Starting phenix.real_space_refine on Tue Mar 26 10:48:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sa4_24944/03_2024/7sa4_24944_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sa4_24944/03_2024/7sa4_24944.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sa4_24944/03_2024/7sa4_24944_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sa4_24944/03_2024/7sa4_24944_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sa4_24944/03_2024/7sa4_24944_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sa4_24944/03_2024/7sa4_24944.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sa4_24944/03_2024/7sa4_24944.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sa4_24944/03_2024/7sa4_24944_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sa4_24944/03_2024/7sa4_24944_updated.pdb" } resolution = 2.55 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 4723 5.49 5 Mg 439 5.21 5 S 164 5.16 5 C 75439 2.51 5 N 27875 2.21 5 O 41423 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "8 GLU 14": "OE1" <-> "OE2" Residue "8 GLU 68": "OE1" <-> "OE2" Residue "8 GLU 102": "OE1" <-> "OE2" Residue "8 GLU 104": "OE1" <-> "OE2" Residue "8 ARG 110": "NH1" <-> "NH2" Residue "8 ARG 132": "NH1" <-> "NH2" Residue "8 ARG 189": "NH1" <-> "NH2" Residue "8 ARG 193": "NH1" <-> "NH2" Residue "8 ARG 194": "NH1" <-> "NH2" Residue "8 GLU 203": "OE1" <-> "OE2" Residue "B ARG 52": "NH1" <-> "NH2" Residue "B ARG 63": "NH1" <-> "NH2" Residue "B ASP 72": "OD1" <-> "OD2" Residue "B ARG 80": "NH1" <-> "NH2" Residue "B GLU 82": "OE1" <-> "OE2" Residue "B ASP 84": "OD1" <-> "OD2" Residue "B ASP 98": "OD1" <-> "OD2" Residue "B GLU 100": "OE1" <-> "OE2" Residue "B ASP 114": "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 ASP 229": "OD1" <-> "OD2" Residue "B GLU 236": "OE1" <-> "OE2" Residue "B PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 269": "NH1" <-> "NH2" Residue "C ARG 13": "NH1" <-> "NH2" Residue "C PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 33": "NH1" <-> "NH2" Residue "C ASP 43": "OD1" <-> "OD2" Residue "C ARG 59": "NH1" <-> "NH2" Residue "C GLU 64": "OE1" <-> "OE2" Residue "C GLU 74": "OE1" <-> "OE2" Residue "C ARG 77": "NH1" <-> "NH2" Residue "C PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 83": "NH1" <-> "NH2" Residue "C GLU 89": "OE1" <-> "OE2" Residue "C ASP 103": "OD1" <-> "OD2" Residue "C ASP 108": "OD1" <-> "OD2" Residue "C PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 168": "OE1" <-> "OE2" Residue "C ARG 169": "NH1" <-> "NH2" Residue "C ASP 181": "OD1" <-> "OD2" Residue "C ARG 184": "NH1" <-> "NH2" Residue "C ASP 200": "OD1" <-> "OD2" Residue "D ARG 21": "NH1" <-> "NH2" Residue "D TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 44": "NH1" <-> "NH2" Residue "D ARG 49": "NH1" <-> "NH2" Residue "D PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 102": "NH1" <-> "NH2" Residue "D PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 140": "OD1" <-> "OD2" Residue "D ASP 154": "OD1" <-> "OD2" Residue "D ARG 162": "NH1" <-> "NH2" Residue "D ARG 170": "NH1" <-> "NH2" Residue "D GLU 197": "OE1" <-> "OE2" Residue "E TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 30": "NH1" <-> "NH2" Residue "E ARG 71": "NH1" <-> "NH2" Residue "E TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 92": "NH1" <-> "NH2" Residue "E ARG 102": "NH1" <-> "NH2" Residue "E ARG 110": "NH1" <-> "NH2" Residue "E ARG 112": "NH1" <-> "NH2" Residue "E ASP 113": "OD1" <-> "OD2" Residue "E ARG 115": "NH1" <-> "NH2" Residue "E PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 123": "OD1" <-> "OD2" Residue "E ARG 148": "NH1" <-> "NH2" Residue "E PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 3": "NH1" <-> "NH2" Residue "F ASP 147": "OD1" <-> "OD2" Residue "F ARG 152": "NH1" <-> "NH2" Residue "F ARG 153": "NH1" <-> "NH2" Residue "F TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 163": "NH1" <-> "NH2" Residue "F ARG 170": "NH1" <-> "NH2" Residue "G ARG 50": "NH1" <-> "NH2" Residue "G ARG 51": "NH1" <-> "NH2" Residue "G ARG 68": "NH1" <-> "NH2" Residue "G GLU 70": "OE1" <-> "OE2" Residue "G PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 149": "OE1" <-> "OE2" Residue "H ASP 36": "OD1" <-> "OD2" Residue "H ARG 62": "NH1" <-> "NH2" Residue "H PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 49": "OE1" <-> "OE2" Residue "J ARG 13": "NH1" <-> "NH2" Residue "J ASP 14": "OD1" <-> "OD2" Residue "J GLU 31": "OE1" <-> "OE2" Residue "J ARG 34": "NH1" <-> "NH2" Residue "J ARG 37": "NH1" <-> "NH2" Residue "J TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 52": "OD1" <-> "OD2" Residue "J ASP 60": "OD1" <-> "OD2" Residue "J TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 89": "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 "J GLU 129": "OE1" <-> "OE2" Residue "K GLU 4": "OE1" <-> "OE2" Residue "K ARG 17": "NH1" <-> "NH2" Residue "K ARG 18": "NH1" <-> "NH2" Residue "K TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 GLU 51": "OE1" <-> "OE2" Residue "L ARG 60": "NH1" <-> "NH2" Residue "L ARG 78": "NH1" <-> "NH2" Residue "L GLU 86": "OE1" <-> "OE2" Residue "L GLU 106": "OE1" <-> "OE2" Residue "L ARG 123": "NH1" <-> "NH2" Residue "L ARG 126": "NH1" <-> "NH2" Residue "L GLU 136": "OE1" <-> "OE2" Residue "M PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 10": "NH1" <-> "NH2" Residue "M ARG 18": "NH1" <-> "NH2" Residue "M PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 31": "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 90": "OE1" <-> "OE2" Residue "M TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 ASP 58": "OD1" <-> "OD2" Residue "N ARG 63": "NH1" <-> "NH2" Residue "N ARG 64": "NH1" <-> "NH2" Residue "N PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 69": "NH1" <-> "NH2" Residue "N TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 96": "NH1" <-> "NH2" Residue "N TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 118": "NH1" <-> "NH2" Residue "O ARG 10": "NH1" <-> "NH2" Residue "O ARG 13": "NH1" <-> "NH2" Residue "O ARG 16": "NH1" <-> "NH2" Residue "O ARG 25": "NH1" <-> "NH2" Residue "O TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 69": "OD1" <-> "OD2" Residue "O ARG 81": "NH1" <-> "NH2" Residue "O ASP 89": "OD1" <-> "OD2" Residue "O ARG 94": "NH1" <-> "NH2" Residue "O ARG 102": "NH1" <-> "NH2" Residue "O ARG 111": "NH1" <-> "NH2" Residue "O PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 21": "NH1" <-> "NH2" Residue "P ASP 24": "OD1" <-> "OD2" Residue "P GLU 27": "OE1" <-> "OE2" Residue "P PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 44": "OE1" <-> "OE2" Residue "P ARG 62": "NH1" <-> "NH2" Residue "P GLU 71": "OE1" <-> "OE2" Residue "P ASP 82": "OD1" <-> "OD2" Residue "P ARG 89": "NH1" <-> "NH2" Residue "P ARG 101": "NH1" <-> "NH2" Residue "P ARG 109": "NH1" <-> "NH2" Residue "Q ARG 3": "NH1" <-> "NH2" Residue "Q ARG 6": "NH1" <-> "NH2" Residue "Q ARG 13": "NH1" <-> "NH2" Residue "Q TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 33": "NH1" <-> "NH2" Residue "Q TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 48": "NH1" <-> "NH2" Residue "Q PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 70": "NH1" <-> "NH2" Residue "Q TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 102": "OD1" <-> "OD2" Residue "R PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 21": "NH1" <-> "NH2" Residue "R GLU 23": "OE1" <-> "OE2" Residue "R GLU 34": "OE1" <-> "OE2" Residue "R PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 68": "NH1" <-> "NH2" Residue "R GLU 70": "OE1" <-> "OE2" Residue "R ARG 78": "NH1" <-> "NH2" Residue "R ARG 79": "NH1" <-> "NH2" Residue "R TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 84": "NH1" <-> "NH2" Residue "S GLU 52": "OE1" <-> "OE2" Residue "S ARG 84": "NH1" <-> "NH2" Residue "S ARG 88": "NH1" <-> "NH2" Residue "S ARG 92": "NH1" <-> "NH2" Residue "S ARG 110": "NH1" <-> "NH2" Residue "T ARG 3": "NH1" <-> "NH2" Residue "T ARG 6": "NH1" <-> "NH2" Residue "T PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 54": "OE1" <-> "OE2" Residue "T GLU 56": "OE1" <-> "OE2" Residue "T TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 89": "OE1" <-> "OE2" Residue "U ARG 6": "NH1" <-> "NH2" 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 "V GLU 7": "OE1" <-> "OE2" Residue "V GLU 11": "OE1" <-> "OE2" Residue "V ARG 19": "NH1" <-> "NH2" Residue "V GLU 55": "OE1" <-> "OE2" Residue "V PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 66": "OD1" <-> "OD2" Residue "W ASP 15": "OD1" <-> "OD2" Residue "W GLU 17": "OE1" <-> "OE2" Residue "W ASP 56": "OD1" <-> "OD2" Residue "W ASP 64": "OD1" <-> "OD2" Residue "W PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 3": "NH1" <-> "NH2" Residue "X ARG 18": "NH1" <-> "NH2" Residue "X ARG 37": "NH1" <-> "NH2" Residue "X PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 45": "NH1" <-> "NH2" Residue "X ARG 50": "NH1" <-> "NH2" Residue "X ARG 57": "NH1" <-> "NH2" Residue "X GLU 70": "OE1" <-> "OE2" Residue "X ARG 74": "NH1" <-> "NH2" Residue "Y ARG 29": "NH1" <-> "NH2" Residue "Y ARG 47": "NH1" <-> "NH2" Residue "Y ARG 52": "NH1" <-> "NH2" Residue "Z ARG 11": "NH1" <-> "NH2" Residue "Z ARG 30": "NH1" <-> "NH2" Residue "Z ARG 45": "NH1" <-> "NH2" Residue "a TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 56": "NH1" <-> "NH2" 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 31": "OD1" <-> "OD2" Residue "b ARG 52": "NH1" <-> "NH2" Residue "c PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 28": "NH1" <-> "NH2" Residue "c GLU 35": "OE1" <-> "OE2" Residue "c ARG 44": "NH1" <-> "NH2" Residue "d ARG 3": "NH1" <-> "NH2" Residue "d PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 30": "NH1" <-> "NH2" Residue "e ARG 40": "NH1" <-> "NH2" Residue "e ARG 42": "NH1" <-> "NH2" Residue "e TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ASP 20": "OD1" <-> "OD2" Residue "f ARG 24": "NH1" <-> "NH2" Residue "g TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ARG 63": "NH1" <-> "NH2" Residue "g ARG 74": "NH1" <-> "NH2" Residue "g GLU 78": "OE1" <-> "OE2" Residue "g ASP 116": "OD1" <-> "OD2" Residue "g ASP 123": "OD1" <-> "OD2" Residue "g ASP 153": "OD1" <-> "OD2" Residue "g ASP 159": "OD1" <-> "OD2" Residue "g ASP 188": "OD1" <-> "OD2" Residue "g PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ARG 208": "NH1" <-> "NH2" Residue "g ARG 225": "NH1" <-> "NH2" Residue "h PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ASP 34": "OD1" <-> "OD2" Residue "h ASP 36": "OD1" <-> "OD2" Residue "h ARG 54": "NH1" <-> "NH2" Residue "h ARG 72": "NH1" <-> "NH2" Residue "h ARG 88": "NH1" <-> "NH2" Residue "h ASP 112": "OD1" <-> "OD2" Residue "h 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 GLU 152": "OE1" <-> "OE2" Residue "h GLU 161": "OE1" <-> "OE2" Residue "h ARG 164": "NH1" <-> "NH2" Residue "h TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 206": "OE1" <-> "OE2" Residue "i ASP 18": "OD1" <-> "OD2" Residue "i ASP 29": "OD1" <-> "OD2" Residue "i ASP 50": "OD1" <-> "OD2" Residue "i GLU 57": "OE1" <-> "OE2" Residue "i GLU 69": "OE1" <-> "OE2" Residue "i ARG 73": "NH1" <-> "NH2" Residue "i ARG 81": "NH1" <-> "NH2" Residue "i GLU 95": "OE1" <-> "OE2" Residue "i ASP 99": "OD1" <-> "OD2" Residue "i PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i GLU 113": "OE1" <-> "OE2" Residue "i GLU 163": "OE1" <-> "OE2" Residue "i ASP 174": "OD1" <-> "OD2" Residue "i PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j GLU 13": "OE1" <-> "OE2" Residue "j PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ASP 41": "OD1" <-> "OD2" 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 PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ARG 157": "NH1" <-> "NH2" Residue "k TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k GLU 23": "OE1" <-> "OE2" Residue "k GLU 40": "OE1" <-> "OE2" Residue "k ASP 41": "OD1" <-> "OD2" Residue "k ARG 45": "NH1" <-> "NH2" Residue "k ARG 79": "NH1" <-> "NH2" Residue "l ARG 4": "NH1" <-> "NH2" Residue "l PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ARG 53": "NH1" <-> "NH2" Residue "l PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 "m GLU 43": "OE1" <-> "OE2" Residue "m GLU 47": "OE1" <-> "OE2" Residue "m ASP 48": "OD1" <-> "OD2" Residue "m PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ASP 54": "OD1" <-> "OD2" Residue "m TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ASP 113": "OD1" <-> "OD2" Residue "m GLU 124": "OE1" <-> "OE2" Residue "m TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ARG 11": "NH1" <-> "NH2" Residue "n TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ARG 41": "NH1" <-> "NH2" Residue "n GLU 59": "OE1" <-> "OE2" Residue "n PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ASP 107": "OD1" <-> "OD2" Residue "n GLU 112": "OE1" <-> "OE2" Residue "n ARG 130": "NH1" <-> "NH2" Residue "o ARG 5": "NH1" <-> "NH2" Residue "o PHE 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ARG 45": "NH1" <-> "NH2" Residue "o TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ARG 89": "NH1" <-> "NH2" Residue "o ASP 91": "OD1" <-> "OD2" Residue "p ARG 37": "NH1" <-> "NH2" Residue "p PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 GLU 25": "OE1" <-> "OE2" Residue "q TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ARG 29": "NH1" <-> "NH2" Residue "r ASP 42": "OD1" <-> "OD2" Residue "r ASP 54": "OD1" <-> "OD2" Residue "r GLU 59": "OE1" <-> "OE2" Residue "r PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r GLU 66": "OE1" <-> "OE2" Residue "r ARG 70": "NH1" <-> "NH2" Residue "r ARG 87": "NH1" <-> "NH2" Residue "r ARG 109": "NH1" <-> "NH2" Residue "s ASP 38": "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 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ARG 85": "NH1" <-> "NH2" Residue "t GLU 14": "OE1" <-> "OE2" Residue "t PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t ASP 49": "OD1" <-> "OD2" Residue "t ARG 72": "NH1" <-> "NH2" Residue "t ARG 89": "NH1" <-> "NH2" Residue "u TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ARG 28": "NH1" <-> "NH2" Residue "u GLU 34": "OE1" <-> "OE2" Residue "u PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ARG 51": "NH1" <-> "NH2" Residue "v ARG 11": "NH1" <-> "NH2" Residue "v ARG 27": "NH1" <-> "NH2" Residue "v ASP 48": "OD1" <-> "OD2" Residue "v GLU 52": "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 ARG 61": "NH1" <-> "NH2" Residue "w ASP 72": "OD1" <-> "OD2" Residue "x PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x ARG 32": "NH1" <-> "NH2" Residue "x PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x ASP 64": "OD1" <-> "OD2" Residue "x GLU 73": "OE1" <-> "OE2" Residue "x PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y ARG 60": "NH1" <-> "NH2" Residue "y ARG 74": "NH1" <-> "NH2" Residue "z GLU 8": "OE1" <-> "OE2" Residue "z ASP 13": "OD1" <-> "OD2" Residue "z PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z GLU 24": "OE1" <-> "OE2" Residue "z ARG 33": "NH1" <-> "NH2" Residue "z GLU 44": "OE1" <-> "OE2" Residue "z ARG 45": "NH1" <-> "NH2" Residue "z ARG 55": "NH1" <-> "NH2" Residue "z ARG 62": "NH1" <-> "NH2" Residue "z GLU 63": "OE1" <-> "OE2" Residue "z ARG 67": "NH1" <-> "NH2" Residue "z ARG 69": "NH1" <-> "NH2" Residue "z TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 150065 Number of models: 1 Model: "" Number of chains: 71 Chain: "1" Number of atoms: 62336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2903, 62336 Classifications: {'RNA': 2903} Modifications used: {'rna2p': 6, 'rna2p_pur': 289, 'rna2p_pyr': 167, 'rna3p': 16, 'rna3p_pur': 1378, 'rna3p_pyr': 1047} Link IDs: {'rna2p': 461, 'rna3p': 2441} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 9 Chain: "2" Number of atoms: 32930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1534, 32930 Unusual residues: {'A3P': 1} Inner-chain residues flagged as termini: ['pdbres=" G 21494 "'] Classifications: {'RNA': 1533, 'undetermined': 1} Modifications used: {'5*END': 1, 'rna2p': 2, 'rna2p_pur': 116, 'rna2p_pyr': 89, 'rna3p': 9, 'rna3p_pur': 752, 'rna3p_pyr': 564} Link IDs: {'rna2p': 206, 'rna3p': 1325, None: 2} Not linked: pdbres=" A 21492 " pdbres="A3P 21493 " Not linked: pdbres="A3P 21493 " pdbres=" G 21494 " Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 2 Chain: "4" 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: "5" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1643 Classifications: {'RNA': 77} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 32, 'rna3p_pyr': 32} Link IDs: {'rna2p': 12, 'rna3p': 64} Chain: "6" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1640 Classifications: {'RNA': 77} Modifications used: {'5*END': 1, 'rna2p_pur': 5, 'rna2p_pyr': 4, 'rna3p_pur': 34, 'rna3p_pyr': 34} Link IDs: {'rna2p': 9, 'rna3p': 67} Chain: "7" Number of atoms: 275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 275 Classifications: {'RNA': 13} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 6, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 11} Chain: "8" Number of atoms: 1606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1606 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 6, 'TRANS': 196} 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: "H" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 980 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 5, 'TRANS': 124} Chain: "I" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 984 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 9, 'TRANS': 125} 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: "W" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 582 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 74} Chain: "X" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "Y" Number of atoms: 501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 501 Classifications: {'peptide': 62} Modifications used: {'COO': 1} Link IDs: {'TRANS': 61} Chain: "Z" Number of atoms: 448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 448 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "a" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 522 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "b" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 444 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "c" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 426 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 2, 'TRANS': 49} Chain: "d" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "e" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 