN B 153 GLN C 36 GLN C 167 ASN C 173 GLN D 41 GLN D 90 GLN E 5 HIS E 21 ASN E 63 GLN F 20 ASN F 115 HIS G 43 ASN G 66 ASN G 128 HIS J 136 GLN L 93 ASN N 62 ASN O 98 GLN ** P 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 75 GLN S 7 HIS S 15 GLN S 61 ASN T 48 GLN T 72 GLN U 40 ASN U 45 HIS U 54 GLN ** U 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 24 ASN ** Y 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 36 GLN a 41 HIS ** g 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 190 ASN ** h 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 41 GLN h 140 ASN i 36 GLN i 40 GLN i 74 ASN i 131 ASN ** j 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 11 HIS k 46 GLN k 68 GLN o 56 HIS o 64 GLN ** o 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 64 GLN q 77 HIS q 112 GLN s 49 GLN t 35 GLN t 80 GLN w 54 GLN x 56 GLN y 3 ASN y 78 ASN W 12 ASN Total number of N/Q/H flips: 55 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 156844 Z= 0.245 Angle : 0.662 13.933 234723 Z= 0.356 Chirality : 0.036 0.391 29908 Planarity : 0.006 0.130 12506 Dihedral : 23.998 179.385 78634 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.05 % Favored : 96.81 % Rotamer: Outliers : 3.30 % Allowed : 18.94 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -1.46 (0.10), residues: 5614 helix: -0.25 (0.11), residues: 1992 sheet: -1.03 (0.15), residues: 1065 loop : -1.43 (0.11), residues: 2557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP k 42 HIS 0.009 0.001 HIS E 5 PHE 0.021 0.002 PHE k 8 TYR 0.029 0.002 TYR g 213 ARG 0.009 0.001 ARG v 27 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11228 Ramachandran restraints generated. 5614 Oldfield, 0 Emsley, 5614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11228 Ramachandran restraints generated. 5614 Oldfield, 0 Emsley, 5614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1820 residues out of total 4672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 1666 time to evaluate : 6.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 114 ASP cc_start: 0.8621 (m-30) cc_final: 0.8114 (m-30) REVERT: B 117 GLN cc_start: 0.8643 (tt0) cc_final: 0.8442 (tp-100) REVERT: B 130 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8437 (pp) REVERT: B 145 GLU cc_start: 0.8822 (mt-10) cc_final: 0.8288 (mt-10) REVERT: B 203 ARG cc_start: 0.8605 (ptp-110) cc_final: 0.8319 (ptp-110) REVERT: B 240 PHE cc_start: 0.9174 (t80) cc_final: 0.8955 (t80) REVERT: B 251 GLN cc_start: 0.8598 (tm-30) cc_final: 0.8040 (tm-30) REVERT: C 126 ASN cc_start: 0.8860 (m-40) cc_final: 0.8608 (m110) REVERT: C 128 ARG cc_start: 0.8334 (mtt90) cc_final: 0.7601 (mtp180) REVERT: C 137 SER cc_start: 0.9144 (m) cc_final: 0.8783 (p) REVERT: C 199 SER cc_start: 0.9126 (m) cc_final: 0.8903 (m) REVERT: D 136 GLN cc_start: 0.9248 (tp-100) cc_final: 0.8754 (tp40) REVERT: D 140 ASP cc_start: 0.8677 (m-30) cc_final: 0.8381 (m-30) REVERT: D 156 ASN cc_start: 0.9010 (m-40) cc_final: 0.8746 (m-40) REVERT: D 168 ASP cc_start: 0.8486 (t0) cc_final: 0.8157 (t70) REVERT: D 188 MET cc_start: 0.9330 (mmm) cc_final: 0.8851 (mtm) REVERT: E 42 GLU cc_start: 0.9256 (OUTLIER) cc_final: 0.8685 (pm20) REVERT: E 135 GLN cc_start: 0.8177 (pm20) cc_final: 0.7053 (pm20) REVERT: E 177 PHE cc_start: 0.6700 (m-10) cc_final: 0.6373 (m-80) REVERT: F 39 ASP cc_start: 0.8737 (p0) cc_final: 0.8498 (p0) REVERT: F 42 GLU cc_start: 0.8251 (mt-10) cc_final: 0.7971 (mp0) REVERT: F 58 TYR cc_start: 0.7382 (m-80) cc_final: 0.7029 (m-80) REVERT: F 83 PHE cc_start: 0.8494 (m-80) cc_final: 0.8033 (m-80) REVERT: F 88 GLN cc_start: 0.8692 (pt0) cc_final: 0.8468 (pt0) REVERT: F 137 ASP cc_start: 0.9003 (t0) cc_final: 0.8737 (t0) REVERT: F 147 ASP cc_start: 0.8840 (OUTLIER) cc_final: 0.8344 (t0) REVERT: F 155 GLU cc_start: 0.8174 (tm-30) cc_final: 0.7639 (tm-30) REVERT: F 167 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.8323 (pt0) REVERT: G 25 TYR cc_start: 0.8920 (t80) cc_final: 0.8698 (t80) REVERT: J 16 TYR cc_start: 0.9220 (m-80) cc_final: 0.8850 (m-80) REVERT: J 31 GLU cc_start: 0.8763 (tp30) cc_final: 0.8540 (tp30) REVERT: J 52 ASP cc_start: 0.8634 (m-30) cc_final: 0.8371 (m-30) REVERT: J 58 ASN cc_start: 0.9361 (m-40) cc_final: 0.8920 (m-40) REVERT: J 60 ASP cc_start: 0.8917 (p0) cc_final: 0.8569 (p0) REVERT: J 96 ARG cc_start: 0.8717 (ttt-90) cc_final: 0.8406 (mmm-85) REVERT: J 106 LYS cc_start: 0.9291 (tttp) cc_final: 0.9073 (ttmm) REVERT: K 12 ASP cc_start: 0.8546 (p0) cc_final: 0.8232 (p0) REVERT: K 88 ASN cc_start: 0.8671 (t0) cc_final: 0.8242 (t0) REVERT: K 103 VAL cc_start: 0.8995 (OUTLIER) cc_final: 0.8788 (m) REVERT: K 121 GLU cc_start: 0.8929 (tt0) cc_final: 0.8600 (tt0) REVERT: L 55 MET cc_start: 0.9169 (tpp) cc_final: 0.8730 (tpt) REVERT: L 81 ASP cc_start: 0.8873 (t0) cc_final: 0.8604 (t0) REVERT: M 3 GLN cc_start: 0.9103 (tt0) cc_final: 0.8835 (tt0) REVERT: M 47 GLU cc_start: 0.8609 (tp30) cc_final: 0.8261 (tp30) REVERT: M 65 ILE cc_start: 0.9455 (mt) cc_final: 0.9253 (mm) REVERT: M 110 GLU cc_start: 0.8838 (tt0) cc_final: 0.8257 (tm-30) REVERT: M 127 LYS cc_start: 0.9201 (ttmm) cc_final: 0.8953 (ttmm) REVERT: M 133 LYS cc_start: 0.8985 (tppt) cc_final: 0.8769 (tptt) REVERT: N 9 GLN cc_start: 0.8390 (tt0) cc_final: 0.8033 (tt0) REVERT: N 20 MET cc_start: 0.9342 (ttp) cc_final: 0.8932 (ttp) REVERT: N 53 THR cc_start: 0.9544 (OUTLIER) cc_final: 0.9119 (p) REVERT: N 72 ASP cc_start: 0.8285 (t70) cc_final: 0.8019 (t70) REVERT: N 94 TYR cc_start: 0.9416 (m-80) cc_final: 0.8930 (m-80) REVERT: N 95 THR cc_start: 0.9588 (m) cc_final: 0.9162 (p) REVERT: O 58 ILE cc_start: 0.8928 (mp) cc_final: 0.8639 (mp) REVERT: O 61 GLN cc_start: 0.8696 (mp10) cc_final: 0.8248 (mp10) REVERT: O 62 LEU cc_start: 0.9021 (mm) cc_final: 0.8619 (tp) REVERT: O 76 LYS cc_start: 0.9031 (mmmm) cc_final: 0.8777 (mmmt) REVERT: O 85 LYS cc_start: 0.9405 (mttt) cc_final: 0.9178 (ttmt) REVERT: O 93 ASP cc_start: 0.8323 (t0) cc_final: 0.7927 (t0) REVERT: O 98 GLN cc_start: 0.8306 (mm-40) cc_final: 0.8007 (mm110) REVERT: P 16 ASP cc_start: 0.8478 (p0) cc_final: 0.8228 (p0) REVERT: P 82 ASP cc_start: 0.8978 (t70) cc_final: 0.8679 (t0) REVERT: P 112 GLU cc_start: 0.7908 (pp20) cc_final: 0.7512 (pp20) REVERT: Q 102 ASP cc_start: 0.8532 (t0) cc_final: 0.8156 (t0) REVERT: Q 107 THR cc_start: 0.9390 (m) cc_final: 0.9057 (p) REVERT: R 2 TYR cc_start: 0.9446 (p90) cc_final: 0.9155 (p90) REVERT: R 34 GLU cc_start: 0.8548 (mm-30) cc_final: 0.8000 (mm-30) REVERT: R 37 GLU cc_start: 0.7794 (pm20) cc_final: 0.7516 (pm20) REVERT: R 94 THR cc_start: 0.9297 (m) cc_final: 0.8581 (p) REVERT: S 2 GLU cc_start: 0.8848 (mp0) cc_final: 0.8645 (mp0) REVERT: S 62 ASP cc_start: 0.8545 (t0) cc_final: 0.7988 (t0) REVERT: S 73 LYS cc_start: 0.8908 (mttt) cc_final: 0.8707 (mttt) REVERT: S 94 ASP cc_start: 0.7942 (m-30) cc_final: 0.7733 (m-30) REVERT: T 1 MET cc_start: 0.6684 (tpt) cc_final: 0.4160 (mmm) REVERT: T 24 MET cc_start: 0.8692 (tpt) cc_final: 0.8398 (tpp) REVERT: T 56 GLU cc_start: 0.9086 (mm-30) cc_final: 0.8764 (tp30) REVERT: T 91 GLN cc_start: 0.8963 (mm-40) cc_final: 0.8321 (mm-40) REVERT: U 7 ARG cc_start: 0.8412 (ttt-90) cc_final: 0.8121 (ttt-90) REVERT: U 10 GLU cc_start: 0.8343 (tt0) cc_final: 0.7872 (tm-30) REVERT: U 26 LYS cc_start: 0.8976 (mmmt) cc_final: 0.8361 (mmmm) REVERT: U 29 LEU cc_start: 0.9370 (mm) cc_final: 0.9119 (mm) REVERT: U 37 GLU cc_start: 0.8091 (tp30) cc_final: 0.7108 (tp30) REVERT: U 41 LEU cc_start: 0.8934 (mt) cc_final: 0.8565 (mt) REVERT: U 60 GLU cc_start: 0.8225 (tt0) cc_final: 0.7898 (tt0) REVERT: U 96 PHE cc_start: 0.8935 (m-80) cc_final: 0.7751 (m-10) REVERT: V 11 GLU cc_start: 0.7773 (pm20) cc_final: 0.7535 (pm20) REVERT: V 18 ARG cc_start: 0.8568 (mpt-90) cc_final: 0.8230 (mpt-90) REVERT: V 25 LYS cc_start: 0.9010 (mttt) cc_final: 0.8733 (mtpp) REVERT: V 48 MET cc_start: 0.8921 (tpp) cc_final: 0.8549 (tpp) REVERT: V 73 LYS cc_start: 0.8917 (mtpp) cc_final: 0.8580 (mmtt) REVERT: V 75 GLN cc_start: 0.9200 (tp40) cc_final: 0.8908 (tp-100) REVERT: V 76 ASP cc_start: 0.8826 (t0) cc_final: 0.8599 (t0) REVERT: V 82 TYR cc_start: 0.9345 (p90) cc_final: 0.8992 (p90) REVERT: V 83 LYS cc_start: 0.9469 (mttt) cc_final: 0.9205 (mttp) REVERT: X 11 ARG cc_start: 0.8797 (ttm-80) cc_final: 0.8558 (mtp85) REVERT: X 35 SER cc_start: 0.9391 (m) cc_final: 0.9067 (t) REVERT: X 43 GLU cc_start: 0.8994 (mt-10) cc_final: 0.8627 (tt0) REVERT: X 70 GLU cc_start: 0.8548 (tm-30) cc_final: 0.8134 (tm-30) REVERT: X 77 LYS cc_start: 0.8594 (mmmt) cc_final: 0.8328 (mmmt) REVERT: Y 13 GLU cc_start: 0.8580 (mt-10) cc_final: 0.8330 (mt-10) REVERT: Y 16 THR cc_start: 0.9442 (p) cc_final: 0.8785 (p) REVERT: Y 17 GLU cc_start: 0.9150 (tp30) cc_final: 0.8791 (mm-30) REVERT: Y 31 GLN cc_start: 0.9411 (mt0) cc_final: 0.9162 (mt0) REVERT: Y 45 GLN cc_start: 0.8987 (mt0) cc_final: 0.8785 (mt0) REVERT: Y 55 THR cc_start: 0.9274 (m) cc_final: 0.8995 (p) REVERT: Y 59 GLU cc_start: 0.9002 (tp30) cc_final: 0.8753 (tp30) REVERT: Z 6 LYS cc_start: 0.8455 (mtmm) cc_final: 0.7595 (mtmm) REVERT: Z 58 GLU cc_start: 0.7283 (tp30) cc_final: 0.6692 (tp30) REVERT: a 1 MET cc_start: 0.7291 (mpp) cc_final: 0.7017 (mmt) REVERT: a 22 MET cc_start: 0.4232 (pmm) cc_final: 0.3586 (pmm) REVERT: b 12 LYS cc_start: 0.8902 (mmmt) cc_final: 0.8426 (mmmt) REVERT: b 31 ASP cc_start: 0.8459 (t70) cc_final: 0.8195 (t0) REVERT: b 36 GLU cc_start: 0.8253 (pt0) cc_final: 0.7978 (pt0) REVERT: b 46 ASP cc_start: 0.9020 (m-30) cc_final: 0.8771 (m-30) REVERT: b 48 TYR cc_start: 0.8596 (m-80) cc_final: 0.7851 (m-10) REVERT: c 33 LYS cc_start: 0.8393 (mptt) cc_final: 0.8032 (mmtm) REVERT: c 34 LEU cc_start: 0.7910 (tp) cc_final: 0.7648 (tp) REVERT: c 37 LYS cc_start: 0.9107 (tttt) cc_final: 0.8853 (ttmm) REVERT: c 39 PHE cc_start: 0.8703 (t80) cc_final: 0.8396 (t80) REVERT: d 2 LYS cc_start: 0.9262 (tttt) cc_final: 0.9008 (ttpp) REVERT: e 64 TYR cc_start: 0.7847 (m-80) cc_final: 0.7645 (m-80) REVERT: f 2 LYS cc_start: 0.8603 (mmmm) cc_final: 0.7983 (tttm) REVERT: f 35 GLN cc_start: 0.9065 (mt0) cc_final: 0.8319 (mt0) REVERT: g 23 TRP cc_start: 0.7729 (p-90) cc_final: 0.7424 (p-90) REVERT: g 24 ASN cc_start: 0.4840 (t0) cc_final: 0.4196 (t0) REVERT: g 69 PHE cc_start: 0.7459 (m-80) cc_final: 0.7032 (m-80) REVERT: g 93 ASN cc_start: 0.7885 (p0) cc_final: 0.7617 (p0) REVERT: g 100 MET cc_start: 0.7323 (ptp) cc_final: 0.7101 (mtp) REVERT: g 108 ARG cc_start: 0.7625 (ttp80) cc_final: 0.7333 (ttp80) REVERT: g 179 LEU cc_start: 0.7941 (mm) cc_final: 0.7539 (mm) REVERT: h 25 ASN cc_start: 0.7981 (t0) cc_final: 0.7706 (t0) REVERT: h 110 GLU cc_start: 0.8737 (mt-10) cc_final: 0.8485 (mt-10) REVERT: h 123 GLN cc_start: 0.9175 (mm-40) cc_final: 0.8895 (mm-40) REVERT: h 152 GLU cc_start: 0.8084 (tm-30) cc_final: 0.7656 (tm-30) REVERT: h 183 ASP cc_start: 0.8776 (t0) cc_final: 0.7896 (t0) REVERT: h 193 TYR cc_start: 0.8434 (m-80) cc_final: 0.8045 (m-10) REVERT: i 34 ILE cc_start: 0.8805 (tp) cc_final: 0.8549 (mm) REVERT: i 77 LYS cc_start: 0.9497 (mtpp) cc_final: 0.9291 (mtpp) REVERT: i 104 ARG cc_start: 0.8920 (mmm-85) cc_final: 0.8687 (mmt90) REVERT: i 141 ASP cc_start: 0.7835 (m-30) cc_final: 0.7444 (m-30) REVERT: j 41 ASP cc_start: 0.8848 (p0) cc_final: 0.8365 (p0) REVERT: j 65 GLU cc_start: 0.9123 (mm-30) cc_final: 0.8761 (mm-30) REVERT: j 68 ARG cc_start: 0.8830 (mtt90) cc_final: 0.8569 (mtt90) REVERT: j 128 TYR cc_start: 0.8937 (m-80) cc_final: 0.8651 (m-80) REVERT: j 142 ASP cc_start: 0.8555 (t70) cc_final: 0.7945 (t70) REVERT: j 145 GLU cc_start: 0.8334 (pp20) cc_final: 0.8045 (pp20) REVERT: j 152 MET cc_start: 0.8864 (mtp) cc_final: 0.8630 (mtp) REVERT: k 3 HIS cc_start: 0.8326 (m90) cc_final: 0.7966 (m-70) REVERT: k 5 GLU cc_start: 0.8524 (tm-30) cc_final: 0.7666 (tm-30) REVERT: k 23 GLU cc_start: 0.9252 (pp20) cc_final: 0.9021 (pp20) REVERT: k 46 GLN cc_start: 0.7885 (tp-100) cc_final: 0.7585 (tp-100) REVERT: k 61 LEU cc_start: 0.8043 (tt) cc_final: 0.7737 (tt) REVERT: k 62 MET cc_start: 0.8953 (ptp) cc_final: 0.8669 (ptp) REVERT: k 68 GLN cc_start: 0.9019 (mt0) cc_final: 0.8756 (mt0) REVERT: k 75 GLU cc_start: 0.9066 (mt-10) cc_final: 0.8603 (mp0) REVERT: k 88 MET cc_start: 0.7438 (ttp) cc_final: 0.7040 (tmm) REVERT: k 90 MET cc_start: 0.8235 (ttp) cc_final: 0.7931 (tpt) REVERT: k 91 ARG cc_start: 0.8501 (ttt90) cc_final: 0.8218 (ttt-90) REVERT: l 5 ARG cc_start: 0.8050 (tpp-160) cc_final: 0.7839 (tmm160) REVERT: l 33 ASP cc_start: 0.7877 (m-30) cc_final: 0.7641 (m-30) REVERT: l 142 HIS cc_start: 0.8856 (m90) cc_final: 0.8019 (m-70) REVERT: l 148 ASN cc_start: 0.7239 (p0) cc_final: 0.7027 (p0) REVERT: m 5 ASP cc_start: 0.8869 (t0) cc_final: 0.7973 (t0) REVERT: m 75 ILE cc_start: 0.8585 (tp) cc_final: 0.8226 (tp) REVERT: m 127 CYS cc_start: 0.9225 (p) cc_final: 0.9012 (p) REVERT: n 25 ASN cc_start: 0.8835 (p0) cc_final: 0.8464 (p0) REVERT: n 31 ASN cc_start: 0.8581 (m110) cc_final: 0.8328 (m110) REVERT: n 55 VAL cc_start: 0.6639 (m) cc_final: 0.6060 (m) REVERT: n 110 GLN cc_start: 0.8915 (mm110) cc_final: 0.8461 (mm110) REVERT: p 18 ASP cc_start: 0.8426 (p0) cc_final: 0.7999 (p0) REVERT: p 64 GLN cc_start: 0.9033 (OUTLIER) cc_final: 0.8711 (pp30) REVERT: p 68 GLU cc_start: 0.8569 (mm-30) cc_final: 0.8165 (mm-30) REVERT: p 87 LYS cc_start: 0.8999 (ttmm) cc_final: 0.8456 (ttmm) REVERT: p 94 GLU cc_start: 0.8992 (mt-10) cc_final: 0.8601 (mm-30) REVERT: p 101 ASN cc_start: 0.9157 (t0) cc_final: 0.8939 (p0) REVERT: q 25 GLU cc_start: 0.8289 (pm20) cc_final: 0.8028 (mp0) REVERT: q 70 GLU cc_start: 0.8246 (mp0) cc_final: 0.8010 (mp0) REVERT: q 75 GLN cc_start: 0.9126 (pt0) cc_final: 0.8775 (pm20) REVERT: q 90 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8831 (mt) REVERT: q 112 GLN cc_start: 0.8083 (mt0) cc_final: 0.7555 (mt0) REVERT: r 7 ILE cc_start: 0.9230 (tp) cc_final: 0.8731 (pt) REVERT: r 23 TYR cc_start: 0.7663 (t80) cc_final: 0.7207 (t80) REVERT: r 42 ASP cc_start: 0.8436 (p0) cc_final: 0.7810 (t0) REVERT: r 86 TYR cc_start: 0.8417 (t80) cc_final: 0.7995 (t80) REVERT: s 4 GLN cc_start: 0.8022 (mm110) cc_final: 0.7484 (mm-40) REVERT: s 33 ASP cc_start: 0.8896 (t0) cc_final: 0.8481 (p0) REVERT: s 89 MET cc_start: 0.9087 (mmm) cc_final: 0.8716 (mmm) REVERT: t 45 GLU cc_start: 0.8885 (tt0) cc_final: 0.8595 (tt0) REVERT: t 80 GLN cc_start: 0.8369 (tm130) cc_final: 0.7783 (tm-30) REVERT: t 84 ARG cc_start: 0.8826 (tpp80) cc_final: 0.8291 (tpp80) REVERT: t 89 ARG cc_start: 0.6926 (tmm-80) cc_final: 0.6658 (tmm-80) REVERT: u 63 GLN cc_start: 0.8782 (mm-40) cc_final: 0.8172 (mm-40) REVERT: u 66 THR cc_start: 0.8689 (t) cc_final: 0.8416 (p) REVERT: v 60 GLU cc_start: 0.7968 (mp0) cc_final: 0.7205 (mp0) REVERT: v 73 TRP cc_start: 0.9213 (m100) cc_final: 0.8188 (m100) REVERT: v 77 ARG cc_start: 0.8734 (ptm-80) cc_final: 0.8431 (ptm160) REVERT: w 25 ASP cc_start: 0.8087 (t0) cc_final: 0.7820 (t0) REVERT: w 72 ASP cc_start: 0.8365 (p0) cc_final: 0.8113 (p0) REVERT: x 7 LYS cc_start: 0.8332 (mtpp) cc_final: 0.7961 (mtpt) REVERT: x 55 ARG cc_start: 0.9133 (mtm180) cc_final: 0.8745 (mtm180) REVERT: x 77 THR cc_start: 0.7643 (p) cc_final: 0.6679 (t) REVERT: y 13 GLN cc_start: 0.9370 (mt0) cc_final: 0.9104 (mt0) REVERT: y 48 GLN cc_start: 0.9135 (tp-100) cc_final: 0.8921 (tp-100) REVERT: y 60 ARG cc_start: 0.9183 (ttm110) cc_final: 0.8890 (ttm110) REVERT: y 78 ASN cc_start: 0.8720 (m-40) cc_final: 0.8496 (m110) REVERT: z 33 ARG cc_start: 0.7940 (ptp-110) cc_final: 0.7521 (ptt180) REVERT: W 70 GLU cc_start: 0.8648 (mm-30) cc_final: 0.8408 (mm-30) outliers start: 154 outliers final: 83 residues processed: 1721 average time/residue: 1.2609 time to fit residues: 3778.4436 Evaluate side-chains 1574 residues out of total 4672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 1483 time to evaluate : 6.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 42 GLU Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 127 ASN Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain F residue 20 ASN Chi-restraints excluded: chain F residue 147 ASP Chi-restraints excluded: chain F residue 167 GLU Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 144 VAL Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain J residue 139 VAL Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 90 ASN Chi-restraints excluded: chain K residue 103 VAL Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain M residue 73 ILE Chi-restraints excluded: chain N residue 53 THR Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain O residue 18 LEU Chi-restraints excluded: chain O residue 35 ILE Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain O residue 69 ASP Chi-restraints excluded: chain P residue 10 GLN Chi-restraints excluded: chain P residue 73 VAL Chi-restraints excluded: chain P residue 114 LEU Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 53 PHE Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain U residue 8 ASP Chi-restraints excluded: chain U residue 40 ASN Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain V residue 4 ILE Chi-restraints excluded: chain V residue 60 VAL Chi-restraints excluded: chain V residue 66 ASP Chi-restraints excluded: chain V residue 70 ILE Chi-restraints excluded: chain X residue 14 THR Chi-restraints excluded: chain X residue 42 SER Chi-restraints excluded: chain Y residue 34 SER Chi-restraints excluded: chain Y residue 36 GLN Chi-restraints excluded: chain Y residue 40 SER Chi-restraints excluded: chain Y residue 50 VAL Chi-restraints excluded: chain Z residue 41 THR Chi-restraints excluded: chain c residue 14 SER Chi-restraints excluded: chain d residue 8 SER Chi-restraints excluded: chain g residue 141 LEU Chi-restraints excluded: chain h residue 31 ASP Chi-restraints excluded: chain h residue 49 LYS Chi-restraints excluded: chain h residue 186 THR Chi-restraints excluded: chain i residue 110 THR Chi-restraints excluded: chain i residue 169 THR Chi-restraints excluded: chain i residue 204 TYR Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 87 SER Chi-restraints excluded: chain l residue 30 LEU Chi-restraints excluded: chain l residue 101 MET Chi-restraints excluded: chain o residue 32 THR Chi-restraints excluded: chain o residue 44 THR Chi-restraints excluded: chain o residue 84 VAL Chi-restraints excluded: chain o residue 96 VAL Chi-restraints excluded: chain o residue 101 SER Chi-restraints excluded: chain p residue 64 GLN Chi-restraints excluded: chain p residue 81 ASN Chi-restraints excluded: chain p residue 84 VAL Chi-restraints excluded: chain p residue 97 ILE Chi-restraints excluded: chain q residue 3 THR Chi-restraints excluded: chain q residue 63 VAL Chi-restraints excluded: chain q residue 90 LEU Chi-restraints excluded: chain s residue 60 GLN Chi-restraints excluded: chain s residue 79 LEU Chi-restraints excluded: chain t residue 3 LEU Chi-restraints excluded: chain t residue 18 ASP Chi-restraints excluded: chain u residue 68 SER Chi-restraints excluded: chain v residue 33 ILE Chi-restraints excluded: chain v residue 43 LYS Chi-restraints excluded: chain w residue 40 VAL Chi-restraints excluded: chain x residue 20 GLU Chi-restraints excluded: chain x residue 48 THR Chi-restraints excluded: chain x residue 58 VAL Chi-restraints excluded: chain y residue 53 GLU Chi-restraints excluded: chain W residue 71 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1010 random chunks: chunk 509 optimal weight: 20.0000 chunk 284 optimal weight: 10.0000 chunk 763 optimal weight: 10.0000 chunk 624 optimal weight: 2.9990 chunk 253 optimal weight: 10.0000 chunk 918 optimal weight: 10.0000 chunk 992 optimal weight: 5.9990 chunk 818 optimal weight: 3.9990 chunk 911 optimal weight: 30.0000 chunk 313 optimal weight: 10.0000 chunk 737 optimal weight: 9.9990 overall best weight: 6.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 70 ASN C 36 GLN ** P 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 75 GLN Q 52 GLN R 18 GLN S 60 HIS T 48 GLN U 40 ASN ** U 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 25 GLN Y 36 GLN Y 38 GLN Z 34 HIS b 42 HIS d 6 GLN ** e 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 190 HIS ** j 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 73 ASN n 50 GLN o 64 GLN p 64 GLN q 6 GLN y 55 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 156844 Z= 0.347 Angle : 0.677 13.613 234723 Z= 0.364 Chirality : 0.037 0.385 29908 Planarity : 0.006 0.133 12506 Dihedral : 23.827 179.974 78634 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.95 % Favored : 95.92 % Rotamer: Outliers : 5.50 % Allowed : 21.10 % Favored : 73.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -0.76 (0.11), residues: 5614 helix: 0.51 (0.11), residues: 1982 sheet: -0.78 (0.16), residues: 1032 loop : -1.12 (0.11), residues: 2600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP l 103 HIS 0.011 0.001 HIS o 15 PHE 0.025 0.002 PHE h 130 TYR 0.031 0.002 TYR g 213 ARG 0.012 0.001 ARG q 14 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11228 Ramachandran restraints generated. 5614 Oldfield, 0 Emsley, 5614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11228 Ramachandran restraints generated. 5614 Oldfield, 0 Emsley, 5614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1795 residues out of total 4672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 257 poor density : 1538 time to evaluate : 6.