504 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "f" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 302 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "g" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1760 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 7, 'TRANS': 217} Chain: "h" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1636 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 7, 'TRANS': 200} Chain: "i" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "j" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1152 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 5, 'TRANS': 150} Chain: "k" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 848 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "l" Number of atoms: 1181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1181 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain: "m" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "n" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1022 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "o" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 790 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 5, 'TRANS': 93} Chain: "p" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 877 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "q" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 957 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, '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: "1" Number of atoms: 292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 292 Unusual residues: {' MG': 292} Classifications: {'undetermined': 292} Link IDs: {None: 291} Chain: "2" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 127 Unusual residues: {' MG': 127} Classifications: {'undetermined': 127} Link IDs: {None: 126} Chain: "4" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Unusual residues: {' MG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "5" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Unusual residues: {' MG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "f" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "i" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "r" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM A0LPZ SG CYS a 16 18.900 144.562 169.705 1.00 76.36 S ATOM A0LQB SG CYS a 18 15.750 143.847 168.906 1.00 80.05 S ATOM A0LUU SG CYS a 40 18.593 143.860 167.040 1.00 73.57 S ATOM A0NFV SG CYS f 11 78.944 85.050 99.750 1.00 44.27 S ATOM A0NGK SG CYS f 14 80.850 83.365 102.331 1.00 41.69 S ATOM A0NJF SG CYS f 27 82.377 83.843 98.700 1.00 42.78 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb="MG MG 13145 " occ=0.50 Time building chain proxies: 57.65, per 1000 atoms: 0.38 Number of scatterers: 150065 At special positions: 0 Unit cell: (231, 258.3, 267.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 164 16.00 P 4723 15.00 Mg 439 11.99 O 41423 8.00 N 27875 7.00 C 75439 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: 73.43 Conformation dependent library (CDL) restraints added in 7.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN a 101 " pdb="ZN ZN a 101 " - pdb=" SG CYS a 18 " pdb="ZN ZN a 101 " - pdb=" SG CYS a 16 " pdb="ZN ZN a 101 " - pdb=" SG CYS a 40 " pdb=" ZN f 101 " pdb="ZN ZN f 101 " - pdb=" SG CYS f 14 " pdb="ZN ZN f 101 " - pdb=" SG CYS f 27 " pdb="ZN ZN f 101 " - pdb=" SG CYS f 11 " pdb="ZN ZN f 101 " - pdb=" ND1 HIS f 33 " Number of angles added : 3 12136 Ramachandran restraints generated. 6068 Oldfield, 0 Emsley, 6068 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11352 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: 191 helices and 78 sheets defined 39.9% alpha, 19.7% beta 1615 base pairs and 2437 stacking pairs defined. Time for finding SS restraints: 80.18 Creating SS restraints... Processing helix chain '8' and resid 12 through 34 Processing helix chain '8' and resid 60 through 71 removed outlier: 3.960A pdb=" N TRP 8 64 " --> pdb=" O GLY 8 60 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA 8 65 " --> pdb=" O ASP 8 61 " (cutoff:3.500A) Processing helix chain '8' and resid 121 through 127 Processing helix chain '8' and resid 149 through 187 removed outlier: 3.673A pdb=" N HIS 8 184 " --> pdb=" O ARG 8 180 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N HIS 8 185 " --> pdb=" O ARG 8 181 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE 8 187 " --> pdb=" O PHE 8 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 16 removed outlier: 7.444A pdb=" N HIS B 15 " --> pdb=" O PRO B 11 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N VAL B 16 " --> pdb=" O GLY B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 35 removed outlier: 5.307A pdb=" N GLU B 35 " --> pdb=" O ALA B 31 " (cutoff:3.500A) 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: 3.935A pdb=" N ALA B 211 " --> pdb=" O LYS B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 226 removed outlier: 3.885A pdb=" N MET B 225 " --> pdb=" O ARG B 221 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N ASN B 226 " --> pdb=" O GLY B 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 221 through 226' Processing helix chain 'B' and resid 260 through 268 removed outlier: 4.867A pdb=" N LYS B 265 " --> pdb=" O LYS B 261 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N PHE B 266 " --> pdb=" O ARG B 262 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ILE B 267 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N VAL B 268 " --> pdb=" O ASP B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 202 removed outlier: 3.860A pdb=" N MET B 201 " --> pdb=" O ALA B 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 61 removed outlier: 5.236A 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 97 through 103 removed outlier: 5.048A pdb=" N PHE C 101 " --> pdb=" O SER C 97 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ALA C 102 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ASP C 103 " --> pdb=" O GLU C 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 97 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: 5.565A 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 removed outlier: 3.502A pdb=" N LEU D 134 " --> pdb=" O LYS D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 163 removed outlier: 4.458A 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: 3.558A pdb=" N VAL E 12 " --> pdb=" O TYR E 8 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N VAL E 13 " --> pdb=" O LYS E 9 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N LYS E 14 " --> pdb=" O ASP E 10 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 46 removed outlier: 5.057A pdb=" N ILE E 44 " --> pdb=" O VAL E 40 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N ALA E 45 " --> pdb=" O GLY E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 62 removed outlier: 3.900A pdb=" N GLY E 62 " --> pdb=" O ALA E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 111 removed outlier: 4.917A pdb=" N VAL E 108 " --> pdb=" O ILE E 104 " (cutoff:3.500A) Proline residue: E 109 - end of helix Processing helix chain 'E' and resid 162 through 174 Processing helix chain 'E' and resid 134 through 139 removed outlier: 3.589A pdb=" N ILE E 137 " --> pdb=" O GLU E 134 " (cutoff:3.500A) Proline residue: E 139 - end of helix Processing helix chain 'F' and resid 2 through 7 removed outlier: 3.994A pdb=" N ALA F 7 " --> pdb=" O ARG F 3 " (cutoff:3.500A) Processing helix chain 'F' and resid 60 through 81 Processing helix chain 'F' and resid 137 through 153 removed outlier: 3.870A 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 49 Processing helix chain 'G' and resid 50 through 73 removed outlier: 3.991A pdb=" N LEU G 54 " --> pdb=" O ARG G 50 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ALA G 56 " --> pdb=" O ALA G 52 " (cutoff:3.500A) removed outlier: 4.358A 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 'H' and resid 3 through 22 removed outlier: 4.801A pdb=" N ALA H 22 " --> pdb=" O VAL H 18 " (cutoff:3.500A) Processing helix chain 'H' and resid 33 through 48 Processing helix chain 'H' and resid 62 through 68 Proline residue: H 68 - end of helix Processing helix chain 'H' and resid 71 through 78 removed outlier: 4.503A pdb=" N ALA H 75 " --> pdb=" O CYS H 71 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N PHE H 76 " --> pdb=" O LEU H 72 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N VAL H 77 " --> pdb=" O LYS H 73 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLY H 78 " --> pdb=" O ASP H 74 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 71 through 78' Processing helix chain 'H' and resid 94 through 106 removed outlier: 4.170A pdb=" N GLU H 98 " --> pdb=" O ARG H 94 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N PHE H 99 " --> pdb=" O LEU H 95 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA H 100 " --> pdb=" O PHE H 96 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N PHE H 106 " --> pdb=" O ALA H 102 " (cutoff:3.500A) Processing helix chain 'I' and resid 23 through 29 removed outlier: 4.933A pdb=" N LEU I 27 " --> pdb=" O VAL I 23 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLY I 28 " --> pdb=" O GLY I 24 " (cutoff:3.500A) Processing helix chain 'I' and resid 33 through 48 removed outlier: 4.798A pdb=" N PHE I 37 " --> pdb=" O ASN I 33 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N CYS I 38 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N SER I 47 " --> pdb=" O ALA I 43 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ILE I 48 " --> pdb=" O LYS I 44 " (cutoff:3.500A) Processing helix chain 'I' and resid 74 through 84 Processing helix chain 'I' and resid 101 through 117 removed outlier: 3.779A pdb=" N THR I 111 " --> pdb=" O GLU I 107 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LYS I 112 " --> pdb=" O ILE I 108 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N ALA I 114 " --> pdb=" O GLN I 110 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N ASP I 115 " --> pdb=" O THR I 111 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N THR I 117 " --> pdb=" O ALA I 113 " (cutoff:3.500A) Processing helix chain 'I' and resid 120 through 136 removed outlier: 3.963A pdb=" N MET I 124 " --> pdb=" O ASP I 120 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 38 Processing helix chain 'J' and resid 88 through 96 Processing helix chain 'J' and resid 97 through 110 removed outlier: 4.399A 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: 3.876A pdb=" N LEU J 122 " --> pdb=" O MET J 118 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N LYS J 123 " --> pdb=" O PHE J 119 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 72 removed outlier: 4.328A 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: 4.472A pdb=" N ARG K 108 " --> pdb=" O THR K 104 " (cutoff:3.500A) removed outlier: 5.478A 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 37 through 42 removed outlier: 3.592A pdb=" N ARG L 41 " --> pdb=" O GLY L 37 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N SER L 42 " --> pdb=" O GLN L 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 37 through 42' Processing helix chain 'L' and resid 56 through 62 Proline residue: L 62 - end of helix Processing helix chain 'L' and resid 68 through 75 removed outlier: 4.018A pdb=" N ALA L 72 " --> pdb=" O SER L 68 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE L 73 " --> pdb=" O ARG L 69 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N ALA L 75 " --> pdb=" O ALA L 71 " (cutoff:3.500A) Processing helix chain 'L' and resid 78 through 85 removed outlier: 3.932A pdb=" N LEU L 82 " --> pdb=" O ARG L 78 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ALA L 83 " --> pdb=" O LEU L 79 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LYS L 84 " --> pdb=" O SER L 80 " (cutoff:3.500A) removed outlier: 3.644A 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: 3.901A pdb=" N LYS M 123 " --> pdb=" O LEU M 119 " (cutoff:3.500A) removed outlier: 3.802A 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: 4.207A pdb=" N ARG N 46 " --> pdb=" O LYS N 42 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL N 47 " --> pdb=" O GLU N 43 " (cutoff:3.500A) Proline residue: N 50 - end of helix removed outlier: 4.346A 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: 5.006A 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: 4.537A pdb=" N ARG O 13 " --> pdb=" O ARG O 9 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N ALA O 14 " --> pdb=" O ARG O 10 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 63 removed outlier: 4.088A pdb=" N GLN O 61 " --> pdb=" O ALA O 57 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU O 62 " --> pdb=" O ILE O 58 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N LYS O 63 " --> pdb=" O ALA O 59 " (cutoff:3.500A) Processing helix chain 'O' and resid 67 through 86 Processing helix chain 'O' and resid 101 through 114 Processing helix chain 'P' and resid 2 through 13 removed outlier: 4.125A pdb=" N GLN P 12 " --> pdb=" O LEU P 8 " (cutoff:3.500A) Processing helix chain 'P' and resid 97 through 104 removed outlier: 4.590A pdb=" N ARG P 101 " --> pdb=" O LEU P 97 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N GLU P 102 " --> pdb=" O TYR P 98 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ARG P 103 " --> pdb=" O TYR P 99 " (cutoff:3.500A) removed outlier: 5.250A 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 'Q' and resid 6 through 22 Processing helix chain 'Q' and resid 26 through 31 removed outlier: 3.610A pdb=" N ARG Q 30 " --> pdb=" O GLY Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 36 through 73 removed outlier: 3.702A pdb=" N ARG Q 51 " --> pdb=" O TYR Q 47 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LYS Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) removed outlier: 3.595A 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: 3.748A pdb=" N LEU S 19 " --> pdb=" O GLN S 15 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N VAL S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE S 24 " --> pdb=" O VAL S 20 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 39 Processing helix chain 'S' and resid 41 through 61 removed outlier: 3.615A pdb=" N VAL S 45 " --> pdb=" O LYS S 41 " (cutoff:3.500A) Processing helix chain 'T' and resid 3 through 11 removed outlier: 4.188A 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: 3.722A pdb=" N VAL U 70 " --> pdb=" O GLN U 66 " (cutoff:3.500A) removed outlier: 4.941A 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: 3.950A pdb=" N LYS V 53 " --> pdb=" O ASN V 49 " (cutoff:3.500A) Processing helix chain 'V' and resid 54 through 59 removed outlier: 4.001A 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: 3.936A pdb=" N GLU Y 8 " --> pdb=" O LYS Y 4 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N LYS Y 9 " --> pdb=" O GLU Y 5 " (cutoff:3.500A) Processing helix chain 'Y' and resid 10 through 35 removed outlier: 3.851A pdb=" N GLY Y 35 " --> pdb=" O GLN Y 31 " (cutoff:3.500A) Processing helix chain 'Y' and resid 39 through 62 removed outlier: 4.714A pdb=" N LEU Y 43 " --> pdb=" O GLN Y 39 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LYS Y 44 " --> pdb=" O SER Y 40 " (cutoff:3.500A) removed outlier: 4.927A 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 44 through 52 removed outlier: 5.883A pdb=" N GLN a 48 " --> pdb=" O PHE a 44 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ARG a 49 " --> pdb=" O THR a 45 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL a 51 " --> pdb=" O LYS a 47 " (cutoff:3.500A) removed outlier: 4.595A 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 19 removed outlier: 4.833A pdb=" N HIS b 19 " --> pdb=" O MET b 15 " (cutoff:3.500A) Processing helix chain 'd' and resid 8 through 16 Processing helix chain 'd' and resid 17 through 25 removed outlier: 3.974A pdb=" N THR d 24 " --> pdb=" O ALA d 20 " (cutoff:3.500A) removed outlier: 5.254A 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: 5.132A pdb=" N LYS e 36 " --> pdb=" O ILE e 32 " (cutoff:3.500A) removed outlier: 5.255A 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: 4.570A pdb=" N GLY e 56 " --> pdb=" O LYS e 52 " (cutoff:3.500A) removed outlier: 4.905A 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 27 through 32 removed outlier: 5.686A pdb=" N PHE g 32 " --> pdb=" O LYS g 28 " (cutoff:3.500A) Processing helix chain 'g' and resid 42 through 64 Proline residue: g 48 - end of helix Processing helix chain 'g' and resid 73 through 88 removed outlier: 6.173A pdb=" N SER g 77 " --> pdb=" O LYS g 73 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N GLU g 78 " --> pdb=" O ARG g 74 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N ALA g 79 " --> pdb=" O ALA g 75 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N CYS g 87 " --> pdb=" O ALA g 83 " (cutoff:3.500A) Processing helix chain 'g' and resid 103 through 122 removed outlier: 4.110A pdb=" N GLN g 109 " --> pdb=" O LYS g 105 " (cutoff:3.500A) Processing helix chain 'g' and resid 130 through 148 Processing helix chain 'g' and resid 165 through 170 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 removed outlier: 3.591A pdb=" N ARG h 11 " --> pdb=" O PRO h 7 " (cutoff:3.500A) 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: 4.063A pdb=" N GLU h 85 " --> pdb=" O GLY h 81 " (cutoff:3.500A) Processing helix chain 'h' and resid 108 through 113 removed outlier: 3.939A pdb=" N ASP h 112 " --> pdb=" O LYS h 108 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N ALA h 113 " --> pdb=" O PRO h 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 108 through 113' Processing helix chain 'h' and resid 114 through 127 Processing helix chain 'h' and resid 129 through 145 Processing helix chain 'i' and resid 7 through 16 removed outlier: 4.272A pdb=" N LEU i 11 " --> pdb=" O PRO i 7 " (cutoff:3.500A) Processing helix chain 'i' and resid 27 through 32 removed outlier: 3.540A pdb=" N LYS i 31 " --> pdb=" O ALA i 27 " (cutoff:3.500A) Processing helix chain 'i' and resid 49 through 66 Processing helix chain 'i' and resid 68 through 83 removed outlier: 5.355A 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: 3.604A pdb=" N LYS i 121 " --> pdb=" O LEU i 117 " (cutoff:3.500A) Processing helix chain 'i' and resid 146 through 151 removed outlier: 4.429A pdb=" N LYS i 151 " --> pdb=" O GLU i 147 " (cutoff:3.500A) Processing helix chain 'i' and resid 152 through 166 removed outlier: 3.675A