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 117 GLN cc_start: 0.8680 (tt0) cc_final: 0.8387 (tp-100) REVERT: B 130 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8387 (pp) REVERT: B 180 GLU cc_start: 0.8534 (mt-10) cc_final: 0.8204 (tt0) REVERT: B 201 MET cc_start: 0.8713 (ptp) cc_final: 0.8416 (ptm) REVERT: B 251 GLN cc_start: 0.8572 (tm-30) cc_final: 0.8141 (tm-30) REVERT: C 11 MET cc_start: 0.8894 (mtp) cc_final: 0.8690 (mtp) REVERT: C 126 ASN cc_start: 0.8850 (m-40) cc_final: 0.8639 (m110) REVERT: C 128 ARG cc_start: 0.8279 (mtt90) cc_final: 0.7485 (ttp-170) REVERT: C 137 SER cc_start: 0.9084 (m) cc_final: 0.8782 (p) REVERT: D 136 GLN cc_start: 0.9219 (tp-100) cc_final: 0.8830 (tp40) REVERT: D 156 ASN cc_start: 0.9033 (m-40) cc_final: 0.8711 (t0) REVERT: D 188 MET cc_start: 0.9445 (OUTLIER) cc_final: 0.8977 (mtm) REVERT: E 20 PHE cc_start: 0.8720 (m-80) cc_final: 0.8449 (m-80) REVERT: E 42 GLU cc_start: 0.9262 (pt0) cc_final: 0.8673 (pm20) REVERT: E 114 PHE cc_start: 0.8997 (t80) cc_final: 0.8633 (t80) REVERT: E 130 MET cc_start: 0.8838 (ppp) cc_final: 0.8589 (ppp) REVERT: E 135 GLN cc_start: 0.8162 (pm20) cc_final: 0.6955 (pm20) REVERT: E 177 PHE cc_start: 0.6808 (m-10) cc_final: 0.6582 (m-10) REVERT: F 39 ASP cc_start: 0.8723 (p0) cc_final: 0.8419 (p0) REVERT: F 58 TYR cc_start: 0.7595 (m-80) cc_final: 0.7098 (m-80) REVERT: F 83 PHE cc_start: 0.8502 (m-80) cc_final: 0.8022 (m-80) REVERT: F 101 ASN cc_start: 0.8955 (p0) cc_final: 0.8581 (p0) REVERT: F 137 ASP cc_start: 0.9079 (t0) cc_final: 0.8826 (t0) REVERT: F 155 GLU cc_start: 0.8155 (tm-30) cc_final: 0.7527 (tm-30) REVERT: G 1 MET cc_start: 0.5798 (ttt) cc_final: 0.5568 (ttm) REVERT: G 25 TYR cc_start: 0.8807 (t80) cc_final: 0.8606 (t80) REVERT: J 58 ASN cc_start: 0.9111 (m-40) cc_final: 0.8774 (m-40) REVERT: J 96 ARG cc_start: 0.8706 (ttt-90) cc_final: 0.8354 (mmm-85) REVERT: J 106 LYS cc_start: 0.9323 (tttp) cc_final: 0.9102 (ttmm) REVERT: K 12 ASP cc_start: 0.8481 (p0) cc_final: 0.8051 (p0) REVERT: K 88 ASN cc_start: 0.8496 (t0) cc_final: 0.8138 (t0) REVERT: K 121 GLU cc_start: 0.8914 (tt0) cc_final: 0.8608 (tt0) REVERT: L 55 MET cc_start: 0.9117 (tpp) cc_final: 0.8812 (tpt) REVERT: L 76 GLU cc_start: 0.8056 (mt-10) cc_final: 0.7661 (mt-10) REVERT: L 81 ASP cc_start: 0.8695 (t0) cc_final: 0.8420 (t0) REVERT: M 3 GLN cc_start: 0.9212 (tt0) cc_final: 0.8892 (tt0) REVERT: M 47 GLU cc_start: 0.8673 (tp30) cc_final: 0.8303 (tp30) REVERT: M 110 GLU cc_start: 0.8900 (tt0) cc_final: 0.8281 (tm-30) REVERT: M 115 GLU cc_start: 0.8477 (tp30) cc_final: 0.8133 (tp30) REVERT: N 9 GLN cc_start: 0.8506 (tt0) cc_final: 0.8160 (tt0) REVERT: N 20 MET cc_start: 0.9343 (ttp) cc_final: 0.8930 (ttp) REVERT: N 72 ASP cc_start: 0.8406 (t70) cc_final: 0.8092 (t70) REVERT: O 40 ILE cc_start: 0.8911 (mt) cc_final: 0.8709 (mp) REVERT: O 58 ILE cc_start: 0.9123 (mp) cc_final: 0.8880 (mp) REVERT: O 61 GLN cc_start: 0.8807 (mp10) cc_final: 0.8574 (mp10) REVERT: O 68 LYS cc_start: 0.8698 (mmtp) cc_final: 0.8437 (mmtm) REVERT: O 93 ASP cc_start: 0.8572 (t0) cc_final: 0.8270 (t0) REVERT: O 98 GLN cc_start: 0.8174 (mm-40) cc_final: 0.7902 (mm110) REVERT: O 112 GLU cc_start: 0.9122 (mm-30) cc_final: 0.8910 (pp20) REVERT: P 8 LEU cc_start: 0.9151 (mm) cc_final: 0.8798 (mm) REVERT: P 13 MET cc_start: 0.8849 (tpp) cc_final: 0.8561 (mmm) REVERT: P 16 ASP cc_start: 0.8576 (p0) cc_final: 0.8220 (p0) REVERT: P 24 ASP cc_start: 0.8400 (m-30) cc_final: 0.7916 (m-30) REVERT: Q 102 ASP cc_start: 0.8463 (t0) cc_final: 0.8149 (t0) REVERT: R 2 TYR cc_start: 0.9470 (p90) cc_final: 0.9110 (p90) REVERT: R 31 GLU cc_start: 0.8156 (mp0) cc_final: 0.7896 (mp0) REVERT: R 37 GLU cc_start: 0.7951 (pm20) cc_final: 0.7593 (pm20) REVERT: R 48 LYS cc_start: 0.9165 (ptpp) cc_final: 0.8809 (ptpp) REVERT: R 55 ASP cc_start: 0.8579 (p0) cc_final: 0.8146 (p0) REVERT: R 60 LYS cc_start: 0.9167 (mttp) cc_final: 0.8863 (pttt) REVERT: R 62 GLU cc_start: 0.8163 (tp30) cc_final: 0.7879 (tp30) REVERT: R 94 THR cc_start: 0.9307 (OUTLIER) cc_final: 0.8678 (p) REVERT: S 2 GLU cc_start: 0.8807 (mp0) cc_final: 0.8571 (mp0) REVERT: S 62 ASP cc_start: 0.8447 (t0) cc_final: 0.8160 (t0) REVERT: S 73 LYS cc_start: 0.8848 (mttt) cc_final: 0.8575 (mttm) REVERT: T 24 MET cc_start: 0.8647 (tpt) cc_final: 0.8427 (tpp) REVERT: T 56 GLU cc_start: 0.9196 (mm-30) cc_final: 0.8887 (tp30) REVERT: T 91 GLN cc_start: 0.8991 (mm-40) cc_final: 0.8381 (mm-40) REVERT: U 10 GLU cc_start: 0.8407 (tt0) cc_final: 0.7844 (tm-30) REVERT: U 22 ARG cc_start: 0.8746 (mtm-85) cc_final: 0.8263 (mtm-85) REVERT: U 29 LEU cc_start: 0.9381 (mm) cc_final: 0.9089 (mm) REVERT: U 81 ASP cc_start: 0.7712 (t70) cc_final: 0.7263 (t70) REVERT: U 96 PHE cc_start: 0.8797 (m-80) cc_final: 0.8320 (m-10) REVERT: V 75 GLN cc_start: 0.9159 (tp40) cc_final: 0.8894 (tp-100) REVERT: V 77 VAL cc_start: 0.9398 (p) cc_final: 0.9025 (p) REVERT: V 90 ASP cc_start: 0.8928 (m-30) cc_final: 0.8507 (t0) REVERT: X 35 SER cc_start: 0.9386 (m) cc_final: 0.9070 (t) REVERT: X 43 GLU cc_start: 0.8980 (mt-10) cc_final: 0.8556 (tt0) REVERT: X 70 GLU cc_start: 0.8560 (tm-30) cc_final: 0.8162 (tm-30) REVERT: Y 13 GLU cc_start: 0.8484 (mt-10) cc_final: 0.8264 (mt-10) REVERT: Y 15 ASN cc_start: 0.9341 (m-40) cc_final: 0.9107 (m-40) REVERT: Y 17 GLU cc_start: 0.9121 (tp30) cc_final: 0.8785 (mm-30) REVERT: Y 31 GLN cc_start: 0.9448 (mt0) cc_final: 0.9175 (mt0) REVERT: Y 36 GLN cc_start: 0.9163 (mm110) cc_final: 0.8878 (mm-40) REVERT: Y 55 THR cc_start: 0.9306 (OUTLIER) cc_final: 0.9025 (p) REVERT: Y 59 GLU cc_start: 0.9014 (tp30) cc_final: 0.8760 (tp30) REVERT: Z 6 LYS cc_start: 0.8570 (mtmm) cc_final: 0.7797 (mtmm) REVERT: Z 58 GLU cc_start: 0.7533 (tp30) cc_final: 0.6968 (tp30) REVERT: a 22 MET cc_start: 0.4578 (pmm) cc_final: 0.3830 (pmm) REVERT: b 12 LYS cc_start: 0.8949 (mmmt) cc_final: 0.8357 (mmmt) REVERT: b 36 GLU cc_start: 0.8339 (pt0) cc_final: 0.7924 (pt0) REVERT: b 46 ASP cc_start: 0.8966 (m-30) cc_final: 0.8665 (m-30) REVERT: b 48 TYR cc_start: 0.8772 (m-80) cc_final: 0.8154 (m-10) REVERT: c 6 ARG cc_start: 0.8175 (ttm-80) cc_final: 0.6369 (ttm-80) REVERT: c 33 LYS cc_start: 0.8368 (mptt) cc_final: 0.8039 (mmtm) REVERT: c 34 LEU cc_start: 0.7902 (tp) cc_final: 0.7593 (tp) REVERT: c 37 LYS cc_start: 0.9103 (tttt) cc_final: 0.8693 (tppt) REVERT: c 39 PHE cc_start: 0.8785 (t80) cc_final: 0.8221 (t80) REVERT: d 2 LYS cc_start: 0.9345 (tttt) cc_final: 0.9122 (ttpt) REVERT: d 28 ARG cc_start: 0.8837 (mtm-85) cc_final: 0.8575 (mtm-85) REVERT: f 2 LYS cc_start: 0.8609 (mmmm) cc_final: 0.8030 (tttm) REVERT: f 35 GLN cc_start: 0.8998 (mt0) cc_final: 0.8365 (mt0) REVERT: g 23 TRP cc_start: 0.7590 (p-90) cc_final: 0.7363 (p-90) REVERT: g 42 ASN cc_start: 0.6200 (t0) cc_final: 0.5962 (t0) REVERT: g 93 ASN cc_start: 0.7946 (p0) cc_final: 0.7703 (p0) REVERT: g 100 MET cc_start: 0.7445 (ptp) cc_final: 0.7046 (mtm) REVERT: g 108 ARG cc_start: 0.7828 (ttp80) cc_final: 0.7613 (ttp80) REVERT: h 25 ASN cc_start: 0.8132 (t0) cc_final: 0.7826 (t0) REVERT: h 42 TYR cc_start: 0.8919 (t80) cc_final: 0.8669 (t80) REVERT: h 152 GLU cc_start: 0.8161 (tm-30) cc_final: 0.7752 (tm-30) REVERT: h 181 ASP cc_start: 0.8535 (t70) cc_final: 0.8114 (t70) REVERT: h 183 ASP cc_start: 0.8737 (t0) cc_final: 0.8019 (t0) REVERT: h 193 TYR cc_start: 0.8470 (m-80) cc_final: 0.8089 (m-10) REVERT: h 201 TRP cc_start: 0.8687 (OUTLIER) cc_final: 0.7576 (m-10) REVERT: i 32 CYS cc_start: 0.7480 (p) cc_final: 0.6818 (p) REVERT: i 34 ILE cc_start: 0.8760 (tp) cc_final: 0.8560 (mm) REVERT: i 141 ASP cc_start: 0.7868 (m-30) cc_final: 0.7485 (m-30) REVERT: i 164 GLN cc_start: 0.9148 (OUTLIER) cc_final: 0.7994 (mp10) REVERT: i 174 ASP cc_start: 0.7380 (t0) cc_final: 0.7152 (p0) REVERT: j 41 ASP cc_start: 0.8643 (p0) cc_final: 0.8203 (p0) REVERT: j 128 TYR cc_start: 0.8921 (m-80) cc_final: 0.8639 (m-80) REVERT: j 145 GLU cc_start: 0.8467 (pp20) cc_final: 0.8163 (pp20) REVERT: k 3 HIS cc_start: 0.8407 (m90) cc_final: 0.7948 (m-70) REVERT: k 5 GLU cc_start: 0.8635 (tm-30) cc_final: 0.7962 (tm-30) REVERT: k 24 ARG cc_start: 0.9035 (mtt-85) cc_final: 0.8749 (ptp-170) REVERT: k 56 LYS cc_start: 0.8558 (mttm) cc_final: 0.8310 (mttm) REVERT: k 62 MET cc_start: 0.8726 (ptp) cc_final: 0.8432 (ptp) REVERT: k 75 GLU cc_start: 0.9017 (mt-10) cc_final: 0.8542 (mp0) REVERT: l 33 ASP cc_start: 0.8105 (m-30) cc_final: 0.7751 (m-30) REVERT: l 142 HIS cc_start: 0.8757 (m90) cc_final: 0.7938 (m-70) REVERT: l 148 ASN cc_start: 0.7199 (p0) cc_final: 0.6977 (p0) REVERT: m 5 ASP cc_start: 0.8763 (t0) cc_final: 0.7995 (t0) REVERT: m 75 ILE cc_start: 0.8507 (OUTLIER) cc_final: 0.8137 (tp) REVERT: m 106 THR cc_start: 0.8631 (OUTLIER) cc_final: 0.8361 (p) REVERT: m 127 CYS cc_start: 0.9295 (p) cc_final: 0.9052 (p) REVERT: n 19 VAL cc_start: 0.8495 (t) cc_final: 0.8249 (m) REVERT: n 100 LYS cc_start: 0.9177 (mptt) cc_final: 0.8972 (mmtt) REVERT: n 107 ASP cc_start: 0.9015 (OUTLIER) cc_final: 0.8672 (t0) REVERT: o 49 PHE cc_start: 0.8626 (m-80) cc_final: 0.8189 (m-80) REVERT: o 63 ASP cc_start: 0.8291 (OUTLIER) cc_final: 0.8051 (m-30) REVERT: p 18 ASP cc_start: 0.8224 (p0) cc_final: 0.7750 (p0) REVERT: p 64 GLN cc_start: 0.9195 (OUTLIER) cc_final: 0.8931 (pp30) REVERT: p 68 GLU cc_start: 0.8637 (mm-30) cc_final: 0.8320 (mm-30) REVERT: p 87 LYS cc_start: 0.8940 (ttmm) cc_final: 0.8382 (ttmm) REVERT: q 7 LEU cc_start: 0.9487 (mt) cc_final: 0.9256 (mp) REVERT: q 70 GLU cc_start: 0.8860 (mp0) cc_final: 0.8425 (mp0) REVERT: q 75 GLN cc_start: 0.9179 (pt0) cc_final: 0.8714 (pm20) REVERT: q 90 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8835 (mt) REVERT: q 112 GLN cc_start: 0.8252 (mt0) cc_final: 0.7559 (mt0) REVERT: r 41 GLU cc_start: 0.8512 (mt-10) cc_final: 0.8050 (mt-10) REVERT: r 42 ASP cc_start: 0.8435 (p0) cc_final: 0.7845 (t0) REVERT: r 66 GLU cc_start: 0.8784 (pm20) cc_final: 0.8357 (pm20) REVERT: r 75 MET cc_start: 0.9275 (tmm) cc_final: 0.8917 (tmm) REVERT: s 4 GLN cc_start: 0.8136 (mm110) cc_final: 0.7538 (mm-40) REVERT: s 42 TRP cc_start: 0.9147 (t60) cc_final: 0.8898 (t60) REVERT: s 89 MET cc_start: 0.9193 (mmm) cc_final: 0.8971 (mmm) REVERT: t 64 ARG cc_start: 0.8935 (mmm160) cc_final: 0.7936 (tpp-160) REVERT: t 80 GLN cc_start: 0.8171 (tm130) cc_final: 0.7842 (tm-30) REVERT: t 89 ARG cc_start: 0.7274 (tmm-80) cc_final: 0.6620 (tmm-80) REVERT: u 2 VAL cc_start: 0.8552 (OUTLIER) cc_final: 0.8250 (t) REVERT: u 63 GLN cc_start: 0.8873 (mm-40) cc_final: 0.8290 (mm-40) REVERT: v 60 GLU cc_start: 0.8037 (mp0) cc_final: 0.7201 (mp0) REVERT: v 73 TRP cc_start: 0.9389 (m100) cc_final: 0.8523 (m100) REVERT: w 25 ASP cc_start: 0.8040 (t0) cc_final: 0.7736 (m-30) REVERT: x 18 LYS cc_start: 0.8115 (mmtp) cc_final: 0.7788 (mmtp) REVERT: x 44 MET cc_start: 0.9111 (mpp) cc_final: 0.8806 (mpp) REVERT: x 53 ASN cc_start: 0.9179 (p0) cc_final: 0.8468 (p0) REVERT: x 55 ARG cc_start: 0.9002 (mtm180) cc_final: 0.8647 (mtm180) REVERT: y 13 GLN cc_start: 0.9360 (mt0) cc_final: 0.9069 (mt0) REVERT: y 15 GLU cc_start: 0.8954 (tm-30) cc_final: 0.8563 (tp30) REVERT: y 24 ARG cc_start: 0.8729 (mmm160) cc_final: 0.8253 (mmp80) REVERT: y 60 ARG cc_start: 0.9108 (ttm110) cc_final: 0.8797 (ttm110) REVERT: z 33 ARG cc_start: 0.7833 (ptp-110) cc_final: 0.7352 (ptt180) REVERT: W 17 GLU cc_start: 0.8430 (mm-30) cc_final: 0.8199 (mm-30) outliers start: 257 outliers final: 165 residues processed: 1666 average time/residue: 1.2847 time to fit residues: 3768.5230 Evaluate side-chains 1635 residues out of total 4672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 1457 time to evaluate : 6.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 157 SER Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 183 GLU Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 145 ASP Chi-restraints excluded: chain D residue 188 MET Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain E residue 127 ASN Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 114 ASP Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 21 VAL Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 139 PHE Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 55 ILE Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain J residue 139 VAL Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 90 ASN Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 91 ASP Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 26 VAL Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain N residue 53 THR Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain O residue 12 THR Chi-restraints excluded: chain O residue 18 LEU Chi-restraints excluded: chain O residue 35 ILE Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain O residue 67 ASN Chi-restraints excluded: chain O residue 69 ASP Chi-restraints excluded: chain P residue 10 GLN Chi-restraints excluded: chain P residue 27 GLU Chi-restraints excluded: chain P residue 60 THR Chi-restraints excluded: chain P residue 73 VAL Chi-restraints excluded: chain P residue 114 LEU Chi-restraints excluded: chain Q residue 97 ASP Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain Q residue 107 THR Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 43 ASN Chi-restraints excluded: chain R residue 53 PHE Chi-restraints excluded: chain R residue 76 LYS Chi-restraints excluded: chain R residue 94 THR Chi-restraints excluded: chain R residue 101 ILE Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 85 ILE Chi-restraints excluded: chain S residue 86 MET Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 17 SER Chi-restraints excluded: chain T residue 32 LEU Chi-restraints excluded: chain T residue 43 ILE Chi-restraints excluded: chain U residue 13 VAL Chi-restraints excluded: chain U residue 19 LYS Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain U residue 36 VAL Chi-restraints excluded: chain U residue 49 VAL Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain V residue 4 ILE Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain V residue 66 ASP Chi-restraints excluded: chain V residue 70 ILE Chi-restraints excluded: chain X residue 14 THR Chi-restraints excluded: chain X residue 65 ASP Chi-restraints excluded: chain Y residue 34 SER Chi-restraints excluded: chain Y residue 50 VAL Chi-restraints excluded: chain Y residue 55 THR Chi-restraints excluded: chain Z residue 10 THR Chi-restraints excluded: chain Z residue 41 THR Chi-restraints excluded: chain Z residue 57 VAL Chi-restraints excluded: chain a residue 53 THR Chi-restraints excluded: chain c residue 5 ILE Chi-restraints excluded: chain c residue 9 ILE Chi-restraints excluded: chain c residue 12 VAL Chi-restraints excluded: chain c residue 14 SER Chi-restraints excluded: chain c residue 42 VAL Chi-restraints excluded: chain d residue 4 THR Chi-restraints excluded: chain d residue 8 SER Chi-restraints excluded: chain d residue 24 THR Chi-restraints excluded: chain d residue 45 SER Chi-restraints excluded: chain e residue 44 LEU Chi-restraints excluded: chain f residue 3 VAL Chi-restraints excluded: chain f residue 20 ASP Chi-restraints excluded: chain g residue 141 LEU Chi-restraints excluded: chain g residue 199 VAL Chi-restraints excluded: chain g residue 204 ASP Chi-restraints excluded: chain g residue 207 ILE Chi-restraints excluded: chain h residue 31 ASP Chi-restraints excluded: chain h residue 49 LYS Chi-restraints excluded: chain h residue 53 SER Chi-restraints excluded: chain h residue 55 ILE Chi-restraints excluded: chain h residue 186 THR Chi-restraints excluded: chain h residue 201 TRP Chi-restraints excluded: chain i residue 164 GLN Chi-restraints excluded: chain i residue 169 THR Chi-restraints excluded: chain i residue 204 TYR Chi-restraints excluded: chain j residue 55 GLU Chi-restraints excluded: chain j residue 72 ILE Chi-restraints excluded: chain k residue 18 VAL Chi-restraints excluded: chain k residue 26 THR Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 54 LEU Chi-restraints excluded: chain k residue 60 VAL Chi-restraints excluded: chain k residue 64 VAL Chi-restraints excluded: chain k residue 82 ASP Chi-restraints excluded: chain k residue 85 ILE Chi-restraints excluded: chain k residue 97 THR Chi-restraints excluded: chain l residue 30 LEU Chi-restraints excluded: chain l residue 54 SER Chi-restraints excluded: chain l residue 101 MET Chi-restraints excluded: chain m residue 75 ILE Chi-restraints excluded: chain m residue 106 THR Chi-restraints excluded: chain n residue 72 ILE Chi-restraints excluded: chain n residue 90 TYR Chi-restraints excluded: chain n residue 107 ASP Chi-restraints excluded: chain o residue 6 ILE Chi-restraints excluded: chain o residue 10 LEU Chi-restraints excluded: chain o residue 44 THR Chi-restraints excluded: chain o residue 63 ASP Chi-restraints excluded: chain o residue 69 THR Chi-restraints excluded: chain o residue 78 GLU Chi-restraints excluded: chain o residue 84 VAL Chi-restraints excluded: chain o residue 96 VAL Chi-restraints excluded: chain p residue 31 ILE Chi-restraints excluded: chain p residue 55 SER Chi-restraints excluded: chain p residue 64 GLN Chi-restraints excluded: chain p residue 81 ASN Chi-restraints excluded: chain p residue 82 LEU Chi-restraints excluded: chain p residue 84 VAL Chi-restraints excluded: chain p residue 97 ILE Chi-restraints excluded: chain q residue 3 THR Chi-restraints excluded: chain q residue 49 LEU Chi-restraints excluded: chain q residue 90 LEU Chi-restraints excluded: chain s residue 48 LEU Chi-restraints excluded: chain s residue 60 GLN Chi-restraints excluded: chain s residue 79 LEU Chi-restraints excluded: chain t residue 3 LEU Chi-restraints excluded: chain t residue 18 ASP Chi-restraints excluded: chain t residue 25 THR Chi-restraints excluded: chain u residue 2 VAL Chi-restraints excluded: chain u residue 68 SER Chi-restraints excluded: chain v residue 43 LYS Chi-restraints excluded: chain v residue 70 THR Chi-restraints excluded: chain w residue 21 ILE Chi-restraints excluded: chain w residue 40 VAL Chi-restraints excluded: chain x residue 48 THR Chi-restraints excluded: chain x residue 58 VAL Chi-restraints excluded: chain y residue 43 ASP Chi-restraints excluded: chain W residue 31 VAL Chi-restraints excluded: chain W residue 35 SER Chi-restraints excluded: chain W residue 59 LEU Chi-restraints excluded: chain W residue 71 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1010 random chunks: chunk 907 optimal weight: 7.9990 chunk 690 optimal weight: 10.0000 chunk 476 optimal weight: 3.9990 chunk 101 optimal weight: 10.0000 chunk 438 optimal weight: 10.0000 chunk 616 optimal weight: 5.9990 chunk 922 optimal weight: 20.0000 chunk 976 optimal weight: 8.9990 chunk 481 optimal weight: 0.4980 chunk 873 optimal weight: 4.9990 chunk 263 optimal weight: 10.0000 overall best weight: 4.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 90 GLN E 5 HIS F 38 ASN ** P 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 75 GLN Q 52 GLN ** Q 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 48 GLN ** Y 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 38 GLN ** e 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 6 HIS h 139 GLN ** h 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 196 ASN ** j 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 28 ASN l 122 ASN o 64 GLN p 64 GLN q 6 GLN r 14 HIS w 54 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 156844 Z= 0.260 Angle : 0.631 13.850 234723 Z= 0.342 Chirality : 0.035 0.391 29908 Planarity : 0.006 0.126 12506 Dihedral : 23.770 179.671 78633 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.31 % Favored : 96.58 % Rotamer: Outliers : 5.31 % Allowed : 22.75 % Favored : 71.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -0.47 (0.11), residues: 5614 helix: 0.83 (0.12), residues: 1978 sheet: -0.72 (0.16), residues: 1071 loop : -0.97 (0.12), residues: 2565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP l 103 HIS 0.009 0.001 HIS E 5 PHE 0.025 0.002 PHE l 26 TYR 0.030 0.002 TYR g 213 ARG 0.026 0.001 ARG l 5 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11228 Ramachandran restraints generated. 5614 Oldfield, 0 Emsley, 5614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11228 Ramachandran restraints generated. 5614 Oldfield, 0 Emsley, 5614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1795 residues out of total 4672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 248 poor density : 1547 time to evaluate : 6.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 117 GLN cc_start: 0.8683 (tt0) cc_final: 0.8379 (tp-100) REVERT: B 145 GLU cc_start: 0.8748 (mt-10) cc_final: 0.8322 (mt-10) REVERT: B 203 ARG cc_start: 0.8699 (ptp-110) cc_final: 0.8059 (ptp-110) REVERT: B 240 PHE cc_start: 0.9160 (t80) cc_final: 0.8881 (t80) REVERT: B 251 GLN cc_start: 0.8547 (tm-30) cc_final: 0.8102 (tm-30) REVERT: C 11 MET cc_start: 0.8867 (mtp) cc_final: 0.8653 (mtp) REVERT: C 137 SER cc_start: 0.9077 (m) cc_final: 0.8799 (p) REVERT: D 136 GLN cc_start: 0.9196 (tp-100) cc_final: 0.8715 (tp-100) REVERT: D 156 ASN cc_start: 0.8975 (m-40) cc_final: 0.8657 (t0) REVERT: D 188 MET cc_start: 0.9430 (OUTLIER) cc_final: 0.8894 (mtm) REVERT: E 42 GLU cc_start: 0.9254 (OUTLIER) cc_final: 0.8612 (pm20) REVERT: E 83 TYR cc_start: 0.8391 (m-80) cc_final: 0.8114 (m-80) REVERT: E 114 PHE cc_start: 0.8920 (t80) cc_final: 0.8621 (t80) REVERT: E 130 MET cc_start: 0.8705 (ppp) cc_final: 0.8397 (ppp) REVERT: E 135 GLN cc_start: 0.8011 (pm20) cc_final: 0.6783 (pm20) REVERT: E 138 PHE cc_start: 0.8948 (m-80) cc_final: 0.8578 (m-80) REVERT: F 39 ASP cc_start: 0.8775 (p0) cc_final: 0.8516 (p0) REVERT: F 58 TYR cc_start: 0.7454 (m-80) cc_final: 0.6936 (m-80) REVERT: F 83 PHE cc_start: 0.8427 (m-80) cc_final: 0.7940 (m-80) REVERT: F 101 ASN cc_start: 0.9121 (p0) cc_final: 0.8737 (p0) REVERT: F 130 GLU cc_start: 0.8409 (tp30) cc_final: 0.7731 (tp30) REVERT: F 133 LEU cc_start: 0.9528 (OUTLIER) cc_final: 0.9257 (pt) REVERT: F 137 ASP cc_start: 0.9035 (t0) cc_final: 0.8795 (t0) REVERT: G 1 MET cc_start: 0.5794 (ttt) cc_final: 0.5591 (ttm) REVERT: J 90 GLU cc_start: 0.7044 (pm20) cc_final: 0.6690 (pm20) REVERT: J 96 ARG cc_start: 0.8730 (ttt-90) cc_final: 0.8308 (mmm-85) REVERT: K 12 ASP cc_start: 0.8444 (p0) cc_final: 0.8019 (p0) REVERT: K 88 ASN cc_start: 0.8481 (t0) cc_final: 0.8133 (t0) REVERT: K 121 GLU cc_start: 0.8895 (tt0) cc_final: 0.8668 (tt0) REVERT: L 76 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7801 (tt0) REVERT: L 81 ASP cc_start: 0.8837 (t0) cc_final: 0.8439 (t0) REVERT: M 3 GLN cc_start: 0.9200 (tt0) cc_final: 0.8859 (tt0) REVERT: M 47 GLU cc_start: 0.8715 (tp30) cc_final: 0.8311 (tp30) REVERT: M 65 ILE cc_start: 0.9447 (mt) cc_final: 0.9209 (mm) REVERT: M 110 GLU cc_start: 0.8863 (tt0) cc_final: 0.8255 (tm-30) REVERT: M 115 GLU cc_start: 0.8508 (tp30) cc_final: 0.8279 (tp30) REVERT: M 119 LEU cc_start: 0.9585 (OUTLIER) cc_final: 0.9279 (mm) REVERT: N 9 GLN cc_start: 0.8423 (tt0) cc_final: 0.8096 (tt0) REVERT: N 20 MET cc_start: 0.9321 (ttp) cc_final: 0.9006 (ttp) REVERT: N 72 ASP cc_start: 0.8344 (t70) cc_final: 0.7997 (t70) REVERT: O 40 ILE cc_start: 0.8909 (mt) cc_final: 0.8690 (mp) REVERT: O 61 GLN cc_start: 0.8799 (mp10) cc_final: 0.8564 (mp10) REVERT: O 93 ASP cc_start: 0.8561 (t0) cc_final: 0.8180 (t0) REVERT: O 98 GLN cc_start: 0.8159 (mm-40) cc_final: 0.7901 (mm110) REVERT: P 13 MET cc_start: 0.8770 (tpp) cc_final: 0.8403 (mmm) REVERT: P 24 ASP cc_start: 0.8278 (m-30) cc_final: 0.7818 (m-30) REVERT: P 112 GLU cc_start: 0.7945 (pp20) cc_final: 0.7538 (pp20) REVERT: Q 102 ASP cc_start: 0.8444 (t0) cc_final: 0.8114 (t0) REVERT: R 2 TYR cc_start: 0.9420 (p90) cc_final: 0.9052 (p90) REVERT: R 31 GLU cc_start: 0.8031 (mp0) cc_final: 0.7791 (mp0) REVERT: R 32 THR cc_start: 0.9382 (m) cc_final: 0.9131 (p) REVERT: R 34 GLU cc_start: 0.8521 (mm-30) cc_final: 0.8169 (mm-30) REVERT: R 37 GLU cc_start: 0.8013 (pm20) cc_final: 0.7638 (pm20) REVERT: R 48 LYS cc_start: 0.9146 (ptpp) cc_final: 0.8761 (ptpp) REVERT: R 60 LYS cc_start: 0.9220 (mttp) cc_final: 0.8991 (mmtp) REVERT: R 62 GLU cc_start: 0.8125 (tp30) cc_final: 0.7499 (tp30) REVERT: R 85 LYS cc_start: 0.8928 (ttmm) cc_final: 0.8605 (mtpp) REVERT: R 94 THR cc_start: 0.9355 (m) cc_final: 0.8736 (p) REVERT: S 2 GLU cc_start: 0.8813 (mp0) cc_final: 0.8567 (mp0) REVERT: S 31 GLN cc_start: 0.8476 (mp10) cc_final: 0.8111 (mp10) REVERT: S 73 LYS cc_start: 0.8854 (mttt) cc_final: 0.8585 (mttm) REVERT: S 94 ASP cc_start: 0.7866 (m-30) cc_final: 0.7635 (m-30) REVERT: T 56 GLU cc_start: 0.9167 (mm-30) cc_final: 0.8858 (tp30) REVERT: T 91 GLN cc_start: 0.9033 (mm-40) cc_final: 0.8429 (mm-40) REVERT: U 8 ASP cc_start: 0.8129 (OUTLIER) cc_final: 0.7641 (t0) REVERT: U 10 GLU cc_start: 0.8386 (tt0) cc_final: 0.7757 (tm-30) REVERT: U 22 ARG cc_start: 0.8770 (mtm-85) cc_final: 0.8275 (mtm-85) REVERT: U 29 LEU cc_start: 0.9393 (mm) cc_final: 0.9120 (mm) REVERT: U 37 GLU cc_start: 0.8309 (pp20) cc_final: 0.8099 (pp20) REVERT: U 81 ASP cc_start: 0.7720 (t70) cc_final: 0.7490 (t0) REVERT: V 2 PHE cc_start: 0.7375 (m-80) cc_final: 0.5915 (m-10) REVERT: V 48 MET cc_start: 0.8891 (tpt) cc_final: 0.8620 (tpt) REVERT: V 59 GLU cc_start: 0.8354 (pt0) cc_final: 0.8123 (pt0) REVERT: V 75 GLN cc_start: 0.9188 (tp40) cc_final: 0.8956 (tp-100) REVERT: V 90 ASP cc_start: 0.8886 (m-30) cc_final: 0.8404 (t0) REVERT: X 35 SER cc_start: 0.9380 (m) cc_final: 0.9041 (t) REVERT: X 43 GLU cc_start: 0.9021 (mt-10) cc_final: 0.8604 (tt0) REVERT: X 70 GLU cc_start: 0.8565 (tm-30) cc_final: 0.8156 (tm-30) REVERT: X 77 LYS cc_start: 0.8407 (mmmt) cc_final: 0.8204 (mmmm) REVERT: Y 13 GLU cc_start: 0.8568 (mt-10) cc_final: 0.8324 (mt-10) REVERT: Y 15 ASN cc_start: 0.9413 (m-40) cc_final: 0.9068 (m-40) REVERT: Y 17 GLU cc_start: 0.9142 (tp30) cc_final: 0.8822 (mm-30) REVERT: Y 24 GLU cc_start: 0.8715 (mt-10) cc_final: 0.8497 (mt-10) REVERT: Y 31 GLN cc_start: 0.9421 (mt0) cc_final: 0.9152 (mt0) REVERT: Y 36 GLN cc_start: 0.9161 (mm110) cc_final: 0.8928 (mm-40) REVERT: Y 59 GLU cc_start: 0.9046 (tp30) cc_final: 0.8764 (tp30) REVERT: Z 58 GLU cc_start: 0.7543 (tp30) cc_final: 0.7083 (tp30) REVERT: a 1 MET cc_start: 0.6931 (mpp) cc_final: 0.6411 (mmt) REVERT: a 22 MET cc_start: 0.4651 (pmm) cc_final: 0.3905 (pmm) REVERT: b 12 LYS cc_start: 0.8915 (mmmt) cc_final: 0.8335 (mmmt) REVERT: b 36 GLU cc_start: 0.8331 (pt0) cc_final: 0.7882 (pt0) REVERT: b 46 ASP cc_start: 0.8956 (m-30) cc_final: 0.8634 (m-30) REVERT: b 48 TYR cc_start: 0.8758 (m-80) cc_final: 0.8083 (m-10) REVERT: c 17 THR cc_start: 0.7691 (OUTLIER) cc_final: 0.7380 (p) REVERT: c 33 LYS cc_start: 0.8362 (mptt) cc_final: 0.8029 (mmtm) REVERT: c 34 LEU cc_start: 0.7780 (tp) cc_final: 0.7457 (tp) REVERT: c 37 LYS cc_start: 0.9068 (tttt) cc_final: 0.8695 (tppt) REVERT: c 39 PHE cc_start: 0.8694 (t80) cc_final: 0.8296 (t80) REVERT: d 2 LYS cc_start: 0.9239 (tttt) cc_final: 0.9018 (ttpp) REVERT: d 28 ARG cc_start: 0.8838 (mtm-85) cc_final: 0.8598 (mtm-85) REVERT: f 18 LYS cc_start: 0.8828 (ttmt) cc_final: 0.8433 (ttmt) REVERT: f 35 GLN cc_start: 0.8965 (mt0) cc_final: 0.8676 (mt0) REVERT: g 93 ASN cc_start: 0.7961 (p0) cc_final: 0.6109 (t0) REVERT: g 95 ARG cc_start: 0.6851 (ttt180) cc_final: 0.6615 (ttt180) REVERT: g 108 ARG cc_start: 0.7799 (ttp80) cc_final: 0.7583 (ttp80) REVERT: g 169 GLU cc_start: 0.7277 (mm-30) cc_final: 0.7035 (mm-30) REVERT: h 25 ASN cc_start: 0.8234 (t0) cc_final: 0.7988 (t0) REVERT: h 42 TYR cc_start: 0.9011 (t80) cc_final: 0.8645 (t80) REVERT: h 152 GLU cc_start: 0.8144 (tm-30) cc_final: 0.7772 (tm-30) REVERT: h 181 ASP cc_start: 0.8494 (t70) cc_final: 0.8061 (t70) REVERT: h 183 ASP cc_start: 0.8660 (t0) cc_final: 0.8084 (t0) REVERT: h 187 SER cc_start: 0.8100 (t) cc_final: 0.7694 (p) REVERT: h 193 TYR cc_start: 0.8360 (m-80) cc_final: 0.7974 (m-10) REVERT: h 201 TRP cc_start: 0.8650 (OUTLIER) cc_final: 0.7693 (m-10) REVERT: i 32 CYS cc_start: 0.7342 (p) cc_final: 0.6650 (p) REVERT: i 34 ILE cc_start: 0.8759 (tp) cc_final: 0.8542 (mm) REVERT: i 103 TYR cc_start: 0.8843 (t80) cc_final: 0.8574 (t80) REVERT: i 107 PHE cc_start: 0.8998 (m-10) cc_final: 0.8660 (m-80) REVERT: i 141 ASP cc_start: 0.7900 (m-30) cc_final: 0.7592 (m-30) REVERT: i 160 GLU cc_start: 0.9275 (OUTLIER) cc_final: 0.8957 (mp0) REVERT: i 163 GLU cc_start: 0.8145 (pp20) cc_final: 0.7668 (pp20) REVERT: i 164 GLN cc_start: 0.8690 (OUTLIER) cc_final: 0.8064 (mp10) REVERT: i 174 ASP cc_start: 0.7449 (t0) cc_final: 0.7109 (p0) REVERT: j 41 ASP cc_start: 0.8810 (p0) cc_final: 0.8386 (p0) REVERT: j 65 GLU cc_start: 0.8675 (tp30) cc_final: 0.8363 (tp30) REVERT: j 93 ARG cc_start: 0.8774 (mpp80) cc_final: 0.8345 (mpp80) REVERT: j 128 TYR cc_start: 0.8923 (m-80) cc_final: 0.8545 (m-80) REVERT: j 145 GLU cc_start: 0.8521 (pp20) cc_final: 0.8227 (pp20) REVERT: j 152 MET cc_start: 0.9033 (mtp) cc_final: 0.8760 (mtm) REVERT: k 3 HIS cc_start: 0.8228 (m90) cc_final: 0.7866 (m-70) REVERT: k 9 MET cc_start: 0.8727 (mtp) cc_final: 0.8441 (mtp) REVERT: k 59 TYR cc_start: 0.8372 (m-80) cc_final: 0.7814 (m-80) REVERT: k 75 GLU cc_start: 0.9042 (mt-10) cc_final: 0.8649 (mt-10) REVERT: k 88 MET cc_start: 0.7283 (OUTLIER) cc_final: 0.5681 (tmm) REVERT: k 90 MET cc_start: 0.8281 (ttm) cc_final: 0.7775 (mtp) REVERT: l 33 ASP cc_start: 0.8092 (m-30) cc_final: 0.7864 (m-30) REVERT: l 99 LEU cc_start: 0.9340 (pp) cc_final: 0.9068 (tp) REVERT: l 142 HIS cc_start: 0.8694 (m90) cc_final: 0.7922 (m-70) REVERT: m 5 ASP cc_start: 0.8750 (t0) cc_final: 0.8035 (t0) REVERT: m 30 SER cc_start: 0.9434 (p) cc_final: 0.9105 (t) REVERT: m 75 ILE cc_start: 0.8500 (tp) cc_final: 0.8259 (tp) REVERT: m 127 CYS cc_start: 0.9274 (p) cc_final: 0.9063 (p) REVERT: n 19 VAL cc_start: 0.8296 (t) cc_final: 0.8020 (m) REVERT: n 25 ASN cc_start: 0.8954 (p0) cc_final: 0.8729 (p0) REVERT: n 27 LYS cc_start: 0.8734 (mmtm) cc_final: 0.8529 (mmtt) REVERT: n 100 LYS cc_start: 0.9137 (mptt) cc_final: 0.8913 (mmtt) REVERT: n 107 ASP cc_start: 0.8955 (OUTLIER) cc_final: 0.8563 (t0) REVERT: o 49 PHE cc_start: 0.8694 (m-80) cc_final: 0.8417 (m-80) REVERT: p 14 LYS cc_start: 0.8289 (tptt) cc_final: 0.8008 (tptt) REVERT: p 18 ASP cc_start: 0.8240 (p0) cc_final: 0.7699 (p0) REVERT: p 68 GLU cc_start: 0.8589 (mm-30) cc_final: 0.8269 (mm-30) REVERT: p 87 LYS cc_start: 0.8927 (ttmm) cc_final: 0.8384 (ttmm) REVERT: p 101 ASN cc_start: 0.9142 (t0) cc_final: 0.8736 (p0) REVERT: q 7 LEU cc_start: 0.9502 (mt) cc_final: 0.9289 (mp) REVERT: q 70 GLU cc_start: 0.8926 (mp0) cc_final: 0.8475 (mp0) REVERT: q 75 GLN cc_start: 0.9189 (pt0) cc_final: 0.8663 (pm20) REVERT: q 90 LEU cc_start: 0.9138 (tp) cc_final: 0.8908 (mt) REVERT: r 41 GLU cc_start: 0.8445 (mt-10) cc_final: 0.8179 (mt-10) REVERT: r 42 ASP cc_start: 0.8485 (p0) cc_final: 0.7913 (t0) REVERT: r 66 GLU cc_start: 0.8716 (pm20) cc_final: 0.8245 (pm20) REVERT: r 75 MET cc_start: 0.9338 (tmm) cc_final: 0.8835 (tmm) REVERT: r 86 TYR cc_start: 0.8469 (t80) cc_final: 0.8208 (t80) REVERT: s 4 GLN cc_start: 0.8108 (mm110) cc_final: 0.7505 (mm-40) REVERT: s 89 MET cc_start: 0.9129 (mmm) cc_final: 0.8733 (mmm) REVERT: t 62 GLN cc_start: 0.9113 (tt0) cc_final: 0.8819 (tp40) REVERT: t 64 ARG cc_start: 0.8801 (mmm160) cc_final: 0.8089 (tpp-160) REVERT: t 80 GLN cc_start: 0.8199 (tm130) cc_final: 0.7901 (tm-30) REVERT: t 89 ARG cc_start: 0.7242 (tmm-80) cc_final: 0.6865 (tmm-80) REVERT: u 2 VAL cc_start: 0.8621 (OUTLIER) cc_final: 0.8346 (t) REVERT: u 63 GLN cc_start: 0.8887 (mm-40) cc_final: 0.8266 (mm-40) REVERT: v 11 ARG cc_start: 0.8043 (mmm-85) cc_final: 0.7601 (mmm-85) REVERT: v 60 GLU cc_start: 0.7977 (mp0) cc_final: 0.7597 (mp0) REVERT: v 73 TRP cc_start: 0.9344 (m100) cc_final: 0.8569 (m100) REVERT: w 25 ASP cc_start: 0.8106 (t0) cc_final: 0.7678 (m-30) REVERT: x 7 LYS cc_start: 0.8372 (mtpp) cc_final: 0.7984 (mtpt) REVERT: x 32 ARG cc_start: 0.7385 (ttp80) cc_final: 0.6976 (ttp80) REVERT: x 53 ASN cc_start: 0.9138 (p0) cc_final: 0.8472 (p0) REVERT: x 55 ARG cc_start: 0.9027 (mtm180) cc_final: 0.8739 (mtm180) REVERT: y 13 GLN cc_start: 0.9337 (mt0) cc_final: 0.9091 (mt0) REVERT: y 24 ARG cc_start: 0.8764 (mmm160) cc_final: 0.8303 (mmp80) REVERT: y 60 ARG cc_start: 0.9110 (ttm110) cc_final: 0.8865 (ttm110) REVERT: z 33 ARG cc_start: 0.7781 (ptp-110) cc_final: 0.7331 (ptt180) REVERT: W 17 GLU cc_start: 0.8395 (mm-30) cc_final: 0.8179 (mm-30) outliers start: 248 outliers final: 164 residues processed: 1657 average time/residue: 1.3200 time to fit residues: 3871.2759 Evaluate side-chains 1635 residues out of total 4672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 1459 time to evaluate : 6.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 157 SER Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 183 GLU Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 188 MET Chi-restraints excluded: chain D residue 199 MET Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 42 GLU Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain E residue 127 ASN Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 20 ASN Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 88 GLN Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 21 VAL Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 139 PHE Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 55 ILE Chi-restraints excluded: chain J residue 60 ASP Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 90 ASN Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain M residue 119 LEU Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain O residue 12 THR Chi-restraints excluded: chain O residue 18 LEU Chi-restraints excluded: chain O residue 35 ILE Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain O residue 69 ASP Chi-restraints excluded: chain P residue 10 GLN Chi-restraints excluded: chain P residue 60 THR Chi-restraints excluded: chain P residue 73 VAL Chi-restraints excluded: chain P residue 97 LEU Chi-restraints excluded: chain P residue 114 LEU Chi-restraints excluded: chain Q residue 97 ASP Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain Q residue 107 THR Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 43 ASN Chi-restraints excluded: chain R residue 53 PHE Chi-restraints excluded: chain R residue 101 ILE Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 86 MET Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 17 SER Chi-restraints excluded: chain T residue 32 LEU Chi-restraints excluded: chain T residue 43 ILE Chi-restraints excluded: chain U residue 8 ASP Chi-restraints excluded: chain U residue 13 VAL Chi-restraints excluded: chain U residue 18 ASP Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain U residue 49 VAL Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain V residue 4 ILE Chi-restraints excluded: chain V residue 60 VAL Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain V residue 66 ASP Chi-restraints excluded: chain V residue 70 ILE Chi-restraints excluded: chain X residue 14 THR Chi-restraints excluded: chain X residue 65 ASP Chi-restraints excluded: chain Y residue 34 SER Chi-restraints excluded: chain Y residue 50 VAL Chi-restraints excluded: chain Z residue 10 THR Chi-restraints excluded: chain Z residue 41 THR Chi-restraints excluded: chain Z residue 57 VAL Chi-restraints excluded: chain c residue 5 ILE Chi-restraints excluded: chain c residue 9 ILE Chi-restraints excluded: chain c residue 14 SER Chi-restraints excluded: chain c residue 17 THR Chi-restraints excluded: chain d residue 8 SER Chi-restraints excluded: chain d residue 24 THR Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain d residue 45 SER Chi-restraints excluded: chain g residue 4 VAL Chi-restraints excluded: chain g residue 141 LEU Chi-restraints excluded: chain g residue 204 ASP Chi-restraints excluded: chain g residue 220 THR Chi-restraints excluded: chain h residue 31 ASP Chi-restraints excluded: chain h residue 49 LYS Chi-restraints excluded: chain h residue 53 SER Chi-restraints excluded: chain h residue 55 ILE Chi-restraints excluded: chain h residue 186 THR Chi-restraints excluded: chain h residue 201 TRP Chi-restraints excluded: chain i residue 160 GLU Chi-restraints excluded: chain i residue 164 GLN Chi-restraints excluded: chain i residue 169 THR Chi-restraints excluded: chain i residue 204 TYR Chi-restraints excluded: chain j residue 11 LEU Chi-restraints excluded: chain j residue 90 THR Chi-restraints excluded: chain k residue 7 VAL Chi-restraints excluded: chain k residue 18 VAL Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 64 VAL Chi-restraints excluded: chain k residue 82 ASP Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain k residue 85 ILE Chi-restraints excluded: chain k residue 88 MET Chi-restraints excluded: chain k residue 97 THR Chi-restraints excluded: chain l residue 30 LEU Chi-restraints excluded: chain l residue 54 SER Chi-restraints excluded: chain l residue 144 MET Chi-restraints excluded: chain m residue 99 LEU Chi-restraints excluded: chain n residue 72 ILE Chi-restraints excluded: chain n residue 98 LEU Chi-restraints excluded: chain n residue 107 ASP Chi-restraints excluded: chain o residue 6 ILE Chi-restraints excluded: chain o residue 10 LEU Chi-restraints excluded: chain o residue 15 HIS Chi-restraints excluded: chain o residue 44 THR Chi-restraints excluded: chain o residue 69 THR Chi-restraints excluded: chain o residue 78 GLU Chi-restraints excluded: chain o residue 80 THR Chi-restraints excluded: chain o residue 84 VAL Chi-restraints excluded: chain o residue 96 VAL Chi-restraints excluded: chain o residue 101 SER Chi-restraints excluded: chain p residue 46 THR Chi-restraints excluded: chain p residue 55 SER Chi-restraints excluded: chain p residue 64 GLN Chi-restraints excluded: chain p residue 81 ASN Chi-restraints excluded: chain p residue 82 LEU Chi-restraints excluded: chain p residue 84 VAL Chi-restraints excluded: chain p residue 97 ILE Chi-restraints excluded: chain q residue 47 SER Chi-restraints excluded: chain r residue 34 LEU Chi-restraints excluded: chain r residue 48 LEU Chi-restraints excluded: chain s residue 48 LEU Chi-restraints excluded: chain s residue 60 GLN Chi-restraints excluded: chain s residue 79 LEU Chi-restraints excluded: chain t residue 3 LEU Chi-restraints excluded: chain t residue 18 ASP Chi-restraints excluded: chain u residue 2 VAL Chi-restraints excluded: chain u residue 68 SER Chi-restraints excluded: chain v residue 43 LYS Chi-restraints excluded: chain v residue 70 THR Chi-restraints excluded: chain w residue 21 ILE Chi-restraints excluded: chain w residue 40 VAL Chi-restraints excluded: chain x residue 44 MET Chi-restraints excluded: chain x residue 48 THR Chi-restraints excluded: chain x residue 58 VAL Chi-restraints excluded: chain x residue 63 THR Chi-restraints excluded: chain y residue 27 MET Chi-restraints excluded: chain y residue 43 ASP Chi-restraints excluded: chain W residue 31 VAL Chi-restraints excluded: chain W residue 59 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1010 random chunks: chunk 813 optimal weight: 8.9990 chunk 554 optimal weight: 20.0000 chunk 14 optimal weight: 20.0000 chunk 726 optimal weight: 7.9990 chunk 402 optimal weight: 30.0000 chunk 833 optimal weight: 5.9990 chunk 674 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 498 optimal weight: 8.9990 chunk 876 optimal weight: 3.9990 chunk 246 optimal weight: 10.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 53 HIS C 36 GLN D 90 GLN ** P 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 75 GLN ** Q 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 48 GLN ** U 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 78 GLN ** X 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 26 HIS f 13 ASN ** g 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 109 GLN ** g 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 122 ASN m 118 GLN p 64 GLN s 66 GLN ** x 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.2764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 156844 Z= 0.373 Angle : 0.688 13.499 234723 Z= 0.368 Chirality : 0.038 0.388 29908 Planarity : 0.006 0.132 12506 Dihedral : 23.753 179.595 78631 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 16.69 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.31 % Favored : 95.58 % Rotamer: Outliers : 6.16 % Allowed : 23.50 % Favored : 70.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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 (0.11), residues: 5614 helix: 0.82 (0.12), residues: 1988 sheet: -0.63 (0.16), residues: 1048 loop : -0.94 (0.12), residues: 2578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP g 23 HIS 0.014 0.001 HIS o 70 PHE 0.033 0.002 PHE U 96 TYR 0.031 0.002 TYR g 213 ARG 0.011 0.001 ARG V 93 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11228 Ramachandran restraints generated. 5614 Oldfield, 0 Emsley, 5614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11228 Ramachandran restraints generated. 5614 Oldfield, 0 Emsley, 5614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1808 residues out of total 4672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 288 poor density : 1520 time to evaluate : 6.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 117 GLN cc_start: 0.8720 (tt0) cc_final: 0.8328 (tp-100) REVERT: B 180 GLU cc_start: 0.8570 (mt-10) cc_final: 0.8280 (tt0) REVERT: B 201 MET cc_start: 0.8786 (ptp) cc_final: 0.8579 (ptm) REVERT: B 203 ARG cc_start: 0.8777 (ptp-110) cc_final: 0.8123 (ptp-170) REVERT: B 251 GLN cc_start: 0.8615 (tm-30) cc_final: 0.8175 (tm-30) REVERT: C 11 MET cc_start: 0.8907 (mtp) cc_final: 0.8655 (mtp) REVERT: C 128 ARG cc_start: 0.8368 (mtt90) cc_final: 0.7504 (ttt-90) REVERT: C 137 SER cc_start: 0.9121 (m) cc_final: 0.8826 (p) REVERT: D 136 GLN cc_start: 0.9177 (tp-100) cc_final: 0.8780 (tp40) REVERT: D 156 ASN cc_start: 0.8998 (m-40) cc_final: 0.8681 (t0) REVERT: E 42 GLU cc_start: 0.9240 (pt0) cc_final: 0.8677 (pm20) REVERT: E 130 MET cc_start: 0.8807 (ppp) cc_final: 0.8513 (ppp) REVERT: E 135 GLN cc_start: 0.7975 (pm20) cc_final: 0.6628 (pm20) REVERT: E 138 PHE cc_start: 0.8911 (m-80) cc_final: 0.8563 (m-80) REVERT: E 177 PHE cc_start: 0.6740 (m-10) cc_final: 0.6512 (m-10) REVERT: F 39 ASP cc_start: 0.8824 (p0) cc_final: 0.8593 (p0) REVERT: F 58 TYR cc_start: 0.7605 (m-80) cc_final: 0.7052 (m-80) REVERT: F 62 TRP cc_start: 0.8638 (m100) cc_final: 0.8342 (m100) REVERT: F 83 PHE cc_start: 0.8449 (m-80) cc_final: 0.7992 (m-80) REVERT: F 101 ASN cc_start: 0.8926 (p0) cc_final: 0.8545 (p0) REVERT: F 124 GLU cc_start: 0.8558 (tm-30) cc_final: 0.8358 (tm-30) REVERT: F 130 GLU cc_start: 0.8388 (tp30) cc_final: 0.7743 (tp30) REVERT: F 137 ASP cc_start: 0.9076 (t0) cc_final: 0.8822 (t0) REVERT: J 31 GLU cc_start: 0.8664 (tp30) cc_final: 0.8420 (tp30) REVERT: J 96 ARG cc_start: 0.8675 (ttt-90) cc_final: 0.8266 (mmm-85) REVERT: J 98 GLU cc_start: 0.8944 (mp0) cc_final: 0.8716 (mp0) REVERT: K 12 ASP cc_start: 0.8535 (p0) cc_final: 0.8143 (p0) REVERT: K 88 ASN cc_start: 0.8467 (t0) cc_final: 0.8105 (t0) REVERT: L 76 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7771 (tt0) REVERT: L 81 ASP cc_start: 0.8875 (t0) cc_final: 0.8440 (t0) REVERT: M 3 GLN cc_start: 0.9222 (tt0) cc_final: 0.8877 (tt0) REVERT: M 47 GLU cc_start: 0.8758 (tp30) cc_final: 0.8365 (tp30) REVERT: M 110 GLU cc_start: 0.8881 (tt0) cc_final: 0.8227 (tm-30) REVERT: M 133 LYS cc_start: 0.9017 (tppt) cc_final: 0.8778 (tptt) REVERT: N 9 GLN cc_start: 0.8593 (tt0) cc_final: 0.8337 (tt0) REVERT: N 20 MET cc_start: 0.9334 (ttp) cc_final: 0.8896 (ttp) REVERT: N 72 ASP cc_start: 0.8395 (t70) cc_final: 0.8043 (t70) REVERT: N 117 ASP cc_start: 0.8624 (m-30) cc_final: 0.8379 (p0) REVERT: O 40 ILE cc_start: 0.8956 (mt) cc_final: 0.8727 (mp) REVERT: O 76 LYS cc_start: 0.9423 (mmmm) cc_final: 0.9168 (mmmm) REVERT: O 88 LYS cc_start: 0.9144 (mmmt) cc_final: 0.8928 (mmmt) REVERT: O 93 ASP cc_start: 0.8578 (t0) cc_final: 0.8277 (t0) REVERT: O 98 GLN cc_start: 0.8118 (mm-40) cc_final: 0.7832 (mm110) REVERT: P 24 ASP cc_start: 0.8399 (m-30) cc_final: 0.7947 (m-30) REVERT: P 98 TYR cc_start: 0.9231 (m-80) cc_final: 0.8674 (m-80) REVERT: P 112 GLU cc_start: 0.8000 (pp20) cc_final: 0.7517 (pp20) REVERT: Q 11 ARG cc_start: 0.8670 (tpp80) cc_final: 0.8469 (tpp-160) REVERT: Q 102 ASP cc_start: 0.8471 (t0) cc_final: 0.8217 (t0) REVERT: R 2 TYR cc_start: 0.9418 (p90) cc_final: 0.9211 (p90) REVERT: R 31 GLU cc_start: 0.8087 (mp0) cc_final: 0.7784 (mp0) REVERT: R 34 GLU cc_start: 0.8674 (mm-30) cc_final: 0.8420 (mm-30) REVERT: R 37 GLU cc_start: 0.8077 (pm20) cc_final: 0.7847 (pm20) REVERT: R 48 LYS cc_start: 0.9124 (ptpp) cc_final: 0.8742 (ptpp) REVERT: R 55 ASP cc_start: 0.8593 (p0) cc_final: 0.8117 (p0) REVERT: R 60 LYS cc_start: 0.9234 (mttp) cc_final: 0.8853 (pttt) REVERT: R 62 GLU cc_start: 0.8103 (tp30) cc_final: 0.7425 (tp30) REVERT: R 85 LYS cc_start: 0.9027 (ttmm) cc_final: 0.8510 (mtpp) REVERT: S 2 GLU cc_start: 0.8791 (mp0) cc_final: 0.8542 (mp0) REVERT: S 62 ASP cc_start: 0.8580 (t0) cc_final: 0.8081 (t0) REVERT: S 73 LYS cc_start: 0.8899 (mttt) cc_final: 0.8645 (mttm) REVERT: T 24 MET cc_start: 0.8633 (tpt) cc_final: 0.8420 (tpp) REVERT: T 56 GLU cc_start: 0.9224 (mm-30) cc_final: 0.8908 (tp30) REVERT: T 91 GLN cc_start: 0.9018 (mm-40) cc_final: 0.8479 (mm110) REVERT: U 8 ASP cc_start: 0.8213 (p0) cc_final: 0.7701 (t0) REVERT: U 10 GLU cc_start: 0.8436 (tt0) cc_final: 0.7890 (tm-30) REVERT: U 22 ARG cc_start: 0.8849 (mtm-85) cc_final: 0.8345 (mtm-85) REVERT: U 29 LEU cc_start: 0.9371 (mm) cc_final: 0.9067 (mm) REVERT: U 46 GLN cc_start: 0.8716 (tp-100) cc_final: 0.8498 (tp-100) REVERT: V 48 MET cc_start: 0.9238 (tpt) cc_final: 0.8678 (tpt) REVERT: V 50 MET cc_start: 0.9285 (mtp) cc_final: 0.9002 (mtp) REVERT: V 75 GLN cc_start: 0.9276 (tp40) cc_final: 0.9057 (tp-100) REVERT: V 90 ASP cc_start: 0.8983 (m-30) cc_final: 0.8453 (t0) REVERT: X 35 SER cc_start: 0.9419 (m) cc_final: 0.9095 (t) REVERT: X 43 GLU cc_start: 0.9020 (mt-10) cc_final: 0.8583 (tt0) REVERT: X 70 GLU cc_start: 0.8518 (tm-30) cc_final: 0.8104 (tm-30) REVERT: Y 13 GLU cc_start: 0.8593 (mt-10) cc_final: 0.8349 (mt-10) REVERT: Y 15 ASN cc_start: 0.9412 (m-40) cc_final: 0.9030 (m-40) REVERT: Y 17 GLU cc_start: 0.9131 (tp30) cc_final: 0.8783 (mm-30) REVERT: Y 24 GLU cc_start: 0.8750 (mt-10) cc_final: 0.8482 (mt-10) REVERT: Y 31 GLN cc_start: 0.9435 (mt0) cc_final: 0.9201 (mt0) REVERT: Y 36 GLN cc_start: 0.9154 (mm110) cc_final: 0.8901 (mm-40) REVERT: Y 45 GLN cc_start: 0.9069 (mt0) cc_final: 0.8831 (mm-40) REVERT: Y 55 THR cc_start: 0.9350 (OUTLIER) cc_final: 0.9069 (p) REVERT: Y 59 GLU cc_start: 0.9100 (tp30) cc_final: 0.8803 (tp30) REVERT: Z 3 LYS cc_start: 0.9182 (tppt) cc_final: 0.8953 (tppt) REVERT: Z 6 LYS cc_start: 0.8982 (mtmm) cc_final: 0.8686 (mtmm) REVERT: Z 58 GLU cc_start: 0.7623 (tp30) cc_final: 0.7148 (tp30) REVERT: a 22 MET cc_start: 0.4833 (pmm) cc_final: 0.4125 (pmm) REVERT: b 12 LYS cc_start: 0.9030 (mmmt) cc_final: 0.8394 (mmmt) REVERT: b 36 GLU cc_start: 0.8283 (pt0) cc_final: 0.7824 (pt0) REVERT: b 46 ASP cc_start: 0.8923 (m-30) cc_final: 0.8611 (m-30) REVERT: b 48 TYR cc_start: 0.8836 (m-80) cc_final: 0.8221 (m-10) REVERT: c 10 LYS cc_start: 0.7559 (ptmt) cc_final: 0.6984 (ptpp) REVERT: c 17 THR cc_start: 0.7776 (OUTLIER) cc_final: 0.7400 (p) REVERT: c 28 ARG cc_start: 0.8336 (mpt180) cc_final: 0.7929 (mpt180) REVERT: c 34 LEU cc_start: 0.7806 (tp) cc_final: 0.7453 (tp) REVERT: c 37 LYS cc_start: 0.9078 (tttt) cc_final: 0.8773 (tppt) REVERT: c 39 PHE cc_start: 0.8662 (t80) cc_final: 0.8272 (t80) REVERT: d 2 LYS cc_start: 0.9289 (tttt) cc_final: 0.9074 (tttm) REVERT: d 28 ARG cc_start: 0.8859 (mtm-85) cc_final: 0.8624 (mtm-85) REVERT: f 18 LYS cc_start: 0.8847 (ttmt) cc_final: 0.8427 (ttmt) REVERT: f 35 GLN cc_start: 0.8947 (mt0) cc_final: 0.8418 (mt0) REVERT: g 93 ASN cc_start: 0.7845 (p0) cc_final: 0.5861 (t0) REVERT: h 41 GLN cc_start: 0.9250 (pp30) cc_final: 0.8941 (pp30) REVERT: h 42 TYR cc_start: 0.9033 (t80) cc_final: 0.8607 (t80) REVERT: h 152 GLU cc_start: 0.8173 (tm-30) cc_final: 0.7690 (tm-30) REVERT: h 181 ASP cc_start: 0.8533 (t70) cc_final: 0.8133 (t70) REVERT: h 183 ASP cc_start: 0.8635 (t0) cc_final: 0.8321 (t0) REVERT: h 187 SER cc_start: 0.8256 (t) cc_final: 0.7697 (p) REVERT: h 201 TRP cc_start: 0.8680 (OUTLIER) cc_final: 0.7572 (m-10) REVERT: i 11 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8331 (mt) REVERT: i 32 CYS cc_start: 0.7311 (p) cc_final: 0.6592 (p) REVERT: i 34 ILE cc_start: 0.8761 (tp) cc_final: 0.8556 (mm) REVERT: i 107 PHE cc_start: 0.8910 (m-10) cc_final: 0.8583 (m-80) REVERT: i 141 ASP cc_start: 0.7892 (m-30) cc_final: 0.7489 (m-30) REVERT: i 160 GLU cc_start: 0.9278 (OUTLIER) cc_final: 0.9052 (mp0) REVERT: i 164 GLN cc_start: 0.8688 (OUTLIER) cc_final: 0.8182 (mp10) REVERT: j 41 ASP cc_start: 0.8732 (p0) cc_final: 0.8407 (p0) REVERT: j 65 GLU cc_start: 0.8722 (tp30) cc_final: 0.8339 (tp30) REVERT: j 69 ARG cc_start: 0.8743 (ttm-80) cc_final: 0.8438 (ttm-80) REVERT: j 76 LEU cc_start: 0.9019 (tt) cc_final: 0.8784 (tt) REVERT: j 93 ARG cc_start: 0.8797 (mpp80) cc_final: 0.8372 (mpp80) REVERT: j 128 TYR cc_start: 0.8921 (m-80) cc_final: 0.8538 (m-80) REVERT: k 3 HIS cc_start: 0.8259 (m90) cc_final: 0.7811 (m-70) REVERT: k 9 MET cc_start: 0.8661 (mtp) cc_final: 0.8396 (mtp) REVERT: k 14 GLN cc_start: 0.8660 (mp10) cc_final: 0.8266 (mp10) REVERT: k 24 ARG cc_start: 0.9131 (ptp90) cc_final: 0.8879 (ptp-170) REVERT: k 59 TYR cc_start: 0.8262 (m-80) cc_final: 0.7727 (m-80) REVERT: k 75 GLU cc_start: 0.9099 (mt-10) cc_final: 0.8839 (mt-10) REVERT: k 88 MET cc_start: 0.7538 (OUTLIER) cc_final: 0.6594 (tmm) REVERT: l 142 HIS cc_start: 0.8652 (m90) cc_final: 0.7905 (m90) REVERT: m 5 ASP cc_start: 0.8741 (t0) cc_final: 0.8087 (t0) REVERT: m 30 SER cc_start: 0.9471 (p) cc_final: 0.9109 (t) REVERT: m 73 GLU cc_start: 0.8681 (tp30) cc_final: 0.8323 (tt0) REVERT: n 20 PHE cc_start: 0.7757 (m-80) cc_final: 0.7444 (m-80) REVERT: n 25 ASN cc_start: 0.8909 (p0) cc_final: 0.8690 (p0) REVERT: n 27 LYS cc_start: 0.8588 (mmtm) cc_final: 0.8306 (mmtm) REVERT: n 57 MET cc_start: 0.8654 (mpp) cc_final: 0.8346 (mpp) REVERT: n 100 LYS cc_start: 0.9142 (mptt) cc_final: 0.8935 (mmtt) REVERT: n 107 ASP cc_start: 0.8954 (OUTLIER) cc_final: 0.8500 (t0) REVERT: o 49 PHE cc_start: 0.8651 (m-80) cc_final: 0.8391 (m-80) REVERT: o 63 ASP cc_start: 0.8212 (OUTLIER) cc_final: 0.7994 (m-30) REVERT: p 14 LYS cc_start: 0.8291 (tptt) cc_final: 0.8005 (tptt) REVERT: p 18 ASP cc_start: 0.8422 (p0) cc_final: 0.7863 (p0) REVERT: p 64 GLN cc_start: 0.9097 (OUTLIER) cc_final: 0.8772 (pp30) REVERT: p 68 GLU cc_start: 0.8595 (mm-30) cc_final: 0.8319 (mm-30) REVERT: p 87 LYS cc_start: 0.8902 (ttmm) cc_final: 0.8357 (ttmm) REVERT: p 101 ASN cc_start: 0.9142 (t0) cc_final: 0.8725 (p0) REVERT: q 7 LEU cc_start: 0.9593 (mt) cc_final: 0.9353 (mp) REVERT: q 75 GLN cc_start: 0.9195 (pt0) cc_final: 0.8658 (pm20) REVERT: q 79 VAL cc_start: 0.9347 (t) cc_final: 0.9099 (p) REVERT: q 90 LEU cc_start: 0.9134 (tp) cc_final: 0.8865 (mt) REVERT: q 112 GLN cc_start: 0.8777 (mt0) cc_final: 0.7927 (mt0) REVERT: r 41 GLU cc_start: 0.8533 (mt-10) cc_final: 0.8119 (mt-10) REVERT: r 42 ASP cc_start: 0.8365 (p0) cc_final: 0.7732 (t0) REVERT: r 75 MET cc_start: 0.9379 (tmm) cc_final: 0.8972 (tmm) REVERT: r 86 TYR cc_start: 0.8478 (t80) cc_final: 0.8214 (t80) REVERT: s 4 GLN cc_start: 0.8360 (mm110) cc_final: 0.7712 (mm-40) REVERT: s 10 GLU cc_start: 0.9227 (tp30) cc_final: 0.8961 (tp30) REVERT: t 62 GLN cc_start: 0.9152 (tt0) cc_final: 0.8884 (tp40) REVERT: t 80 GLN cc_start: 0.8214 (tm130) cc_final: 0.7916 (tm-30) REVERT: t 89 ARG cc_start: 0.7169 (tmm-80) cc_final: 0.6514 (tmm-80) REVERT: u 2 VAL cc_start: 0.8840 (OUTLIER) cc_final: 0.8580 (t) REVERT: u 12 LYS cc_start: 0.7657 (ttmt) cc_final: 0.7451 (mtpp) REVERT: u 48 GLU cc_start: 0.8798 (mt-10) cc_final: 0.8595 (mt-10) REVERT: u 63 GLN cc_start: 0.8902 (mm-40) cc_final: 0.8319 (mm-40) REVERT: v 13 VAL cc_start: 0.9410 (t) cc_final: 0.9068 (m) REVERT: v 60 GLU cc_start: 0.7995 (mp0) cc_final: 0.7588 (mp0) REVERT: v 73 TRP cc_start: 0.9414 (m100) cc_final: 0.8505 (m100) REVERT: w 25 ASP cc_start: 0.8285 (t0) cc_final: 0.8070 (t0) REVERT: x 7 LYS cc_start: 0.8240 (mtpp) cc_final: 0.7837 (mtpt) REVERT: x 53 ASN cc_start: 0.9155 (p0) cc_final: 0.8656 (p0) REVERT: x 55 ARG cc_start: 0.8967 (mtm180) cc_final: 0.8718 (mtm180) REVERT: y 13 GLN cc_start: 0.9322 (mt0) cc_final: 0.9075 (mt0) REVERT: z 33 ARG cc_start: 0.7889 (ptp-110) cc_final: 0.7349 (ptt180) REVERT: W 39 ARG cc_start: 0.8862 (mtp85) cc_final: 0.8658 (mtp85) outliers start: 288 outliers final: 204 residues processed: 1641 average time/residue: 1.2327 time to fit residues: 3549.8800 Evaluate side-chains 1680 residues out of total 4672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 215 poor density : 1465 time to evaluate : 6.