pdb=" N LYS i 156 " --> pdb=" O GLN i 152 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N GLU i 166 " --> pdb=" O ALA i 162 " (cutoff:3.500A) Processing helix chain 'i' and resid 187 through 192 removed outlier: 5.046A pdb=" N SER i 192 " --> pdb=" O ARG i 188 " (cutoff:3.500A) Processing helix chain 'i' and resid 196 through 206 removed outlier: 3.786A pdb=" N ILE i 200 " --> pdb=" O ASN i 196 " (cutoff:3.500A) Processing helix chain 'j' and resid 55 through 71 removed outlier: 4.067A pdb=" N ASN j 70 " --> pdb=" O LYS j 66 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N MET j 71 " --> pdb=" O ALA j 67 " (cutoff:3.500A) Processing helix chain 'j' and resid 109 through 119 removed outlier: 4.020A pdb=" N ALA j 113 " --> pdb=" O GLY j 109 " (cutoff:3.500A) Processing helix chain 'j' and resid 132 through 148 removed outlier: 5.603A 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: 3.767A pdb=" N SER k 15 " --> pdb=" O HIS k 11 " (cutoff:3.500A) removed outlier: 5.187A 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 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 111 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: 3.909A 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: 4.226A pdb=" N VAL o 84 " --> pdb=" O THR o 80 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ASP o 85 " --> pdb=" O GLU o 81 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N ASP o 91 " --> pdb=" O LEU o 87 " (cutoff:3.500A) Processing helix chain 'p' and resid 46 through 51 removed outlier: 4.343A pdb=" N GLY p 51 " --> pdb=" O ALA p 47 " (cutoff:3.500A) Processing helix chain 'p' and resid 54 through 59 removed outlier: 4.080A pdb=" N SER p 58 " --> pdb=" O GLY p 54 " (cutoff:3.500A) removed outlier: 4.340A 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 75 Processing helix chain 'p' and resid 93 through 104 removed outlier: 4.578A 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 removed outlier: 3.700A pdb=" N TYR q 117 " --> pdb=" O ALA q 113 " (cutoff:3.500A) Processing helix chain 'r' and resid 14 through 22 removed outlier: 3.628A pdb=" N SER r 21 " --> pdb=" O ILE r 17 " (cutoff:3.500A) removed outlier: 4.394A 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: 4.332A pdb=" N LEU r 48 " --> pdb=" O LYS r 44 " (cutoff:3.500A) removed outlier: 5.586A 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: 3.784A pdb=" N PHE r 63 " --> pdb=" O GLU r 59 " (cutoff:3.500A) removed outlier: 4.786A 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 56 through 61 removed outlier: 4.253A pdb=" N GLN s 60 " --> pdb=" O SER s 56 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N ARG s 61 " --> pdb=" O PRO s 57 " (cutoff:3.500A) No H-bonds generated for 'chain 's' and resid 56 through 61' 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: 4.164A pdb=" N GLY t 41 " --> pdb=" O ASN t 37 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N HIS t 42 " --> pdb=" O HIS t 38 " (cutoff:3.500A) Processing helix chain 't' and resid 49 through 74 removed outlier: 3.686A 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: 3.652A pdb=" N ALA w 15 " --> pdb=" O CYS w 11 " (cutoff:3.500A) Processing helix chain 'w' and resid 25 through 34 removed outlier: 5.423A 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 removed outlier: 3.509A pdb=" N GLN w 54 " --> pdb=" O LYS w 50 " (cutoff:3.500A) Processing helix chain 'x' and resid 12 through 26 Processing helix chain 'x' and resid 63 through 68 removed outlier: 3.892A pdb=" N VAL x 67 " --> pdb=" O THR x 63 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N GLY x 68 " --> pdb=" O ASP x 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'x' and resid 63 through 68' Processing helix chain 'x' and resid 70 through 76 removed outlier: 4.135A pdb=" N PHE x 74 " --> pdb=" O LYS x 70 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA x 75 " --> pdb=" O LEU x 71 " (cutoff:3.500A) Proline residue: x 76 - end of helix No H-bonds generated for 'chain 'x' and resid 70 through 76' Processing helix chain 'y' and resid 4 through 41 Processing helix chain 'y' and resid 44 through 65 Proline residue: y 56 - end of helix Processing helix chain 'y' and resid 68 through 87 removed outlier: 5.317A pdb=" N ALA y 87 " --> pdb=" O ILE y 83 " (cutoff:3.500A) Processing helix chain 'z' and resid 11 through 27 Processing helix chain 'z' and resid 28 through 37 removed outlier: 4.920A pdb=" N PHE z 37 " --> pdb=" O ARG z 33 " (cutoff:3.500A) Processing helix chain 'z' and resid 40 through 69 removed outlier: 4.841A pdb=" N ARG z 62 " --> pdb=" O LYS z 58 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLU z 63 " --> pdb=" O LYS z 59 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N THR z 68 " --> pdb=" O ASN z 64 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ARG z 69 " --> pdb=" O ALA z 65 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain '8' and resid 36 through 40 removed outlier: 4.699A pdb=" N ALA 8 36 " --> pdb=" O ASP 8 59 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ASP 8 59 " --> pdb=" O ALA 8 36 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LEU 8 55 " --> pdb=" O LEU 8 40 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N LEU 8 58 " --> pdb=" O ILE 8 2 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N ILE 8 2 " --> pdb=" O LEU 8 58 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N LEU 8 3 " --> pdb=" O PHE 8 98 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain '8' and resid 109 through 115 removed outlier: 6.532A pdb=" N ARG 8 110 " --> pdb=" O ALA 8 133 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N ALA 8 133 " --> pdb=" O ARG 8 110 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N GLU 8 112 " --> pdb=" O VAL 8 131 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N VAL 8 131 " --> pdb=" O GLU 8 112 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N LEU 8 114 " --> pdb=" O SER 8 129 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ILE 8 140 " --> pdb=" O HIS 8 135 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'B' and resid 2 through 5 Processing sheet with id= 4, first strand: chain 'B' and resid 75 through 78 removed outlier: 4.488A pdb=" N ASP B 114 " --> pdb=" O VAL B 78 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N GLY B 127 " --> pdb=" O GLN B 115 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N GLN B 117 " --> pdb=" O GLY B 127 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'B' and resid 80 through 83 removed outlier: 5.305A pdb=" N ASN B 90 " --> pdb=" O ALA B 106 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'B' and resid 138 through 142 removed outlier: 3.761A pdb=" N SER B 139 " --> pdb=" O ILE B 164 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N THR B 173 " --> pdb=" O VAL B 165 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLU B 180 " --> pdb=" O LEU B 176 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'C' and resid 11 through 16 removed outlier: 3.802A pdb=" N VAL C 20 " --> pdb=" O THR C 16 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL C 26 " --> pdb=" O VAL C 9 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N SER C 199 " --> pdb=" O LYS C 8 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N ASP C 200 " --> pdb=" O THR C 112 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N THR C 112 " --> pdb=" O ASP C 200 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'C' and resid 32 through 35 removed outlier: 6.576A pdb=" N GLN C 49 " --> pdb=" O THR C 35 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'C' and resid 179 through 182 Processing sheet with id= 10, first strand: chain 'C' and resid 24 through 28 Processing sheet with id= 11, first strand: chain 'C' and resid 46 through 51 removed outlier: 5.628A pdb=" N ARG C 46 " --> pdb=" O LEU C 84 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'C' and resid 105 through 108 removed outlier: 6.486A pdb=" N LYS C 105 " --> pdb=" O VAL C 177 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'D' and resid 1 through 6 removed outlier: 3.591A pdb=" N MET D 1 " --> pdb=" O VAL D 14 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N SER D 10 " --> pdb=" O LEU D 5 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'D' and resid 117 through 120 removed outlier: 5.601A pdb=" N ARG D 117 " --> pdb=" O ASP D 184 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'E' and resid 65 through 69 removed outlier: 5.627A pdb=" N GLY E 39 " --> pdb=" O GLY E 151 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N GLY E 151 " --> pdb=" O GLY E 39 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'F' and resid 16 through 19 Processing sheet with id= 17, first strand: chain 'F' and resid 41 through 45 Processing sheet with id= 18, first strand: chain 'F' and resid 82 through 89 removed outlier: 6.012A pdb=" N THR F 129 " --> pdb=" O LEU F 89 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'F' and resid 94 through 98 Processing sheet with id= 20, first strand: chain 'G' and resid 17 through 21 removed outlier: 4.085A pdb=" N ASP G 17 " --> pdb=" O LEU G 5 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N GLN G 2 " --> pdb=" O ALA G 39 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'G' and resid 76 through 83 removed outlier: 6.341A pdb=" N GLU G 76 " --> pdb=" O LYS G 141 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ILE G 143 " --> pdb=" O GLU G 76 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN G 133 " --> pdb=" O GLU G 114 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N GLU G 114 " --> pdb=" O GLN G 133 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'H' and resid 23 through 28 removed outlier: 3.796A pdb=" N LEU H 23 " --> pdb=" O GLU H 87 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'I' and resid 55 through 60 removed outlier: 3.885A pdb=" N VAL I 69 " --> pdb=" O VAL I 57 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'J' and resid 52 through 57 removed outlier: 4.617A pdb=" N ASP J 19 " --> pdb=" O LEU J 140 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'J' and resid 74 through 78 removed outlier: 7.291A pdb=" N GLY J 83 " --> pdb=" O THR J 78 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'K' and resid 6 through 9 removed outlier: 4.020A pdb=" N THR K 6 " --> pdb=" O CYS K 21 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LYS K 40 " --> pdb=" O ILE K 22 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ASP K 37 " --> pdb=" O VAL K 62 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'K' and resid 8 through 11 Processing sheet with id= 28, first strand: chain 'M' and resid 62 through 65 removed outlier: 3.644A pdb=" N TYR M 103 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N LEU M 33 " --> pdb=" O LEU M 102 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LYS M 100 " --> pdb=" O ALA M 35 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'M' and resid 73 through 76 removed outlier: 6.849A pdb=" N ILE M 73 " --> pdb=" O GLU M 90 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'M' and resid 30 through 36 removed outlier: 7.877A pdb=" N SER M 30 " --> pdb=" O LYS M 133 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N LYS M 127 " --> pdb=" O VAL M 36 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'N' and resid 33 through 37 removed outlier: 5.851A pdb=" N ALA N 108 " --> pdb=" O PHE N 102 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N PHE N 102 " --> pdb=" O ALA N 108 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N MET N 110 " --> pdb=" O CYS N 100 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'O' and resid 49 through 52 removed outlier: 3.606A pdb=" N VAL O 49 " --> pdb=" O VAL O 39 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'P' and resid 38 through 45 removed outlier: 6.553A pdb=" N THR P 25 " --> pdb=" O LYS P 87 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'P' and resid 49 through 53 removed outlier: 3.694A pdb=" N ALA P 49 " --> pdb=" O THR P 60 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ARG P 53 " --> pdb=" O HIS P 56 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N SER P 57 " --> pdb=" O THR P 76 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'R' and resid 11 through 15 removed outlier: 3.569A pdb=" N MET R 40 " --> pdb=" O VAL R 4 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'R' and resid 18 through 21 removed outlier: 4.111A pdb=" N GLN R 18 " --> pdb=" O ILE R 98 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ASP R 95 " --> pdb=" O VAL R 64 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LYS R 60 " --> pdb=" O THR R 99 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N GLU R 31 " --> pdb=" O VAL R 63 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'R' and resid 57 through 60 Processing sheet with id= 38, first strand: chain 'R' and resid 65 through 68 Processing sheet with id= 39, first strand: chain 'R' and resid 71 through 78 removed outlier: 4.066A pdb=" N TYR R 83 " --> pdb=" O ARG R 78 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'S' and resid 2 through 8 removed outlier: 4.793A pdb=" N THR S 100 " --> pdb=" O GLY S 79 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'S' and resid 81 through 88 removed outlier: 4.182A pdb=" N ARG S 92 " --> pdb=" O ARG S 88 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'T' and resid 28 through 33 removed outlier: 6.404A pdb=" N ASN T 28 " --> pdb=" O LEU T 87 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N LYS T 66 " --> pdb=" O ARG T 77 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N ASP T 79 " --> pdb=" O LYS T 64 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LYS T 64 " --> pdb=" O ASP T 79 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LYS T 81 " --> pdb=" O VAL T 62 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL T 62 " --> pdb=" O LYS T 81 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ALA T 83 " --> pdb=" O THR T 60 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N THR T 60 " --> pdb=" O ALA T 83 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N VAL T 85 " --> pdb=" O VAL T 58 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N VAL T 58 " --> pdb=" O VAL T 85 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'U' and resid 40 through 45 No H-bonds generated for sheet with id= 43 Processing sheet with id= 44, first strand: chain 'U' and resid 82 through 87 removed outlier: 7.390A pdb=" N ARG U 82 " --> pdb=" O LYS U 97 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N ARG U 94 " --> pdb=" O ILE U 103 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLU U 101 " --> pdb=" O PHE U 96 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'V' and resid 69 through 72 removed outlier: 6.668A pdb=" N ALA V 39 " --> pdb=" O ARG V 9 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE V 89 " --> pdb=" O PRO V 27 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'W' and resid 45 through 48 removed outlier: 5.962A pdb=" N ILE W 82 " --> pdb=" O GLY W 48 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'W' and resid 51 through 54 removed outlier: 4.114A pdb=" N THR W 58 " --> pdb=" O GLY W 54 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'X' and resid 12 through 19 removed outlier: 4.512A pdb=" N ASN X 23 " --> pdb=" O SER X 19 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'X' and resid 35 through 41 Processing sheet with id= 50, first strand: chain 'Z' and resid 33 through 39 removed outlier: 4.161A pdb=" N HIS Z 34 " --> pdb=" O GLN Z 9 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N MET Z 54 " --> pdb=" O THR Z 10 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'a' and resid 20 through 25 removed outlier: 4.378A pdb=" N ASN a 20 " --> pdb=" O CYS a 16 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'b' and resid 29 through 32 removed outlier: 4.204A pdb=" N GLU b 36 " --> pdb=" O ASP b 31 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'c' and resid 19 through 25 removed outlier: 6.096A pdb=" N HIS c 19 " --> pdb=" O SER c 13 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ILE c 48 " --> pdb=" O SER c 14 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N LEU c 34 " --> pdb=" O GLU c 51 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'e' and resid 22 through 25 removed outlier: 5.522A pdb=" N PHE e 22 " --> pdb=" O VAL e 50 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'f' and resid 1 through 5 removed outlier: 6.402A pdb=" N HIS f 33 " --> pdb=" O CYS f 27 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N CYS f 27 " --> pdb=" O HIS f 33 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N ILE f 23 " --> pdb=" O GLN f 37 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'g' and resid 15 through 18 removed outlier: 5.287A pdb=" N HIS g 15 " --> pdb=" O ILE g 41 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N HIS g 39 " --> pdb=" O GLY g 17 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'g' and resid 89 through 93 Processing sheet with id= 58, first strand: chain 'h' and resid 53 through 59 Processing sheet with id= 59, first strand: chain 'h' and resid 164 through 170 removed outlier: 5.800A pdb=" N ARG h 164 " --> pdb=" O GLY h 155 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ASP h 181 " --> pdb=" O LYS h 204 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'i' and resid 141 through 145 removed outlier: 4.012A pdb=" N ASP i 141 " --> pdb=" O PHE i 182 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N MET i 178 " --> pdb=" O ILE i 145 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'j' and resid 11 through 16 removed outlier: 6.683A pdb=" N LEU j 36 " --> pdb=" O ILE j 16 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'j' and resid 83 through 88 removed outlier: 7.309A pdb=" N HIS j 83 " --> pdb=" O PRO j 98 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ALA j 99 " --> pdb=" O ASN j 122 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N ASN j 122 " --> pdb=" O ALA j 99 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'j' and resid 33 through 41 removed outlier: 6.604A pdb=" N ARG j 45 " --> pdb=" O ASP j 41 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'k' and resid 38 through 42 removed outlier: 3.538A pdb=" N ARG k 38 " --> pdb=" O ASN k 63 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N TYR k 59 " --> pdb=" O TRP k 42 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N HIS k 3 " --> pdb=" O THR k 92 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG k 86 " --> pdb=" O MET k 9 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'k' and resid 43 through 46 Processing sheet with id= 66, first strand: chain 'l' and resid 72 through 79 removed outlier: 6.317A pdb=" N THR l 72 " --> pdb=" O VAL l 91 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N TYR l 85 " --> pdb=" O ARG l 78 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'm' and resid 23 through 29 removed outlier: 6.249A pdb=" N ALA m 23 " --> pdb=" O LEU m 63 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP m 48 " --> pdb=" O THR m 62 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'm' and resid 74 through 77 removed outlier: 6.604A pdb=" N VAL m 103 " --> pdb=" O ILE m 126 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'n' and resid 5 through 11 removed outlier: 6.905A pdb=" N LYS n 22 " --> pdb=" O LEU n 63 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N LEU n 63 " --> pdb=" O LYS n 22 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N GLY n 24 " --> pdb=" O LEU n 61 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'o' and resid 36 through 40 removed outlier: 6.223A pdb=" N ARG o 5 " --> pdb=" O GLY o 103 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'o' and resid 44 through 52 Processing sheet with id= 72, first strand: chain 'p' and resid 29 through 36 removed outlier: 3.698A pdb=" N ASN p 29 " --> pdb=" O SER p 26 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N VAL p 84 " --> pdb=" O THR p 108 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'q' and resid 29 through 32 removed outlier: 5.047A pdb=" N LEU q 81 " --> pdb=" O VAL q 98 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N HIS q 96 " --> pdb=" O ARG q 83 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'q' and resid 36 through 41 removed outlier: 4.904A pdb=" N LYS q 51 " --> pdb=" O ILE q 67 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N PHE q 61 " --> pdb=" O LEU q 57 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'u' and resid 4 through 10 removed outlier: 3.800A pdb=" N PHE u 16 " --> pdb=" O HIS u 9 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'v' and resid 7 through 11 removed outlier: 7.015A pdb=" N GLU v 60 " --> pdb=" O VAL v 76 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N SER v 72 " --> pdb=" O CYS v 64 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 'v' and resid 19 through 30 No H-bonds generated for sheet with id= 77 Processing sheet with id= 78, first strand: chain 'x' and resid 30 through 34 removed outlier: 4.542A pdb=" N LEU x 47 " --> pdb=" O VAL x 62 " (cutoff:3.500A) 2175 hydrogen bonds defined for protein. 