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 157 SER Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 183 GLU Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 199 MET Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 61 SER Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain E residue 127 ASN Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 20 ASN Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 88 GLN Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 21 VAL Chi-restraints excluded: chain G residue 130 VAL Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 139 PHE Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 55 ILE Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 60 ASP Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain J residue 139 VAL Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 90 ASN Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 26 VAL Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain N residue 53 THR Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain O residue 12 THR Chi-restraints excluded: chain O residue 18 LEU Chi-restraints excluded: chain O residue 35 ILE Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain O residue 67 ASN Chi-restraints excluded: chain O residue 69 ASP Chi-restraints excluded: chain P residue 10 GLN Chi-restraints excluded: chain P residue 60 THR Chi-restraints excluded: chain P residue 73 VAL Chi-restraints excluded: chain P residue 85 SER Chi-restraints excluded: chain P residue 97 LEU Chi-restraints excluded: chain P residue 114 LEU Chi-restraints excluded: chain Q residue 4 VAL Chi-restraints excluded: chain Q residue 97 ASP Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain Q residue 107 THR Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 43 ASN Chi-restraints excluded: chain R residue 53 PHE Chi-restraints excluded: chain R residue 101 ILE Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 85 ILE Chi-restraints excluded: chain S residue 86 MET Chi-restraints excluded: chain S residue 104 THR Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 17 SER Chi-restraints excluded: chain T residue 32 LEU Chi-restraints excluded: chain U residue 9 ASP Chi-restraints excluded: chain U residue 13 VAL Chi-restraints excluded: chain U residue 18 ASP Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain U residue 49 VAL Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain V residue 3 THR Chi-restraints excluded: chain V residue 4 ILE Chi-restraints excluded: chain V residue 7 GLU Chi-restraints excluded: chain V residue 38 LEU Chi-restraints excluded: chain V residue 60 VAL Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain V residue 66 ASP Chi-restraints excluded: chain V residue 70 ILE Chi-restraints excluded: chain X residue 14 THR Chi-restraints excluded: chain X residue 65 ASP Chi-restraints excluded: chain Y residue 34 SER Chi-restraints excluded: chain Y residue 50 VAL Chi-restraints excluded: chain Y residue 55 THR Chi-restraints excluded: chain Z residue 10 THR Chi-restraints excluded: chain Z residue 40 ASP Chi-restraints excluded: chain Z residue 41 THR Chi-restraints excluded: chain Z residue 57 VAL Chi-restraints excluded: chain a residue 28 VAL Chi-restraints excluded: chain b residue 3 VAL Chi-restraints excluded: chain c residue 5 ILE Chi-restraints excluded: chain c residue 9 ILE Chi-restraints excluded: chain c residue 12 VAL Chi-restraints excluded: chain c residue 17 THR Chi-restraints excluded: chain c residue 42 VAL Chi-restraints excluded: chain d residue 4 THR Chi-restraints excluded: chain d residue 8 SER Chi-restraints excluded: chain d residue 24 THR Chi-restraints excluded: chain d residue 45 SER Chi-restraints excluded: chain e residue 6 THR Chi-restraints excluded: chain e residue 29 LEU Chi-restraints excluded: chain e residue 38 THR Chi-restraints excluded: chain e residue 44 LEU Chi-restraints excluded: chain f residue 3 VAL Chi-restraints excluded: chain g residue 4 VAL Chi-restraints excluded: chain g residue 6 MET Chi-restraints excluded: chain g residue 20 THR Chi-restraints excluded: chain g residue 23 TRP Chi-restraints excluded: chain g residue 127 ASP Chi-restraints excluded: chain g residue 199 VAL Chi-restraints excluded: chain g residue 204 ASP Chi-restraints excluded: chain g residue 205 ASP Chi-restraints excluded: chain g residue 207 ILE Chi-restraints excluded: chain h residue 31 ASP Chi-restraints excluded: chain h residue 53 SER Chi-restraints excluded: chain h residue 55 ILE Chi-restraints excluded: chain h residue 186 THR Chi-restraints excluded: chain h residue 201 TRP Chi-restraints excluded: chain i residue 11 LEU Chi-restraints excluded: chain i residue 160 GLU Chi-restraints excluded: chain i residue 164 GLN Chi-restraints excluded: chain i residue 204 TYR Chi-restraints excluded: chain j residue 11 LEU Chi-restraints excluded: chain j residue 52 LYS Chi-restraints excluded: chain j residue 90 THR Chi-restraints excluded: chain k residue 18 VAL Chi-restraints excluded: chain k residue 26 THR Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 64 VAL Chi-restraints excluded: chain k residue 82 ASP Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain k residue 85 ILE Chi-restraints excluded: chain k residue 88 MET Chi-restraints excluded: chain k residue 97 THR Chi-restraints excluded: chain l residue 30 LEU Chi-restraints excluded: chain l residue 54 SER Chi-restraints excluded: chain l residue 144 MET Chi-restraints excluded: chain m residue 61 LEU Chi-restraints excluded: chain n residue 29 VAL Chi-restraints excluded: chain n residue 72 ILE Chi-restraints excluded: chain n residue 90 TYR Chi-restraints excluded: chain n residue 98 LEU Chi-restraints excluded: chain n residue 107 ASP Chi-restraints excluded: chain n residue 111 VAL Chi-restraints excluded: chain o residue 6 ILE Chi-restraints excluded: chain o residue 10 LEU Chi-restraints excluded: chain o residue 15 HIS Chi-restraints excluded: chain o residue 44 THR Chi-restraints excluded: chain o residue 63 ASP Chi-restraints excluded: chain o residue 69 THR Chi-restraints excluded: chain o residue 78 GLU Chi-restraints excluded: chain o residue 80 THR Chi-restraints excluded: chain o residue 84 VAL Chi-restraints excluded: chain o residue 96 VAL Chi-restraints excluded: chain p residue 31 ILE Chi-restraints excluded: chain p residue 46 THR Chi-restraints excluded: chain p residue 55 SER Chi-restraints excluded: chain p residue 64 GLN Chi-restraints excluded: chain p residue 81 ASN Chi-restraints excluded: chain p residue 82 LEU Chi-restraints excluded: chain p residue 84 VAL Chi-restraints excluded: chain p residue 97 ILE Chi-restraints excluded: chain q residue 3 THR Chi-restraints excluded: chain q residue 47 SER Chi-restraints excluded: chain s residue 48 LEU Chi-restraints excluded: chain s residue 79 LEU Chi-restraints excluded: chain t residue 3 LEU Chi-restraints excluded: chain t residue 18 ASP Chi-restraints excluded: chain u residue 2 VAL Chi-restraints excluded: chain u residue 29 ASN Chi-restraints excluded: chain u residue 68 SER Chi-restraints excluded: chain u residue 74 LEU Chi-restraints excluded: chain v residue 43 LYS Chi-restraints excluded: chain v residue 55 ILE Chi-restraints excluded: chain v residue 70 THR Chi-restraints excluded: chain w residue 21 ILE Chi-restraints excluded: chain w residue 40 VAL Chi-restraints excluded: chain w residue 67 LEU Chi-restraints excluded: chain x residue 5 LEU Chi-restraints excluded: chain x residue 48 THR Chi-restraints excluded: chain x residue 58 VAL Chi-restraints excluded: chain y residue 27 MET Chi-restraints excluded: chain y residue 43 ASP Chi-restraints excluded: chain W residue 59 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1010 random chunks: chunk 328 optimal weight: 10.0000 chunk 879 optimal weight: 5.9990 chunk 192 optimal weight: 10.0000 chunk 573 optimal weight: 30.0000 chunk 241 optimal weight: 10.0000 chunk 977 optimal weight: 8.9990 chunk 811 optimal weight: 2.9990 chunk 452 optimal weight: 10.0000 chunk 81 optimal weight: 10.0000 chunk 323 optimal weight: 10.0000 chunk 513 optimal weight: 8.9990 overall best weight: 7.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 36 GLN D 90 GLN E 27 GLN ** P 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 75 GLN Q 52 GLN ** Q 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 48 GLN T 59 ASN ** U 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 27 ASN Y 38 GLN ** g 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 25 ASN ** h 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 139 GLN ** i 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 61 GLN k 68 GLN ** l 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 148 ASN m 118 GLN p 64 GLN s 66 GLN v 45 HIS ** x 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8815 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.093 156844 Z= 0.379 Angle : 0.688 13.389 234723 Z= 0.368 Chirality : 0.038 0.382 29908 Planarity : 0.006 0.130 12506 Dihedral : 23.759 179.967 78631 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 16.64 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.15 % Favored : 95.76 % Rotamer: Outliers : 6.53 % Allowed : 24.06 % Favored : 69.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.45 (0.11), residues: 5614 helix: 0.80 (0.12), residues: 1984 sheet: -0.70 (0.16), residues: 1060 loop : -0.93 (0.12), residues: 2570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP l 103 HIS 0.025 0.001 HIS o 70 PHE 0.029 0.002 PHE U 96 TYR 0.032 0.002 TYR g 213 ARG 0.011 0.001 ARG F 170 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11228 Ramachandran restraints generated. 5614 Oldfield, 0 Emsley, 5614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11228 Ramachandran restraints generated. 5614 Oldfield, 0 Emsley, 5614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1803 residues out of total 4672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 305 poor density : 1498 time to evaluate : 6.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 117 GLN cc_start: 0.8711 (tt0) cc_final: 0.8467 (tp-100) REVERT: B 145 GLU cc_start: 0.8728 (mt-10) cc_final: 0.8431 (mt-10) REVERT: B 203 ARG cc_start: 0.8769 (ptp-110) cc_final: 0.8096 (ptp-170) REVERT: B 240 PHE cc_start: 0.9227 (t80) cc_final: 0.8979 (t80) REVERT: B 251 GLN cc_start: 0.8624 (tm-30) cc_final: 0.8173 (tm-30) REVERT: C 11 MET cc_start: 0.8889 (mtp) cc_final: 0.8636 (mtp) REVERT: C 128 ARG cc_start: 0.8431 (mtt90) cc_final: 0.8200 (mtt-85) REVERT: C 137 SER cc_start: 0.9090 (m) cc_final: 0.8797 (p) REVERT: D 1 MET cc_start: 0.8528 (mmt) cc_final: 0.7959 (mmt) REVERT: D 136 GLN cc_start: 0.9173 (tp-100) cc_final: 0.8775 (tp40) REVERT: D 156 ASN cc_start: 0.9016 (m-40) cc_final: 0.8690 (t0) REVERT: E 42 GLU cc_start: 0.9223 (OUTLIER) cc_final: 0.8639 (pm20) REVERT: E 94 GLU cc_start: 0.8806 (pp20) cc_final: 0.8583 (pp20) REVERT: E 130 MET cc_start: 0.8799 (ppp) cc_final: 0.8345 (ppp) REVERT: E 138 PHE cc_start: 0.8894 (m-80) cc_final: 0.8584 (m-80) REVERT: E 177 PHE cc_start: 0.6793 (m-10) cc_final: 0.6500 (m-80) REVERT: F 39 ASP cc_start: 0.8823 (p0) cc_final: 0.8557 (p0) REVERT: F 58 TYR cc_start: 0.7599 (m-80) cc_final: 0.7105 (m-80) REVERT: F 83 PHE cc_start: 0.8414 (m-80) cc_final: 0.7940 (m-80) REVERT: F 101 ASN cc_start: 0.8925 (p0) cc_final: 0.8518 (p0) REVERT: F 130 GLU cc_start: 0.8420 (tp30) cc_final: 0.7858 (tp30) REVERT: F 137 ASP cc_start: 0.9050 (t0) cc_final: 0.8787 (t0) REVERT: J 31 GLU cc_start: 0.8665 (tp30) cc_final: 0.8438 (tp30) REVERT: J 98 GLU cc_start: 0.8927 (mp0) cc_final: 0.8719 (mp0) REVERT: K 12 ASP cc_start: 0.8574 (p0) cc_final: 0.8155 (p0) REVERT: K 88 ASN cc_start: 0.8449 (t0) cc_final: 0.8171 (t0) REVERT: L 76 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7716 (tt0) REVERT: L 81 ASP cc_start: 0.8879 (t0) cc_final: 0.8431 (t0) REVERT: M 3 GLN cc_start: 0.9225 (tt0) cc_final: 0.8899 (tt0) REVERT: M 22 GLN cc_start: 0.8617 (mm110) cc_final: 0.8256 (mm-40) REVERT: M 47 GLU cc_start: 0.8800 (tp30) cc_final: 0.8375 (tp30) REVERT: M 110 GLU cc_start: 0.8862 (tt0) cc_final: 0.8221 (tm-30) REVERT: N 9 GLN cc_start: 0.8616 (tt0) cc_final: 0.8386 (tt0) REVERT: N 20 MET cc_start: 0.9329 (ttp) cc_final: 0.8890 (ttp) REVERT: N 72 ASP cc_start: 0.8429 (t70) cc_final: 0.8098 (t70) REVERT: O 40 ILE cc_start: 0.8950 (mt) cc_final: 0.8712 (mp) REVERT: O 52 SER cc_start: 0.9594 (m) cc_final: 0.8768 (p) REVERT: O 76 LYS cc_start: 0.9398 (mmmm) cc_final: 0.9095 (mmmm) REVERT: O 88 LYS cc_start: 0.9081 (mmmt) cc_final: 0.8852 (mmmt) REVERT: O 93 ASP cc_start: 0.8601 (t0) cc_final: 0.8306 (t0) REVERT: O 98 GLN cc_start: 0.8085 (mm-40) cc_final: 0.7781 (mm110) REVERT: P 13 MET cc_start: 0.8549 (mmm) cc_final: 0.8274 (mmm) REVERT: P 24 ASP cc_start: 0.8395 (m-30) cc_final: 0.7964 (m-30) REVERT: P 98 TYR cc_start: 0.9240 (m-80) cc_final: 0.8934 (m-80) REVERT: Q 102 ASP cc_start: 0.8483 (t0) cc_final: 0.8233 (t0) REVERT: R 2 TYR cc_start: 0.9426 (p90) cc_final: 0.9101 (p90) REVERT: R 31 GLU cc_start: 0.8130 (mp0) cc_final: 0.7777 (mp0) REVERT: R 34 GLU cc_start: 0.8649 (mm-30) cc_final: 0.8340 (mm-30) REVERT: R 48 LYS cc_start: 0.9142 (ptpp) cc_final: 0.8762 (ptpp) REVERT: R 60 LYS cc_start: 0.9245 (mttp) cc_final: 0.8888 (pttt) REVERT: R 62 GLU cc_start: 0.8214 (tp30) cc_final: 0.7524 (tp30) REVERT: R 94 THR cc_start: 0.9349 (OUTLIER) cc_final: 0.8727 (p) REVERT: S 1 MET cc_start: 0.8507 (ttm) cc_final: 0.7950 (ttt) REVERT: S 62 ASP cc_start: 0.8485 (t0) cc_final: 0.8189 (t0) REVERT: S 73 LYS cc_start: 0.8878 (mttt) cc_final: 0.8656 (mttm) REVERT: S 94 ASP cc_start: 0.7863 (m-30) cc_final: 0.7625 (m-30) REVERT: T 91 GLN cc_start: 0.9014 (mm-40) cc_final: 0.8492 (mm110) REVERT: U 8 ASP cc_start: 0.8249 (OUTLIER) cc_final: 0.7724 (t0) REVERT: U 10 GLU cc_start: 0.8429 (tt0) cc_final: 0.7886 (tm-30) REVERT: U 22 ARG cc_start: 0.8845 (mtm-85) cc_final: 0.8244 (mtm-85) REVERT: U 27 ASN cc_start: 0.9011 (p0) cc_final: 0.8526 (p0) REVERT: U 29 LEU cc_start: 0.9371 (mm) cc_final: 0.9048 (mm) REVERT: U 46 GLN cc_start: 0.8720 (tp-100) cc_final: 0.8513 (tp-100) REVERT: V 48 MET cc_start: 0.9257 (tpt) cc_final: 0.8774 (tpt) REVERT: V 75 GLN cc_start: 0.9211 (tp40) cc_final: 0.8981 (tp-100) REVERT: V 90 ASP cc_start: 0.8869 (OUTLIER) cc_final: 0.8348 (t0) REVERT: X 35 SER cc_start: 0.9391 (m) cc_final: 0.9086 (t) REVERT: X 43 GLU cc_start: 0.9025 (mt-10) cc_final: 0.8608 (tt0) REVERT: X 70 GLU cc_start: 0.8559 (tm-30) cc_final: 0.8130 (tm-30) REVERT: Y 13 GLU cc_start: 0.8588 (mt-10) cc_final: 0.8328 (mt-10) REVERT: Y 15 ASN cc_start: 0.9392 (m-40) cc_final: 0.8981 (m-40) REVERT: Y 17 GLU cc_start: 0.9143 (tp30) cc_final: 0.8791 (mm-30) REVERT: Y 24 GLU cc_start: 0.8764 (mt-10) cc_final: 0.8467 (mt-10) REVERT: Y 31 GLN cc_start: 0.9429 (mt0) cc_final: 0.9189 (mt0) REVERT: Y 36 GLN cc_start: 0.9130 (mm110) cc_final: 0.8887 (mm-40) REVERT: Y 55 THR cc_start: 0.9365 (OUTLIER) cc_final: 0.9081 (p) REVERT: Y 59 GLU cc_start: 0.9121 (tp30) cc_final: 0.8815 (tp30) REVERT: Z 6 LYS cc_start: 0.8958 (mtmm) cc_final: 0.8608 (mtmm) REVERT: Z 58 GLU cc_start: 0.7787 (tp30) cc_final: 0.7260 (tp30) REVERT: a 22 MET cc_start: 0.4750 (pmm) cc_final: 0.4084 (pmm) REVERT: b 12 LYS cc_start: 0.8938 (mmmt) cc_final: 0.8373 (mmmt) REVERT: b 48 TYR cc_start: 0.8874 (m-80) cc_final: 0.8318 (m-10) REVERT: c 10 LYS cc_start: 0.7564 (ptmt) cc_final: 0.7023 (ptpp) REVERT: c 17 THR cc_start: 0.7831 (OUTLIER) cc_final: 0.7487 (p) REVERT: c 34 LEU cc_start: 0.7801 (tp) cc_final: 0.7453 (tp) REVERT: c 37 LYS cc_start: 0.9068 (tttt) cc_final: 0.8747 (tppt) REVERT: c 39 PHE cc_start: 0.8640 (t80) cc_final: 0.8242 (t80) REVERT: d 2 LYS cc_start: 0.9370 (tttt) cc_final: 0.9094 (tttm) REVERT: d 28 ARG cc_start: 0.8833 (mtm-85) cc_final: 0.8601 (mtm-85) REVERT: f 35 GLN cc_start: 0.8940 (mt0) cc_final: 0.8441 (mt0) REVERT: g 93 ASN cc_start: 0.7676 (p0) cc_final: 0.7465 (p0) REVERT: g 140 GLU cc_start: 0.6951 (pp20) cc_final: 0.6316 (pp20) REVERT: g 145 GLU cc_start: 0.8980 (mm-30) cc_final: 0.8736 (mm-30) REVERT: g 169 GLU cc_start: 0.7410 (mm-30) cc_final: 0.6877 (mm-30) REVERT: h 41 GLN cc_start: 0.9273 (pp30) cc_final: 0.9009 (pp30) REVERT: h 42 TYR cc_start: 0.9044 (t80) cc_final: 0.8636 (t80) REVERT: h 152 GLU cc_start: 0.8115 (tm-30) cc_final: 0.7771 (tm-30) REVERT: h 168 TYR cc_start: 0.8556 (m-80) cc_final: 0.8053 (m-80) REVERT: h 181 ASP cc_start: 0.8516 (t70) cc_final: 0.8143 (t70) REVERT: h 183 ASP cc_start: 0.8643 (t0) cc_final: 0.8356 (t0) REVERT: h 187 SER cc_start: 0.8247 (t) cc_final: 0.7596 (p) REVERT: h 201 TRP cc_start: 0.8643 (OUTLIER) cc_final: 0.7608 (m-10) REVERT: i 4 TYR cc_start: 0.8284 (t80) cc_final: 0.7413 (t80) REVERT: i 11 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8225 (mt) REVERT: i 32 CYS cc_start: 0.7229 (p) cc_final: 0.6483 (p) REVERT: i 107 PHE cc_start: 0.8891 (m-10) cc_final: 0.8561 (m-80) REVERT: i 141 ASP cc_start: 0.7926 (m-30) cc_final: 0.7514 (m-30) REVERT: i 164 GLN cc_start: 0.8679 (OUTLIER) cc_final: 0.8338 (mp10) REVERT: j 41 ASP cc_start: 0.8808 (p0) cc_final: 0.8522 (p0) REVERT: j 65 GLU cc_start: 0.8775 (tp30) cc_final: 0.8514 (tp30) REVERT: j 76 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8820 (tt) REVERT: j 86 LYS cc_start: 0.9273 (mmtt) cc_final: 0.8728 (mmmm) REVERT: j 93 ARG cc_start: 0.8823 (mpp80) cc_final: 0.8393 (mpp80) REVERT: j 128 TYR cc_start: 0.8929 (m-80) cc_final: 0.8580 (m-80) REVERT: j 145 GLU cc_start: 0.8593 (pp20) cc_final: 0.8329 (pp20) REVERT: k 3 HIS cc_start: 0.8299 (m90) cc_final: 0.7895 (m170) REVERT: k 5 GLU cc_start: 0.8412 (tm-30) cc_final: 0.8164 (tm-30) REVERT: k 14 GLN cc_start: 0.8642 (mp10) cc_final: 0.8171 (mp10) REVERT: k 24 ARG cc_start: 0.9025 (ptp90) cc_final: 0.8684 (ptp-170) REVERT: k 75 GLU cc_start: 0.9164 (mt-10) cc_final: 0.8836 (mt-10) REVERT: m 5 ASP cc_start: 0.8744 (t0) cc_final: 0.8083 (t0) REVERT: m 30 SER cc_start: 0.9439 (p) cc_final: 0.9057 (t) REVERT: n 22 LYS cc_start: 0.7072 (ptpp) cc_final: 0.6818 (ptpp) REVERT: n 25 ASN cc_start: 0.8841 (p0) cc_final: 0.8576 (p0) REVERT: n 27 LYS cc_start: 0.8599 (mmtm) cc_final: 0.8313 (mmtm) REVERT: n 57 MET cc_start: 0.8646 (mpp) cc_final: 0.8298 (mpp) REVERT: n 61 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8566 (tp) REVERT: n 81 HIS cc_start: 0.8791 (t-90) cc_final: 0.8501 (t-90) REVERT: n 100 LYS cc_start: 0.9109 (mptt) cc_final: 0.8865 (mmtt) REVERT: n 107 ASP cc_start: 0.8918 (OUTLIER) cc_final: 0.8473 (t0) REVERT: o 63 ASP cc_start: 0.8232 (OUTLIER) cc_final: 0.8012 (m-30) REVERT: o 97 ASP cc_start: 0.8411 (t0) cc_final: 0.8172 (t0) REVERT: p 14 LYS cc_start: 0.8150 (tptt) cc_final: 0.7949 (tptt) REVERT: p 18 ASP cc_start: 0.8302 (p0) cc_final: 0.7796 (p0) REVERT: p 68 GLU cc_start: 0.8619 (mm-30) cc_final: 0.8350 (mm-30) REVERT: p 87 LYS cc_start: 0.8863 (ttmm) cc_final: 0.8419 (ttmm) REVERT: p 101 ASN cc_start: 0.9155 (t0) cc_final: 0.8713 (p0) REVERT: q 7 LEU cc_start: 0.9582 (mt) cc_final: 0.9374 (mp) REVERT: q 25 GLU cc_start: 0.8483 (pm20) cc_final: 0.8205 (pm20) REVERT: q 75 GLN cc_start: 0.9204 (pt0) cc_final: 0.8904 (pp30) REVERT: q 79 VAL cc_start: 0.9379 (t) cc_final: 0.9125 (p) REVERT: q 90 LEU cc_start: 0.9133 (tp) cc_final: 0.8858 (mt) REVERT: q 112 GLN cc_start: 0.8730 (mt0) cc_final: 0.8071 (mt0) REVERT: r 41 GLU cc_start: 0.8487 (mt-10) cc_final: 0.8262 (mt-10) REVERT: r 42 ASP cc_start: 0.8379 (p0) cc_final: 0.7726 (t0) REVERT: r 75 MET cc_start: 0.9380 (tmm) cc_final: 0.8981 (tmm) REVERT: r 86 TYR cc_start: 0.8473 (t80) cc_final: 0.8212 (t80) REVERT: s 4 GLN cc_start: 0.8254 (mm110) cc_final: 0.7592 (mm-40) REVERT: s 66 GLN cc_start: 0.8781 (OUTLIER) cc_final: 0.8537 (mm-40) REVERT: s 89 MET cc_start: 0.9216 (mmm) cc_final: 0.8781 (mmm) REVERT: t 62 GLN cc_start: 0.9149 (tt0) cc_final: 0.8886 (tp40) REVERT: t 80 GLN cc_start: 0.8202 (tm130) cc_final: 0.7957 (tm-30) REVERT: t 89 ARG cc_start: 0.7272 (tmm-80) cc_final: 0.6698 (tmm-80) REVERT: u 2 VAL cc_start: 0.8823 (OUTLIER) cc_final: 0.8551 (t) REVERT: u 48 GLU cc_start: 0.8784 (mt-10) cc_final: 0.8567 (mt-10) REVERT: u 63 GLN cc_start: 0.8913 (mm-40) cc_final: 0.8372 (mm-40) REVERT: v 13 VAL cc_start: 0.9465 (t) cc_final: 0.9176 (m) REVERT: v 60 GLU cc_start: 0.7946 (mp0) cc_final: 0.7465 (mp0) REVERT: v 73 TRP cc_start: 0.9415 (m100) cc_final: 0.8495 (m100) REVERT: w 25 ASP cc_start: 0.8358 (t0) cc_final: 0.8111 (t0) REVERT: x 53 ASN cc_start: 0.9200 (p0) cc_final: 0.8742 (p0) REVERT: y 13 GLN cc_start: 0.9337 (mt0) cc_final: 0.9033 (mt0) REVERT: z 33 ARG cc_start: 0.7837 (ptp-110) cc_final: 0.7292 (ptt180) REVERT: W 15 ASP cc_start: 0.8798 (t0) cc_final: 0.8520 (t0) REVERT: W 17 GLU cc_start: 0.8371 (mm-30) cc_final: 0.8154 (mm-30) outliers start: 305 outliers final: 226 residues processed: 1626 average time/residue: 1.2185 time to fit residues: 3492.3324 Evaluate side-chains 1678 residues out of total 4672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 241 poor density : 1437 time to evaluate : 6.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 183 GLU Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain D residue 199 MET Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 42 GLU Chi-restraints excluded: chain E residue 61 SER Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain E residue 127 ASN Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 20 ASN Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 88 GLN Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 21 VAL Chi-restraints excluded: chain G residue 94 ILE Chi-restraints excluded: chain G residue 130 VAL Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 139 PHE Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 55 ILE Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 60 ASP Chi-restraints excluded: chain J residue 67 ASN Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain J residue 139 VAL Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 90 ASN Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain L residue 143 GLU Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 26 VAL Chi-restraints excluded: chain M residue 73 ILE Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain N residue 53 THR Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain O residue 12 THR Chi-restraints excluded: chain O residue 18 LEU Chi-restraints excluded: chain O residue 35 ILE Chi-restraints excluded: chain O residue 38 GLN Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain O residue 69 ASP Chi-restraints excluded: chain P residue 60 THR Chi-restraints excluded: chain P residue 73 VAL Chi-restraints excluded: chain P residue 85 SER Chi-restraints excluded: chain P residue 97 LEU Chi-restraints excluded: chain P residue 114 LEU Chi-restraints excluded: chain Q residue 4 VAL Chi-restraints excluded: chain Q residue 97 ASP Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain Q residue 107 THR Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 43 ASN Chi-restraints excluded: chain R residue 53 PHE Chi-restraints excluded: chain R residue 94 THR Chi-restraints excluded: chain R residue 101 ILE Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 78 GLU Chi-restraints excluded: chain S residue 85 ILE Chi-restraints excluded: chain S residue 86 MET Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 17 SER Chi-restraints excluded: chain T residue 32 LEU Chi-restraints excluded: chain U residue 8 ASP Chi-restraints excluded: chain U residue 13 VAL Chi-restraints excluded: chain U residue 18 ASP Chi-restraints excluded: chain U residue 25 VAL Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain U residue 36 VAL Chi-restraints excluded: chain U residue 49 VAL Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain U residue 100 SER Chi-restraints excluded: chain V residue 3 THR Chi-restraints excluded: chain V residue 4 ILE Chi-restraints excluded: chain V residue 60 VAL Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain V residue 66 ASP Chi-restraints excluded: chain V residue 90 ASP Chi-restraints excluded: chain X residue 14 THR Chi-restraints excluded: chain X residue 65 ASP Chi-restraints excluded: chain Y residue 21 LEU Chi-restraints excluded: chain Y residue 34 SER Chi-restraints excluded: chain Y residue 50 VAL Chi-restraints excluded: chain Y residue 55 THR Chi-restraints excluded: chain Z residue 10 THR Chi-restraints excluded: chain Z residue 40 ASP Chi-restraints excluded: chain Z residue 41 THR Chi-restraints excluded: chain Z residue 57 VAL Chi-restraints excluded: chain a residue 28 VAL Chi-restraints excluded: chain a residue 51 VAL Chi-restraints excluded: chain b residue 3 VAL Chi-restraints excluded: chain c residue 5 ILE Chi-restraints excluded: chain c residue 9 ILE Chi-restraints excluded: chain c residue 14 SER Chi-restraints excluded: chain c residue 17 THR Chi-restraints excluded: chain c residue 42 VAL Chi-restraints excluded: chain d residue 4 THR Chi-restraints excluded: chain d residue 8 SER Chi-restraints excluded: chain d residue 24 THR Chi-restraints excluded: chain d residue 45 SER Chi-restraints excluded: chain e residue 6 THR Chi-restraints excluded: chain e residue 29 LEU Chi-restraints excluded: chain e residue 32 ILE Chi-restraints excluded: chain e residue 38 THR Chi-restraints excluded: chain e residue 44 LEU Chi-restraints excluded: chain e residue 54 ASP Chi-restraints excluded: chain f residue 3 VAL Chi-restraints excluded: chain g residue 4 VAL Chi-restraints excluded: chain g residue 8 ASP Chi-restraints excluded: chain g residue 23 TRP Chi-restraints excluded: chain g residue 127 ASP Chi-restraints excluded: chain g residue 141 LEU Chi-restraints excluded: chain g residue 204 ASP Chi-restraints excluded: chain g residue 205 ASP Chi-restraints excluded: chain h residue 31 ASP Chi-restraints excluded: chain h residue 53 SER Chi-restraints excluded: chain h residue 55 ILE Chi-restraints excluded: chain h residue 186 THR Chi-restraints excluded: chain h residue 201 TRP Chi-restraints excluded: chain i residue 11 LEU Chi-restraints excluded: chain i residue 110 THR Chi-restraints excluded: chain i residue 164 GLN Chi-restraints excluded: chain i residue 190 ASP Chi-restraints excluded: chain i residue 204 TYR Chi-restraints excluded: chain j residue 11 LEU Chi-restraints excluded: chain j residue 76 LEU Chi-restraints excluded: chain j residue 90 THR Chi-restraints excluded: chain k residue 7 VAL Chi-restraints excluded: chain k residue 18 VAL Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 46 GLN Chi-restraints excluded: chain k residue 82 ASP Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain k residue 85 ILE Chi-restraints excluded: chain k residue 97 THR Chi-restraints excluded: chain l residue 30 LEU Chi-restraints excluded: chain l residue 54 SER Chi-restraints excluded: chain l residue 144 MET Chi-restraints excluded: chain m residue 11 LEU Chi-restraints excluded: chain m residue 27 MET Chi-restraints excluded: chain m residue 61 LEU Chi-restraints excluded: chain n residue 29 VAL Chi-restraints excluded: chain n residue 55 VAL Chi-restraints excluded: chain n residue 61 LEU Chi-restraints excluded: chain n residue 72 ILE Chi-restraints excluded: chain n residue 90 TYR Chi-restraints excluded: chain n residue 98 LEU Chi-restraints excluded: chain n residue 107 ASP Chi-restraints excluded: chain n residue 111 VAL Chi-restraints excluded: chain o residue 6 ILE Chi-restraints excluded: chain o residue 10 LEU Chi-restraints excluded: chain o residue 15 HIS Chi-restraints excluded: chain o residue 44 THR Chi-restraints excluded: chain o residue 63 ASP Chi-restraints excluded: chain o residue 70 HIS Chi-restraints excluded: chain o residue 78 GLU Chi-restraints excluded: chain o residue 80 THR Chi-restraints excluded: chain o residue 84 VAL Chi-restraints excluded: chain o residue 96 VAL Chi-restraints excluded: chain p residue 31 ILE Chi-restraints excluded: chain p residue 46 THR Chi-restraints excluded: chain p residue 55 SER Chi-restraints excluded: chain p residue 64 GLN Chi-restraints excluded: chain p residue 81 ASN Chi-restraints excluded: chain p residue 82 LEU Chi-restraints excluded: chain p residue 83 GLU Chi-restraints excluded: chain p residue 84 VAL Chi-restraints excluded: chain p residue 97 ILE Chi-restraints excluded: chain q residue 3 THR Chi-restraints excluded: chain q residue 39 THR Chi-restraints excluded: chain q residue 47 SER Chi-restraints excluded: chain q residue 63 VAL Chi-restraints excluded: chain r residue 43 VAL Chi-restraints excluded: chain s residue 34 VAL Chi-restraints excluded: chain s residue 48 LEU Chi-restraints excluded: chain s residue 66 GLN Chi-restraints excluded: chain s residue 79 LEU Chi-restraints excluded: chain t residue 3 LEU Chi-restraints excluded: chain t residue 18 ASP Chi-restraints excluded: chain u residue 2 VAL Chi-restraints excluded: chain u residue 29 ASN Chi-restraints excluded: chain u residue 68 SER Chi-restraints excluded: chain v residue 43 LYS Chi-restraints excluded: chain v residue 51 ASN Chi-restraints excluded: chain v residue 70 THR Chi-restraints excluded: chain w residue 21 ILE Chi-restraints excluded: chain w residue 40 VAL Chi-restraints excluded: chain x residue 5 LEU Chi-restraints excluded: chain x residue 44 MET Chi-restraints excluded: chain x residue 48 THR Chi-restraints excluded: chain x residue 58 VAL Chi-restraints excluded: chain x residue 63 THR Chi-restraints excluded: chain y residue 27 MET Chi-restraints excluded: chain y residue 43 ASP Chi-restraints excluded: chain W residue 59 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1010 random chunks: chunk 942 optimal weight: 0.9980 chunk 110 optimal weight: 30.0000 chunk 556 optimal weight: 4.9990 chunk 713 optimal weight: 5.9990 chunk 552 optimal weight: 10.0000 chunk 822 optimal weight: 6.9990 chunk 545 optimal weight: 9.9990 chunk 973 optimal weight: 6.9990 chunk 609 optimal weight: 0.9990 chunk 593 optimal weight: 10.0000 chunk 449 optimal weight: 10.0000 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 36 GLN ** M 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 52 GLN ** Q 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 24 ASN ** g 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 139 GLN ** i 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 118 GLN n 5 GLN p 64 GLN x 53 ASN y 70 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 156844 Z= 0.237 Angle : 0.631 13.644 234723 Z= 0.340 Chirality : 0.035 0.401 29908 Planarity : 0.006 0.125 12506 Dihedral : 23.726 179.941 78631 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.94 % Favored : 95.99 % Rotamer: Outliers : 5.71 % Allowed : 25.86 % Favored : 68.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.30 (0.11), residues: 5614 helix: 0.93 (0.12), residues: 1999 sheet: -0.69 (0.16), residues: 1056 loop : -0.82 (0.12), residues: 2559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP l 103 HIS 0.017 0.001 HIS o 70 PHE 0.036 0.002 PHE l 26 TYR 0.046 0.002 TYR G 25 ARG 0.014 0.001 ARG w 48 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11228 Ramachandran restraints generated. 5614 Oldfield, 0 Emsley, 5614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11228 Ramachandran restraints generated. 5614 Oldfield, 0 Emsley, 5614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1775 residues out of total 4672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 267 poor density : 1508 time to evaluate : 6.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 117 GLN cc_start: 0.8662 (tt0) cc_final: 0.8446 (tp-100) REVERT: B 180 GLU cc_start: 0.8484 (mt-10) cc_final: 0.8216 (tt0) REVERT: B 203 ARG cc_start: 0.8737 (ptp-110) cc_final: 0.8137 (ptp-170) REVERT: B 251 GLN cc_start: 0.8591 (tm-30) cc_final: 0.8105 (tm-30) REVERT: C 11 MET cc_start: 0.8781 (mtp) cc_final: 0.8552 (mtp) REVERT: C 137 SER cc_start: 0.9076 (m) cc_final: 0.8809 (p) REVERT: D 1 MET cc_start: 0.8538 (mmt) cc_final: 0.8037 (mmt) REVERT: D 136 GLN cc_start: 0.9193 (tp-100) cc_final: 0.8763 (tp40) REVERT: D 156 ASN cc_start: 0.8988 (m-40) cc_final: 0.8660 (t0) REVERT: E 42 GLU cc_start: 0.9215 (OUTLIER) cc_final: 0.8613 (pm20) REVERT: E 130 MET cc_start: 0.8876 (ppp) cc_final: 0.8444 (ppp) REVERT: E 138 PHE cc_start: 0.8880 (m-80) cc_final: 0.8559 (m-80) REVERT: E 177 PHE cc_start: 0.6783 (m-10) cc_final: 0.6533 (m-80) REVERT: F 39 ASP cc_start: 0.8830 (p0) cc_final: 0.8573 (p0) REVERT: F 58 TYR cc_start: 0.7574 (m-80) cc_final: 0.7076 (m-80) REVERT: F 62 TRP cc_start: 0.8600 (m100) cc_final: 0.8287 (m100) REVERT: F 83 PHE cc_start: 0.8322 (m-80) cc_final: 0.7853 (m-80) REVERT: F 101 ASN cc_start: 0.9011 (p0) cc_final: 0.8679 (p0) REVERT: F 130 GLU cc_start: 0.8432 (tp30) cc_final: 0.7857 (tp30) REVERT: F 137 ASP cc_start: 0.8992 (t0) cc_final: 0.8732 (t0) REVERT: J 2 LYS cc_start: 0.9482 (OUTLIER) cc_final: 0.9100 (mttt) REVERT: J 31 GLU cc_start: 0.8684 (tp30) cc_final: 0.8450 (tp30) REVERT: J 91 GLU cc_start: 0.8677 (pm20) cc_final: 0.8359 (pm20) REVERT: J 96 ARG cc_start: 0.8673 (ttt-90) cc_final: 0.8298 (mmm-85) REVERT: J 98 GLU cc_start: 0.8921 (mp0) cc_final: 0.8268 (mp0) REVERT: J 102 GLU cc_start: 0.8653 (mt-10) cc_final: 0.8394 (mt-10) REVERT: K 12 ASP cc_start: 0.8499 (p0) cc_final: 0.8089 (p0) REVERT: K 88 ASN cc_start: 0.8529 (t0) cc_final: 0.8106 (t0) REVERT: L 76 GLU cc_start: 0.8041 (mt-10) cc_final: 0.7754 (tt0) REVERT: L 81 ASP cc_start: 0.8858 (t0) cc_final: 0.8453 (t0) REVERT: M 3 GLN cc_start: 0.9210 (tt0) cc_final: 0.8890 (tt0) REVERT: M 22 GLN cc_start: 0.8428 (mm110) cc_final: 0.8027 (mm-40) REVERT: M 47 GLU cc_start: 0.8728 (tp30) cc_final: 0.8307 (tp30) REVERT: M 110 GLU cc_start: 0.8878 (tt0) cc_final: 0.8272 (tm-30) REVERT: M 136 MET cc_start: 0.7861 (ttp) cc_final: 0.7656 (ttp) REVERT: N 9 GLN cc_start: 0.8483 (tt0) cc_final: 0.8218 (tt0) REVERT: N 20 MET cc_start: 0.9299 (ttp) cc_final: 0.8986 (ttp) REVERT: N 72 ASP cc_start: 0.8375 (t70) cc_final: 0.7976 (t70) REVERT: O 40 ILE cc_start: 0.8944 (mt) cc_final: 0.8703 (mp) REVERT: O 52 SER cc_start: 0.9595 (m) cc_final: 0.8821 (p) REVERT: O 76 LYS cc_start: 0.9367 (mmmm) cc_final: 0.9063 (mmmm) REVERT: O 88 LYS cc_start: 0.9101 (mmmt) cc_final: 0.8883 (mmmt) REVERT: O 93 ASP cc_start: 0.8540 (t0) cc_final: 0.8210 (t0) REVERT: P 8 LEU cc_start: 0.9118 (mm) cc_final: 0.8787 (mm) REVERT: P 13 MET cc_start: 0.8563 (mmm) cc_final: 0.8238 (mmm) REVERT: P 24 ASP cc_start: 0.8169 (m-30) cc_final: 0.7730 (m-30) REVERT: P 98 TYR cc_start: 0.9153 (m-80) cc_final: 0.8700 (m-80) REVERT: P 112 GLU cc_start: 0.8059 (pp20) cc_final: 0.7696 (pp20) REVERT: Q 102 ASP cc_start: 0.8494 (t0) cc_final: 0.8222 (t0) REVERT: R 2 TYR cc_start: 0.9370 (p90) cc_final: 0.9130 (p90) REVERT: R 31 GLU cc_start: 0.8123 (mp0) cc_final: 0.7779 (mp0) REVERT: R 34 GLU cc_start: 0.8668 (mm-30) cc_final: 0.8404 (mm-30) REVERT: R 48 LYS cc_start: 0.9137 (ptpp) cc_final: 0.8766 (ptpp) REVERT: R 60 LYS cc_start: 0.9244 (mttp) cc_final: 0.8890 (pttt) REVERT: R 62 GLU cc_start: 0.8205 (tp30) cc_final: 0.7584 (tp30) REVERT: R 74 ILE cc_start: 0.9473 (mp) cc_final: 0.9258 (mt) REVERT: R 94 THR cc_start: 0.9328 (m) cc_final: 0.8766 (p) REVERT: S 1 MET cc_start: 0.8400 (ttm) cc_final: 0.8045 (ttt) REVERT: S 8 ARG cc_start: 0.8902 (mtp85) cc_final: 0.8392 (mtp85) REVERT: S 62 ASP cc_start: 0.8598 (t0) cc_final: 0.8193 (t0) REVERT: S 73 LYS cc_start: 0.8860 (mttt) cc_final: 0.8583 (mtpp) REVERT: T 91 GLN cc_start: 0.9046 (mm-40) cc_final: 0.8513 (mm110) REVERT: U 10 GLU cc_start: 0.8420 (tt0) cc_final: 0.7867 (tm-30) REVERT: U 22 ARG cc_start: 0.8841 (mtm-85) cc_final: 0.8251 (mtm-85) REVERT: U 29 LEU cc_start: 0.9414 (mm) cc_final: 0.9084 (mm) REVERT: U 46 GLN cc_start: 0.8801 (tp-100) cc_final: 0.8576 (tp-100) REVERT: V 90 ASP cc_start: 0.8836 (OUTLIER) cc_final: 0.8326 (t0) REVERT: X 35 SER cc_start: 0.9371 (m) cc_final: 0.9028 (t) REVERT: X 43 GLU cc_start: 0.9038 (mt-10) cc_final: 0.8695 (tt0) REVERT: X 67 VAL cc_start: 0.9593 (t) cc_final: 0.9386 (p) REVERT: X 70 GLU cc_start: 0.8565 (tm-30) cc_final: 0.8145 (tm-30) REVERT: Y 13 GLU cc_start: 0.8548 (mt-10) cc_final: 0.8285 (mt-10) REVERT: Y 15 ASN cc_start: 0.9431 (m-40) cc_final: 0.9012 (m110) REVERT: Y 17 GLU cc_start: 0.9137 (tp30) cc_final: 0.8792 (mm-30) REVERT: Y 24 GLU cc_start: 0.8752 (mt-10) cc_final: 0.8437 (mt-10) REVERT: Y 31 GLN cc_start: 0.9417 (mt0) cc_final: 0.9155 (mt0) REVERT: Y 36 GLN cc_start: 0.9030 (mm110) cc_final: 0.8811 (mm-40) REVERT: Y 45 GLN cc_start: 0.9107 (mt0) cc_final: 0.8884 (mm-40) REVERT: Y 55 THR cc_start: 0.9338 (OUTLIER) cc_final: 0.9066 (p) REVERT: Y 59 GLU cc_start: 0.9151 (tp30) cc_final: 0.8858 (tp30) REVERT: Z 6 LYS cc_start: 0.8948 (mtmm) cc_final: 0.8668 (mtmm) REVERT: Z 58 GLU cc_start: 0.7875 (tp30) cc_final: 0.7331 (tp30) REVERT: a 1 MET cc_start: 0.6942 (mpp) cc_final: 0.6422 (mpp) REVERT: a 22 MET cc_start: 0.5067 (pmm) cc_final: 0.4477 (pmm) REVERT: b 12 LYS cc_start: 0.8919 (mmmt) cc_final: 0.8340 (mmmt) REVERT: c 10 LYS cc_start: 0.7487 (ptmt) cc_final: 0.6916 (ptpp) REVERT: c 17 THR cc_start: 0.7685 (OUTLIER) cc_final: 0.7411 (p) REVERT: c 28 ARG cc_start: 0.8432 (mpt180) cc_final: 0.8145 (mpt180) REVERT: c 34 LEU cc_start: 0.7681 (tp) cc_final: 0.7362 (tp) REVERT: c 37 LYS cc_start: 0.9090 (tttt) cc_final: 0.8774 (tppt) REVERT: c 39 PHE cc_start: 0.8653 (t80) cc_final: 0.8252 (t80) REVERT: d 2 LYS cc_start: 0.9337 (tttt) cc_final: 0.9072 (tttm) REVERT: d 28 ARG cc_start: 0.8815 (mtm-85) cc_final: 0.8563 (mtm-85) REVERT: f 35 GLN cc_start: 0.8951 (mt0) cc_final: 0.8696 (mt0) REVERT: g 93 ASN cc_start: 0.7677 (p0) cc_final: 0.5628 (t0) REVERT: g 145 GLU cc_start: 0.9023 (mm-30) cc_final: 0.8801 (mm-30) REVERT: g 169 GLU cc_start: 0.7184 (mm-30) cc_final: 0.6685 (mm-30) REVERT: h 41 GLN cc_start: 0.9297 (pp30) cc_final: 0.9002 (pp30) REVERT: h 42 TYR cc_start: 0.9072 (t80) cc_final: 0.8642 (t80) REVERT: h 152 GLU cc_start: 0.8009 (tm-30) cc_final: 0.7637 (tm-30) REVERT: h 168 TYR cc_start: 0.8538 (m-80) cc_final: 0.7688 (m-80) REVERT: h 181 ASP cc_start: 0.8480 (t70) cc_final: 0.8114 (t70) REVERT: h 183 ASP cc_start: 0.8635 (t0) cc_final: 0.8364 (t0) REVERT: h 184 TYR cc_start: 0.8765 (t80) cc_final: 0.8545 (t80) REVERT: h 187 SER cc_start: 0.8027 (t) cc_final: 0.7212 (p) REVERT: h 201 TRP cc_start: 0.8455 (OUTLIER) cc_final: 0.7586 (m-10) REVERT: i 4 TYR cc_start: 0.8030 (t80) cc_final: 0.7167 (t80) REVERT: i 11 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8279 (mt) REVERT: i 103 TYR cc_start: 0.8838 (t80) cc_final: 0.8623 (t80) REVERT: i 107 PHE cc_start: 0.8857 (m-10) cc_final: 0.8538 (m-80) REVERT: i 141 ASP cc_start: 0.7909 (m-30) cc_final: 0.7581 (m-30) REVERT: i 164 GLN cc_start: 0.8603 (OUTLIER) cc_final: 0.8292 (mp10) REVERT: j 23 LYS cc_start: 0.8146 (ttpp) cc_final: 0.7587 (ptmt) REVERT: j 41 ASP cc_start: 0.8847 (p0) cc_final: 0.8606 (p0) REVERT: j 45 ARG cc_start: 0.9026 (mmm-85) cc_final: 0.8447 (mmm-85) REVERT: j 65 GLU cc_start: 0.8697 (tp30) cc_final: 0.8397 (tp30) REVERT: j 76 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8813 (tt) REVERT: j 86 LYS cc_start: 0.9259 (mmtt) cc_final: 0.8687 (mmmm) REVERT: j 93 ARG cc_start: 0.8828 (mpp80) cc_final: 0.8385 (mpp80) REVERT: j 128 TYR cc_start: 0.8920 (m-80) cc_final: 0.8593 (m-80) REVERT: j 142 ASP cc_start: 0.8700 (t70) cc_final: 0.7879 (t70) REVERT: j 145 GLU cc_start: 0.8569 (pp20) cc_final: 0.8297 (pp20) REVERT: k 3 HIS cc_start: 0.8214 (m90) cc_final: 0.7809 (m-70) REVERT: k 5 GLU cc_start: 0.8374 (tm-30) cc_final: 0.7913 (tm-30) REVERT: k 9 MET cc_start: 0.8644 (mtp) cc_final: 0.8342 (mtp) REVERT: k 14 GLN cc_start: 0.8539 (mp10) cc_final: 0.8006 (mp10) REVERT: k 42 TRP cc_start: 0.8223 (m-10) cc_final: 0.8017 (m100) REVERT: k 59 TYR cc_start: 0.8278 (m-80) cc_final: 0.7641 (m-80) REVERT: k 75 GLU cc_start: 0.9162 (mt-10) cc_final: 0.8835 (mt-10) REVERT: k 90 MET cc_start: 0.7993 (ttm) cc_final: 0.7517 (mtp) REVERT: l 142 HIS cc_start: 0.8636 (m90) cc_final: 0.7872 (m90) REVERT: m 5 ASP cc_start: 0.8723 (t0) cc_final: 0.8028 (t0) REVERT: m 30 SER cc_start: 0.9435 (p) cc_final: 0.9126 (t) REVERT: m 45 PHE cc_start: 0.9271 (m-80) cc_final: 0.9005 (m-80) REVERT: m 73 GLU cc_start: 0.8652 (tp30) cc_final: 0.8418 (tt0) REVERT: m 126 ILE cc_start: 0.8840 (mm) cc_final: 0.8531 (tp) REVERT: n 22 LYS cc_start: 0.6996 (ptpp) cc_final: 0.6746 (ptpp) REVERT: n 57 MET cc_start: 0.8654 (mpp) cc_final: 0.8314 (mpp) REVERT: n 61 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8611 (tp) REVERT: n 81 HIS cc_start: 0.8780 (t-90) cc_final: 0.8454 (t-90) REVERT: n 100 LYS cc_start: 0.9099 (mptt) cc_final: 0.8880 (mmtt) REVERT: n 107 ASP cc_start: 0.8915 (OUTLIER) cc_final: 0.8420 (t0) REVERT: o 15 HIS cc_start: 0.7172 (OUTLIER) cc_final: 0.5468 (t70) REVERT: o 63 ASP cc_start: 0.8183 (OUTLIER) cc_final: 0.7932 (m-30) REVERT: o 97 ASP cc_start: 0.8463 (t0) cc_final: 0.8262 (t0) REVERT: p 18 ASP cc_start: 0.8237 (p0) cc_final: 0.7864 (p0) REVERT: p 68 GLU cc_start: 0.8552 (mm-30) cc_final: 0.8237 (mm-30) REVERT: p 101 ASN cc_start: 0.9147 (t0) cc_final: 0.8713 (p0) REVERT: q 7 LEU cc_start: 0.9556 (mt) cc_final: 0.9322 (mp) REVERT: q 90 LEU cc_start: 0.9118 (tp) cc_final: 0.8851 (mt) REVERT: q 112 GLN cc_start: 0.8720 (mt0) cc_final: 0.7864 (mt0) REVERT: q 117 TYR cc_start: 0.8690 (m-80) cc_final: 0.8428 (m-80) REVERT: r 41 GLU cc_start: 0.8425 (mt-10) cc_final: 0.8032 (mt-10) REVERT: r 42 ASP cc_start: 0.8339 (p0) cc_final: 0.7744 (t0) REVERT: r 59 GLU cc_start: 0.8752 (mm-30) cc_final: 0.7913 (mt-10) REVERT: r 75 MET cc_start: 0.9375 (tmm) cc_final: 0.9012 (tmm) REVERT: r 86 TYR cc_start: 0.8507 (t80) cc_final: 0.8225 (t80) REVERT: s 4 GLN cc_start: 0.8226 (mm110) cc_final: 0.7610 (mm-40) REVERT: s 89 MET cc_start: 0.9188 (mmm) cc_final: 0.8868 (mmm) REVERT: t 62 GLN cc_start: 0.9116 (tt0) cc_final: 0.8901 (tp40) REVERT: t 80 GLN cc_start: 0.8219 (tm130) cc_final: 0.7900 (tm-30) REVERT: t 89 ARG cc_start: 0.7256 (tmm-80) cc_final: 0.6720 (tmm-80) REVERT: u 2 VAL cc_start: 0.8801 (OUTLIER) cc_final: 0.8547 (t) REVERT: u 63 GLN cc_start: 0.8890 (mm-40) cc_final: 0.8336 (mm-40) REVERT: v 6 ARG cc_start: 0.8453 (mtp85) cc_final: 0.7904 (mtp85) REVERT: v 13 VAL cc_start: 0.9470 (t) cc_final: 0.9194 (m) REVERT: v 60 GLU cc_start: 0.8030 (mp0) cc_final: 0.7659 (mp0) REVERT: v 73 TRP cc_start: 0.9369 (m100) cc_final: 0.8421 (m100) REVERT: w 25 ASP cc_start: 0.8385 (t0) cc_final: 0.8144 (t0) REVERT: x 7 LYS cc_start: 0.8165 (mtpp) cc_final: 0.7760 (mtpt) REVERT: y 13 GLN cc_start: 0.9307 (mt0) cc_final: 0.9029 (mt0) REVERT: y 24 ARG cc_start: 0.8800 (mmm160) cc_final: 0.8451 (mmp-170) REVERT: y 27 MET cc_start: 0.9113 (OUTLIER) cc_final: 0.8713 (tmm) REVERT: z 33 ARG cc_start: 0.7795 (ptp-110) cc_final: 0.7262 (ptt180) REVERT: W 15 ASP cc_start: 0.8861 (t0) cc_final: 0.8554 (t0) REVERT: W 17 GLU cc_start: 0.8356 (mm-30) cc_final: 0.8125 (mm-30) REVERT: W 64 ASP cc_start: 0.8734 (m-30) cc_final: 0.8447 (m-30) outliers start: 267 outliers final: 204 residues processed: 1621 average time/residue: 1.2219 time to fit residues: 3484.7241 Evaluate side-chains 1694 residues out of total 4672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 219 poor density : 1475 time to evaluate : 6.