6429 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 4058 hydrogen bonds 6352 hydrogen bond angles 0 basepair planarities 1615 basepair parallelities 2437 stacking parallelities Total time for adding SS restraints: 321.95 Time building geometry restraints manager: 78.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.54: 152664 1.54 - 1.90: 9770 1.90 - 2.25: 0 2.25 - 2.60: 0 2.60 - 2.96: 3 Bond restraints: 162437 Sorted by residual: bond pdb=" O3' G 21276 " pdb=" P C 21277 " ideal model delta sigma weight residual 1.607 2.958 -1.351 1.50e-02 4.44e+03 8.11e+03 bond pdb=" O3' C 21383 " pdb=" P C 21384 " ideal model delta sigma weight residual 1.607 2.915 -1.308 1.50e-02 4.44e+03 7.60e+03 bond pdb=" O3' G 2 147 " pdb=" P G 2 148 " ideal model delta sigma weight residual 1.607 2.901 -1.294 1.50e-02 4.44e+03 7.44e+03 bond pdb=" C4 5MU 1 747 " pdb=" C5 5MU 1 747 " ideal model delta sigma weight residual 1.802 1.471 0.331 2.00e-02 2.50e+03 2.74e+02 bond pdb=" C4 5MU 11939 " pdb=" C5 5MU 11939 " ideal model delta sigma weight residual 1.802 1.474 0.328 2.00e-02 2.50e+03 2.69e+02 ... (remaining 162432 not shown) Histogram of bond angle deviations from ideal: 66.02 - 87.30: 6 87.30 - 108.58: 55795 108.58 - 129.85: 183988 129.85 - 151.13: 2903 151.13 - 172.41: 3 Bond angle restraints: 242695 Sorted by residual: angle pdb=" O3' G 2 147 " pdb=" P G 2 148 " pdb=" O5' G 2 148 " ideal model delta sigma weight residual 104.00 67.46 36.54 1.50e+00 4.44e-01 5.94e+02 angle pdb=" O3' C 21383 " pdb=" P C 21384 " pdb=" O5' C 21384 " ideal model delta sigma weight residual 104.00 68.83 35.17 1.50e+00 4.44e-01 5.50e+02 angle pdb=" O3' G 2 147 " pdb=" P G 2 148 " pdb=" OP1 G 2 148 " ideal model delta sigma weight residual 108.00 172.41 -64.41 3.00e+00 1.11e-01 4.61e+02 angle pdb=" O3' G 21276 " pdb=" P C 21277 " pdb=" OP2 C 21277 " ideal model delta sigma weight residual 108.00 172.19 -64.19 3.00e+00 1.11e-01 4.58e+02 angle pdb=" O3' G 21276 " pdb=" P C 21277 " pdb=" O5' C 21277 " ideal model delta sigma weight residual 104.00 72.72 31.28 1.50e+00 4.44e-01 4.35e+02 ... (remaining 242690 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 91135 35.95 - 71.90: 11461 71.90 - 107.85: 1252 107.85 - 143.80: 21 143.80 - 179.75: 39 Dihedral angle restraints: 103908 sinusoidal: 86316 harmonic: 17592 Sorted by residual: dihedral pdb=" O4' G7M 12069 " pdb=" C4' G7M 12069 " pdb=" C3' G7M 12069 " pdb=" C2' G7M 12069 " ideal model delta sinusoidal sigma weight residual -35.00 43.23 -78.23 1 8.00e+00 1.56e-02 1.19e+02 dihedral pdb=" O4' U 1 138 " pdb=" C1' U 1 138 " pdb=" N1 U 1 138 " pdb=" C2 U 1 138 " ideal model delta sinusoidal sigma weight residual -160.00 15.49 -175.49 1 1.50e+01 4.44e-03 8.52e+01 dihedral pdb=" O4' U 2 467 " pdb=" C1' U 2 467 " pdb=" N1 U 2 467 " pdb=" C2 U 2 467 " ideal model delta sinusoidal sigma weight residual 200.00 28.77 171.23 1 1.50e+01 4.44e-03 8.48e+01 ... (remaining 103905 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.109: 30887 1.109 - 2.217: 0 2.217 - 3.326: 0 3.326 - 4.435: 0 4.435 - 5.544: 3 Chirality restraints: 30890 Sorted by residual: chirality pdb=" C2' G7M 12069 " pdb=" C3' G7M 12069 " pdb=" O2' G7M 12069 " pdb=" C1' G7M 12069 " both_signs ideal model delta sigma weight residual False -2.75 2.79 -5.54 2.00e-01 2.50e+01 7.68e+02 chirality pdb=" C3' G7M 12069 " pdb=" C4' G7M 12069 " pdb=" O3' G7M 12069 " pdb=" C2' G7M 12069 " both_signs ideal model delta sigma weight residual False -2.48 2.20 -4.68 2.00e-01 2.50e+01 5.47e+02 chirality pdb=" C4' G7M 12069 " pdb=" C5' G7M 12069 " pdb=" O4' G7M 12069 " pdb=" C3' G7M 12069 " both_signs ideal model delta sigma weight residual False -2.50 2.16 -4.66 2.00e-01 2.50e+01 5.42e+02 ... (remaining 30887 not shown) Planarity restraints: 13216 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 2MG 21516 " 0.061 2.00e-02 2.50e+03 6.07e-01 8.29e+03 pdb=" C4' 2MG 21516 " 0.445 2.00e-02 2.50e+03 pdb=" O4' 2MG 21516 " 0.635 2.00e-02 2.50e+03 pdb=" C3' 2MG 21516 " -0.593 2.00e-02 2.50e+03 pdb=" O3' 2MG 21516 " -0.649 2.00e-02 2.50e+03 pdb=" C2' 2MG 21516 " -0.169 2.00e-02 2.50e+03 pdb=" O2' 2MG 21516 " 0.987 2.00e-02 2.50e+03 pdb=" C1' 2MG 21516 " 0.223 2.00e-02 2.50e+03 pdb=" N9 2MG 21516 " -0.941 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMC 12498 " -0.068 2.00e-02 2.50e+03 5.97e-01 8.02e+03 pdb=" C4' OMC 12498 " -0.437 2.00e-02 2.50e+03 pdb=" O4' OMC 12498 " -0.601 2.00e-02 2.50e+03 pdb=" C3' OMC 12498 " 0.609 2.00e-02 2.50e+03 pdb=" O3' OMC 12498 " 0.647 2.00e-02 2.50e+03 pdb=" C2' OMC 12498 " 0.174 2.00e-02 2.50e+03 pdb=" O2' OMC 12498 " -0.991 2.00e-02 2.50e+03 pdb=" C1' OMC 12498 " -0.227 2.00e-02 2.50e+03 pdb=" N1 OMC 12498 " 0.894 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' A3P 21493 " 0.853 2.00e-02 2.50e+03 5.84e-01 7.67e+03 pdb=" C4' A3P 21493 " -0.228 2.00e-02 2.50e+03 pdb=" O4' A3P 21493 " -0.781 2.00e-02 2.50e+03 pdb=" C3' A3P 21493 " 0.294 2.00e-02 2.50e+03 pdb=" O3' A3P 21493 " -0.860 2.00e-02 2.50e+03 pdb=" C2' A3P 21493 " 0.631 2.00e-02 2.50e+03 pdb=" O2' A3P 21493 " 0.500 2.00e-02 2.50e+03 pdb=" C1' A3P 21493 " -0.453 2.00e-02 2.50e+03 pdb=" N9 A3P 21493 " 0.043 2.00e-02 2.50e+03 ... (remaining 13213 not shown) Histogram of nonbonded interaction distances: 1.12 - 1.88: 9 1.88 - 2.63: 5703 2.63 - 3.39: 193966 3.39 - 4.14: 540104 4.14 - 4.90: 716992 Nonbonded interactions: 1456774 Sorted by model distance: nonbonded pdb="MG MG 21714 " pdb="MG MG 21715 " model vdw 1.125 1.300 nonbonded pdb=" O6 G 1 570 " pdb="MG MG 13084 " model vdw 1.854 2.170 nonbonded pdb=" OP1 G 11332 " pdb="MG MG 13153 " model vdw 1.854 2.170 nonbonded pdb=" OP2 A 2 596 " pdb="MG MG 21697 " model vdw 1.857 2.170 nonbonded pdb=" OP1 C 12427 " pdb="MG MG 13151 " model vdw 1.863 2.170 ... (remaining 1456769 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain '5' and ((resid 0 and (name O5' or name C5' or name C4' or name O4' or na \ me C3' or name O3' or name C2' or name O2' or name C1' or name N1 or name C2 or \ name O2 or name N3 or name C4 or name N4 or name C5 or name C6 )) or resid 1 thr \ ough 76)) selection = chain '6' } 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=0.50 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: 5.060 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: 0.180 Extract box with map and model: 17.960 Check model and map are aligned: 1.620 Set scattering table: 1.020 Process input model: 671.900 Find NCS groups from input model: 3.480 Set up NCS constraints: 0.470 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: 0.040 Load rotamer database and sin/cos tables:12.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 714.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 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 : 0.011 1.351 162437 Z= 0.631 Angle : 0.854 64.409 242695 Z= 0.441 Chirality : 0.067 5.544 30890 Planarity : 0.018 0.607 13216 Dihedral : 23.369 179.747 92556 Min Nonbonded Distance : 1.125 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.61 % Favored : 96.34 % Rotamer: Outliers : 0.06 % Allowed : 0.52 % Favored : 99.42 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.10), residues: 6068 helix: 0.79 (0.11), residues: 2105 sheet: -0.79 (0.14), residues: 1105 loop : -0.73 (0.11), residues: 2858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.096 0.004 TRP g 23 HIS 0.017 0.003 HIS e 31 PHE 0.044 0.003 PHE a 64 TYR 0.038 0.003 TYR g 213 ARG 0.036 0.002 ARG B 217 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12136 Ramachandran restraints generated. 6068 Oldfield, 0 Emsley, 6068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12136 Ramachandran restraints generated. 6068 Oldfield, 0 Emsley, 6068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1923 residues out of total 5041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1920 time to evaluate : 6.309 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: B 97 LYS cc_start: 0.8700 (mmmm) cc_final: 0.8456 (mmtt) REVERT: C 103 ASP cc_start: 0.7297 (p0) cc_final: 0.6870 (p0) REVERT: C 139 SER cc_start: 0.9095 (m) cc_final: 0.8894 (m) REVERT: E 15 LYS cc_start: 0.8634 (ttmt) cc_final: 0.8408 (ttmm) REVERT: H 38 MET cc_start: 0.1625 (mmt) cc_final: 0.1021 (mpp) REVERT: J 34 ARG cc_start: 0.8447 (ttp80) cc_final: 0.8150 (ttt90) REVERT: J 102 GLU cc_start: 0.8356 (mt-10) cc_final: 0.8134 (mt-10) REVERT: M 44 ARG cc_start: 0.8322 (mtt-85) cc_final: 0.8122 (mtt-85) REVERT: M 82 MET cc_start: 0.8724 (mmp) cc_final: 0.8388 (mmm) REVERT: T 4 GLU cc_start: 0.7824 (tp30) cc_final: 0.7513 (tp30) REVERT: Y 4 LYS cc_start: 0.8328 (tmtt) cc_final: 0.8047 (tptp) REVERT: c 30 LYS cc_start: 0.8838 (mmtp) cc_final: 0.8549 (mmtp) REVERT: g 36 ASN cc_start: 0.6333 (t0) cc_final: 0.5996 (t0) REVERT: g 190 ASN cc_start: 0.8761 (p0) cc_final: 0.8532 (p0) REVERT: h 89 LYS cc_start: 0.8126 (mmpt) cc_final: 0.7696 (mmmt) REVERT: h 132 ARG cc_start: 0.7662 (ttm-80) cc_final: 0.7129 (ttt90) REVERT: h 199 LYS cc_start: 0.9269 (mttt) cc_final: 0.9027 (mttm) REVERT: j 66 LYS cc_start: 0.8409 (mttt) cc_final: 0.8148 (mtmt) REVERT: l 90 GLU cc_start: 0.7145 (mm-30) cc_final: 0.6855 (mm-30) REVERT: l 101 MET cc_start: 0.8438 (mtm) cc_final: 0.8148 (mtp) REVERT: p 20 VAL cc_start: 0.8982 (t) cc_final: 0.8637 (m) REVERT: p 68 GLU cc_start: 0.7665 (mt-10) cc_final: 0.7371 (mt-10) REVERT: p 105 PHE cc_start: 0.8971 (m-80) cc_final: 0.8676 (m-80) REVERT: t 53 ARG cc_start: 0.8813 (ttm110) cc_final: 0.8566 (ttm110) REVERT: u 23 ASP cc_start: 0.8700 (t0) cc_final: 0.8495 (t70) REVERT: v 15 ASP cc_start: 0.8317 (p0) cc_final: 0.8116 (p0) REVERT: w 25 ASP cc_start: 0.8258 (t0) cc_final: 0.7888 (t0) REVERT: w 54 GLN cc_start: 0.8505 (tt0) cc_final: 0.8221 (tt0) outliers start: 3 outliers final: 3 residues processed: 1922 average time/residue: 2.3711 time to fit residues: 6398.6301 Evaluate side-chains 1664 residues out of total 5041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1661 time to evaluate : 6.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 8 residue 8 SER Chi-restraints excluded: chain 8 residue 203 GLU Chi-restraints excluded: chain j residue 164 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1063 random chunks: chunk 897 optimal weight: 4.9990 chunk 805 optimal weight: 7.9990 chunk 447 optimal weight: 10.0000 chunk 275 optimal weight: 10.0000 chunk 543 optimal weight: 0.8980 chunk 430 optimal weight: 0.7980 chunk 833 optimal weight: 8.9990 chunk 322 optimal weight: 7.9990 chunk 506 optimal weight: 0.8980 chunk 620 optimal weight: 40.0000 chunk 965 optimal weight: 3.9990 overall best weight: 2.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 8 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 85 HIS 8 86 HIS 8 167 GLN 8 179 GLN C 32 ASN C 42 ASN ** C 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 62 GLN D 156 ASN D 195 GLN E 127 ASN F 45 HIS F 104 ASN F 128 GLN ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 9 GLN ** M 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 97 GLN O 100 HIS P 75 GLN Q 72 ASN R 86 GLN R 91 GLN S 7 HIS S 57 ASN T 28 ASN T 48 GLN T 59 ASN U 69 ASN V 49 ASN V 75 GLN ** V 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 76 ASN Y 15 ASN Y 20 ASN Y 31 GLN a 61 ASN b 42 HIS d 29 GLN ** g 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 58 ASN ** g 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 19 ASN h 100 GLN i 40 GLN ** i 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 116 GLN j 73 ASN j 89 HIS k 11 HIS ** k 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 67 GLN n 50 GLN n 75 GLN n 126 GLN o 20 GLN s 60 GLN s 66 GLN t 35 GLN t 37 ASN t 40 GLN u 18 GLN u 26 ASN v 47 HIS w 31 ASN w 52 GLN y 3 ASN y 52 ASN Total number of N/Q/H flips: 60 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.0855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 162437 Z= 0.222 Angle : 0.643 24.915 242695 Z= 0.343 Chirality : 0.036 0.341 30890 Planarity : 0.006 0.139 13216 Dihedral : 23.972 179.504 80459 Min Nonbonded Distance : 1.087 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.48 % Favored : 96.51 % Rotamer: Outliers : 2.56 % Allowed : 14.26 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.10), residues: 6068 helix: 1.40 (0.11), residues: 2108 sheet: -0.68 (0.14), residues: 1122 loop : -0.60 (0.11), residues: 2838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP l 103 HIS 0.009 0.001 HIS V 80 PHE 0.023 0.002 PHE t 43 TYR 0.031 0.002 TYR g 213 ARG 0.008 0.001 ARG J 95 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12136 Ramachandran restraints generated. 6068 Oldfield, 0 Emsley, 6068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12136 Ramachandran restraints generated. 6068 Oldfield, 0 Emsley, 6068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1843 residues out of total 5041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 1714 time to evaluate : 6.398 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: 8 14 GLU cc_start: 0.9016 (mp0) cc_final: 0.8757 (mp0) REVERT: 8 46 ARG cc_start: 0.7668 (OUTLIER) cc_final: 0.7373 (mtm110) REVERT: 8 56 ILE cc_start: 0.8771 (OUTLIER) cc_final: 0.8562 (mp) REVERT: B 97 LYS cc_start: 0.8684 (mmmm) cc_final: 0.8431 (mmtt) REVERT: B 167 ARG cc_start: 0.7996 (ttp80) cc_final: 0.7757 (ttp80) REVERT: D 111 GLU cc_start: 0.8637 (tp30) cc_final: 0.8069 (tp30) REVERT: D 166 LYS cc_start: 0.8370 (mmmt) cc_final: 0.7943 (mtpt) REVERT: E 112 ARG cc_start: 0.7898 (ttp80) cc_final: 0.7608 (ttm-80) REVERT: F 6 LYS cc_start: 0.8183 (mptt) cc_final: 0.7852 (mptt) REVERT: F 45 HIS cc_start: 0.7459 (t70) cc_final: 0.7191 (t70) REVERT: H 38 MET cc_start: 0.1579 (mmt) cc_final: 0.0917 (mpp) REVERT: H 86 MET cc_start: 0.2741 (mmt) cc_final: 0.1835 (mmt) REVERT: J 34 ARG cc_start: 0.8326 (ttp80) cc_final: 0.8047 (ttt90) REVERT: J 95 ARG cc_start: 0.7285 (ttm-80) cc_final: 0.6960 (ttm-80) REVERT: J 102 GLU cc_start: 0.8364 (mt-10) cc_final: 0.8143 (mt-10) REVERT: M 10 ARG cc_start: 0.8160 (OUTLIER) cc_final: 0.7433 (mtp85) REVERT: M 44 ARG cc_start: 0.8227 (mtt-85) cc_final: 0.8014 (mtt-85) REVERT: M 82 MET cc_start: 0.8517 (mmp) cc_final: 0.8168 (mmm) REVERT: P 71 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.8011 (mt-10) REVERT: Q 75 SER cc_start: 0.9122 (p) cc_final: 0.8894 (p) REVERT: Q 87 SER cc_start: 0.8945 (m) cc_final: 0.8738 (m) REVERT: S 98 LYS cc_start: 0.9081 (OUTLIER) cc_final: 0.8795 (mttm) REVERT: S 99 ARG cc_start: 0.8617 (mtt-85) cc_final: 0.8407 (mtt-85) REVERT: T 9 LYS cc_start: 0.8926 (OUTLIER) cc_final: 0.8605 (mmtp) REVERT: V 46 LYS cc_start: 0.8923 (mmtm) cc_final: 0.8581 (mptt) REVERT: W 68 LYS cc_start: 0.9029 (OUTLIER) cc_final: 0.8163 (ttmm) REVERT: X 11 ARG cc_start: 0.8580 (OUTLIER) cc_final: 0.7578 (mtp85) REVERT: Y 44 LYS cc_start: 0.9041 (OUTLIER) cc_final: 0.8602 (ttmm) REVERT: b 37 LYS cc_start: 0.8595 (mtmp) cc_final: 0.8384 (mtpt) REVERT: c 30 LYS cc_start: 0.8699 (mmtp) cc_final: 0.8369 (mmtp) REVERT: g 10 LEU cc_start: 0.8217 (mt) cc_final: 0.7968 (tm) REVERT: g 27 MET cc_start: 0.8538 (mmm) cc_final: 0.8326 (mmm) REVERT: g 58 ASN cc_start: 0.8080 (OUTLIER) cc_final: 0.7299 (t0) REVERT: g 139 ARG cc_start: 0.7556 (mmt90) cc_final: 0.7308 (mtt180) REVERT: h 132 ARG cc_start: 0.7631 (ttm-80) cc_final: 0.7177 (ttt90) REVERT: j 45 ARG cc_start: 0.8003 (mtp85) cc_final: 0.7713 (mtp85) REVERT: j 66 LYS cc_start: 0.8345 (mttt) cc_final: 0.8091 (mtmt) REVERT: l 139 GLU cc_start: 0.7539 (pt0) cc_final: 0.7329 (pt0) REVERT: n 57 MET cc_start: 0.7265 (mtp) cc_final: 0.6997 (mtp) REVERT: o 7 ARG cc_start: 0.8048 (OUTLIER) cc_final: 0.6551 (mpt-90) REVERT: o 88 MET cc_start: 0.7653 (mmm) cc_final: 0.7322 (mmm) REVERT: p 68 GLU cc_start: 0.7642 (mt-10) cc_final: 0.7378 (mt-10) REVERT: p 105 PHE cc_start: 0.8889 (m-80) cc_final: 0.8541 (m-80) REVERT: t 53 ARG cc_start: 0.8718 (ttm110) cc_final: 0.8445 (ttm110) REVERT: v 15 ASP cc_start: 0.8334 (p0) cc_final: 0.8131 (p0) REVERT: v 58 VAL cc_start: 0.8787 (t) cc_final: 0.8561 (t) outliers start: 129 outliers final: 48 residues processed: 1747 average time/residue: 2.2845 time to fit residues: 5662.1024 Evaluate side-chains 1693 residues out of total 5041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 1634 time to evaluate : 6.