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 157 SER Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 183 GLU Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 23 ASN Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 42 GLU Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain E residue 127 ASN Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 20 ASN Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 88 GLN Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 21 VAL Chi-restraints excluded: chain G residue 94 ILE Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 139 PHE Chi-restraints excluded: chain J residue 2 LYS Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 55 ILE Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 60 ASP Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain J residue 139 VAL Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain L residue 143 GLU Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 26 VAL Chi-restraints excluded: chain M residue 73 ILE Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 115 LEU Chi-restraints excluded: chain O residue 12 THR Chi-restraints excluded: chain O residue 18 LEU Chi-restraints excluded: chain O residue 35 ILE Chi-restraints excluded: chain O residue 38 GLN Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain O residue 69 ASP Chi-restraints excluded: chain P residue 60 THR Chi-restraints excluded: chain P residue 73 VAL Chi-restraints excluded: chain P residue 97 LEU Chi-restraints excluded: chain P residue 114 LEU Chi-restraints excluded: chain Q residue 4 VAL Chi-restraints excluded: chain Q residue 97 ASP Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain Q residue 107 THR Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 43 ASN Chi-restraints excluded: chain R residue 53 PHE Chi-restraints excluded: chain R residue 101 ILE Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 78 GLU Chi-restraints excluded: chain S residue 85 ILE Chi-restraints excluded: chain S residue 86 MET Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 32 LEU Chi-restraints excluded: chain T residue 43 ILE Chi-restraints excluded: chain U residue 8 ASP Chi-restraints excluded: chain U residue 13 VAL Chi-restraints excluded: chain U residue 18 ASP Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain U residue 36 VAL Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain V residue 3 THR Chi-restraints excluded: chain V residue 4 ILE Chi-restraints excluded: chain V residue 60 VAL Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain V residue 66 ASP Chi-restraints excluded: chain V residue 70 ILE Chi-restraints excluded: chain V residue 90 ASP Chi-restraints excluded: chain X residue 14 THR Chi-restraints excluded: chain X residue 65 ASP Chi-restraints excluded: chain Y residue 21 LEU Chi-restraints excluded: chain Y residue 34 SER Chi-restraints excluded: chain Y residue 50 VAL Chi-restraints excluded: chain Y residue 55 THR Chi-restraints excluded: chain Z residue 10 THR Chi-restraints excluded: chain Z residue 41 THR Chi-restraints excluded: chain Z residue 57 VAL Chi-restraints excluded: chain a residue 51 VAL Chi-restraints excluded: chain b residue 3 VAL Chi-restraints excluded: chain c residue 9 ILE Chi-restraints excluded: chain c residue 14 SER Chi-restraints excluded: chain c residue 17 THR Chi-restraints excluded: chain c residue 42 VAL Chi-restraints excluded: chain d residue 8 SER Chi-restraints excluded: chain d residue 24 THR Chi-restraints excluded: chain d residue 45 SER Chi-restraints excluded: chain e residue 6 THR Chi-restraints excluded: chain e residue 32 ILE Chi-restraints excluded: chain e residue 44 LEU Chi-restraints excluded: chain e residue 54 ASP Chi-restraints excluded: chain f residue 3 VAL Chi-restraints excluded: chain g residue 4 VAL Chi-restraints excluded: chain g residue 23 TRP Chi-restraints excluded: chain g residue 115 LYS Chi-restraints excluded: chain g residue 127 ASP Chi-restraints excluded: chain g residue 204 ASP Chi-restraints excluded: chain g residue 207 ILE Chi-restraints excluded: chain h residue 31 ASP Chi-restraints excluded: chain h residue 53 SER Chi-restraints excluded: chain h residue 55 ILE Chi-restraints excluded: chain h residue 186 THR Chi-restraints excluded: chain h residue 201 TRP Chi-restraints excluded: chain i residue 11 LEU Chi-restraints excluded: chain i residue 164 GLN Chi-restraints excluded: chain i residue 190 ASP Chi-restraints excluded: chain i residue 204 TYR Chi-restraints excluded: chain j residue 11 LEU Chi-restraints excluded: chain j residue 22 SER Chi-restraints excluded: chain j residue 76 LEU Chi-restraints excluded: chain j residue 90 THR Chi-restraints excluded: chain k residue 7 VAL Chi-restraints excluded: chain k residue 18 VAL Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 46 GLN Chi-restraints excluded: chain k residue 82 ASP Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain k residue 85 ILE Chi-restraints excluded: chain k residue 97 THR Chi-restraints excluded: chain l residue 30 LEU Chi-restraints excluded: chain l residue 54 SER Chi-restraints excluded: chain l residue 144 MET Chi-restraints excluded: chain m residue 11 LEU Chi-restraints excluded: chain m residue 61 LEU Chi-restraints excluded: chain n residue 29 VAL Chi-restraints excluded: chain n residue 55 VAL Chi-restraints excluded: chain n residue 61 LEU Chi-restraints excluded: chain n residue 72 ILE Chi-restraints excluded: chain n residue 90 TYR Chi-restraints excluded: chain n residue 98 LEU Chi-restraints excluded: chain n residue 107 ASP Chi-restraints excluded: chain n residue 111 VAL Chi-restraints excluded: chain o residue 6 ILE Chi-restraints excluded: chain o residue 10 LEU Chi-restraints excluded: chain o residue 15 HIS Chi-restraints excluded: chain o residue 18 ILE Chi-restraints excluded: chain o residue 44 THR Chi-restraints excluded: chain o residue 63 ASP Chi-restraints excluded: chain o residue 70 HIS Chi-restraints excluded: chain o residue 78 GLU Chi-restraints excluded: chain o residue 80 THR Chi-restraints excluded: chain o residue 84 VAL Chi-restraints excluded: chain o residue 96 VAL Chi-restraints excluded: chain p residue 46 THR Chi-restraints excluded: chain p residue 55 SER Chi-restraints excluded: chain p residue 64 GLN Chi-restraints excluded: chain p residue 81 ASN Chi-restraints excluded: chain p residue 82 LEU Chi-restraints excluded: chain p residue 84 VAL Chi-restraints excluded: chain p residue 86 VAL Chi-restraints excluded: chain p residue 97 ILE Chi-restraints excluded: chain q residue 3 THR Chi-restraints excluded: chain q residue 39 THR Chi-restraints excluded: chain q residue 47 SER Chi-restraints excluded: chain q residue 63 VAL Chi-restraints excluded: chain r residue 43 VAL Chi-restraints excluded: chain s residue 34 VAL Chi-restraints excluded: chain s residue 48 LEU Chi-restraints excluded: chain s residue 79 LEU Chi-restraints excluded: chain t residue 3 LEU Chi-restraints excluded: chain t residue 18 ASP Chi-restraints excluded: chain u residue 2 VAL Chi-restraints excluded: chain u residue 68 SER Chi-restraints excluded: chain v residue 51 ASN Chi-restraints excluded: chain v residue 70 THR Chi-restraints excluded: chain w residue 21 ILE Chi-restraints excluded: chain w residue 40 VAL Chi-restraints excluded: chain x residue 5 LEU Chi-restraints excluded: chain x residue 44 MET Chi-restraints excluded: chain x residue 48 THR Chi-restraints excluded: chain x residue 58 VAL Chi-restraints excluded: chain x residue 63 THR Chi-restraints excluded: chain y residue 27 MET Chi-restraints excluded: chain y residue 28 MET Chi-restraints excluded: chain y residue 43 ASP Chi-restraints excluded: chain y residue 85 LYS Chi-restraints excluded: chain W residue 71 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1010 random chunks: chunk 602 optimal weight: 9.9990 chunk 388 optimal weight: 30.0000 chunk 581 optimal weight: 6.9990 chunk 293 optimal weight: 10.0000 chunk 191 optimal weight: 20.0000 chunk 188 optimal weight: 10.0000 chunk 618 optimal weight: 9.9990 chunk 663 optimal weight: 10.0000 chunk 481 optimal weight: 10.0000 chunk 90 optimal weight: 10.0000 chunk 765 optimal weight: 5.9990 overall best weight: 8.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 36 GLN N 23 ASN O 98 GLN ** P 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 18 GLN T 48 GLN U 40 ASN ** U 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 75 GLN ** X 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 15 HIS ** g 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 100 ASN ** i 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 68 GLN m 118 GLN n 5 GLN p 64 GLN s 49 GLN ** x 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 70 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8825 moved from start: 0.3190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.097 156844 Z= 0.440 Angle : 0.726 13.234 234723 Z= 0.385 Chirality : 0.040 0.385 29908 Planarity : 0.007 0.133 12506 Dihedral : 23.735 179.575 78631 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 17.67 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.61 % Favored : 95.32 % Rotamer: Outliers : 5.82 % Allowed : 26.11 % Favored : 68.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.47 (0.11), residues: 5614 helix: 0.76 (0.11), residues: 1996 sheet: -0.71 (0.16), residues: 1063 loop : -0.93 (0.12), residues: 2555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP l 103 HIS 0.018 0.001 HIS o 70 PHE 0.028 0.002 PHE U 96 TYR 0.033 0.002 TYR g 213 ARG 0.011 0.001 ARG v 27 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11228 Ramachandran restraints generated. 5614 Oldfield, 0 Emsley, 5614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11228 Ramachandran restraints generated. 5614 Oldfield, 0 Emsley, 5614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1721 residues out of total 4672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 272 poor density : 1449 time to evaluate : 6.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 117 GLN cc_start: 0.8765 (tt0) cc_final: 0.8461 (tp40) REVERT: B 145 GLU cc_start: 0.8709 (mt-10) cc_final: 0.8453 (mt-10) REVERT: B 203 ARG cc_start: 0.8813 (ptp-110) cc_final: 0.8130 (ptp-170) REVERT: B 251 GLN cc_start: 0.8638 (tm-30) cc_final: 0.8191 (tm-30) REVERT: C 11 MET cc_start: 0.8877 (mtp) cc_final: 0.8600 (mtp) REVERT: C 137 SER cc_start: 0.9105 (m) cc_final: 0.8802 (p) REVERT: D 136 GLN cc_start: 0.9179 (tp-100) cc_final: 0.8776 (tp40) REVERT: D 156 ASN cc_start: 0.9009 (m-40) cc_final: 0.8692 (t0) REVERT: D 170 ARG cc_start: 0.8413 (ptp-170) cc_final: 0.7837 (mtm-85) REVERT: E 130 MET cc_start: 0.8773 (ppp) cc_final: 0.8267 (ppp) REVERT: E 138 PHE cc_start: 0.8899 (m-80) cc_final: 0.8601 (m-80) REVERT: E 177 PHE cc_start: 0.6897 (m-10) cc_final: 0.6622 (m-80) REVERT: F 39 ASP cc_start: 0.8856 (p0) cc_final: 0.8610 (p0) REVERT: F 58 TYR cc_start: 0.7634 (m-80) cc_final: 0.7102 (m-80) REVERT: F 83 PHE cc_start: 0.8384 (m-80) cc_final: 0.7952 (m-80) REVERT: F 101 ASN cc_start: 0.8943 (p0) cc_final: 0.8711 (p0) REVERT: F 130 GLU cc_start: 0.8435 (tp30) cc_final: 0.7893 (tp30) REVERT: F 137 ASP cc_start: 0.9073 (t0) cc_final: 0.8820 (t0) REVERT: J 31 GLU cc_start: 0.8706 (tp30) cc_final: 0.8452 (tp30) REVERT: J 75 TYR cc_start: 0.9112 (m-80) cc_final: 0.8875 (m-80) REVERT: J 86 GLN cc_start: 0.9111 (tt0) cc_final: 0.8692 (tt0) REVERT: J 98 GLU cc_start: 0.8930 (mp0) cc_final: 0.8718 (mp0) REVERT: K 12 ASP cc_start: 0.8615 (p0) cc_final: 0.8391 (p0) REVERT: K 88 ASN cc_start: 0.8382 (t0) cc_final: 0.8088 (t0) REVERT: L 76 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7758 (tt0) REVERT: L 81 ASP cc_start: 0.8911 (t0) cc_final: 0.8485 (t0) REVERT: M 3 GLN cc_start: 0.9233 (tt0) cc_final: 0.8925 (tt0) REVERT: M 22 GLN cc_start: 0.8620 (mm110) cc_final: 0.8237 (mm-40) REVERT: M 47 GLU cc_start: 0.8749 (tp30) cc_final: 0.8361 (tp30) REVERT: M 110 GLU cc_start: 0.8853 (tt0) cc_final: 0.8224 (tm-30) REVERT: M 136 MET cc_start: 0.7969 (ttp) cc_final: 0.7762 (ttp) REVERT: N 20 MET cc_start: 0.9338 (ttp) cc_final: 0.8894 (ttp) REVERT: N 72 ASP cc_start: 0.8476 (t70) cc_final: 0.8131 (t70) REVERT: O 40 ILE cc_start: 0.8948 (mt) cc_final: 0.8689 (mp) REVERT: O 52 SER cc_start: 0.9642 (m) cc_final: 0.8891 (p) REVERT: O 76 LYS cc_start: 0.9420 (mmmm) cc_final: 0.9119 (mmmm) REVERT: O 88 LYS cc_start: 0.9081 (mmmt) cc_final: 0.8824 (mmmt) REVERT: O 93 ASP cc_start: 0.8573 (t0) cc_final: 0.8200 (t0) REVERT: P 13 MET cc_start: 0.8649 (mmm) cc_final: 0.8331 (mmm) REVERT: P 24 ASP cc_start: 0.8460 (m-30) cc_final: 0.7987 (m-30) REVERT: P 98 TYR cc_start: 0.9271 (m-80) cc_final: 0.9000 (m-80) REVERT: P 112 GLU cc_start: 0.8098 (pp20) cc_final: 0.7698 (pp20) REVERT: Q 102 ASP cc_start: 0.8525 (t0) cc_final: 0.8277 (t0) REVERT: R 2 TYR cc_start: 0.9405 (p90) cc_final: 0.9186 (p90) REVERT: R 31 GLU cc_start: 0.8121 (mp0) cc_final: 0.7771 (mp0) REVERT: R 48 LYS cc_start: 0.9147 (ptpp) cc_final: 0.8769 (ptpp) REVERT: R 55 ASP cc_start: 0.8610 (p0) cc_final: 0.8141 (p0) REVERT: R 60 LYS cc_start: 0.9214 (mttp) cc_final: 0.8779 (pttt) REVERT: R 62 GLU cc_start: 0.8239 (tp30) cc_final: 0.7547 (tp30) REVERT: R 85 LYS cc_start: 0.9084 (ttmm) cc_final: 0.8686 (mtpp) REVERT: R 94 THR cc_start: 0.9344 (OUTLIER) cc_final: 0.8720 (p) REVERT: S 1 MET cc_start: 0.8342 (ttm) cc_final: 0.8114 (ttm) REVERT: S 62 ASP cc_start: 0.8610 (t0) cc_final: 0.8159 (t0) REVERT: S 95 ARG cc_start: 0.8577 (tpp80) cc_final: 0.8231 (tpp80) REVERT: T 91 GLN cc_start: 0.9164 (mm-40) cc_final: 0.8638 (mm110) REVERT: U 8 ASP cc_start: 0.8369 (OUTLIER) cc_final: 0.7673 (t0) REVERT: U 10 GLU cc_start: 0.8435 (tt0) cc_final: 0.7879 (tm-30) REVERT: U 22 ARG cc_start: 0.8863 (mtm-85) cc_final: 0.8284 (mtm-85) REVERT: U 27 ASN cc_start: 0.9008 (p0) cc_final: 0.8533 (p0) REVERT: U 29 LEU cc_start: 0.9321 (mm) cc_final: 0.8974 (mm) REVERT: U 46 GLN cc_start: 0.8698 (tp-100) cc_final: 0.8495 (tp-100) REVERT: V 90 ASP cc_start: 0.8850 (OUTLIER) cc_final: 0.8366 (t0) REVERT: X 35 SER cc_start: 0.9369 (m) cc_final: 0.9087 (t) REVERT: X 70 GLU cc_start: 0.8587 (tm-30) cc_final: 0.8161 (tm-30) REVERT: Y 13 GLU cc_start: 0.8596 (mt-10) cc_final: 0.8325 (mt-10) REVERT: Y 15 ASN cc_start: 0.9393 (m-40) cc_final: 0.8981 (m-40) REVERT: Y 17 GLU cc_start: 0.9153 (tp30) cc_final: 0.8800 (mm-30) REVERT: Y 24 GLU cc_start: 0.8801 (mt-10) cc_final: 0.8477 (mt-10) REVERT: Y 31 GLN cc_start: 0.9441 (mt0) cc_final: 0.9203 (mt0) REVERT: Y 36 GLN cc_start: 0.9111 (mm110) cc_final: 0.8881 (mm-40) REVERT: Y 55 THR cc_start: 0.9392 (OUTLIER) cc_final: 0.9113 (p) REVERT: Y 59 GLU cc_start: 0.9205 (tp30) cc_final: 0.8898 (tp30) REVERT: Z 6 LYS cc_start: 0.8941 (mtmm) cc_final: 0.8572 (mtmm) REVERT: Z 58 GLU cc_start: 0.7818 (tp30) cc_final: 0.7252 (tp30) REVERT: a 22 MET cc_start: 0.4833 (pmm) cc_final: 0.4229 (pmm) REVERT: b 12 LYS cc_start: 0.8926 (mmmt) cc_final: 0.8362 (mmmt) REVERT: c 10 LYS cc_start: 0.7593 (ptmt) cc_final: 0.7017 (ptpp) REVERT: c 17 THR cc_start: 0.7839 (OUTLIER) cc_final: 0.7476 (p) REVERT: c 34 LEU cc_start: 0.7753 (tp) cc_final: 0.7438 (tp) REVERT: c 37 LYS cc_start: 0.9067 (tttt) cc_final: 0.8595 (tppt) REVERT: c 39 PHE cc_start: 0.8669 (t80) cc_final: 0.8276 (t80) REVERT: d 2 LYS cc_start: 0.9371 (tttt) cc_final: 0.9078 (ttpt) REVERT: g 73 LYS cc_start: 0.3455 (OUTLIER) cc_final: 0.2911 (mptt) REVERT: g 145 GLU cc_start: 0.9014 (mm-30) cc_final: 0.8770 (mm-30) REVERT: g 154 MET cc_start: 0.7479 (tpp) cc_final: 0.7277 (tpp) REVERT: g 165 ASP cc_start: 0.5252 (t0) cc_final: 0.5014 (t0) REVERT: g 169 GLU cc_start: 0.7395 (mm-30) cc_final: 0.6872 (mm-30) REVERT: h 41 GLN cc_start: 0.9301 (pp30) cc_final: 0.8973 (pp30) REVERT: h 42 TYR cc_start: 0.9092 (t80) cc_final: 0.8657 (t80) REVERT: h 152 GLU cc_start: 0.8212 (tm-30) cc_final: 0.7914 (tm-30) REVERT: h 168 TYR cc_start: 0.8616 (m-80) cc_final: 0.8208 (m-80) REVERT: h 181 ASP cc_start: 0.8523 (t70) cc_final: 0.8159 (t70) REVERT: h 183 ASP cc_start: 0.8662 (t0) cc_final: 0.8393 (t0) REVERT: h 187 SER cc_start: 0.8265 (t) cc_final: 0.7646 (p) REVERT: h 201 TRP cc_start: 0.8703 (OUTLIER) cc_final: 0.7600 (m-10) REVERT: i 107 PHE cc_start: 0.8841 (m-10) cc_final: 0.8541 (m-80) REVERT: i 141 ASP cc_start: 0.7817 (m-30) cc_final: 0.7397 (m-30) REVERT: i 164 GLN cc_start: 0.8719 (OUTLIER) cc_final: 0.8412 (mp10) REVERT: j 41 ASP cc_start: 0.8726 (p0) cc_final: 0.8480 (p0) REVERT: j 65 GLU cc_start: 0.8792 (tp30) cc_final: 0.8569 (tp30) REVERT: j 76 LEU cc_start: 0.9035 (tt) cc_final: 0.8814 (tt) REVERT: j 86 LYS cc_start: 0.9287 (mmtt) cc_final: 0.8746 (mmmm) REVERT: j 93 ARG cc_start: 0.8817 (mpp80) cc_final: 0.8385 (mpp80) REVERT: j 128 TYR cc_start: 0.8918 (m-80) cc_final: 0.8585 (m-80) REVERT: j 145 GLU cc_start: 0.8619 (pp20) cc_final: 0.8348 (pp20) REVERT: k 3 HIS cc_start: 0.8242 (m90) cc_final: 0.7775 (m170) REVERT: k 9 MET cc_start: 0.8708 (mtp) cc_final: 0.8420 (mtp) REVERT: k 14 GLN cc_start: 0.8629 (mp10) cc_final: 0.7978 (mp10) REVERT: k 59 TYR cc_start: 0.8324 (m-80) cc_final: 0.7694 (m-80) REVERT: k 75 GLU cc_start: 0.9181 (mt-10) cc_final: 0.8873 (mt-10) REVERT: k 90 MET cc_start: 0.7939 (ttp) cc_final: 0.7613 (mtp) REVERT: l 5 ARG cc_start: 0.7987 (tmm160) cc_final: 0.7778 (tmm160) REVERT: l 103 TRP cc_start: 0.9161 (m-10) cc_final: 0.8701 (m-90) REVERT: m 5 ASP cc_start: 0.8753 (t0) cc_final: 0.8124 (t0) REVERT: m 30 SER cc_start: 0.9440 (p) cc_final: 0.9117 (t) REVERT: m 73 GLU cc_start: 0.8547 (tp30) cc_final: 0.8281 (tt0) REVERT: m 96 MET cc_start: 0.9083 (tpp) cc_final: 0.8866 (tpp) REVERT: m 126 ILE cc_start: 0.8755 (mm) cc_final: 0.8473 (tp) REVERT: n 22 LYS cc_start: 0.7040 (ptpp) cc_final: 0.6822 (ptpp) REVERT: n 57 MET cc_start: 0.8604 (mpp) cc_final: 0.8260 (mpp) REVERT: n 61 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8654 (tp) REVERT: n 81 HIS cc_start: 0.8879 (t-90) cc_final: 0.8492 (t-90) REVERT: n 100 LYS cc_start: 0.9100 (mptt) cc_final: 0.8883 (mmtt) REVERT: n 107 ASP cc_start: 0.8866 (OUTLIER) cc_final: 0.8301 (t0) REVERT: o 63 ASP cc_start: 0.8244 (OUTLIER) cc_final: 0.8038 (m-30) REVERT: p 15 GLN cc_start: 0.8176 (pp30) cc_final: 0.7823 (pp30) REVERT: p 18 ASP cc_start: 0.8266 (p0) cc_final: 0.7678 (p0) REVERT: p 68 GLU cc_start: 0.8526 (mm-30) cc_final: 0.8263 (mm-30) REVERT: p 85 MET cc_start: 0.8855 (mmm) cc_final: 0.8505 (mmp) REVERT: q 7 LEU cc_start: 0.9594 (mt) cc_final: 0.9365 (mp) REVERT: q 79 VAL cc_start: 0.9347 (t) cc_final: 0.9114 (p) REVERT: q 90 LEU cc_start: 0.9093 (tp) cc_final: 0.8786 (mt) REVERT: q 112 GLN cc_start: 0.8755 (mt0) cc_final: 0.8086 (mt0) REVERT: r 41 GLU cc_start: 0.8432 (mt-10) cc_final: 0.7942 (mt-10) REVERT: r 42 ASP cc_start: 0.8336 (p0) cc_final: 0.7546 (t70) REVERT: r 59 GLU cc_start: 0.8744 (mm-30) cc_final: 0.7922 (mt-10) REVERT: r 75 MET cc_start: 0.9338 (tmm) cc_final: 0.9010 (tmm) REVERT: r 86 TYR cc_start: 0.8477 (t80) cc_final: 0.8180 (t80) REVERT: s 4 GLN cc_start: 0.8291 (mm110) cc_final: 0.7634 (mm-40) REVERT: s 39 GLU cc_start: 0.8574 (tp30) cc_final: 0.8161 (tp30) REVERT: s 42 TRP cc_start: 0.8948 (t60) cc_final: 0.8299 (t60) REVERT: s 66 GLN cc_start: 0.8754 (mt0) cc_final: 0.8465 (mm-40) REVERT: s 89 MET cc_start: 0.9212 (mmm) cc_final: 0.8866 (mmm) REVERT: t 62 GLN cc_start: 0.9142 (tt0) cc_final: 0.8935 (tp40) REVERT: t 80 GLN cc_start: 0.8181 (tm130) cc_final: 0.7950 (tm-30) REVERT: t 89 ARG cc_start: 0.7260 (tmm-80) cc_final: 0.6651 (tmm-80) REVERT: u 2 VAL cc_start: 0.8747 (OUTLIER) cc_final: 0.8261 (t) REVERT: u 48 GLU cc_start: 0.8960 (mt-10) cc_final: 0.8596 (tt0) REVERT: u 63 GLN cc_start: 0.8851 (mm-40) cc_final: 0.8352 (mm-40) REVERT: v 60 GLU cc_start: 0.7987 (mp0) cc_final: 0.7731 (mp0) REVERT: v 65 ARG cc_start: 0.8107 (OUTLIER) cc_final: 0.7850 (ttp80) REVERT: v 73 TRP cc_start: 0.9438 (m100) cc_final: 0.8528 (m100) REVERT: w 25 ASP cc_start: 0.8468 (t0) cc_final: 0.8172 (t0) REVERT: z 33 ARG cc_start: 0.7865 (ptp-110) cc_final: 0.7304 (ptt180) REVERT: W 15 ASP cc_start: 0.8937 (t0) cc_final: 0.8603 (t0) REVERT: W 17 GLU cc_start: 0.8392 (mm-30) cc_final: 0.8162 (mm-30) REVERT: W 64 ASP cc_start: 0.8784 (m-30) cc_final: 0.8458 (m-30) outliers start: 272 outliers final: 222 residues processed: 1570 average time/residue: 1.2047 time to fit residues: 3338.9430 Evaluate side-chains 1667 residues out of total 4672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 235 poor density : 1432 time to evaluate : 6.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 157 SER Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 183 GLU Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 199 MET Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 23 ASN Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 61 SER Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain E residue 127 ASN Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 20 ASN Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 88 GLN Chi-restraints excluded: chain F residue 114 ASP Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 94 ILE Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 139 PHE Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 55 ILE Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 60 ASP Chi-restraints excluded: chain J residue 67 ASN Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain J residue 139 VAL Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 90 ASN Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 26 VAL Chi-restraints excluded: chain M residue 73 ILE Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain N residue 53 THR Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain O residue 12 THR Chi-restraints excluded: chain O residue 18 LEU Chi-restraints excluded: chain O residue 35 ILE Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain O residue 69 ASP Chi-restraints excluded: chain O residue 98 GLN Chi-restraints excluded: chain P residue 10 GLN Chi-restraints excluded: chain P residue 60 THR Chi-restraints excluded: chain P residue 73 VAL Chi-restraints excluded: chain P residue 97 LEU Chi-restraints excluded: chain P residue 114 LEU Chi-restraints excluded: chain Q residue 4 VAL Chi-restraints excluded: chain Q residue 97 ASP Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain Q residue 107 THR Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 18 GLN Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 43 ASN Chi-restraints excluded: chain R residue 53 PHE Chi-restraints excluded: chain R residue 94 THR Chi-restraints excluded: chain R residue 101 ILE Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 78 GLU Chi-restraints excluded: chain S residue 85 ILE Chi-restraints excluded: chain S residue 86 MET Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 17 SER Chi-restraints excluded: chain T residue 32 LEU Chi-restraints excluded: chain U residue 8 ASP Chi-restraints excluded: chain U residue 9 ASP Chi-restraints excluded: chain U residue 13 VAL Chi-restraints excluded: chain U residue 18 ASP Chi-restraints excluded: chain U residue 25 VAL Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain U residue 36 VAL Chi-restraints excluded: chain U residue 40 ASN Chi-restraints excluded: chain U residue 49 VAL Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain U residue 100 SER Chi-restraints excluded: chain V residue 3 THR Chi-restraints excluded: chain V residue 4 ILE Chi-restraints excluded: chain V residue 60 VAL Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain V residue 66 ASP Chi-restraints excluded: chain V residue 90 ASP Chi-restraints excluded: chain X residue 14 THR Chi-restraints excluded: chain X residue 65 ASP Chi-restraints excluded: chain Y residue 21 LEU Chi-restraints excluded: chain Y residue 34 SER Chi-restraints excluded: chain Y residue 50 VAL Chi-restraints excluded: chain Y residue 55 THR Chi-restraints excluded: chain Z residue 10 THR Chi-restraints excluded: chain Z residue 40 ASP Chi-restraints excluded: chain Z residue 41 THR Chi-restraints excluded: chain Z residue 57 VAL Chi-restraints excluded: chain a residue 28 VAL Chi-restraints excluded: chain a residue 51 VAL Chi-restraints excluded: chain b residue 3 VAL Chi-restraints excluded: chain b residue 26 THR Chi-restraints excluded: chain c residue 9 ILE Chi-restraints excluded: chain c residue 17 THR Chi-restraints excluded: chain c residue 42 VAL Chi-restraints excluded: chain c residue 48 ILE Chi-restraints excluded: chain d residue 8 SER Chi-restraints excluded: chain d residue 24 THR Chi-restraints excluded: chain d residue 45 SER Chi-restraints excluded: chain e residue 6 THR Chi-restraints excluded: chain e residue 32 ILE Chi-restraints excluded: chain e residue 38 THR Chi-restraints excluded: chain e residue 44 LEU Chi-restraints excluded: chain e residue 54 ASP Chi-restraints excluded: chain g residue 23 TRP Chi-restraints excluded: chain g residue 73 LYS Chi-restraints excluded: chain g residue 115 LYS Chi-restraints excluded: chain g residue 127 ASP Chi-restraints excluded: chain g residue 204 ASP Chi-restraints excluded: chain g residue 205 ASP Chi-restraints excluded: chain g residue 207 ILE Chi-restraints excluded: chain h residue 31 ASP Chi-restraints excluded: chain h residue 53 SER Chi-restraints excluded: chain h residue 55 ILE Chi-restraints excluded: chain h residue 116 VAL Chi-restraints excluded: chain h residue 186 THR Chi-restraints excluded: chain h residue 201 TRP Chi-restraints excluded: chain i residue 110 THR Chi-restraints excluded: chain i residue 164 GLN Chi-restraints excluded: chain i residue 190 ASP Chi-restraints excluded: chain i residue 204 TYR Chi-restraints excluded: chain j residue 11 LEU Chi-restraints excluded: chain j residue 30 ILE Chi-restraints excluded: chain j residue 90 THR Chi-restraints excluded: chain j residue 149 SER Chi-restraints excluded: chain k residue 7 VAL Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 46 GLN Chi-restraints excluded: chain k residue 82 ASP Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain k residue 85 ILE Chi-restraints excluded: chain k residue 97 THR Chi-restraints excluded: chain l residue 30 LEU Chi-restraints excluded: chain l residue 54 SER Chi-restraints excluded: chain l residue 136 LYS Chi-restraints excluded: chain l residue 144 MET Chi-restraints excluded: chain m residue 11 LEU Chi-restraints excluded: chain m residue 61 LEU Chi-restraints excluded: chain n residue 29 VAL Chi-restraints excluded: chain n residue 55 VAL Chi-restraints excluded: chain n residue 61 LEU Chi-restraints excluded: chain n residue 72 ILE Chi-restraints excluded: chain n residue 90 TYR Chi-restraints excluded: chain n residue 98 LEU Chi-restraints excluded: chain n residue 107 ASP Chi-restraints excluded: chain n residue 111 VAL Chi-restraints excluded: chain o residue 6 ILE Chi-restraints excluded: chain o residue 10 LEU Chi-restraints excluded: chain o residue 15 HIS Chi-restraints excluded: chain o residue 18 ILE Chi-restraints excluded: chain o residue 44 THR Chi-restraints excluded: chain o residue 63 ASP Chi-restraints excluded: chain o residue 70 HIS Chi-restraints excluded: chain o residue 78 GLU Chi-restraints excluded: chain o residue 80 THR Chi-restraints excluded: chain o residue 84 VAL Chi-restraints excluded: chain o residue 96 VAL Chi-restraints excluded: chain p residue 46 THR Chi-restraints excluded: chain p residue 55 SER Chi-restraints excluded: chain p residue 64 GLN Chi-restraints excluded: chain p residue 81 ASN Chi-restraints excluded: chain p residue 82 LEU Chi-restraints excluded: chain p residue 84 VAL Chi-restraints excluded: chain p residue 97 ILE Chi-restraints excluded: chain q residue 3 THR Chi-restraints excluded: chain q residue 39 THR Chi-restraints excluded: chain q residue 47 SER Chi-restraints excluded: chain q residue 63 VAL Chi-restraints excluded: chain r residue 9 ILE Chi-restraints excluded: chain r residue 43 VAL Chi-restraints excluded: chain r residue 69 LEU Chi-restraints excluded: chain s residue 46 LEU Chi-restraints excluded: chain s residue 48 LEU Chi-restraints excluded: chain s residue 79 LEU Chi-restraints excluded: chain t residue 3 LEU Chi-restraints excluded: chain t residue 18 ASP Chi-restraints excluded: chain u residue 2 VAL Chi-restraints excluded: chain u residue 29 ASN Chi-restraints excluded: chain u residue 68 SER Chi-restraints excluded: chain v residue 51 ASN Chi-restraints excluded: chain v residue 55 ILE Chi-restraints excluded: chain v residue 65 ARG Chi-restraints excluded: chain v residue 70 THR Chi-restraints excluded: chain w residue 21 ILE Chi-restraints excluded: chain w residue 40 VAL Chi-restraints excluded: chain w residue 67 LEU Chi-restraints excluded: chain x residue 5 LEU Chi-restraints excluded: chain x residue 44 MET Chi-restraints excluded: chain x residue 48 THR Chi-restraints excluded: chain x residue 58 VAL Chi-restraints excluded: chain y residue 27 MET Chi-restraints excluded: chain y residue 28 MET Chi-restraints excluded: chain y residue 43 ASP Chi-restraints excluded: chain W residue 59 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1010 random chunks: chunk 885 optimal weight: 5.9990 chunk 932 optimal weight: 1.9990 chunk 850 optimal weight: 10.0000 chunk 907 optimal weight: 10.0000 chunk 546 optimal weight: 8.9990 chunk 395 optimal weight: 20.0000 chunk 712 optimal weight: 7.9990 chunk 278 optimal weight: 10.0000 chunk 819 optimal weight: 9.9990 chunk 857 optimal weight: 20.0000 chunk 903 optimal weight: 9.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 36 GLN N 23 ASN ** P 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 18 GLN T 48 GLN ** U 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 139 GLN ** i 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 68 GLN ** l 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 64 GLN y 70 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8815 moved from start: 0.3255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.087 156844 Z= 0.363 Angle : 0.690 13.319 234723 Z= 0.368 Chirality : 0.038 0.384 29908 Planarity : 0.006 0.129 12506 Dihedral : 23.750 179.754 78631 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 17.02 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.52 % Favored : 95.40 % Rotamer: Outliers : 5.71 % Allowed : 26.20 % Favored : 68.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.50 (0.11), residues: 5614 helix: 0.74 (0.12), residues: 1996 sheet: -0.75 (0.16), residues: 1075 loop : -0.94 (0.12), residues: 2543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP l 103 HIS 0.015 0.001 HIS o 70 PHE 0.028 0.002 PHE U 96 TYR 0.033 0.002 TYR D 35 ARG 0.010 0.001 ARG v 27 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11228 Ramachandran restraints generated. 5614 Oldfield, 0 Emsley, 5614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11228 Ramachandran restraints generated. 5614 Oldfield, 0 Emsley, 5614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1735 residues out of total 4672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 267 poor density : 1468 time to evaluate : 6.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 180 GLU cc_start: 0.8568 (mt-10) cc_final: 0.8279 (tt0) REVERT: B 203 ARG cc_start: 0.8793 (ptp-110) cc_final: 0.8188 (ptp-170) REVERT: B 251 GLN cc_start: 0.8646 (tm-30) cc_final: 0.8194 (tm-30) REVERT: C 11 MET cc_start: 0.8844 (mtp) cc_final: 0.8565 (mtp) REVERT: C 137 SER cc_start: 0.9107 (m) cc_final: 0.8823 (p) REVERT: D 1 MET cc_start: 0.8460 (mmt) cc_final: 0.7992 (mmt) REVERT: D 136 GLN cc_start: 0.9171 (tp-100) cc_final: 0.8768 (tp40) REVERT: D 156 ASN cc_start: 0.9009 (m-40) cc_final: 0.8694 (t0) REVERT: D 170 ARG cc_start: 0.8377 (ptp-170) cc_final: 0.7818 (mtm-85) REVERT: E 130 MET cc_start: 0.8827 (ppp) cc_final: 0.8605 (ppp) REVERT: E 138 PHE cc_start: 0.8900 (m-80) cc_final: 0.8592 (m-80) REVERT: E 177 PHE cc_start: 0.6866 (m-10) cc_final: 0.6604 (m-80) REVERT: F 39 ASP cc_start: 0.8856 (p0) cc_final: 0.8614 (p0) REVERT: F 58 TYR cc_start: 0.7611 (m-80) cc_final: 0.7079 (m-80) REVERT: F 83 PHE cc_start: 0.8346 (m-80) cc_final: 0.7916 (m-80) REVERT: F 101 ASN cc_start: 0.8961 (p0) cc_final: 0.8747 (p0) REVERT: F 130 GLU cc_start: 0.8433 (tp30) cc_final: 0.7900 (tp30) REVERT: F 137 ASP cc_start: 0.9050 (t0) cc_final: 0.8804 (t0) REVERT: G 33 GLN cc_start: 0.8964 (mt0) cc_final: 0.8597 (mt0) REVERT: J 2 LYS cc_start: 0.9444 (OUTLIER) cc_final: 0.8457 (mmtp) REVERT: J 31 GLU cc_start: 0.8672 (tp30) cc_final: 0.8409 (tp30) REVERT: J 75 TYR cc_start: 0.9084 (m-80) cc_final: 0.8842 (m-80) REVERT: J 86 GLN cc_start: 0.9079 (tt0) cc_final: 0.8646 (tt0) REVERT: J 98 GLU cc_start: 0.8929 (mp0) cc_final: 0.8725 (mp0) REVERT: K 12 ASP cc_start: 0.8528 (p0) cc_final: 0.8287 (p0) REVERT: K 20 MET cc_start: 0.8897 (ttp) cc_final: 0.8619 (ttm) REVERT: K 88 ASN cc_start: 0.8386 (t0) cc_final: 0.8094 (t0) REVERT: L 76 GLU cc_start: 0.8056 (mt-10) cc_final: 0.7660 (tt0) REVERT: L 81 ASP cc_start: 0.8895 (t0) cc_final: 0.8485 (t0) REVERT: M 3 GLN cc_start: 0.9221 (tt0) cc_final: 0.8918 (tt0) REVERT: M 22 GLN cc_start: 0.8481 (mm110) cc_final: 0.8080 (mm-40) REVERT: M 47 GLU cc_start: 0.8748 (tp30) cc_final: 0.8326 (tp30) REVERT: M 110 GLU cc_start: 0.8864 (tt0) cc_final: 0.8228 (tm-30) REVERT: N 20 MET cc_start: 0.9324 (ttp) cc_final: 0.9006 (ttp) REVERT: N 72 ASP cc_start: 0.8426 (t70) cc_final: 0.8075 (t70) REVERT: O 40 ILE cc_start: 0.8953 (mt) cc_final: 0.8719 (mp) REVERT: O 52 SER cc_start: 0.9642 (m) cc_final: 0.8895 (p) REVERT: O 61 GLN cc_start: 0.8287 (mp10) cc_final: 0.8057 (mp10) REVERT: O 76 LYS cc_start: 0.9402 (mmmm) cc_final: 0.9092 (mmmm) REVERT: O 88 LYS cc_start: 0.9048 (mmmt) cc_final: 0.8738 (mmmt) REVERT: O 93 ASP cc_start: 0.8581 (t0) cc_final: 0.8278 (t0) REVERT: P 8 LEU cc_start: 0.9105 (mm) cc_final: 0.8835 (mm) REVERT: P 13 MET cc_start: 0.8634 (mmm) cc_final: 0.8316 (mmm) REVERT: P 24 ASP cc_start: 0.8422 (m-30) cc_final: 0.7947 (m-30) REVERT: P 112 GLU cc_start: 0.8116 (pp20) cc_final: 0.7750 (pp20) REVERT: Q 102 ASP cc_start: 0.8503 (t0) cc_final: 0.8214 (t0) REVERT: R 2 TYR cc_start: 0.9390 (p90) cc_final: 0.9164 (p90) REVERT: R 31 GLU cc_start: 0.8170 (mp0) cc_final: 0.7809 (mp0) REVERT: R 48 LYS cc_start: 0.9138 (ptpp) cc_final: 0.8764 (ptpp) REVERT: R 60 LYS cc_start: 0.9242 (mttp) cc_final: 0.8846 (pttt) REVERT: R 62 GLU cc_start: 0.8224 (tp30) cc_final: 0.7544 (tp30) REVERT: R 85 LYS cc_start: 0.9029 (ttmm) cc_final: 0.8630 (mtpp) REVERT: R 94 THR cc_start: 0.9326 (OUTLIER) cc_final: 0.8721 (p) REVERT: S 1 MET cc_start: 0.8363 (ttm) cc_final: 0.8114 (ttm) REVERT: S 62 ASP cc_start: 0.8644 (t0) cc_final: 0.8195 (t0) REVERT: T 91 GLN cc_start: 0.9068 (mm-40) cc_final: 0.8565 (mm110) REVERT: U 8 ASP cc_start: 0.8340 (OUTLIER) cc_final: 0.7646 (t0) REVERT: U 10 GLU cc_start: 0.8404 (tt0) cc_final: 0.7838 (tm-30) REVERT: U 22 ARG cc_start: 0.8884 (mtm-85) cc_final: 0.8318 (mtm-85) REVERT: U 27 ASN cc_start: 0.9002 (p0) cc_final: 0.8518 (p0) REVERT: U 29 LEU cc_start: 0.9360 (mm) cc_final: 0.9017 (mm) REVERT: U 46 GLN cc_start: 0.8762 (tp-100) cc_final: 0.8546 (tp-100) REVERT: V 90 ASP cc_start: 0.8806 (OUTLIER) cc_final: 0.8319 (t0) REVERT: X 35 SER cc_start: 0.9390 (m) cc_final: 0.9084 (t) REVERT: X 43 GLU cc_start: 0.8997 (mt-10) cc_final: 0.8662 (tt0) REVERT: X 70 GLU cc_start: 0.8575 (tm-30) cc_final: 0.8157 (tm-30) REVERT: Y 13 GLU cc_start: 0.8583 (mt-10) cc_final: 0.8371 (mt-10) REVERT: Y 15 ASN cc_start: 0.9425 (m-40) cc_final: 0.9052 (m-40) REVERT: Y 17 GLU cc_start: 0.9142 (tp30) cc_final: 0.8796 (mm-30) REVERT: Y 24 GLU cc_start: 0.8795 (mt-10) cc_final: 0.8470 (mt-10) REVERT: Y 31 GLN cc_start: 0.9429 (mt0) cc_final: 0.9186 (mt0) REVERT: Y 36 GLN cc_start: 0.9097 (mm110) cc_final: 0.8875 (mm-40) REVERT: Y 55 THR cc_start: 0.9374 (OUTLIER) cc_final: 0.9097 (p) REVERT: Y 59 GLU cc_start: 0.9202 (tp30) cc_final: 0.8890 (tp30) REVERT: Z 6 LYS cc_start: 0.8944 (mtmm) cc_final: 0.8612 (mtmm) REVERT: Z 58 GLU cc_start: 0.7747 (tp30) cc_final: 0.7181 (tp30) REVERT: a 1 MET cc_start: 0.6994 (mpp) cc_final: 0.6192 (mmm) REVERT: a 22 MET cc_start: 0.4846 (pmm) cc_final: 0.4277 (pmm) REVERT: b 12 LYS cc_start: 0.8901 (mmmt) cc_final: 0.8324 (mmmt) REVERT: c 10 LYS cc_start: 0.7562 (ptmt) cc_final: 0.6986 (ptpp) REVERT: c 17 THR cc_start: 0.7798 (OUTLIER) cc_final: 0.7490 (p) REVERT: c 34 LEU cc_start: 0.7724 (tp) cc_final: 0.7441 (tp) REVERT: c 37 LYS cc_start: 0.9045 (tttt) cc_final: 0.8726 (tppt) REVERT: c 39 PHE cc_start: 0.8621 (t80) cc_final: 0.8244 (t80) REVERT: d 2 LYS cc_start: 0.9362 (tttt) cc_final: 0.9076 (ttpp) REVERT: g 73 LYS cc_start: 0.3538 (OUTLIER) cc_final: 0.3028 (mptt) REVERT: g 145 GLU cc_start: 0.9032 (mm-30) cc_final: 0.8806 (mm-30) REVERT: g 154 MET cc_start: 0.7409 (tpp) cc_final: 0.7201 (tpp) REVERT: g 169 GLU cc_start: 0.7371 (mm-30) cc_final: 0.6929 (mm-30) REVERT: h 41 GLN cc_start: 0.9279 (pp30) cc_final: 0.8945 (pp30) REVERT: h 42 TYR cc_start: 0.9098 (t80) cc_final: 0.8660 (t80) REVERT: h 152 GLU cc_start: 0.8183 (tm-30) cc_final: 0.7865 (tm-30) REVERT: h 168 TYR cc_start: 0.8618 (m-80) cc_final: 0.8167 (m-80) REVERT: h 181 ASP cc_start: 0.8524 (t70) cc_final: 0.8163 (t70) REVERT: h 183 ASP cc_start: 0.8647 (t0) cc_final: 0.8379 (t0) REVERT: h 187 SER cc_start: 0.8187 (t) cc_final: 0.7428 (p) REVERT: h 201 TRP cc_start: 0.8612 (OUTLIER) cc_final: 0.7649 (m-10) REVERT: i 107 PHE cc_start: 0.8788 (m-10) cc_final: 0.8484 (m-80) REVERT: i 141 ASP cc_start: 0.7899 (m-30) cc_final: 0.7487 (m-30) REVERT: i 164 GLN cc_start: 0.8717 (OUTLIER) cc_final: 0.8448 (mp10) REVERT: j 41 ASP cc_start: 0.8729 (p0) cc_final: 0.8500 (p0) REVERT: j 65 GLU cc_start: 0.8780 (tp30) cc_final: 0.8559 (tp30) REVERT: j 86 LYS cc_start: 0.9280 (mmtt) cc_final: 0.8749 (mmmm) REVERT: j 93 ARG cc_start: 0.8866 (mpp80) cc_final: 0.8428 (mpp80) REVERT: j 128 TYR cc_start: 0.8931 (m-80) cc_final: 0.8597 (m-80) REVERT: j 145 GLU cc_start: 0.8613 (pp20) cc_final: 0.8387 (pp20) REVERT: k 3 HIS cc_start: 0.8215 (m90) cc_final: 0.7760 (m-70) REVERT: k 9 MET cc_start: 0.8664 (mtp) cc_final: 0.8376 (mtp) REVERT: k 14 GLN cc_start: 0.8617 (mp10) cc_final: 0.7997 (mp10) REVERT: k 24 ARG cc_start: 0.9062 (ptp90) cc_final: 0.8657 (ptp90) REVERT: k 42 TRP cc_start: 0.8212 (m-10) cc_final: 0.7954 (m100) REVERT: k 59 TYR cc_start: 0.8239 (m-80) cc_final: 0.7591 (m-80) REVERT: k 75 GLU cc_start: 0.9175 (mt-10) cc_final: 0.8873 (mt-10) REVERT: k 90 MET cc_start: 0.8001 (ttp) cc_final: 0.7654 (mtp) REVERT: l 5 ARG cc_start: 0.8000 (tmm160) cc_final: 0.7764 (tmm160) REVERT: l 116 MET cc_start: 0.8936 (tpp) cc_final: 0.8480 (tpp) REVERT: m 5 ASP cc_start: 0.8763 (t0) cc_final: 0.8092 (t0) REVERT: m 30 SER cc_start: 0.9416 (p) cc_final: 0.9098 (t) REVERT: m 73 GLU cc_start: 0.8491 (tp30) cc_final: 0.8232 (tt0) REVERT: m 126 ILE cc_start: 0.8759 (mm) cc_final: 0.8500 (tp) REVERT: n 6 TYR cc_start: 0.8125 (m-80) cc_final: 0.7890 (m-80) REVERT: n 22 LYS cc_start: 0.6784 (ptpp) cc_final: 0.6482 (ptpp) REVERT: n 57 MET cc_start: 0.8535 (mpp) cc_final: 0.8197 (mpp) REVERT: n 61 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8678 (tp) REVERT: n 81 HIS cc_start: 0.8917 (t-90) cc_final: 0.8538 (t-90) REVERT: n 100 LYS cc_start: 0.9124 (mptt) cc_final: 0.8909 (mmtt) REVERT: n 107 ASP cc_start: 0.8924 (OUTLIER) cc_final: 0.8447 (t0) REVERT: o 15 HIS cc_start: 0.7647 (OUTLIER) cc_final: 0.6529 (t70) REVERT: p 15 GLN cc_start: 0.8257 (pp30) cc_final: 0.7850 (pp30) REVERT: p 18 ASP cc_start: 0.8261 (p0) cc_final: 0.7686 (p0) REVERT: p 68 GLU cc_start: 0.8549 (mm-30) cc_final: 0.8295 (mm-30) REVERT: p 85 MET cc_start: 0.8798 (mmm) cc_final: 0.8310 (mmp) REVERT: p 87 LYS cc_start: 0.8739 (ttmm) cc_final: 0.8459 (ttmm) REVERT: p 101 ASN cc_start: 0.9215 (t0) cc_final: 0.8813 (p0) REVERT: q 7 LEU cc_start: 0.9570 (mt) cc_final: 0.9355 (mp) REVERT: q 75 GLN cc_start: 0.9174 (pt0) cc_final: 0.8766 (pp30) REVERT: q 79 VAL cc_start: 0.9341 (t) cc_final: 0.9111 (p) REVERT: q 90 LEU cc_start: 0.9134 (tp) cc_final: 0.8850 (mt) REVERT: q 112 GLN cc_start: 0.8751 (mt0) cc_final: 0.8103 (mt0) REVERT: r 41 GLU cc_start: 0.8395 (mt-10) cc_final: 0.7930 (mt-10) REVERT: r 42 ASP cc_start: 0.8363 (p0) cc_final: 0.7641 (t70) REVERT: r 75 MET cc_start: 0.9340 (tmm) cc_final: 0.9027 (tmm) REVERT: r 86 TYR cc_start: 0.8492 (t80) cc_final: 0.8214 (t80) REVERT: s 4 GLN cc_start: 0.8275 (mm110) cc_final: 0.7624 (mm-40) REVERT: s 66 GLN cc_start: 0.8747 (mt0) cc_final: 0.8480 (mm-40) REVERT: s 89 MET cc_start: 0.9178 (mmm) cc_final: 0.8876 (mmm) REVERT: t 62 GLN cc_start: 0.9142 (tt0) cc_final: 0.8932 (tp40) REVERT: t 80 GLN cc_start: 0.8111 (tm130) cc_final: 0.7846 (tm-30) REVERT: t 89 ARG cc_start: 0.7242 (tmm-80) cc_final: 0.6645 (tmm-80) REVERT: u 2 VAL cc_start: 0.8719 (OUTLIER) cc_final: 0.8378 (t) REVERT: u 48 GLU cc_start: 0.8976 (mt-10) cc_final: 0.8621 (tt0) REVERT: u 63 GLN cc_start: 0.8870 (mm-40) cc_final: 0.8361 (mm-40) REVERT: v 11 ARG cc_start: 0.8054 (mmm-85) cc_final: 0.7431 (mmm-85) REVERT: v 13 VAL cc_start: 0.9494 (t) cc_final: 0.9251 (m) REVERT: v 60 GLU cc_start: 0.8248 (mp0) cc_final: 0.7953 (mp0) REVERT: v 65 ARG cc_start: 0.8139 (OUTLIER) cc_final: 0.7882 (ttp80) REVERT: v 73 TRP cc_start: 0.9414 (m100) cc_final: 0.8475 (m100) REVERT: z 33 ARG cc_start: 0.7848 (ptp-110) cc_final: 0.7295 (ptt180) REVERT: W 15 ASP cc_start: 0.8824 (t0) cc_final: 0.8508 (t0) REVERT: W 17 GLU cc_start: 0.8379 (mm-30) cc_final: 0.8162 (mm-30) REVERT: W 64 ASP cc_start: 0.8821 (m-30) cc_final: 0.8490 (m-30) outliers start: 267 outliers final: 228 residues processed: 1586 average time/residue: 1.2262 time to fit residues: 3425.6066 Evaluate side-chains 1691 residues out of total 4672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 242 poor density : 1449 time to evaluate : 6.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 53 HIS Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 157 SER Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 183 GLU Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 199 MET Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 23 ASN Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 61 SER Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain E residue 127 ASN Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 20 ASN Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 88 GLN Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 21 VAL Chi-restraints excluded: chain G residue 94 ILE Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 139 PHE Chi-restraints excluded: chain J residue 2 LYS Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 55 ILE Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 60 ASP Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain J residue 139 VAL Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 90 ASN Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 26 VAL Chi-restraints excluded: chain M residue 73 ILE Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain N residue 53 THR Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain O residue 12 THR Chi-restraints excluded: chain O residue 18 LEU Chi-restraints excluded: chain O residue 35 ILE Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain O residue 69 ASP Chi-restraints excluded: chain O residue 98 GLN Chi-restraints excluded: chain P residue 10 GLN Chi-restraints excluded: chain P residue 60 THR Chi-restraints excluded: chain P residue 73 VAL Chi-restraints excluded: chain P residue 97 LEU Chi-restraints excluded: chain P residue 114 LEU Chi-restraints excluded: chain Q residue 4 VAL Chi-restraints excluded: chain Q residue 97 ASP Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain Q residue 107 THR Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 43 ASN Chi-restraints excluded: chain R residue 53 PHE Chi-restraints excluded: chain R residue 94 THR Chi-restraints excluded: chain R residue 101 ILE Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 78 GLU Chi-restraints excluded: chain S residue 85 ILE Chi-restraints excluded: chain S residue 86 MET Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 17 SER Chi-restraints excluded: chain T residue 32 LEU Chi-restraints excluded: chain U residue 8 ASP Chi-restraints excluded: chain U residue 9 ASP Chi-restraints excluded: chain U residue 13 VAL Chi-restraints excluded: chain U residue 18 ASP Chi-restraints excluded: chain U residue 25 VAL Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain U residue 36 VAL Chi-restraints excluded: chain U residue 49 VAL Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain V residue 3 THR Chi-restraints excluded: chain V residue 4 ILE Chi-restraints excluded: chain V residue 30 ILE Chi-restraints excluded: chain V residue 60 VAL Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain V residue 66 ASP Chi-restraints excluded: chain V residue 70 ILE Chi-restraints excluded: chain V residue 90 ASP Chi-restraints excluded: chain X residue 14 THR Chi-restraints excluded: chain X residue 65 ASP Chi-restraints excluded: chain Y residue 21 LEU Chi-restraints excluded: chain Y residue 34 SER Chi-restraints excluded: chain Y residue 50 VAL Chi-restraints excluded: chain Y residue 55 THR Chi-restraints excluded: chain Z residue 10 THR Chi-restraints excluded: chain Z residue 40 ASP Chi-restraints excluded: chain Z residue 41 THR Chi-restraints excluded: chain Z residue 57 VAL Chi-restraints excluded: chain a residue 28 VAL Chi-restraints excluded: chain a residue 51 VAL Chi-restraints excluded: chain b residue 3 VAL Chi-restraints excluded: chain c residue 9 ILE Chi-restraints excluded: chain c residue 17 THR Chi-restraints excluded: chain c residue 42 VAL Chi-restraints excluded: chain c residue 48 ILE Chi-restraints excluded: chain d residue 8 SER Chi-restraints excluded: chain d residue 24 THR Chi-restraints excluded: chain d residue 45 SER Chi-restraints excluded: chain e residue 6 THR Chi-restraints excluded: chain e residue 32 ILE Chi-restraints excluded: chain e residue 38 THR Chi-restraints excluded: chain e residue 44 LEU Chi-restraints excluded: chain e residue 54 ASP Chi-restraints excluded: chain g residue 23 TRP Chi-restraints excluded: chain g residue 73 LYS Chi-restraints excluded: chain g residue 126 PHE Chi-restraints excluded: chain g residue 127 ASP Chi-restraints excluded: chain g residue 204 ASP Chi-restraints excluded: chain g residue 205 ASP Chi-restraints excluded: chain g residue 207 ILE Chi-restraints excluded: chain h residue 31 ASP Chi-restraints excluded: chain h residue 53 SER Chi-restraints excluded: chain h residue 55 ILE Chi-restraints excluded: chain h residue 186 THR Chi-restraints excluded: chain h residue 201 TRP Chi-restraints excluded: chain i residue 19 LEU Chi-restraints excluded: chain i residue 110 THR Chi-restraints excluded: chain i residue 164 GLN Chi-restraints excluded: chain i residue 190 ASP Chi-restraints excluded: chain i residue 204 TYR Chi-restraints excluded: chain j residue 11 LEU Chi-restraints excluded: chain j residue 22 SER Chi-restraints excluded: chain j residue 30 ILE Chi-restraints excluded: chain j residue 90 THR Chi-restraints excluded: chain j residue 149 SER Chi-restraints excluded: chain k residue 7 VAL Chi-restraints excluded: chain k residue 18 VAL Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 46 GLN Chi-restraints excluded: chain k residue 82 ASP Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain k residue 85 ILE Chi-restraints excluded: chain k residue 97 THR Chi-restraints excluded: chain l residue 30 LEU Chi-restraints excluded: chain l residue 54 SER Chi-restraints excluded: chain l residue 136 LYS Chi-restraints excluded: chain l residue 144 MET Chi-restraints excluded: chain m residue 11 LEU Chi-restraints excluded: chain m residue 27 MET Chi-restraints excluded: chain m residue 61 LEU Chi-restraints excluded: chain n residue 5 GLN Chi-restraints excluded: chain n residue 29 VAL Chi-restraints excluded: chain n residue 55 VAL Chi-restraints excluded: chain n residue 61 LEU Chi-restraints excluded: chain n residue 72 ILE Chi-restraints excluded: chain n residue 90 TYR Chi-restraints excluded: chain n residue 98 LEU Chi-restraints excluded: chain n residue 107 ASP Chi-restraints excluded: chain n residue 111 VAL Chi-restraints excluded: chain o residue 6 ILE Chi-restraints excluded: chain o residue 10 LEU Chi-restraints excluded: chain o residue 15 HIS Chi-restraints excluded: chain o residue 18 ILE Chi-restraints excluded: chain o residue 44 THR Chi-restraints excluded: chain o residue 60 ASP Chi-restraints excluded: chain o residue 70 HIS Chi-restraints excluded: chain o residue 78 GLU Chi-restraints excluded: chain o residue 80 THR Chi-restraints excluded: chain o residue 84 VAL Chi-restraints excluded: chain o residue 96 VAL Chi-restraints excluded: chain p residue 31 ILE Chi-restraints excluded: chain p residue 46 THR Chi-restraints excluded: chain p residue 55 SER Chi-restraints excluded: chain p residue 64 GLN Chi-restraints excluded: chain p residue 81 ASN Chi-restraints excluded: chain p residue 82 LEU Chi-restraints excluded: chain p residue 84 VAL Chi-restraints excluded: chain p residue 97 ILE Chi-restraints excluded: chain q residue 3 THR Chi-restraints excluded: chain q residue 39 THR Chi-restraints excluded: chain q residue 47 SER Chi-restraints excluded: chain q residue 53 CYS Chi-restraints excluded: chain q residue 63 VAL Chi-restraints excluded: chain r residue 43 VAL Chi-restraints excluded: chain r residue 48 LEU Chi-restraints excluded: chain s residue 48 LEU Chi-restraints excluded: chain s residue 79 LEU Chi-restraints excluded: chain t residue 3 LEU Chi-restraints excluded: chain t residue 18 ASP Chi-restraints excluded: chain u residue 2 VAL Chi-restraints excluded: chain u residue 29 ASN Chi-restraints excluded: chain u residue 68 SER Chi-restraints excluded: chain v residue 51 ASN Chi-restraints excluded: chain v residue 65 ARG Chi-restraints excluded: chain v residue 70 THR Chi-restraints excluded: chain w residue 21 ILE Chi-restraints excluded: chain w residue 40 VAL Chi-restraints excluded: chain w residue 67 LEU Chi-restraints excluded: chain x residue 5 LEU Chi-restraints excluded: chain x residue 44 MET Chi-restraints excluded: chain x residue 48 THR Chi-restraints excluded: chain x residue 58 VAL Chi-restraints excluded: chain y residue 27 MET Chi-restraints excluded: chain y residue 28 MET Chi-restraints excluded: chain y residue 43 ASP Chi-restraints excluded: chain W residue 59 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1010 random chunks: chunk 595 optimal weight: 10.0000 chunk 959 optimal weight: 9.9990 chunk 585 optimal weight: 1.9990 chunk 455 optimal weight: 50.0000 chunk 666 optimal weight: 0.8980 chunk 1006 optimal weight: 8.9990 chunk 926 optimal weight: 10.0000 chunk 801 optimal weight: 6.9990 chunk 83 optimal weight: 10.0000 chunk 618 optimal weight: 5.9990 chunk 491 optimal weight: 7.