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 8 residue 46 ARG Chi-restraints excluded: chain 8 residue 48 SER Chi-restraints excluded: chain 8 residue 56 ILE Chi-restraints excluded: chain B residue 70 ASN Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain D residue 7 ASP Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain L residue 51 GLU Chi-restraints excluded: chain M residue 10 ARG Chi-restraints excluded: chain M residue 95 LEU Chi-restraints excluded: chain M residue 135 VAL Chi-restraints excluded: chain N residue 89 SER Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain P residue 71 GLU Chi-restraints excluded: chain P residue 110 ILE Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain S residue 53 SER Chi-restraints excluded: chain S residue 98 LYS Chi-restraints excluded: chain T residue 9 LYS Chi-restraints excluded: chain T residue 10 VAL Chi-restraints excluded: chain T residue 16 VAL Chi-restraints excluded: chain T residue 27 SER Chi-restraints excluded: chain T residue 32 LEU Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain W residue 32 LEU Chi-restraints excluded: chain W residue 68 LYS Chi-restraints excluded: chain X residue 2 SER Chi-restraints excluded: chain X residue 11 ARG Chi-restraints excluded: chain Y residue 24 GLU Chi-restraints excluded: chain Y residue 44 LYS Chi-restraints excluded: chain g residue 35 ARG Chi-restraints excluded: chain g residue 58 ASN Chi-restraints excluded: chain g residue 161 LEU Chi-restraints excluded: chain h residue 53 SER Chi-restraints excluded: chain h residue 187 SER Chi-restraints excluded: chain i residue 143 VAL Chi-restraints excluded: chain j residue 148 ASN Chi-restraints excluded: chain m residue 11 LEU Chi-restraints excluded: chain m residue 94 LYS Chi-restraints excluded: chain n residue 5 GLN Chi-restraints excluded: chain o residue 7 ARG Chi-restraints excluded: chain o residue 80 THR Chi-restraints excluded: chain q residue 112 GLN Chi-restraints excluded: chain r residue 25 VAL Chi-restraints excluded: chain r residue 113 ARG Chi-restraints excluded: chain s residue 47 LYS Chi-restraints excluded: chain s residue 55 SER Chi-restraints excluded: chain v residue 13 VAL Chi-restraints excluded: chain v residue 67 LEU Chi-restraints excluded: chain w residue 42 SER Chi-restraints excluded: chain x residue 58 VAL Chi-restraints excluded: chain x residue 79 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1063 random chunks: chunk 536 optimal weight: 9.9990 chunk 299 optimal weight: 20.0000 chunk 803 optimal weight: 5.9990 chunk 657 optimal weight: 6.9990 chunk 266 optimal weight: 10.0000 chunk 967 optimal weight: 9.9990 chunk 1044 optimal weight: 10.0000 chunk 861 optimal weight: 2.9990 chunk 959 optimal weight: 0.9980 chunk 329 optimal weight: 10.0000 chunk 775 optimal weight: 9.9990 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 8 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 85 HIS 8 179 GLN C 32 ASN C 42 ASN C 49 GLN C 94 GLN D 156 ASN D 195 GLN E 127 ASN ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 45 GLN M 97 GLN Q 56 GLN Q 72 ASN T 59 ASN ** U 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 74 ASN V 49 ASN ** V 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 75 GLN ** V 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 76 ASN Y 15 ASN Y 20 ASN Y 31 GLN a 61 ASN d 29 GLN ** g 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 58 ASN ** g 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 8 ASN h 19 ASN h 100 GLN h 139 GLN i 40 GLN ** i 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 116 GLN j 73 ASN ** k 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 67 GLN n 50 GLN n 75 GLN n 126 GLN o 20 GLN s 66 GLN t 35 GLN t 40 GLN u 26 ASN v 45 HIS w 31 ASN y 3 ASN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.0766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.116 162437 Z= 0.409 Angle : 0.702 24.142 242695 Z= 0.370 Chirality : 0.041 0.330 30890 Planarity : 0.007 0.145 13216 Dihedral : 23.869 179.965 80453 Min Nonbonded Distance : 1.021 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.53 % Favored : 96.46 % Rotamer: Outliers : 3.93 % Allowed : 16.52 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.10), residues: 6068 helix: 1.39 (0.11), residues: 2127 sheet: -0.65 (0.14), residues: 1148 loop : -0.56 (0.11), residues: 2793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP l 103 HIS 0.011 0.002 HIS w 74 PHE 0.022 0.002 PHE t 43 TYR 0.030 0.002 TYR g 213 ARG 0.011 0.001 ARG Q 51 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12136 Ramachandran restraints generated. 6068 Oldfield, 0 Emsley, 6068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12136 Ramachandran restraints generated. 6068 Oldfield, 0 Emsley, 6068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1849 residues out of total 5041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 1651 time to evaluate : 6.475 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: 8 21 LYS cc_start: 0.8717 (mttm) cc_final: 0.8472 (mttm) REVERT: 8 46 ARG cc_start: 0.7587 (OUTLIER) cc_final: 0.7375 (mtm110) REVERT: B 167 ARG cc_start: 0.7992 (ttp80) cc_final: 0.7749 (ttp80) REVERT: C 204 LYS cc_start: 0.9134 (OUTLIER) cc_final: 0.8908 (mttm) REVERT: D 122 GLU cc_start: 0.6682 (pm20) cc_final: 0.6301 (pm20) REVERT: D 144 GLU cc_start: 0.6663 (tm-30) cc_final: 0.6351 (tm-30) REVERT: D 198 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.7019 (mp0) REVERT: F 6 LYS cc_start: 0.8170 (OUTLIER) cc_final: 0.7794 (mptt) REVERT: H 38 MET cc_start: 0.1508 (mmt) cc_final: 0.0812 (mpp) REVERT: H 86 MET cc_start: 0.2821 (mmt) cc_final: 0.1990 (mmt) REVERT: J 96 ARG cc_start: 0.7862 (pmm150) cc_final: 0.7538 (pmm150) REVERT: J 102 GLU cc_start: 0.8350 (mt-10) cc_final: 0.8141 (mt-10) REVERT: K 90 ASN cc_start: 0.8025 (OUTLIER) cc_final: 0.7699 (m-40) REVERT: K 106 GLU cc_start: 0.8425 (mp0) cc_final: 0.8177 (mp0) REVERT: M 44 ARG cc_start: 0.8269 (mtt-85) cc_final: 0.8040 (mtt-85) REVERT: M 82 MET cc_start: 0.8545 (mmp) cc_final: 0.8277 (mmm) REVERT: P 71 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.8044 (mt-10) REVERT: Q 75 SER cc_start: 0.9200 (p) cc_final: 0.8993 (p) REVERT: Q 85 LYS cc_start: 0.9036 (OUTLIER) cc_final: 0.8320 (mptm) REVERT: Q 87 SER cc_start: 0.8948 (m) cc_final: 0.8744 (m) REVERT: R 6 GLN cc_start: 0.7934 (OUTLIER) cc_final: 0.7335 (tm-30) REVERT: S 68 ASP cc_start: 0.8227 (m-30) cc_final: 0.7969 (m-30) REVERT: S 98 LYS cc_start: 0.9119 (OUTLIER) cc_final: 0.8803 (mttm) REVERT: S 99 ARG cc_start: 0.8725 (mtt-85) cc_final: 0.8446 (mtt-85) REVERT: T 9 LYS cc_start: 0.8971 (OUTLIER) cc_final: 0.8689 (mtmt) REVERT: V 46 LYS cc_start: 0.8918 (mmtm) cc_final: 0.8565 (mptp) REVERT: W 68 LYS cc_start: 0.9046 (OUTLIER) cc_final: 0.8336 (ttmm) REVERT: Y 31 GLN cc_start: 0.8526 (mt0) cc_final: 0.8121 (mt0) REVERT: b 53 LYS cc_start: 0.8702 (OUTLIER) cc_final: 0.8391 (tttt) REVERT: c 30 LYS cc_start: 0.8712 (mmtp) cc_final: 0.8467 (mmtp) REVERT: d 1 MET cc_start: 0.7879 (OUTLIER) cc_final: 0.7565 (mtm) REVERT: g 10 LEU cc_start: 0.8202 (mt) cc_final: 0.7950 (tm) REVERT: g 27 MET cc_start: 0.8591 (mmm) cc_final: 0.8308 (mmm) REVERT: g 36 ASN cc_start: 0.6242 (t0) cc_final: 0.5877 (t0) REVERT: g 113 ARG cc_start: 0.8208 (tpt170) cc_final: 0.7992 (tpt90) REVERT: g 139 ARG cc_start: 0.7582 (mmt90) cc_final: 0.7235 (mtt-85) REVERT: g 161 LEU cc_start: 0.9363 (OUTLIER) cc_final: 0.8977 (mp) REVERT: g 173 ILE cc_start: 0.9178 (OUTLIER) cc_final: 0.8906 (mm) REVERT: i 65 TYR cc_start: 0.9228 (m-80) cc_final: 0.8782 (m-80) REVERT: j 45 ARG cc_start: 0.8027 (mtp85) cc_final: 0.7616 (mtp85) REVERT: j 66 LYS cc_start: 0.8330 (mttt) cc_final: 0.7970 (mtmt) REVERT: k 2 ARG cc_start: 0.7833 (OUTLIER) cc_final: 0.7421 (ttp-170) REVERT: k 68 GLN cc_start: 0.8010 (mt0) cc_final: 0.7499 (mt0) REVERT: l 58 GLU cc_start: 0.6744 (mm-30) cc_final: 0.6532 (mm-30) REVERT: l 139 GLU cc_start: 0.7509 (pt0) cc_final: 0.7246 (pt0) REVERT: m 50 LYS cc_start: 0.8339 (tmmt) cc_final: 0.8029 (pttt) REVERT: m 60 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.7009 (tp30) REVERT: o 5 ARG cc_start: 0.6543 (tmm-80) cc_final: 0.6055 (tmm-80) REVERT: o 7 ARG cc_start: 0.8220 (OUTLIER) cc_final: 0.7223 (mpt-90) REVERT: o 88 MET cc_start: 0.7667 (mmm) cc_final: 0.7396 (mmm) REVERT: p 68 GLU cc_start: 0.7683 (mt-10) cc_final: 0.7457 (mt-10) REVERT: p 105 PHE cc_start: 0.8922 (m-80) cc_final: 0.8591 (m-80) REVERT: t 53 ARG cc_start: 0.8844 (ttm110) cc_final: 0.8625 (ttm110) REVERT: w 61 ARG cc_start: 0.8796 (OUTLIER) cc_final: 0.7781 (mpt180) REVERT: x 56 GLN cc_start: 0.8322 (OUTLIER) cc_final: 0.8086 (pm20) REVERT: y 57 ILE cc_start: 0.8729 (OUTLIER) cc_final: 0.8472 (tt) REVERT: y 82 GLN cc_start: 0.8267 (OUTLIER) cc_final: 0.7247 (mp10) REVERT: y 85 LYS cc_start: 0.8617 (OUTLIER) cc_final: 0.8387 (ttpp) outliers start: 198 outliers final: 96 residues processed: 1707 average time/residue: 2.2704 time to fit residues: 5500.5325 Evaluate side-chains 1751 residues out of total 5041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 1632 time to evaluate : 6.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 8 residue 46 ARG Chi-restraints excluded: chain 8 residue 48 SER Chi-restraints excluded: chain 8 residue 93 LEU Chi-restraints excluded: chain 8 residue 109 ILE Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 204 LYS Chi-restraints excluded: chain D residue 139 LYS Chi-restraints excluded: chain D residue 143 LEU Chi-restraints excluded: chain D residue 155 GLU Chi-restraints excluded: chain D residue 198 GLU Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain F residue 6 LYS Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 90 ASN Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain M residue 95 LEU Chi-restraints excluded: chain M residue 135 VAL Chi-restraints excluded: chain N residue 89 SER Chi-restraints excluded: chain O residue 40 ILE Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain O residue 68 LYS Chi-restraints excluded: chain P residue 71 GLU Chi-restraints excluded: chain P residue 110 ILE Chi-restraints excluded: chain Q residue 85 LYS Chi-restraints excluded: chain R residue 6 GLN Chi-restraints excluded: chain S residue 53 SER Chi-restraints excluded: chain S residue 98 LYS Chi-restraints excluded: chain T residue 9 LYS Chi-restraints excluded: chain T residue 10 VAL Chi-restraints excluded: chain T residue 16 VAL Chi-restraints excluded: chain T residue 27 SER Chi-restraints excluded: chain T residue 32 LEU Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain V residue 4 ILE Chi-restraints excluded: chain V residue 8 VAL Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain W residue 32 LEU Chi-restraints excluded: chain W residue 68 LYS Chi-restraints excluded: chain W residue 78 LYS Chi-restraints excluded: chain X residue 2 SER Chi-restraints excluded: chain X residue 43 GLU Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain Y residue 24 GLU Chi-restraints excluded: chain a residue 22 MET Chi-restraints excluded: chain b residue 25 VAL Chi-restraints excluded: chain b residue 53 LYS Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 4 THR Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain f residue 8 LYS Chi-restraints excluded: chain g residue 35 ARG Chi-restraints excluded: chain g residue 110 SER Chi-restraints excluded: chain g residue 133 GLU Chi-restraints excluded: chain g residue 161 LEU Chi-restraints excluded: chain g residue 167 ASP Chi-restraints excluded: chain g residue 173 ILE Chi-restraints excluded: chain g residue 211 THR Chi-restraints excluded: chain g residue 220 THR Chi-restraints excluded: chain h residue 53 SER Chi-restraints excluded: chain h residue 114 LYS Chi-restraints excluded: chain h residue 187 SER Chi-restraints excluded: chain i residue 143 VAL Chi-restraints excluded: chain i residue 166 GLU Chi-restraints excluded: chain j residue 61 GLN Chi-restraints excluded: chain j residue 114 VAL Chi-restraints excluded: chain j residue 148 ASN Chi-restraints excluded: chain j residue 164 ILE Chi-restraints excluded: chain k residue 1 MET Chi-restraints excluded: chain k residue 2 ARG Chi-restraints excluded: chain m residue 11 LEU Chi-restraints excluded: chain m residue 60 GLU Chi-restraints excluded: chain m residue 74 SER Chi-restraints excluded: chain m residue 94 LYS Chi-restraints excluded: chain n residue 5 GLN Chi-restraints excluded: chain n residue 15 SER Chi-restraints excluded: chain n residue 85 ARG Chi-restraints excluded: chain o residue 7 ARG Chi-restraints excluded: chain o residue 17 LEU Chi-restraints excluded: chain p residue 79 ILE Chi-restraints excluded: chain q residue 35 THR Chi-restraints excluded: chain q residue 65 SER Chi-restraints excluded: chain q residue 112 GLN Chi-restraints excluded: chain r residue 25 VAL Chi-restraints excluded: chain r residue 93 ARG Chi-restraints excluded: chain r residue 113 ARG Chi-restraints excluded: chain s residue 47 LYS Chi-restraints excluded: chain s residue 55 SER Chi-restraints excluded: chain s residue 100 SER Chi-restraints excluded: chain u residue 66 THR Chi-restraints excluded: chain u residue 68 SER Chi-restraints excluded: chain u residue 78 VAL Chi-restraints excluded: chain v residue 13 VAL Chi-restraints excluded: chain v residue 18 GLU Chi-restraints excluded: chain v residue 67 LEU Chi-restraints excluded: chain w residue 42 SER Chi-restraints excluded: chain w residue 61 ARG Chi-restraints excluded: chain x residue 29 LYS Chi-restraints excluded: chain x residue 56 GLN Chi-restraints excluded: chain x residue 79 THR Chi-restraints excluded: chain y residue 57 ILE Chi-restraints excluded: chain y residue 82 GLN Chi-restraints excluded: chain y residue 85 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1063 random chunks: chunk 955 optimal weight: 6.9990 chunk 727 optimal weight: 0.9990 chunk 501 optimal weight: 5.9990 chunk 107 optimal weight: 50.0000 chunk 461 optimal weight: 20.0000 chunk 649 optimal weight: 0.7980 chunk 970 optimal weight: 0.5980 chunk 1027 optimal weight: 0.0470 chunk 507 optimal weight: 5.9990 chunk 919 optimal weight: 8.9990 chunk 276 optimal weight: 8.9990 overall best weight: 1.6882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 8 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 85 HIS B 243 HIS C 42 ASN ** C 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 156 ASN D 195 GLN E 127 ASN F 104 ASN ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 3 GLN M 97 GLN P 3 ASN Q 72 ASN T 28 ASN ** U 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 49 ASN ** V 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 75 GLN ** V 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 76 ASN Y 15 ASN Y 20 ASN a 61 ASN d 29 GLN ** g 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 42 ASN g 58 ASN ** g 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 8 ASN h 19 ASN h 100 GLN ** i 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 116 GLN j 73 ASN ** k 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 67 GLN n 50 GLN n 75 GLN n 126 GLN o 20 GLN p 28 ASN s 60 GLN s 66 GLN t 35 GLN t 40 GLN u 26 ASN w 31 ASN w 54 GLN y 3 ASN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.1167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 162437 Z= 0.177 Angle : 0.603 22.041 242695 Z= 0.325 Chirality : 0.034 0.350 30890 Planarity : 0.006 0.129 13216 Dihedral : 23.842 179.489 80453 Min Nonbonded Distance : 1.133 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.18 % Favored : 96.80 % Rotamer: Outliers : 3.37 % Allowed : 18.37 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.11), residues: 6068 helix: 1.71 (0.11), residues: 2116 sheet: -0.60 (0.15), residues: 1141 loop : -0.47 (0.11), residues: 2811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP l 103 HIS 0.006 0.001 HIS w 74 PHE 0.020 0.001 PHE R 53 TYR 0.034 0.002 TYR g 213 ARG 0.013 0.001 ARG J 95 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12136 Ramachandran restraints generated. 6068 Oldfield, 0 Emsley, 6068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12136 Ramachandran restraints generated. 