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 36 GLN ** M 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 75 GLN ** Q 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 18 GLN ** U 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 35 GLN ** g 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 68 GLN ** l 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 118 GLN p 64 GLN q 6 GLN y 70 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.3326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 156844 Z= 0.270 Angle : 0.655 13.455 234723 Z= 0.351 Chirality : 0.036 0.395 29908 Planarity : 0.006 0.127 12506 Dihedral : 23.720 179.959 78631 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 16.13 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.44 % Favored : 95.49 % Rotamer: Outliers : 5.31 % Allowed : 26.99 % Favored : 67.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.44 (0.11), residues: 5614 helix: 0.77 (0.12), residues: 1998 sheet: -0.71 (0.16), residues: 1077 loop : -0.90 (0.12), residues: 2539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP l 103 HIS 0.011 0.001 HIS o 70 PHE 0.037 0.002 PHE E 20 TYR 0.033 0.002 TYR D 35 ARG 0.014 0.001 ARG f 12 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11228 Ramachandran restraints generated. 5614 Oldfield, 0 Emsley, 5614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11228 Ramachandran restraints generated. 5614 Oldfield, 0 Emsley, 5614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1709 residues out of total 4672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 248 poor density : 1461 time to evaluate : 6.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 117 GLN cc_start: 0.8620 (tt0) cc_final: 0.8284 (tp40) REVERT: B 145 GLU cc_start: 0.8725 (mt-10) cc_final: 0.8459 (mt-10) REVERT: B 146 MET cc_start: 0.9005 (mtp) cc_final: 0.8622 (mtp) REVERT: B 203 ARG cc_start: 0.8798 (ptp-110) cc_final: 0.8235 (ptp90) REVERT: B 251 GLN cc_start: 0.8576 (tm-30) cc_final: 0.8094 (tm-30) REVERT: C 11 MET cc_start: 0.8825 (mtp) cc_final: 0.8589 (mtp) REVERT: C 137 SER cc_start: 0.9093 (m) cc_final: 0.8825 (p) REVERT: D 1 MET cc_start: 0.8523 (mmt) cc_final: 0.8125 (mmm) REVERT: D 136 GLN cc_start: 0.9172 (tp-100) cc_final: 0.8765 (tp40) REVERT: D 156 ASN cc_start: 0.8998 (m-40) cc_final: 0.8698 (t0) REVERT: D 195 GLN cc_start: 0.9019 (mm-40) cc_final: 0.8640 (mm-40) REVERT: E 130 MET cc_start: 0.8873 (ppp) cc_final: 0.8367 (ppp) REVERT: E 138 PHE cc_start: 0.8872 (m-80) cc_final: 0.8536 (m-80) REVERT: E 177 PHE cc_start: 0.6834 (m-10) cc_final: 0.6584 (m-10) REVERT: F 39 ASP cc_start: 0.8860 (p0) cc_final: 0.8624 (p0) REVERT: F 58 TYR cc_start: 0.7576 (m-80) cc_final: 0.7047 (m-80) REVERT: F 62 TRP cc_start: 0.8602 (m100) cc_final: 0.8297 (m100) REVERT: F 83 PHE cc_start: 0.8356 (m-80) cc_final: 0.7910 (m-80) REVERT: F 101 ASN cc_start: 0.9002 (p0) cc_final: 0.8691 (p0) REVERT: F 130 GLU cc_start: 0.8429 (tp30) cc_final: 0.7899 (tp30) REVERT: F 137 ASP cc_start: 0.9014 (t0) cc_final: 0.8765 (t0) REVERT: G 33 GLN cc_start: 0.8922 (mt0) cc_final: 0.8582 (mt0) REVERT: J 31 GLU cc_start: 0.8649 (tp30) cc_final: 0.8390 (tp30) REVERT: J 75 TYR cc_start: 0.9066 (m-80) cc_final: 0.8821 (m-80) REVERT: J 86 GLN cc_start: 0.9047 (tt0) cc_final: 0.8610 (tt0) REVERT: J 90 GLU cc_start: 0.8105 (mp0) cc_final: 0.7878 (mp0) REVERT: J 98 GLU cc_start: 0.8915 (mp0) cc_final: 0.8259 (mp0) REVERT: J 102 GLU cc_start: 0.8635 (mt-10) cc_final: 0.8378 (mt-10) REVERT: K 12 ASP cc_start: 0.8554 (p0) cc_final: 0.8123 (p0) REVERT: K 20 MET cc_start: 0.8785 (ttp) cc_final: 0.8575 (ttm) REVERT: K 88 ASN cc_start: 0.8355 (t0) cc_final: 0.8091 (t0) REVERT: L 76 GLU cc_start: 0.7993 (mt-10) cc_final: 0.7670 (tt0) REVERT: L 81 ASP cc_start: 0.8872 (t0) cc_final: 0.8482 (t0) REVERT: L 143 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.8073 (pp20) REVERT: M 3 GLN cc_start: 0.9165 (tt0) cc_final: 0.8854 (tt0) REVERT: M 22 GLN cc_start: 0.8435 (mm110) cc_final: 0.8154 (mm-40) REVERT: M 47 GLU cc_start: 0.8693 (tp30) cc_final: 0.8353 (tp30) REVERT: M 110 GLU cc_start: 0.8856 (tt0) cc_final: 0.8227 (tm-30) REVERT: N 20 MET cc_start: 0.9297 (ttp) cc_final: 0.8966 (ttp) REVERT: N 72 ASP cc_start: 0.8447 (t70) cc_final: 0.8043 (t70) REVERT: O 40 ILE cc_start: 0.8924 (mt) cc_final: 0.8703 (mp) REVERT: O 52 SER cc_start: 0.9626 (m) cc_final: 0.8861 (p) REVERT: O 61 GLN cc_start: 0.8269 (mp10) cc_final: 0.8024 (mp10) REVERT: O 76 LYS cc_start: 0.9377 (mmmm) cc_final: 0.9081 (mmmm) REVERT: O 88 LYS cc_start: 0.9020 (mmmt) cc_final: 0.8809 (mmmt) REVERT: O 93 ASP cc_start: 0.8494 (t0) cc_final: 0.8157 (t0) REVERT: P 13 MET cc_start: 0.8590 (mmm) cc_final: 0.8238 (mmm) REVERT: P 24 ASP cc_start: 0.8307 (m-30) cc_final: 0.7993 (m-30) REVERT: P 98 TYR cc_start: 0.9089 (m-80) cc_final: 0.8584 (m-80) REVERT: P 112 GLU cc_start: 0.8107 (pp20) cc_final: 0.7735 (pp20) REVERT: Q 102 ASP cc_start: 0.8480 (t0) cc_final: 0.8214 (t0) REVERT: R 2 TYR cc_start: 0.9370 (p90) cc_final: 0.9089 (p90) REVERT: R 10 LYS cc_start: 0.8262 (mttp) cc_final: 0.8061 (mttp) REVERT: R 23 GLU cc_start: 0.8417 (mm-30) cc_final: 0.8071 (mm-30) REVERT: R 31 GLU cc_start: 0.8109 (mp0) cc_final: 0.7767 (mp0) REVERT: R 48 LYS cc_start: 0.9119 (ptpp) cc_final: 0.8776 (ptpp) REVERT: R 60 LYS cc_start: 0.9253 (mttp) cc_final: 0.8891 (pttt) REVERT: R 62 GLU cc_start: 0.8217 (tp30) cc_final: 0.7511 (tp30) REVERT: R 85 LYS cc_start: 0.8956 (ttmm) cc_final: 0.8577 (mtpp) REVERT: R 94 THR cc_start: 0.9325 (m) cc_final: 0.8747 (p) REVERT: S 1 MET cc_start: 0.8293 (ttm) cc_final: 0.7976 (ttm) REVERT: S 8 ARG cc_start: 0.8958 (mtp85) cc_final: 0.8391 (mtp85) REVERT: S 62 ASP cc_start: 0.8591 (t0) cc_final: 0.8130 (t0) REVERT: T 54 GLU cc_start: 0.8504 (mm-30) cc_final: 0.8130 (tp30) REVERT: T 91 GLN cc_start: 0.9063 (mm-40) cc_final: 0.8517 (mm110) REVERT: U 10 GLU cc_start: 0.8417 (tt0) cc_final: 0.7850 (tm-30) REVERT: U 22 ARG cc_start: 0.8891 (mtm-85) cc_final: 0.8325 (mtm-85) REVERT: U 27 ASN cc_start: 0.9025 (p0) cc_final: 0.8575 (p0) REVERT: U 29 LEU cc_start: 0.9410 (mm) cc_final: 0.9056 (mm) REVERT: U 46 GLN cc_start: 0.8771 (tp-100) cc_final: 0.8520 (tp-100) REVERT: V 90 ASP cc_start: 0.8794 (OUTLIER) cc_final: 0.8313 (t0) REVERT: X 35 SER cc_start: 0.9367 (m) cc_final: 0.9051 (t) REVERT: X 43 GLU cc_start: 0.8983 (mt-10) cc_final: 0.8651 (tt0) REVERT: Y 13 GLU cc_start: 0.8665 (mt-10) cc_final: 0.8353 (mt-10) REVERT: Y 15 ASN cc_start: 0.9415 (m-40) cc_final: 0.8982 (m110) REVERT: Y 17 GLU cc_start: 0.9136 (tp30) cc_final: 0.8794 (mm-30) REVERT: Y 24 GLU cc_start: 0.8774 (mt-10) cc_final: 0.8443 (mt-10) REVERT: Y 31 GLN cc_start: 0.9430 (mt0) cc_final: 0.9175 (mt0) REVERT: Y 36 GLN cc_start: 0.9047 (mm110) cc_final: 0.8830 (mm-40) REVERT: Y 55 THR cc_start: 0.9348 (OUTLIER) cc_final: 0.9074 (p) REVERT: Y 59 GLU cc_start: 0.9234 (tp30) cc_final: 0.8952 (tp30) REVERT: Z 6 LYS cc_start: 0.8940 (mtmm) cc_final: 0.8698 (mtmm) REVERT: Z 58 GLU cc_start: 0.7865 (tp30) cc_final: 0.7281 (tp30) REVERT: a 22 MET cc_start: 0.4865 (pmm) cc_final: 0.4372 (pmm) REVERT: b 12 LYS cc_start: 0.8913 (mmmt) cc_final: 0.8323 (mmmt) REVERT: c 10 LYS cc_start: 0.7471 (ptmt) cc_final: 0.6906 (ptpp) REVERT: c 17 THR cc_start: 0.7720 (OUTLIER) cc_final: 0.7452 (p) REVERT: c 39 PHE cc_start: 0.8578 (t80) cc_final: 0.8224 (t80) REVERT: c 51 GLU cc_start: 0.7782 (tt0) cc_final: 0.7384 (pt0) REVERT: d 2 LYS cc_start: 0.9370 (tttt) cc_final: 0.9063 (ttpt) REVERT: f 2 LYS cc_start: 0.8587 (mtpp) cc_final: 0.8199 (ttmm) REVERT: g 73 LYS cc_start: 0.3542 (OUTLIER) cc_final: 0.3152 (mptt) REVERT: g 93 ASN cc_start: 0.7197 (p0) cc_final: 0.5116 (t0) REVERT: g 169 GLU cc_start: 0.7321 (mm-30) cc_final: 0.6888 (mm-30) REVERT: h 41 GLN cc_start: 0.9283 (pp30) cc_final: 0.8903 (pp30) REVERT: h 42 TYR cc_start: 0.9064 (t80) cc_final: 0.8645 (t80) REVERT: h 152 GLU cc_start: 0.8141 (tm-30) cc_final: 0.7834 (tm-30) REVERT: h 168 TYR cc_start: 0.8518 (m-80) cc_final: 0.8063 (m-10) REVERT: h 181 ASP cc_start: 0.8505 (t70) cc_final: 0.8152 (t70) REVERT: h 183 ASP cc_start: 0.8661 (t0) cc_final: 0.8392 (t0) REVERT: h 187 SER cc_start: 0.8035 (t) cc_final: 0.7293 (p) REVERT: h 201 TRP cc_start: 0.8508 (OUTLIER) cc_final: 0.7563 (m-10) REVERT: i 141 ASP cc_start: 0.7890 (m-30) cc_final: 0.7589 (m-30) REVERT: i 164 GLN cc_start: 0.8765 (OUTLIER) cc_final: 0.8509 (mp10) REVERT: j 23 LYS cc_start: 0.8099 (ttpp) cc_final: 0.7583 (ptmt) REVERT: j 41 ASP cc_start: 0.8836 (p0) cc_final: 0.8625 (p0) REVERT: j 65 GLU cc_start: 0.8755 (tp30) cc_final: 0.8532 (tp30) REVERT: j 76 LEU cc_start: 0.9068 (tt) cc_final: 0.8860 (tt) REVERT: j 86 LYS cc_start: 0.9267 (mmtt) cc_final: 0.8737 (mmmm) REVERT: j 93 ARG cc_start: 0.8860 (mpp80) cc_final: 0.8420 (mpp80) REVERT: j 95 PHE cc_start: 0.9132 (t80) cc_final: 0.8866 (t80) REVERT: j 128 TYR cc_start: 0.8927 (m-80) cc_final: 0.8635 (m-80) REVERT: j 145 GLU cc_start: 0.8586 (pp20) cc_final: 0.8322 (pp20) REVERT: k 3 HIS cc_start: 0.8262 (m90) cc_final: 0.7947 (m90) REVERT: k 9 MET cc_start: 0.8636 (mtp) cc_final: 0.8371 (mtp) REVERT: k 33 GLU cc_start: 0.8566 (tm-30) cc_final: 0.8169 (tm-30) REVERT: k 42 TRP cc_start: 0.8228 (m-10) cc_final: 0.8027 (m100) REVERT: k 59 TYR cc_start: 0.8251 (m-80) cc_final: 0.7580 (m-80) REVERT: k 75 GLU cc_start: 0.9156 (mt-10) cc_final: 0.8840 (mt-10) REVERT: k 90 MET cc_start: 0.8016 (ttp) cc_final: 0.7646 (mtp) REVERT: l 103 TRP cc_start: 0.9063 (m-10) cc_final: 0.8605 (m-90) REVERT: l 116 MET cc_start: 0.8939 (tpp) cc_final: 0.8529 (tpp) REVERT: l 142 HIS cc_start: 0.8605 (m90) cc_final: 0.7861 (m90) REVERT: m 5 ASP cc_start: 0.8774 (t0) cc_final: 0.8122 (t0) REVERT: m 30 SER cc_start: 0.9428 (p) cc_final: 0.9136 (t) REVERT: m 73 GLU cc_start: 0.8464 (tp30) cc_final: 0.8250 (tt0) REVERT: m 126 ILE cc_start: 0.8788 (mm) cc_final: 0.8485 (tp) REVERT: n 6 TYR cc_start: 0.8086 (m-80) cc_final: 0.7843 (m-80) REVERT: n 22 LYS cc_start: 0.6667 (ptpp) cc_final: 0.6378 (ptpp) REVERT: n 57 MET cc_start: 0.8522 (mpp) cc_final: 0.8190 (mpp) REVERT: n 61 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8674 (tp) REVERT: n 81 HIS cc_start: 0.8902 (t-90) cc_final: 0.8544 (t-90) REVERT: n 100 LYS cc_start: 0.9083 (mptt) cc_final: 0.8861 (mmtt) REVERT: o 15 HIS cc_start: 0.7737 (OUTLIER) cc_final: 0.6973 (t70) REVERT: p 15 GLN cc_start: 0.8202 (pp30) cc_final: 0.7811 (pp30) REVERT: p 18 ASP cc_start: 0.8194 (p0) cc_final: 0.7580 (p0) REVERT: p 68 GLU cc_start: 0.8511 (mm-30) cc_final: 0.8250 (mm-30) REVERT: p 85 MET cc_start: 0.8750 (mmm) cc_final: 0.8248 (mmp) REVERT: p 87 LYS cc_start: 0.8738 (ttmm) cc_final: 0.8435 (ttmm) REVERT: p 101 ASN cc_start: 0.9210 (t0) cc_final: 0.8851 (p0) REVERT: q 76 GLU cc_start: 0.8685 (tt0) cc_final: 0.8461 (tm-30) REVERT: q 79 VAL cc_start: 0.9367 (t) cc_final: 0.9131 (p) REVERT: q 90 LEU cc_start: 0.9099 (tp) cc_final: 0.8821 (mt) REVERT: q 112 GLN cc_start: 0.8733 (mt0) cc_final: 0.8070 (mt0) REVERT: r 41 GLU cc_start: 0.8362 (mt-10) cc_final: 0.7936 (mt-10) REVERT: r 42 ASP cc_start: 0.8339 (p0) cc_final: 0.7651 (t70) REVERT: r 75 MET cc_start: 0.9332 (tmm) cc_final: 0.9039 (tmm) REVERT: r 86 TYR cc_start: 0.8479 (t80) cc_final: 0.8168 (t80) REVERT: s 4 GLN cc_start: 0.8179 (mm110) cc_final: 0.7526 (mm-40) REVERT: s 66 GLN cc_start: 0.8757 (mt0) cc_final: 0.8505 (mm-40) REVERT: s 89 MET cc_start: 0.9181 (mmm) cc_final: 0.8923 (mmm) REVERT: t 62 GLN cc_start: 0.9123 (tt0) cc_final: 0.8910 (tp40) REVERT: t 80 GLN cc_start: 0.8122 (tm130) cc_final: 0.7875 (tm-30) REVERT: t 83 GLU cc_start: 0.8349 (mp0) cc_final: 0.8076 (pm20) REVERT: t 89 ARG cc_start: 0.7210 (tmm-80) cc_final: 0.6818 (tmm-80) REVERT: u 2 VAL cc_start: 0.8489 (OUTLIER) cc_final: 0.8251 (t) REVERT: u 31 ARG cc_start: 0.8666 (tmm-80) cc_final: 0.8329 (ttp80) REVERT: u 48 GLU cc_start: 0.8960 (mt-10) cc_final: 0.8648 (tt0) REVERT: u 63 GLN cc_start: 0.8878 (mm-40) cc_final: 0.8317 (mm-40) REVERT: v 11 ARG cc_start: 0.8095 (mmm-85) cc_final: 0.7457 (mmm-85) REVERT: v 13 VAL cc_start: 0.9507 (t) cc_final: 0.9247 (m) REVERT: v 18 GLU cc_start: 0.9006 (pt0) cc_final: 0.7983 (pm20) REVERT: v 60 GLU cc_start: 0.8252 (mp0) cc_final: 0.7992 (mp0) REVERT: v 73 TRP cc_start: 0.9395 (m100) cc_final: 0.8477 (m100) REVERT: y 24 ARG cc_start: 0.8805 (mmm160) cc_final: 0.8397 (mmp-170) REVERT: z 33 ARG cc_start: 0.7765 (ptp-110) cc_final: 0.7269 (ptt180) REVERT: W 15 ASP cc_start: 0.8890 (t0) cc_final: 0.8560 (t0) REVERT: W 17 GLU cc_start: 0.8373 (mm-30) cc_final: 0.8112 (mm-30) REVERT: W 64 ASP cc_start: 0.8842 (m-30) cc_final: 0.8537 (m-30) outliers start: 248 outliers final: 222 residues processed: 1570 average time/residue: 1.3382 time to fit residues: 3731.0060 Evaluate side-chains 1661 residues out of total 4672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 232 poor density : 1429 time to evaluate : 6.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 157 SER Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 183 GLU Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 199 MET Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 23 ASN Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 61 SER Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain E residue 127 ASN Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 20 ASN Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 88 GLN Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 21 VAL Chi-restraints excluded: chain G residue 94 ILE Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 139 PHE Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 55 ILE Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 60 ASP Chi-restraints excluded: chain J residue 64 VAL Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain J residue 139 VAL Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 90 ASN Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain L residue 143 GLU Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 26 VAL Chi-restraints excluded: chain M residue 73 ILE Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain N residue 53 THR Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain O residue 12 THR Chi-restraints excluded: chain O residue 18 LEU Chi-restraints excluded: chain O residue 35 ILE Chi-restraints excluded: chain O residue 38 GLN Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain O residue 69 ASP Chi-restraints excluded: chain P residue 10 GLN Chi-restraints excluded: chain P residue 60 THR Chi-restraints excluded: chain P residue 73 VAL Chi-restraints excluded: chain P residue 97 LEU Chi-restraints excluded: chain P residue 114 LEU Chi-restraints excluded: chain Q residue 4 VAL Chi-restraints excluded: chain Q residue 97 ASP Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain Q residue 107 THR Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 43 ASN Chi-restraints excluded: chain R residue 53 PHE Chi-restraints excluded: chain R residue 101 ILE Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 78 GLU Chi-restraints excluded: chain S residue 85 ILE Chi-restraints excluded: chain S residue 86 MET Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 17 SER Chi-restraints excluded: chain T residue 32 LEU Chi-restraints excluded: chain U residue 8 ASP Chi-restraints excluded: chain U residue 9 ASP Chi-restraints excluded: chain U residue 13 VAL Chi-restraints excluded: chain U residue 18 ASP Chi-restraints excluded: chain U residue 25 VAL Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain U residue 36 VAL Chi-restraints excluded: chain U residue 49 VAL Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain V residue 4 ILE Chi-restraints excluded: chain V residue 60 VAL Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain V residue 66 ASP Chi-restraints excluded: chain V residue 70 ILE Chi-restraints excluded: chain V residue 90 ASP Chi-restraints excluded: chain X residue 14 THR Chi-restraints excluded: chain X residue 65 ASP Chi-restraints excluded: chain Y residue 21 LEU Chi-restraints excluded: chain Y residue 34 SER Chi-restraints excluded: chain Y residue 50 VAL Chi-restraints excluded: chain Y residue 55 THR Chi-restraints excluded: chain Z residue 10 THR Chi-restraints excluded: chain Z residue 24 LEU Chi-restraints excluded: chain Z residue 41 THR Chi-restraints excluded: chain Z residue 57 VAL Chi-restraints excluded: chain a residue 28 VAL Chi-restraints excluded: chain a residue 51 VAL Chi-restraints excluded: chain b residue 3 VAL Chi-restraints excluded: chain c residue 9 ILE Chi-restraints excluded: chain c residue 17 THR Chi-restraints excluded: chain c residue 42 VAL Chi-restraints excluded: chain c residue 48 ILE Chi-restraints excluded: chain d residue 8 SER Chi-restraints excluded: chain d residue 24 THR Chi-restraints excluded: chain d residue 45 SER Chi-restraints excluded: chain e residue 6 THR Chi-restraints excluded: chain e residue 32 ILE Chi-restraints excluded: chain e residue 38 THR Chi-restraints excluded: chain e residue 44 LEU Chi-restraints excluded: chain e residue 54 ASP Chi-restraints excluded: chain g residue 23 TRP Chi-restraints excluded: chain g residue 73 LYS Chi-restraints excluded: chain g residue 126 PHE Chi-restraints excluded: chain g residue 127 ASP Chi-restraints excluded: chain g residue 204 ASP Chi-restraints excluded: chain g residue 205 ASP Chi-restraints excluded: chain g residue 207 ILE Chi-restraints excluded: chain h residue 31 ASP Chi-restraints excluded: chain h residue 53 SER Chi-restraints excluded: chain h residue 55 ILE Chi-restraints excluded: chain h residue 116 VAL Chi-restraints excluded: chain h residue 186 THR Chi-restraints excluded: chain h residue 201 TRP Chi-restraints excluded: chain i residue 19 LEU Chi-restraints excluded: chain i residue 110 THR Chi-restraints excluded: chain i residue 164 GLN Chi-restraints excluded: chain i residue 190 ASP Chi-restraints excluded: chain i residue 204 TYR Chi-restraints excluded: chain j residue 11 LEU Chi-restraints excluded: chain j residue 22 SER Chi-restraints excluded: chain j residue 30 ILE Chi-restraints excluded: chain j residue 90 THR Chi-restraints excluded: chain j residue 149 SER Chi-restraints excluded: chain k residue 7 VAL Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 46 GLN Chi-restraints excluded: chain k residue 82 ASP Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain k residue 85 ILE Chi-restraints excluded: chain k residue 97 THR Chi-restraints excluded: chain l residue 54 SER Chi-restraints excluded: chain l residue 136 LYS Chi-restraints excluded: chain l residue 144 MET Chi-restraints excluded: chain m residue 11 LEU Chi-restraints excluded: chain m residue 61 LEU Chi-restraints excluded: chain n residue 5 GLN Chi-restraints excluded: chain n residue 29 VAL Chi-restraints excluded: chain n residue 55 VAL Chi-restraints excluded: chain n residue 58 VAL Chi-restraints excluded: chain n residue 61 LEU Chi-restraints excluded: chain n residue 72 ILE Chi-restraints excluded: chain n residue 90 TYR Chi-restraints excluded: chain n residue 111 VAL Chi-restraints excluded: chain o residue 6 ILE Chi-restraints excluded: chain o residue 10 LEU Chi-restraints excluded: chain o residue 15 HIS Chi-restraints excluded: chain o residue 44 THR Chi-restraints excluded: chain o residue 60 ASP Chi-restraints excluded: chain o residue 69 THR Chi-restraints excluded: chain o residue 78 GLU Chi-restraints excluded: chain o residue 80 THR Chi-restraints excluded: chain o residue 84 VAL Chi-restraints excluded: chain o residue 96 VAL Chi-restraints excluded: chain p residue 46 THR Chi-restraints excluded: chain p residue 55 SER Chi-restraints excluded: chain p residue 64 GLN Chi-restraints excluded: chain p residue 81 ASN Chi-restraints excluded: chain p residue 82 LEU Chi-restraints excluded: chain p residue 84 VAL Chi-restraints excluded: chain p residue 97 ILE Chi-restraints excluded: chain q residue 3 THR Chi-restraints excluded: chain q residue 21 VAL Chi-restraints excluded: chain q residue 39 THR Chi-restraints excluded: chain q residue 47 SER Chi-restraints excluded: chain q residue 53 CYS Chi-restraints excluded: chain q residue 63 VAL Chi-restraints excluded: chain r residue 9 ILE Chi-restraints excluded: chain r residue 43 VAL Chi-restraints excluded: chain r residue 48 LEU Chi-restraints excluded: chain s residue 46 LEU Chi-restraints excluded: chain s residue 48 LEU Chi-restraints excluded: chain s residue 79 LEU Chi-restraints excluded: chain t residue 3 LEU Chi-restraints excluded: chain t residue 18 ASP Chi-restraints excluded: chain u residue 2 VAL Chi-restraints excluded: chain u residue 29 ASN Chi-restraints excluded: chain u residue 68 SER Chi-restraints excluded: chain v residue 51 ASN Chi-restraints excluded: chain v residue 70 THR Chi-restraints excluded: chain w residue 21 ILE Chi-restraints excluded: chain w residue 40 VAL Chi-restraints excluded: chain w residue 67 LEU Chi-restraints excluded: chain x residue 5 LEU Chi-restraints excluded: chain x residue 44 MET Chi-restraints excluded: chain x residue 48 THR Chi-restraints excluded: chain x residue 58 VAL Chi-restraints excluded: chain y residue 28 MET Chi-restraints excluded: chain y residue 43 ASP Chi-restraints excluded: chain W residue 59 LEU Chi-restraints excluded: chain W residue 71 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1010 random chunks: chunk 636 optimal weight: 8.9990 chunk 853 optimal weight: 20.0000 chunk 245 optimal weight: 10.0000 chunk 738 optimal weight: 9.9990 chunk 118 optimal weight: 10.0000 chunk 222 optimal weight: 10.0000 chunk 802 optimal weight: 1.9990 chunk 335 optimal weight: 20.0000 chunk 824 optimal weight: 10.0000 chunk 101 optimal weight: 10.0000 chunk 147 optimal weight: 10.0000 overall best weight: 8.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 36 GLN D 90 GLN G 28 ASN O 38 GLN ** P 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 75 GLN ** Q 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 18 GLN T 48 GLN U 40 ASN ** U 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 139 GLN ** i 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 148 ASN ** k 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 68 GLN ** l 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 64 GLN y 70 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.063613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.044291 restraints weight = 572332.111| |-----------------------------------------------------------------------------| r_work (start): 0.2808 rms_B_bonded: 1.98 r_work: 0.2704 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2618 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9032 moved from start: 0.3418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.101 156844 Z= 0.418 Angle : 0.725 15.484 234723 Z= 0.384 Chirality : 0.039 0.385 29908 Planarity : 0.006 0.132 12506 Dihedral : 23.729 179.825 78631 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 18.03 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.06 % Favored : 94.87 % Rotamer: Outliers : 5.48 % Allowed : 27.08 % Favored : 67.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.59 (0.11), residues: 5614 helix: 0.65 (0.12), residues: 1991 sheet: -0.80 (0.16), residues: 1065 loop : -0.97 (0.12), residues: 2558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP l 103 HIS 0.011 0.001 HIS o 70 PHE 0.025 0.002 PHE U 96 TYR 0.031 0.002 TYR g 213 ARG 0.016 0.001 ARG f 12 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 49977.51 seconds wall clock time: 868 minutes 29.36 seconds (52109.36 seconds total)