6068 Oldfield, 0 Emsley, 6068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1866 residues out of total 5041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 1696 time to evaluate : 6.427 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: 8 21 LYS cc_start: 0.8658 (mttm) cc_final: 0.8393 (mttm) REVERT: B 167 ARG cc_start: 0.7961 (ttp80) cc_final: 0.7742 (ttp80) REVERT: C 105 LYS cc_start: 0.8670 (mmtm) cc_final: 0.8330 (mmtm) REVERT: D 111 GLU cc_start: 0.8613 (tp30) cc_final: 0.7953 (tp30) REVERT: D 144 GLU cc_start: 0.6726 (tm-30) cc_final: 0.6509 (tm-30) REVERT: D 198 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.7017 (mp0) REVERT: E 112 ARG cc_start: 0.7930 (ttp80) cc_final: 0.7497 (ttm-80) REVERT: F 6 LYS cc_start: 0.8052 (OUTLIER) cc_final: 0.7824 (mptt) REVERT: H 38 MET cc_start: 0.1539 (mmt) cc_final: 0.0873 (mpp) REVERT: H 86 MET cc_start: 0.2716 (mmt) cc_final: 0.1934 (mmt) REVERT: I 135 MET cc_start: 0.1765 (ttm) cc_final: 0.1285 (ptt) REVERT: J 34 ARG cc_start: 0.8310 (ttp80) cc_final: 0.8024 (ttt90) REVERT: J 102 GLU cc_start: 0.8336 (mt-10) cc_final: 0.8135 (mt-10) REVERT: M 10 ARG cc_start: 0.8125 (OUTLIER) cc_final: 0.7611 (mtp85) REVERT: M 44 ARG cc_start: 0.8231 (mtt-85) cc_final: 0.8014 (mtt-85) REVERT: M 82 MET cc_start: 0.8386 (mmp) cc_final: 0.8131 (mmm) REVERT: P 71 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7960 (mt-10) REVERT: Q 75 SER cc_start: 0.9067 (p) cc_final: 0.8834 (p) REVERT: Q 87 SER cc_start: 0.8926 (m) cc_final: 0.8715 (m) REVERT: S 83 LYS cc_start: 0.8996 (OUTLIER) cc_final: 0.8304 (ptpt) REVERT: S 98 LYS cc_start: 0.9067 (OUTLIER) cc_final: 0.8754 (mttm) REVERT: S 99 ARG cc_start: 0.8695 (mtt-85) cc_final: 0.8465 (mtt-85) REVERT: T 9 LYS cc_start: 0.8911 (OUTLIER) cc_final: 0.8677 (mtpt) REVERT: Y 31 GLN cc_start: 0.8398 (mt0) cc_final: 0.8025 (mt0) REVERT: Y 44 LYS cc_start: 0.9049 (OUTLIER) cc_final: 0.8657 (ttmm) REVERT: b 53 LYS cc_start: 0.8588 (OUTLIER) cc_final: 0.8248 (tttt) REVERT: c 30 LYS cc_start: 0.8795 (mmtp) cc_final: 0.8471 (mmtp) REVERT: d 1 MET cc_start: 0.7840 (OUTLIER) cc_final: 0.7537 (mtm) REVERT: g 10 LEU cc_start: 0.8172 (mt) cc_final: 0.7927 (tm) REVERT: g 27 MET cc_start: 0.8536 (mmm) cc_final: 0.8295 (mmm) REVERT: g 139 ARG cc_start: 0.7417 (mmt90) cc_final: 0.7209 (mtt-85) REVERT: g 161 LEU cc_start: 0.9280 (OUTLIER) cc_final: 0.8841 (mp) REVERT: g 173 ILE cc_start: 0.9134 (OUTLIER) cc_final: 0.8848 (mm) REVERT: h 142 MET cc_start: 0.8955 (OUTLIER) cc_final: 0.8720 (mmm) REVERT: k 2 ARG cc_start: 0.7787 (OUTLIER) cc_final: 0.7381 (ttp-170) REVERT: l 139 GLU cc_start: 0.7493 (pt0) cc_final: 0.7268 (pt0) REVERT: l 143 ARG cc_start: 0.7506 (mtm-85) cc_final: 0.7239 (mtm-85) REVERT: m 60 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.6831 (tp30) REVERT: o 5 ARG cc_start: 0.6416 (tmm-80) cc_final: 0.6198 (tmm-80) REVERT: o 7 ARG cc_start: 0.8117 (OUTLIER) cc_final: 0.6549 (mpt-90) REVERT: p 64 GLN cc_start: 0.8193 (pt0) cc_final: 0.7824 (tm-30) REVERT: p 68 GLU cc_start: 0.7568 (mt-10) cc_final: 0.7336 (mt-10) REVERT: p 105 PHE cc_start: 0.8840 (m-80) cc_final: 0.8503 (m-80) REVERT: t 63 ARG cc_start: 0.9363 (ttp-170) cc_final: 0.9008 (ttm170) REVERT: t 69 TYR cc_start: 0.9232 (t80) cc_final: 0.9012 (t80) REVERT: w 61 ARG cc_start: 0.8749 (OUTLIER) cc_final: 0.7876 (mpt180) REVERT: x 56 GLN cc_start: 0.8287 (OUTLIER) cc_final: 0.8069 (pm20) REVERT: y 57 ILE cc_start: 0.8577 (OUTLIER) cc_final: 0.8216 (tt) REVERT: y 82 GLN cc_start: 0.8235 (OUTLIER) cc_final: 0.7341 (mp10) outliers start: 170 outliers final: 74 residues processed: 1735 average time/residue: 2.3029 time to fit residues: 5648.6471 Evaluate side-chains 1738 residues out of total 5041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 1644 time to evaluate : 6.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 8 residue 2 ILE Chi-restraints excluded: chain 8 residue 161 ILE Chi-restraints excluded: chain 8 residue 202 ILE Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 194 GLU Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain D residue 198 GLU Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 142 ASP Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain F residue 6 LYS Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain H residue 87 GLU Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain L residue 51 GLU Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain M residue 10 ARG Chi-restraints excluded: chain M residue 95 LEU Chi-restraints excluded: chain M residue 126 ILE Chi-restraints excluded: chain M residue 135 VAL Chi-restraints excluded: chain N residue 89 SER Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 68 LYS Chi-restraints excluded: chain P residue 6 LYS Chi-restraints excluded: chain P residue 71 GLU Chi-restraints excluded: chain S residue 53 SER Chi-restraints excluded: chain S residue 83 LYS Chi-restraints excluded: chain S residue 98 LYS Chi-restraints excluded: chain T residue 9 LYS Chi-restraints excluded: chain T residue 10 VAL Chi-restraints excluded: chain T residue 27 SER Chi-restraints excluded: chain T residue 32 LEU Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain V residue 4 ILE Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain W residue 32 LEU Chi-restraints excluded: chain X residue 2 SER Chi-restraints excluded: chain X residue 43 GLU Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain Y residue 24 GLU Chi-restraints excluded: chain Y residue 44 LYS Chi-restraints excluded: chain Z residue 21 LYS Chi-restraints excluded: chain b residue 53 LYS Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain e residue 32 ILE Chi-restraints excluded: chain f residue 8 LYS Chi-restraints excluded: chain g residue 35 ARG Chi-restraints excluded: chain g residue 161 LEU Chi-restraints excluded: chain g residue 167 ASP Chi-restraints excluded: chain g residue 173 ILE Chi-restraints excluded: chain g residue 174 LYS Chi-restraints excluded: chain g residue 220 THR Chi-restraints excluded: chain g residue 223 GLU Chi-restraints excluded: chain h residue 53 SER Chi-restraints excluded: chain h residue 142 MET Chi-restraints excluded: chain h residue 185 ASN Chi-restraints excluded: chain h residue 187 SER Chi-restraints excluded: chain i residue 143 VAL Chi-restraints excluded: chain j residue 114 VAL Chi-restraints excluded: chain j residue 148 ASN Chi-restraints excluded: chain j residue 164 ILE Chi-restraints excluded: chain k residue 2 ARG Chi-restraints excluded: chain m residue 11 LEU Chi-restraints excluded: chain m residue 60 GLU Chi-restraints excluded: chain m residue 94 LYS Chi-restraints excluded: chain m residue 107 SER Chi-restraints excluded: chain n residue 15 SER Chi-restraints excluded: chain n residue 85 ARG Chi-restraints excluded: chain o residue 7 ARG Chi-restraints excluded: chain o residue 17 LEU Chi-restraints excluded: chain p residue 35 THR Chi-restraints excluded: chain p residue 79 ILE Chi-restraints excluded: chain q residue 30 LYS Chi-restraints excluded: chain r residue 25 VAL Chi-restraints excluded: chain s residue 47 LYS Chi-restraints excluded: chain s residue 55 SER Chi-restraints excluded: chain v residue 13 VAL Chi-restraints excluded: chain v residue 67 LEU Chi-restraints excluded: chain w residue 42 SER Chi-restraints excluded: chain w residue 61 ARG Chi-restraints excluded: chain x residue 29 LYS Chi-restraints excluded: chain x residue 56 GLN Chi-restraints excluded: chain x residue 58 VAL Chi-restraints excluded: chain x residue 79 THR Chi-restraints excluded: chain y residue 57 ILE Chi-restraints excluded: chain y residue 82 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1063 random chunks: chunk 855 optimal weight: 8.9990 chunk 583 optimal weight: 7.9990 chunk 14 optimal weight: 10.0000 chunk 765 optimal weight: 9.9990 chunk 423 optimal weight: 10.0000 chunk 876 optimal weight: 10.0000 chunk 710 optimal weight: 3.9990 chunk 1 optimal weight: 10.0000 chunk 524 optimal weight: 5.9990 chunk 922 optimal weight: 7.9990 chunk 259 optimal weight: 7.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 8 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 85 HIS B 117 GLN C 42 ASN C 94 GLN D 41 GLN D 156 ASN D 195 GLN E 127 ASN F 20 ASN I 29 GLN K 88 ASN L 93 ASN P 3 ASN T 28 ASN T 48 GLN T 59 ASN U 40 ASN ** U 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 49 ASN V 51 GLN ** V 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 76 ASN Y 15 ASN Y 20 ASN Y 39 GLN a 61 ASN b 4 GLN d 29 GLN g 42 ASN ** g 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 120 GLN h 8 ASN h 100 GLN h 139 GLN i 40 GLN i 59 GLN i 116 GLN j 73 ASN ** k 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 50 GLN n 75 GLN n 126 GLN o 20 GLN p 24 HIS p 28 ASN p 29 ASN s 60 GLN s 66 GLN t 35 GLN t 40 GLN u 26 ASN u 29 ASN w 31 ASN w 54 GLN y 3 ASN Total number of N/Q/H flips: 51 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.0899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.124 162437 Z= 0.495 Angle : 0.736 23.513 242695 Z= 0.384 Chirality : 0.044 0.334 30890 Planarity : 0.007 0.147 13216 Dihedral : 23.812 178.816 80453 Min Nonbonded Distance : 1.005 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.68 % Favored : 96.31 % Rotamer: Outliers : 4.72 % Allowed : 18.49 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.10), residues: 6068 helix: 1.48 (0.11), residues: 2117 sheet: -0.63 (0.15), residues: 1125 loop : -0.48 (0.11), residues: 2826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP l 103 HIS 0.011 0.002 HIS w 74 PHE 0.023 0.002 PHE G 91 TYR 0.032 0.002 TYR g 213 ARG 0.012 0.001 ARG k 91 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12136 Ramachandran restraints generated. 6068 Oldfield, 0 Emsley, 6068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12136 Ramachandran restraints generated. 6068 Oldfield, 0 Emsley, 6068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1872 residues out of total 5041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 238 poor density : 1634 time to evaluate : 6.409 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: 8 21 LYS cc_start: 0.8689 (mttm) cc_final: 0.8406 (mttm) REVERT: B 167 ARG cc_start: 0.7995 (ttp80) cc_final: 0.7742 (ttp80) REVERT: B 182 ARG cc_start: 0.8900 (OUTLIER) cc_final: 0.8583 (ttt90) REVERT: C 55 LYS cc_start: 0.8593 (tttp) cc_final: 0.8353 (tttp) REVERT: D 122 GLU cc_start: 0.6650 (pm20) cc_final: 0.6447 (pm20) REVERT: D 198 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7013 (mp0) REVERT: F 6 LYS cc_start: 0.8158 (OUTLIER) cc_final: 0.7869 (mptt) REVERT: H 38 MET cc_start: 0.1556 (mmt) cc_final: 0.0783 (mpp) REVERT: H 86 MET cc_start: 0.2714 (mmt) cc_final: 0.1952 (mmt) REVERT: I 35 MET cc_start: 0.4908 (OUTLIER) cc_final: 0.3787 (pp-130) REVERT: I 135 MET cc_start: 0.1671 (ttm) cc_final: 0.1097 (ptt) REVERT: J 102 GLU cc_start: 0.8349 (mt-10) cc_final: 0.8118 (mt-10) REVERT: K 17 ARG cc_start: 0.7836 (mmm-85) cc_final: 0.7598 (mmm160) REVERT: K 106 GLU cc_start: 0.8334 (mp0) cc_final: 0.8101 (mp0) REVERT: M 6 ARG cc_start: 0.7920 (OUTLIER) cc_final: 0.7298 (ptm160) REVERT: M 44 ARG cc_start: 0.8304 (mtt-85) cc_final: 0.8068 (mtt-85) REVERT: P 71 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.8065 (mt-10) REVERT: Q 18 LEU cc_start: 0.9241 (OUTLIER) cc_final: 0.8947 (mm) REVERT: Q 75 SER cc_start: 0.9207 (p) cc_final: 0.9002 (p) REVERT: Q 85 LYS cc_start: 0.9038 (OUTLIER) cc_final: 0.8555 (mptm) REVERT: R 6 GLN cc_start: 0.7983 (OUTLIER) cc_final: 0.7360 (tm-30) REVERT: R 97 LYS cc_start: 0.8860 (OUTLIER) cc_final: 0.8617 (ttmt) REVERT: S 23 LEU cc_start: 0.9263 (OUTLIER) cc_final: 0.8812 (mp) REVERT: S 83 LYS cc_start: 0.9137 (OUTLIER) cc_final: 0.8352 (ptpt) REVERT: S 98 LYS cc_start: 0.9138 (OUTLIER) cc_final: 0.8753 (mttm) REVERT: T 9 LYS cc_start: 0.8967 (OUTLIER) cc_final: 0.8649 (mmtp) REVERT: W 68 LYS cc_start: 0.9093 (OUTLIER) cc_final: 0.8556 (ttmm) REVERT: X 11 ARG cc_start: 0.8708 (OUTLIER) cc_final: 0.8387 (mtp85) REVERT: Y 31 GLN cc_start: 0.8461 (mt0) cc_final: 0.8090 (mt0) REVERT: b 53 LYS cc_start: 0.8689 (OUTLIER) cc_final: 0.8365 (tttt) REVERT: d 1 MET cc_start: 0.7897 (OUTLIER) cc_final: 0.7593 (mtm) REVERT: g 10 LEU cc_start: 0.8209 (mt) cc_final: 0.7940 (tm) REVERT: g 27 MET cc_start: 0.8641 (mmm) cc_final: 0.8321 (mmm) REVERT: g 36 ASN cc_start: 0.6286 (t0) cc_final: 0.5862 (t0) REVERT: g 52 GLU cc_start: 0.7423 (pt0) cc_final: 0.7069 (pt0) REVERT: g 139 ARG cc_start: 0.7454 (mmt90) cc_final: 0.7221 (mtt-85) REVERT: g 173 ILE cc_start: 0.9153 (OUTLIER) cc_final: 0.8861 (mm) REVERT: i 65 TYR cc_start: 0.9261 (m-80) cc_final: 0.8938 (m-80) REVERT: i 78 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7696 (tm-30) REVERT: i 156 LYS cc_start: 0.8251 (OUTLIER) cc_final: 0.7832 (ttmt) REVERT: k 2 ARG cc_start: 0.7927 (OUTLIER) cc_final: 0.7401 (ttp-170) REVERT: l 58 GLU cc_start: 0.6794 (mm-30) cc_final: 0.6394 (mm-30) REVERT: l 139 GLU cc_start: 0.7575 (pt0) cc_final: 0.7323 (pt0) REVERT: l 143 ARG cc_start: 0.7392 (mtm-85) cc_final: 0.7104 (mtm-85) REVERT: m 60 GLU cc_start: 0.7570 (OUTLIER) cc_final: 0.7067 (tp30) REVERT: m 83 LEU cc_start: 0.9291 (OUTLIER) cc_final: 0.9055 (tt) REVERT: n 57 MET cc_start: 0.7468 (mtp) cc_final: 0.7259 (mtp) REVERT: n 114 LYS cc_start: 0.8996 (OUTLIER) cc_final: 0.7191 (tptp) REVERT: o 5 ARG cc_start: 0.6432 (tmm-80) cc_final: 0.6127 (tmm-80) REVERT: o 7 ARG cc_start: 0.8250 (OUTLIER) cc_final: 0.6627 (mpt-90) REVERT: p 15 GLN cc_start: 0.7389 (OUTLIER) cc_final: 0.7169 (tp40) REVERT: p 64 GLN cc_start: 0.8228 (OUTLIER) cc_final: 0.7708 (tm-30) REVERT: p 68 GLU cc_start: 0.7638 (mt-10) cc_final: 0.7289 (mt-10) REVERT: p 105 PHE cc_start: 0.8902 (m-80) cc_final: 0.8601 (m-80) REVERT: s 92 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7222 (mt-10) REVERT: w 61 ARG cc_start: 0.8808 (OUTLIER) cc_final: 0.7697 (mpt180) REVERT: x 32 ARG cc_start: 0.8045 (OUTLIER) cc_final: 0.7575 (ttp-110) REVERT: x 56 GLN cc_start: 0.8313 (OUTLIER) cc_final: 0.8054 (pm20) REVERT: y 57 ILE cc_start: 0.8887 (OUTLIER) cc_final: 0.8618 (tt) REVERT: y 82 GLN cc_start: 0.8268 (OUTLIER) cc_final: 0.7256 (mp10) REVERT: y 85 LYS cc_start: 0.8626 (OUTLIER) cc_final: 0.8421 (ttpp) REVERT: z 4 ILE cc_start: 0.7107 (OUTLIER) cc_final: 0.6659 (mt) outliers start: 238 outliers final: 117 residues processed: 1708 average time/residue: 2.3348 time to fit residues: 5663.6987 Evaluate side-chains 1764 residues out of total 5041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 1611 time to evaluate : 6.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 8 residue 2 ILE Chi-restraints excluded: chain 8 residue 48 SER Chi-restraints excluded: chain 8 residue 109 ILE Chi-restraints excluded: chain 8 residue 161 ILE Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 125 LYS Chi-restraints excluded: chain B residue 182 ARG Chi-restraints excluded: chain B residue 194 GLU Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain D residue 139 LYS Chi-restraints excluded: chain D residue 143 LEU Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 198 GLU Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 125 ARG Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain F residue 6 LYS Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain H residue 87 GLU Chi-restraints excluded: chain I residue 35 MET Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain M residue 6 ARG Chi-restraints excluded: chain M residue 95 LEU Chi-restraints excluded: chain M residue 126 ILE Chi-restraints excluded: chain M residue 135 VAL Chi-restraints excluded: chain N residue 89 SER Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain O residue 68 LYS Chi-restraints excluded: chain P residue 71 GLU Chi-restraints excluded: chain P residue 110 ILE Chi-restraints excluded: chain P residue 111 LYS Chi-restraints excluded: chain Q residue 18 LEU Chi-restraints excluded: chain Q residue 85 LYS Chi-restraints excluded: chain R residue 6 GLN Chi-restraints excluded: chain R residue 97 LYS Chi-restraints excluded: chain S residue 23 LEU Chi-restraints excluded: chain S residue 53 SER Chi-restraints excluded: chain S residue 83 LYS Chi-restraints excluded: chain S residue 98 LYS Chi-restraints excluded: chain T residue 9 LYS Chi-restraints excluded: chain T residue 10 VAL Chi-restraints excluded: chain T residue 16 VAL Chi-restraints excluded: chain T residue 27 SER Chi-restraints excluded: chain T residue 32 LEU Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain V residue 8 VAL Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain W residue 32 LEU Chi-restraints excluded: chain W residue 68 LYS Chi-restraints excluded: chain X residue 2 SER Chi-restraints excluded: chain X residue 11 ARG Chi-restraints excluded: chain X residue 43 GLU Chi-restraints excluded: chain X residue 71 LEU Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain Y residue 24 GLU Chi-restraints excluded: chain Z residue 21 LYS Chi-restraints excluded: chain Z residue 39 GLU Chi-restraints excluded: chain b residue 25 VAL Chi-restraints excluded: chain b residue 53 LYS Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain e residue 32 ILE Chi-restraints excluded: chain f residue 8 LYS Chi-restraints excluded: chain g residue 35 ARG Chi-restraints excluded: chain g residue 110 SER Chi-restraints excluded: chain g residue 161 LEU Chi-restraints excluded: chain g residue 167 ASP Chi-restraints excluded: chain g residue 173 ILE Chi-restraints excluded: chain g residue 174 LYS Chi-restraints excluded: chain g residue 211 THR Chi-restraints excluded: chain g residue 220 THR Chi-restraints excluded: chain h residue 53 SER Chi-restraints excluded: chain h residue 119 SER Chi-restraints excluded: chain h residue 162 ILE Chi-restraints excluded: chain h residue 185 ASN Chi-restraints excluded: chain h residue 187 SER Chi-restraints excluded: chain i residue 78 GLU Chi-restraints excluded: chain i residue 143 VAL Chi-restraints excluded: chain i residue 156 LYS Chi-restraints excluded: chain i residue 166 GLU Chi-restraints excluded: chain j residue 61 GLN Chi-restraints excluded: chain j residue 114 VAL Chi-restraints excluded: chain j residue 164 ILE Chi-restraints excluded: chain k residue 2 ARG Chi-restraints excluded: chain k residue 90 MET Chi-restraints excluded: chain l residue 23 LEU Chi-restraints excluded: chain m residue 11 LEU Chi-restraints excluded: chain m residue 60 GLU Chi-restraints excluded: chain m residue 74 SER Chi-restraints excluded: chain m residue 83 LEU Chi-restraints excluded: chain m residue 94 LYS Chi-restraints excluded: chain n residue 5 GLN Chi-restraints excluded: chain n residue 15 SER Chi-restraints excluded: chain n residue 61 LEU Chi-restraints excluded: chain n residue 85 ARG Chi-restraints excluded: chain n residue 114 LYS Chi-restraints excluded: chain o residue 7 ARG Chi-restraints excluded: chain o residue 17 LEU Chi-restraints excluded: chain o residue 80 THR Chi-restraints excluded: chain p residue 15 GLN Chi-restraints excluded: chain p residue 35 THR Chi-restraints excluded: chain p residue 64 GLN Chi-restraints excluded: chain p residue 79 ILE Chi-restraints excluded: chain q residue 30 LYS Chi-restraints excluded: chain q residue 35 THR Chi-restraints excluded: chain q residue 112 GLN Chi-restraints excluded: chain r residue 25 VAL Chi-restraints excluded: chain r residue 30 SER Chi-restraints excluded: chain r residue 113 ARG Chi-restraints excluded: chain s residue 19 LYS Chi-restraints excluded: chain s residue 47 LYS Chi-restraints excluded: chain s residue 55 SER Chi-restraints excluded: chain s residue 92 GLU Chi-restraints excluded: chain s residue 100 SER Chi-restraints excluded: chain u residue 66 THR Chi-restraints excluded: chain u residue 68 SER Chi-restraints excluded: chain u residue 78 VAL Chi-restraints excluded: chain v residue 13 VAL Chi-restraints excluded: chain v residue 18 GLU Chi-restraints excluded: chain v residue 33 ILE Chi-restraints excluded: chain v residue 67 LEU Chi-restraints excluded: chain w residue 42 SER Chi-restraints excluded: chain w residue 43 ARG Chi-restraints excluded: chain w residue 61 ARG Chi-restraints excluded: chain x residue 21 LYS Chi-restraints excluded: chain x residue 29 LYS Chi-restraints excluded: chain x residue 32 ARG Chi-restraints excluded: chain x residue 56 GLN Chi-restraints excluded: chain x residue 64 ASP Chi-restraints excluded: chain x residue 79 THR Chi-restraints excluded: chain y residue 57 ILE Chi-restraints excluded: chain y residue 82 GLN Chi-restraints excluded: chain y residue 85 LYS Chi-restraints excluded: chain z residue 4 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1063 random chunks: chunk 345 optimal weight: 5.9990 chunk 925 optimal weight: 7.9990 chunk 203 optimal weight: 1.9990 chunk 603 optimal weight: 20.0000 chunk 253 optimal weight: 7.9990 chunk 1028 optimal weight: 10.0000 chunk 853 optimal weight: 0.9980 chunk 476 optimal weight: 6.9990 chunk 85 optimal weight: 5.9990 chunk 340 optimal weight: 7.9990 chunk 539 optimal weight: 4.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8 179 GLN B 117 GLN C 32 ASN C 42 ASN ** C 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 GLN D 195 GLN E 127 ASN F 104 ASN I 106 GLN K 3 GLN M 97 GLN P 3 ASN Q 72 ASN R 86 GLN T 28 ASN T 48 GLN ** U 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 49 ASN V 51 GLN V 75 GLN ** V 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 76 ASN Y 15 ASN Y 20 ASN Y 39 GLN a 61 ASN d 29 GLN g 42 ASN ** g 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 8 ASN h 19 ASN h 100 GLN h 139 GLN i 40 GLN ** i 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 116 GLN j 73 ASN ** k 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 50 GLN n 75 GLN n 126 GLN o 20 GLN p 24 HIS p 28 ASN s 60 GLN s 66 GLN t 35 GLN t 40 GLN u 26 ASN w 31 ASN w 54 GLN y 3 ASN ** y 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 47 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.1040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 162437 Z= 0.313 Angle : 0.651 20.996 242695 Z= 0.347 Chirality : 0.038 0.341 30890 Planarity : 0.006 0.138 13216 Dihedral : 23.821 178.935 80453 Min Nonbonded Distance : 1.043 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.46 % Favored : 96.52 % Rotamer: Outliers : 4.52 % Allowed : 19.42 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.11), residues: 6068 helix: 1.55 (0.11), residues: 2119 sheet: -0.57 (0.15), residues: 1127 loop : -0.46 (0.11), residues: 2822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP l 103 HIS 0.008 0.001 HIS w 74 PHE 0.019 0.002 PHE D 183 TYR 0.037 0.002 TYR g 213 ARG 0.010 0.001 ARG p 98 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12136 Ramachandran restraints generated. 6068 Oldfield, 0 Emsley, 6068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12136 Ramachandran restraints generated. 6068 Oldfield, 0 Emsley, 6068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1859 residues out of total 5041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 228 poor density : 1631 time to evaluate : 6.532 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: 8 21 LYS cc_start: 0.8683 (mttm) cc_final: 0.8469 (mttm) REVERT: 8 25 ARG cc_start: 0.8003 (OUTLIER) cc_final: 0.7795 (tpp-160) REVERT: 8 93 LEU cc_start: 0.7825 (OUTLIER) cc_final: 0.7623 (mm) REVERT: B 115 GLN cc_start: 0.8334 (OUTLIER) cc_final: 0.7996 (mp10) REVERT: B 167 ARG cc_start: 0.7997 (ttp80) cc_final: 0.7759 (ttp80) REVERT: C 33 ARG cc_start: 0.8927 (OUTLIER) cc_final: 0.8433 (ptt-90) REVERT: D 111 GLU cc_start: 0.8583 (tp30) cc_final: 0.8084 (tp30) REVERT: D 198 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.6797 (mp0) REVERT: E 38 MET cc_start: 0.8391 (mtm) cc_final: 0.8105 (ttm) REVERT: E 112 ARG cc_start: 0.7876 (ttp80) cc_final: 0.7553 (ttm-80) REVERT: F 6 LYS cc_start: 0.8103 (OUTLIER) cc_final: 0.7830 (mptt) REVERT: H 38 MET cc_start: 0.1692 (mmt) cc_final: 0.1002 (mpp) REVERT: H 86 MET cc_start: 0.2855 (mmt) cc_final: 0.2094 (mmt) REVERT: I 35 MET cc_start: 0.4885 (OUTLIER) cc_final: 0.3803 (pp-130) REVERT: I 135 MET cc_start: 0.1848 (ttm) cc_final: 0.1194 (ptt) REVERT: J 102 GLU cc_start: 0.8382 (mt-10) cc_final: 0.8160 (mt-10) REVERT: K 17 ARG cc_start: 0.7777 (mmm-85) cc_final: 0.7547 (mmm160) REVERT: K 106 GLU cc_start: 0.8292 (mp0) cc_final: 0.8055 (mp0) REVERT: M 5 LYS cc_start: 0.8849 (OUTLIER) cc_final: 0.8623 (mtmm) REVERT: M 6 ARG cc_start: 0.7909 (OUTLIER) cc_final: 0.7283 (ptm160) REVERT: P 71 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.8025 (mt-10) REVERT: Q 18 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8932 (mm) REVERT: Q 75 SER cc_start: 0.9143 (p) cc_final: 0.8914 (p) REVERT: Q 85 LYS cc_start: 0.8992 (OUTLIER) cc_final: 0.8292 (mptm) REVERT: R 6 GLN cc_start: 0.7933 (OUTLIER) cc_final: 0.7331 (tm-30) REVERT: R 97 LYS cc_start: 0.8837 (OUTLIER) cc_final: 0.8614 (ttmt) REVERT: S 83 LYS cc_start: 0.9055 (OUTLIER) cc_final: 0.8224 (ptpt) REVERT: S 98 LYS cc_start: 0.9109 (OUTLIER) cc_final: 0.8715 (mttm) REVERT: T 9 LYS cc_start: 0.8902 (OUTLIER) cc_final: 0.8639 (mtpt) REVERT: W 68 LYS cc_start: 0.9090 (OUTLIER) cc_final: 0.8594 (ttmm) REVERT: X 76 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7744 (tt0) REVERT: Y 31 GLN cc_start: 0.8401 (mt0) cc_final: 0.8042 (mt0) REVERT: b 53 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8314 (tttt) REVERT: d 1 MET cc_start: 0.7847 (OUTLIER) cc_final: 0.7505 (mtm) REVERT: g 10 LEU cc_start: 0.8219 (mt) cc_final: 0.7965 (tm) REVERT: g 27 MET cc_start: 0.8600 (mmm) cc_final: 0.8314 (mmm) REVERT: g 139 ARG cc_start: 0.7434 (mmt90) cc_final: 0.7224 (mtt-85) REVERT: g 173 ILE cc_start: 0.9140 (OUTLIER) cc_final: 0.8826 (mm) REVERT: i 65 TYR cc_start: 0.9294 (m-80) cc_final: 0.8862 (m-80) REVERT: i 78 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7644 (tm-30) REVERT: i 156 LYS cc_start: 0.8204 (OUTLIER) cc_final: 0.7769 (ttmt) REVERT: k 2 ARG cc_start: 0.7794 (OUTLIER) cc_final: 0.7390 (ttp-170) REVERT: k 44 ARG cc_start: 0.8341 (OUTLIER) cc_final: 0.8089 (tpp80) REVERT: l 139 GLU cc_start: 0.7563 (pt0) cc_final: 0.7288 (pt0) REVERT: l 143 ARG cc_start: 0.7425 (mtm-85) cc_final: 0.7112 (mtm-85) REVERT: m 41 LYS cc_start: 0.8810 (OUTLIER) cc_final: 0.7750 (tmmm) REVERT: m 60 GLU cc_start: 0.7547 (OUTLIER) cc_final: 0.6950 (tp30) REVERT: n 57 MET cc_start: 0.7454 (mtp) cc_final: 0.7217 (mtp) REVERT: o 5 ARG cc_start: 0.6409 (tmm-80) cc_final: 0.6047 (tmm-80) REVERT: o 7 ARG cc_start: 0.8215 (OUTLIER) cc_final: 0.6575 (mpt-90) REVERT: p 15 GLN cc_start: 0.7374 (OUTLIER) cc_final: 0.7150 (tp40) REVERT: p 64 GLN cc_start: 0.8183 (OUTLIER) cc_final: 0.7794 (tm-30) REVERT: p 68 GLU cc_start: 0.7640 (mt-10) cc_final: 0.7388 (mt-10) REVERT: p 105 PHE cc_start: 0.8850 (m-80) cc_final: 0.8517 (m-80) REVERT: s 92 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7171 (mt-10) REVERT: t 63 ARG cc_start: 0.9397 (ttp-170) cc_final: 0.9057 (ttp-170) REVERT: v 49 GLU cc_start: 0.7648 (mm-30) cc_final: 0.7355 (tp30) REVERT: w 61 ARG cc_start: 0.8778 (OUTLIER) cc_final: 0.7838 (mpt180) REVERT: x 56 GLN cc_start: 0.8236 (OUTLIER) cc_final: 0.7973 (pm20) REVERT: y 57 ILE cc_start: 0.8814 (OUTLIER) cc_final: 0.8537 (tt) REVERT: y 82 GLN cc_start: 0.8221 (OUTLIER) cc_final: 0.7249 (mp10) REVERT: z 4 ILE cc_start: 0.7045 (OUTLIER) cc_final: 0.6581 (mt) outliers start: 228 outliers final: 118 residues processed: 1707 average time/residue: 2.3577 time to fit residues: 5703.9281 Evaluate side-chains 1760 residues out of total 5041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 1605 time to evaluate : 6.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 8 residue 2 ILE Chi-restraints excluded: chain 8 residue 25 ARG Chi-restraints excluded: chain 8 residue 48 SER Chi-restraints excluded: chain 8 residue 93 LEU Chi-restraints excluded: chain 8 residue 109 ILE Chi-restraints excluded: chain 8 residue 161 ILE Chi-restraints excluded: chain 8 residue 202 ILE Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 125 LYS Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 194 GLU Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain C residue 33 ARG Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 139 LYS Chi-restraints excluded: chain D residue 143 LEU Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 198 GLU Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 142 ASP Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain F residue 6 LYS Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain H residue 87 GLU Chi-restraints excluded: chain H residue 128 THR Chi-restraints excluded: chain I residue 35 MET Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain M residue 5 LYS Chi-restraints excluded: chain M residue 6 ARG Chi-restraints excluded: chain M residue 95 LEU Chi-restraints excluded: chain M residue 126 ILE Chi-restraints excluded: chain M residue 135 VAL Chi-restraints excluded: chain N residue 89 SER Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain O residue 68 LYS Chi-restraints excluded: chain P residue 71 GLU Chi-restraints excluded: chain P residue 110 ILE Chi-restraints excluded: chain P residue 111 LYS Chi-restraints excluded: chain Q residue 18 LEU Chi-restraints excluded: chain Q residue 85 LYS Chi-restraints excluded: chain R residue 6 GLN Chi-restraints excluded: chain R residue 48 LYS Chi-restraints excluded: chain R residue 97 LYS Chi-restraints excluded: chain S residue 53 SER Chi-restraints excluded: chain S residue 83 LYS Chi-restraints excluded: chain S residue 98 LYS Chi-restraints excluded: chain T residue 9 LYS Chi-restraints excluded: chain T residue 10 VAL Chi-restraints excluded: chain T residue 16 VAL Chi-restraints excluded: chain T residue 27 SER Chi-restraints excluded: chain T residue 32 LEU Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain W residue 32 LEU Chi-restraints excluded: chain W residue 68 LYS Chi-restraints excluded: chain W residue 78 LYS Chi-restraints excluded: chain X residue 2 SER Chi-restraints excluded: chain X residue 43 GLU Chi-restraints excluded: chain X residue 71 LEU Chi-restraints excluded: chain X residue 76 GLU Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain Y residue 24 GLU Chi-restraints excluded: chain Z residue 6 LYS Chi-restraints excluded: chain Z residue 21 LYS Chi-restraints excluded: chain Z residue 39 GLU Chi-restraints excluded: chain b residue 25 VAL Chi-restraints excluded: chain b residue 53 LYS Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 4 THR Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain e residue 32 ILE Chi-restraints excluded: chain f residue 8 LYS Chi-restraints excluded: chain g residue 35 ARG Chi-restraints excluded: chain g residue 110 SER Chi-restraints excluded: chain g residue 161 LEU Chi-restraints excluded: chain g residue 167 ASP Chi-restraints excluded: chain g residue 173 ILE Chi-restraints excluded: chain g residue 211 THR Chi-restraints excluded: chain g residue 220 THR Chi-restraints excluded: chain h residue 53 SER Chi-restraints excluded: chain h residue 185 ASN Chi-restraints excluded: chain h residue 187 SER Chi-restraints excluded: chain i residue 78 GLU Chi-restraints excluded: chain i residue 143 VAL Chi-restraints excluded: chain i residue 156 LYS Chi-restraints excluded: chain i residue 166 GLU Chi-restraints excluded: chain j residue 114 VAL Chi-restraints excluded: chain j residue 164 ILE Chi-restraints excluded: chain k residue 2 ARG Chi-restraints excluded: chain k residue 44 ARG Chi-restraints excluded: chain k residue 52 ASN Chi-restraints excluded: chain k residue 90 MET Chi-restraints excluded: chain k residue 92 THR Chi-restraints excluded: chain l residue 23 LEU Chi-restraints excluded: chain l residue 133 THR Chi-restraints excluded: chain m residue 11 LEU Chi-restraints excluded: chain m residue 41 LYS Chi-restraints excluded: chain m residue 60 GLU Chi-restraints excluded: chain m residue 94 LYS Chi-restraints excluded: chain n residue 5 GLN Chi-restraints excluded: chain n residue 15 SER Chi-restraints excluded: chain n residue 85 ARG Chi-restraints excluded: chain n residue 94 LEU Chi-restraints excluded: chain o residue 7 ARG Chi-restraints excluded: chain o residue 17 LEU Chi-restraints excluded: chain o residue 80 THR Chi-restraints excluded: chain p residue 15 GLN Chi-restraints excluded: chain p residue 35 THR Chi-restraints excluded: chain p residue 64 GLN Chi-restraints excluded: chain p residue 79 ILE Chi-restraints excluded: chain q residue 30 LYS Chi-restraints excluded: chain q residue 65 SER Chi-restraints excluded: chain q residue 112 GLN Chi-restraints excluded: chain r residue 25 VAL Chi-restraints excluded: chain r residue 30 SER Chi-restraints excluded: chain r residue 113 ARG Chi-restraints excluded: chain s residue 47 LYS Chi-restraints excluded: chain s residue 55 SER Chi-restraints excluded: chain s residue 92 GLU Chi-restraints excluded: chain s residue 100 SER Chi-restraints excluded: chain t residue 75 VAL Chi-restraints excluded: chain v residue 13 VAL Chi-restraints excluded: chain v residue 18 GLU Chi-restraints excluded: chain v residue 67 LEU Chi-restraints excluded: chain w residue 42 SER Chi-restraints excluded: chain w residue 43 ARG Chi-restraints excluded: chain w residue 61 ARG Chi-restraints excluded: chain x residue 21 LYS Chi-restraints excluded: chain x residue 29 LYS Chi-restraints excluded: chain x residue 56 GLN Chi-restraints excluded: chain x residue 58 VAL Chi-restraints excluded: chain x residue 64 ASP Chi-restraints excluded: chain x residue 79 THR Chi-restraints excluded: chain y residue 57 ILE Chi-restraints excluded: chain y residue 64 LYS Chi-restraints excluded: chain y residue 82 GLN Chi-restraints excluded: chain z residue 4 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1063 random chunks: chunk 991 optimal weight: 7.9990 chunk 115 optimal weight: 7.9990 chunk 585 optimal weight: 3.9990 chunk 751 optimal weight: 8.9990 chunk 581 optimal weight: 5.9990 chunk 865 optimal weight: 0.7980 chunk 574 optimal weight: 9.9990 chunk 1024 optimal weight: 0.2980 chunk 641 optimal weight: 0.8980 chunk 624 optimal weight: 20.0000 chunk 473 optimal weight: 1.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8 169 GLN B 117 GLN C 42 ASN ** C 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 GLN ** D 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 195 GLN E 127 ASN F 20 ASN K 3 GLN P 3 ASN Q 56 GLN R 86 GLN T 28 ASN T 48 GLN ** U 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 49 ASN V 51 GLN V 75 GLN ** V 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 76 ASN Y 15 ASN Y 20 ASN Y 39 GLN a 61 ASN d 29 GLN g 42 ASN ** g 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 8 ASN h 19 ASN h 100 GLN h 123 GLN i 40 GLN i 59 GLN i 116 GLN j 73 ASN ** k 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 50 GLN n 75 GLN n 126 GLN o 20 GLN p 24 HIS p 28 ASN s 60 GLN s 66 GLN t 35 GLN t 40 GLN u 26 ASN w 31 ASN w 54 GLN w 75 GLN y 3 ASN ** y 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.1194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 162437 Z= 0.179 Angle : 0.615 19.899 242695 Z= 0.332 Chirality : 0.034 0.352 30890 Planarity : 0.006 0.131 13216 Dihedral : 23.848 179.567 80453 Min Nonbonded Distance : 1.100 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.44 % Favored : 96.54 % Rotamer: Outliers : 4.13 % Allowed : 20.37 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.11), residues: 6068 helix: 1.63 (0.11), residues: 2119 sheet: -0.54 (0.15), residues: 1132 loop : -0.41 (0.11), residues: 2817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP l 103 HIS 0.006 0.001 HIS w 74 PHE 0.029 0.002 PHE 8 201 TYR 0.039 0.002 TYR g 213 ARG 0.009 0.000 ARG j 45 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12136 Ramachandran restraints generated. 6068 Oldfield, 0 Emsley, 6068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12136 Ramachandran restraints generated. 6068 Oldfield, 0 Emsley, 6068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1858 residues out of total 5041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 208 poor density : 1650 time to evaluate : 6.467 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: 8 93 LEU cc_start: 0.7785 (OUTLIER) cc_final: 0.7570 (mm) REVERT: B 115 GLN cc_start: 0.8309 (OUTLIER) cc_final: 0.7971 (mp10) REVERT: B 167 ARG cc_start: 0.7956 (ttp80) cc_final: 0.7745 (ttp80) REVERT: D 111 GLU cc_start: 0.8565 (tp30) cc_final: 0.8077 (tp30) REVERT: D 198 GLU cc_start: 0.7551 (OUTLIER) cc_final: 0.6785 (mp0) REVERT: E 112 ARG cc_start: 0.7867 (ttp80) cc_final: 0.7534 (ttm-80) REVERT: F 6 LYS cc_start: 0.8055 (OUTLIER) cc_final: 0.7819 (mptt) REVERT: H 38 MET cc_start: 0.1991 (mmt) cc_final: 0.1302 (mpp) REVERT: H 86 MET cc_start: 0.2835 (mmt) cc_final: 0.2082 (mmt) REVERT: H 116 GLU cc_start: 0.2750 (OUTLIER) cc_final: 0.2166 (pm20) REVERT: I 35 MET cc_start: 0.4856 (OUTLIER) cc_final: 0.3806 (pp-130) REVERT: I 124 MET cc_start: 0.3568 (mmm) cc_final: 0.3168 (tpt) REVERT: I 135 MET cc_start: 0.1693 (ttm) cc_final: 0.1267 (ptt) REVERT: J 34 ARG cc_start: 0.8303 (ttp80) cc_final: 0.8000 (ttt90) REVERT: K 17 ARG cc_start: 0.7741 (mmm-85) cc_final: 0.7524 (mmm160) REVERT: K 106 GLU cc_start: 0.8280 (mp0) cc_final: 0.8073 (mp0) REVERT: M 5 LYS cc_start: 0.8840 (OUTLIER) cc_final: 0.8619 (mtmm) REVERT: M 6 ARG cc_start: 0.7878 (OUTLIER) cc_final: 0.7252 (ptm160) REVERT: P 71 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7996 (mt-10) REVERT: Q 18 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8919 (mm) REVERT: Q 75 SER cc_start: 0.9093 (p) cc_final: 0.8861 (p) REVERT: Q 87 SER cc_start: 0.8934 (m) cc_final: 0.8729 (m) REVERT: R 6 GLN cc_start: 0.7926 (OUTLIER) cc_final: 0.7349 (tm-30) REVERT: R 97 LYS cc_start: 0.8817 (OUTLIER) cc_final: 0.8596 (ttmt) REVERT: S 98 LYS cc_start: 0.9092 (OUTLIER) cc_final: 0.8675 (mttm) REVERT: T 9 LYS cc_start: 0.8866 (OUTLIER) cc_final: 0.8520 (mmtp) REVERT: T 33 LYS cc_start: 0.8694 (mttp) cc_final: 0.8426 (mttp) REVERT: W 68 LYS cc_start: 0.9077 (OUTLIER) cc_final: 0.8581 (ttmm) REVERT: Y 31 GLN cc_start: 0.8368 (mt0) cc_final: 0.7992 (mt0) REVERT: d 1 MET cc_start: 0.7837 (OUTLIER) cc_final: 0.7539 (mtm) REVERT: g 10 LEU cc_start: 0.8205 (mt) cc_final: 0.7950 (tm) REVERT: g 27 MET cc_start: 0.8570 (mmm) cc_final: 0.8301 (mmm) REVERT: g 52 GLU cc_start: 0.7391 (pt0) cc_final: 0.7044 (pt0) REVERT: g 113 ARG cc_start: 0.8257 (tpt90) cc_final: 0.8039 (tpt90) REVERT: g 139 ARG cc_start: 0.7422 (mmt90) cc_final: 0.7211 (mtt-85) REVERT: g 173 ILE cc_start: 0.9136 (OUTLIER) cc_final: 0.8824 (mm) REVERT: h 142 MET cc_start: 0.8963 (OUTLIER) cc_final: 0.8687 (mmm) REVERT: i 65 TYR cc_start: 0.9258 (m-80) cc_final: 0.8765 (m-80) REVERT: i 78 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7603 (tm-30) REVERT: i 156 LYS cc_start: 0.8192 (OUTLIER) cc_final: 0.7757 (ttmt) REVERT: k 2 ARG cc_start: 0.7722 (OUTLIER) cc_final: 0.7482 (ttp-170) REVERT: k 44 ARG cc_start: 0.8306 (OUTLIER) cc_final: 0.8064 (tpp80) REVERT: k 54 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8237 (pp) REVERT: k 102 MET cc_start: 0.6731 (ppp) cc_final: 0.6320 (ppp) REVERT: l 58 GLU cc_start: 0.7178 (OUTLIER) cc_final: 0.6879 (mm-30) REVERT: l 139 GLU cc_start: 0.7555 (pt0) cc_final: 0.7257 (pt0) REVERT: l 143 ARG cc_start: 0.7460 (mtm-85) cc_final: 0.7144 (mtm-85) REVERT: m 60 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.6885 (tp30) REVERT: n 57 MET cc_start: 0.7498 (mtp) cc_final: 0.7072 (mtp) REVERT: o 5 ARG cc_start: 0.6383 (tmm-80) cc_final: 0.5806 (tmm-80) REVERT: o 7 ARG cc_start: 0.8200 (OUTLIER) cc_final: 0.6397 (mpt-90) REVERT: p 15 GLN cc_start: 0.7334 (OUTLIER) cc_final: 0.7112 (tp40) REVERT: p 64 GLN cc_start: 0.8159 (OUTLIER) cc_final: 0.7792 (tm-30) REVERT: p 68 GLU cc_start: 0.7619 (mt-10) cc_final: 0.7392 (mt-10) REVERT: p 105 PHE cc_start: 0.8821 (m-80) cc_final: 0.8525 (m-80) REVERT: s 92 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7100 (mt-10) REVERT: t 47 LYS cc_start: 0.8578 (OUTLIER) cc_final: 0.8377 (mtpp) REVERT: t 63 ARG cc_start: 0.9365 (ttp-170) cc_final: 0.8950 (ttm170) REVERT: v 49 GLU cc_start: 0.7566 (mm-30) cc_final: 0.7307 (tp30) REVERT: w 61 ARG cc_start: 0.8745 (OUTLIER) cc_final: 0.7911 (mpt180) REVERT: x 56 GLN cc_start: 0.8242 (OUTLIER) cc_final: 0.7952 (pm20) REVERT: y 57 ILE cc_start: 0.8752 (OUTLIER) cc_final: 0.8498 (tt) REVERT: y 82 GLN cc_start: 0.8209 (OUTLIER) cc_final: 0.7308 (mp10) REVERT: z 4 ILE cc_start: 0.7006 (OUTLIER) cc_final: 0.6550 (mt) outliers start: 208 outliers final: 112 residues processed: 1712 average time/residue: 2.3713 time to fit residues: 5800.7098 Evaluate side-chains 1774 residues out of total 5041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 1627 time to evaluate : 6.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 8 residue 48 SER Chi-restraints excluded: chain 8 residue 93 LEU Chi-restraints excluded: chain 8 residue 109 ILE Chi-restraints excluded: chain 8 residue 161 ILE Chi-restraints excluded: chain 8 residue 202 ILE Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 194 GLU Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 139 LYS Chi-restraints excluded: chain D residue 143 LEU Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 198 GLU Chi-restraints excluded: chain E residue 32 GLU Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 142 ASP Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 175 PHE Chi-restraints excluded: chain F residue 6 LYS Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain H residue 87 GLU Chi-restraints excluded: chain H residue 116 GLU Chi-restraints excluded: chain H residue 128 THR Chi-restraints excluded: chain I residue 35 MET Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain L residue 51 GLU Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain M residue 5 LYS Chi-restraints excluded: chain M residue 6 ARG Chi-restraints excluded: chain M residue 95 LEU Chi-restraints excluded: chain M residue 126 ILE Chi-restraints excluded: chain M residue 135 VAL Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 89 SER Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain O residue 68 LYS Chi-restraints excluded: chain P residue 71 GLU Chi-restraints excluded: chain P residue 110 ILE Chi-restraints excluded: chain P residue 111 LYS Chi-restraints excluded: chain Q residue 18 LEU Chi-restraints excluded: chain R residue 6 GLN Chi-restraints excluded: chain R residue 48 LYS Chi-restraints excluded: chain R residue 97 LYS Chi-restraints excluded: chain S residue 96 ILE Chi-restraints excluded: chain S residue 98 LYS Chi-restraints excluded: chain T residue 9 LYS Chi-restraints excluded: chain T residue 10 VAL Chi-restraints excluded: chain T residue 16 VAL Chi-restraints excluded: chain T residue 27 SER Chi-restraints excluded: chain T residue 32 LEU Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain W residue 68 LYS Chi-restraints excluded: chain X residue 2 SER Chi-restraints excluded: chain X residue 43 GLU Chi-restraints excluded: chain X residue 71 LEU Chi-restraints excluded: chain Y residue 2 LYS Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain Y residue 24 GLU Chi-restraints excluded: chain Z residue 6 LYS Chi-restraints excluded: chain Z residue 21 LYS Chi-restraints excluded: chain Z residue 39 GLU Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain e residue 32 ILE Chi-restraints excluded: chain f residue 8 LYS Chi-restraints excluded: chain g residue 35 ARG Chi-restraints excluded: chain g residue 110 SER Chi-restraints excluded: chain g residue 143 LYS Chi-restraints excluded: chain g residue 161 LEU Chi-restraints excluded: chain g residue 167 ASP Chi-restraints excluded: chain g residue 173 ILE Chi-restraints excluded: chain g residue 220 THR Chi-restraints excluded: chain h residue 53 SER Chi-restraints excluded: chain h residue 142 MET Chi-restraints excluded: chain h residue 185 ASN Chi-restraints excluded: chain i residue 64 ILE Chi-restraints excluded: chain i residue 78 GLU Chi-restraints excluded: chain i residue 143 VAL Chi-restraints excluded: chain i residue 156 LYS Chi-restraints excluded: chain j residue 61 GLN Chi-restraints excluded: chain j residue 114 VAL Chi-restraints excluded: chain j residue 164 ILE Chi-restraints excluded: chain k residue 2 ARG Chi-restraints excluded: chain k residue 44 ARG Chi-restraints excluded: chain k residue 52 ASN Chi-restraints excluded: chain k residue 54 LEU Chi-restraints excluded: chain k residue 92 THR Chi-restraints excluded: chain l residue 23 LEU Chi-restraints excluded: chain l residue 58 GLU Chi-restraints excluded: chain l residue 133 THR Chi-restraints excluded: chain m residue 11 LEU Chi-restraints excluded: chain m residue 60 GLU Chi-restraints excluded: chain m residue 94 LYS Chi-restraints excluded: chain m residue 107 SER Chi-restraints excluded: chain n residue 15 SER Chi-restraints excluded: chain n residue 85 ARG Chi-restraints excluded: chain n residue 94 LEU Chi-restraints excluded: chain o residue 7 ARG Chi-restraints excluded: chain o residue 17 LEU Chi-restraints excluded: chain o residue 80 THR Chi-restraints excluded: chain p residue 15 GLN Chi-restraints excluded: chain p residue 35 THR Chi-restraints excluded: chain p residue 64 GLN Chi-restraints excluded: chain p residue 79 ILE Chi-restraints excluded: chain q residue 30 LYS Chi-restraints excluded: chain q residue 65 SER Chi-restraints excluded: chain q residue 112 GLN Chi-restraints excluded: chain r residue 25 VAL Chi-restraints excluded: chain r residue 30 SER Chi-restraints excluded: chain r residue 113 ARG Chi-restraints excluded: chain s residue 47 LYS Chi-restraints excluded: chain s residue 55 SER Chi-restraints excluded: chain s residue 92 GLU Chi-restraints excluded: chain t residue 47 LYS Chi-restraints excluded: chain t residue 75 VAL Chi-restraints excluded: chain u residue 68 SER Chi-restraints excluded: chain v residue 13 VAL Chi-restraints excluded: chain v residue 18 GLU Chi-restraints excluded: chain v residue 58 VAL Chi-restraints excluded: chain v residue 67 LEU Chi-restraints excluded: chain w residue 42 SER Chi-restraints excluded: chain w residue 43 ARG Chi-restraints excluded: chain w residue 61 ARG Chi-restraints excluded: chain x residue 21 LYS Chi-restraints excluded: chain x residue 29 LYS Chi-restraints excluded: chain x residue 56 GLN Chi-restraints excluded: chain x residue 58 VAL Chi-restraints excluded: chain x residue 79 THR Chi-restraints excluded: chain y residue 57 ILE Chi-restraints excluded: chain y residue 64 LYS Chi-restraints excluded: chain y residue 82 GLN Chi-restraints excluded: chain z residue 4 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1063 random chunks: chunk 633 optimal weight: 6.9990 chunk 409 optimal weight: 10.0000 chunk 611 optimal weight: 7.9990 chunk 308 optimal weight: 10.0000 chunk 201 optimal weight: 8.9990 chunk 198 optimal weight: 8.9990 chunk 651 optimal weight: 8.9990 chunk 698 optimal weight: 9.9990 chunk 506 optimal weight: 10.0000 chunk 95 optimal weight: 8.9990 chunk 805 optimal weight: 20.0000 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8 179 GLN B 117 GLN C 42 ASN C 94 GLN D 41 GLN D 156 ASN D 195 GLN E 127 ASN L 93 ASN P 3 ASN Q 52 GLN R 86 GLN T 28 ASN T 48 GLN U 69 ASN ** U 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 49 ASN V 51 GLN ** V 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 76 ASN Y 15 ASN Y 20 ASN Y 39 GLN a 61 ASN b 4 GLN d 29 GLN g 42 ASN ** g 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 100 GLN h 139 GLN i 40 GLN i 59 GLN i 116 GLN j 73 ASN ** k 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 50 GLN n 75 GLN n 126 GLN o 20 GLN p 24 HIS p 28 ASN ** p 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 81 ASN ** s 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 66 GLN t 35 GLN t 40 GLN u 26 ASN w 31 ASN w 54 GLN y 3 ASN Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.1014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.132 162437 Z= 0.593 Angle : 0.793 22.353 242695 Z= 0.409 Chirality : 0.048 0.333 30890 Planarity : 0.008 0.151 13216 Dihedral : 23.818 178.718 80453 Min Nonbonded Distance : 0.985 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.84 % Favored : 96.14 % Rotamer: Outliers : 4.52 % Allowed : 20.65 % Favored : 74.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.15 (0.10), residues: 6068 helix: 1.34 (0.11), residues: 2110 sheet: -0.60 (0.15), residues: 1126 loop : -0.49 (0.11), residues: 2832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP l 103 HIS 0.013 0.002 HIS r 14 PHE 0.026 0.003 PHE G 91 TYR 0.037 0.003 TYR g 213 ARG 0.010 0.001 ARG d 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12136 Ramachandran restraints generated. 6068 Oldfield, 0 Emsley, 6068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12136 Ramachandran restraints generated. 6068 Oldfield, 0 Emsley, 6068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1853 residues out of total 5041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 228 poor density : 1625 time to evaluate : 5.894 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: 8 21 LYS cc_start: 0.8791 (mttm) cc_final: 0.8537 (mttm) REVERT: 8 93 LEU cc_start: 0.8024 (OUTLIER) cc_final: 0.7783 (mm) REVERT: B 167 ARG cc_start: 0.8024 (ttp80) cc_final: 0.7758 (ttp80) REVERT: C 33 ARG cc_start: 0.9076 (OUTLIER) cc_final: 0.8479 (ptt-90) REVERT: D 1 MET cc_start: 0.7211 (ptp) cc_final: 0.6869 (ptp) REVERT: D 16 GLU cc_start: 0.7614 (tp30) cc_final: 0.7237 (tp30) REVERT: D 141 MET cc_start: 0.8682 (mtp) cc_final: 0.8380 (mtp) REVERT: D 198 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.6821 (mp0) REVERT: E 38 MET cc_start: 0.8492 (mtm) cc_final: 0.8190 (ttm) REVERT: E 112 ARG cc_start: 0.7871 (ttp80) cc_final: 0.7513 (ttm-80) REVERT: F 6 LYS cc_start: 0.8166 (OUTLIER) cc_final: 0.7851 (mptt) REVERT: H 38 MET cc_start: 0.2124 (mmt) cc_final: 0.1371 (mpp) REVERT: H 86 MET cc_start: 0.2424 (mmt) cc_final: 0.1923 (mmt) REVERT: I 35 MET cc_start: 0.4899 (OUTLIER) cc_final: 0.3725 (pp-130) REVERT: I 135 MET cc_start: 0.1727 (ttm) cc_final: 0.1367 (ttt) REVERT: K 17 ARG cc_start: 0.7850 (mmm-85) cc_final: 0.7592 (mmm160) REVERT: K 90 ASN cc_start: 0.8351 (OUTLIER) cc_final: 0.8067 (m110) REVERT: K 106 GLU cc_start: 0.8344 (mp0) cc_final: 0.8092 (mp0) REVERT: M 5 LYS cc_start: 0.8915 (OUTLIER) cc_final: 0.8704 (mtmm) REVERT: M 6 ARG cc_start: 0.7891 (OUTLIER) cc_final: 0.7222 (ptm160) REVERT: P 71 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.8082 (mt-10) REVERT: Q 18 LEU cc_start: 0.9265 (OUTLIER) cc_final: 0.8968 (mm) REVERT: Q 85 LYS cc_start: 0.9047 (OUTLIER) cc_final: 0.8499 (mptm) REVERT: R 6 GLN cc_start: 0.7989 (OUTLIER) cc_final: 0.7356 (tm-30) REVERT: R 97 LYS cc_start: 0.8868 (OUTLIER) cc_final: 0.8647 (ttmt) REVERT: S 98 LYS cc_start: 0.9140 (OUTLIER) cc_final: 0.8729 (mttm) REVERT: T 9 LYS cc_start: 0.8991 (OUTLIER) cc_final: 0.8687 (mtpt) REVERT: W 68 LYS cc_start: 0.9096 (OUTLIER) cc_final: 0.8615 (ttmm) REVERT: X 11 ARG cc_start: 0.8761 (OUTLIER) cc_final: 0.8482 (mtp85) REVERT: Y 31 GLN cc_start: 0.8458 (mt0) cc_final: 0.8226 (mt0) REVERT: d 1 MET cc_start: 0.7904 (OUTLIER) cc_final: 0.7647 (mtm) REVERT: g 10 LEU cc_start: 0.8241 (mt) cc_final: 0.7981 (tm) REVERT: g 27 MET cc_start: 0.8700 (mmm) cc_final: 0.8341 (mmm) REVERT: g 36 ASN cc_start: 0.6291 (t0) cc_final: 0.5807 (t0) REVERT: g 139 ARG cc_start: 0.7449 (mmt90) cc_final: 0.7235 (mtt-85) REVERT: g 173 ILE cc_start: 0.9129 (OUTLIER) cc_final: 0.8857 (mm) REVERT: i 65 TYR cc_start: 0.9295 (m-80) cc_final: 0.8867 (m-80) REVERT: i 78 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7671 (tm-30) REVERT: i 156 LYS cc_start: 0.8295 (OUTLIER) cc_final: 0.8044 (ttmt) REVERT: k 2 ARG cc_start: 0.7868 (OUTLIER) cc_final: 0.7525 (ttp-170) REVERT: k 44 ARG cc_start: 0.8367 (OUTLIER) cc_final: 0.8075 (tpp80) REVERT: k 54 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8285 (pp) REVERT: k 56 LYS cc_start: 0.8013 (mttm) cc_final: 0.7537 (mmtp) REVERT: k 102 MET cc_start: 0.6778 (ppp) cc_final: 0.6392 (ppp) REVERT: l 58 GLU cc_start: 0.7246 (OUTLIER) cc_final: 0.6566 (mm-30) REVERT: l 139 GLU cc_start: 0.7613 (pt0) cc_final: 0.7359 (pt0) REVERT: l 143 ARG cc_start: 0.7439 (mtm-85) cc_final: 0.7068 (mtm-85) REVERT: m 60 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.7129 (tp30) REVERT: m 83 LEU cc_start: 0.9320 (OUTLIER) cc_final: 0.9089 (tt) REVERT: o 5 ARG cc_start: 0.6358 (tmm-80) cc_final: 0.5868 (tmm-80) REVERT: o 7 ARG cc_start: 0.8282 (OUTLIER) cc_final: 0.6586 (mpt-90) REVERT: p 15 GLN cc_start: 0.7403 (OUTLIER) cc_final: 0.7187 (tp40) REVERT: p 105 PHE cc_start: 0.8906 (m-80) cc_final: 0.8580 (m-80) REVERT: r 78 LYS cc_start: 0.8513 (OUTLIER) cc_final: 0.8131 (tmmm) REVERT: s 92 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7224 (mt-10) REVERT: w 61 ARG cc_start: 0.8821 (OUTLIER) cc_final: 0.7753 (mpt180) REVERT: x 56 GLN cc_start: 0.8295 (OUTLIER) cc_final: 0.7960 (pm20) REVERT: y 82 GLN cc_start: 0.8279 (OUTLIER) cc_final: 0.7218 (mp10) REVERT: y 85 LYS cc_start: 0.8564 (OUTLIER) cc_final: 0.8289 (ttpp) REVERT: z 4 ILE cc_start: 0.7134 (OUTLIER) cc_final: 0.6736 (mt) outliers start: 228 outliers final: 135 residues processed: 1701 average time/residue: 2.3327 time to fit residues: 5613.0447 Evaluate side-chains 1774 residues out of total 5041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 1603 time to evaluate : 6.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 8 residue 2 ILE Chi-restraints excluded: chain 8 residue 48 SER Chi-restraints excluded: chain 8 residue 93 LEU Chi-restraints excluded: chain 8 residue 109 ILE Chi-restraints excluded: chain 8 residue 161 ILE Chi-restraints excluded: chain 8 residue 201 PHE Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 125 LYS Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 194 GLU Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain C residue 33 ARG Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 139 LYS Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 198 GLU Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 32 GLU Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 120 LYS Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 142 ASP Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain F residue 6 LYS Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain H residue 87 GLU Chi-restraints excluded: chain H residue 128 THR Chi-restraints excluded: chain I residue 35 MET Chi-restraints excluded: chain K residue 28 SER Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 90 ASN Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain M residue 5 LYS Chi-restraints excluded: chain M residue 6 ARG Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain M residue 95 LEU Chi-restraints excluded: chain M residue 126 ILE Chi-restraints excluded: chain M residue 135 VAL Chi-restraints excluded: chain N residue 89 SER Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain O residue 68 LYS Chi-restraints excluded: chain P residue 12 GLN Chi-restraints excluded: chain P residue 71 GLU Chi-restraints excluded: chain P residue 110 ILE Chi-restraints excluded: chain P residue 111 LYS Chi-restraints excluded: chain Q residue 18 LEU Chi-restraints excluded: chain Q residue 85 LYS Chi-restraints excluded: chain R residue 6 GLN Chi-restraints excluded: chain R residue 37 GLU Chi-restraints excluded: chain R residue 48 LYS Chi-restraints excluded: chain R residue 97 LYS Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 53 SER Chi-restraints excluded: chain S residue 96 ILE Chi-restraints excluded: chain S residue 98 LYS Chi-restraints excluded: chain T residue 9 LYS Chi-restraints excluded: chain T residue 10 VAL Chi-restraints excluded: chain T residue 16 VAL Chi-restraints excluded: chain T residue 27 SER Chi-restraints excluded: chain T residue 32 LEU Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain V residue 8 VAL Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain W residue 32 LEU Chi-restraints excluded: chain W residue 68 LYS Chi-restraints excluded: chain X residue 2 SER Chi-restraints excluded: chain X residue 11 ARG Chi-restraints excluded: chain X residue 43 GLU Chi-restraints excluded: chain X residue 71 LEU Chi-restraints excluded: chain Y residue 2 LYS Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain Y residue 24 GLU Chi-restraints excluded: chain Z residue 21 LYS Chi-restraints excluded: chain Z residue 39 GLU Chi-restraints excluded: chain b residue 25 VAL Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 4 THR Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain e residue 32 ILE Chi-restraints excluded: chain f residue 8 LYS Chi-restraints excluded: chain g residue 35 ARG Chi-restraints excluded: chain g residue 110 SER Chi-restraints excluded: chain g residue 161 LEU Chi-restraints excluded: chain g residue 167 ASP Chi-restraints excluded: chain g residue 173 ILE Chi-restraints excluded: chain g residue 199 VAL Chi-restraints excluded: chain g residue 211 THR Chi-restraints excluded: chain g residue 220 THR Chi-restraints excluded: chain h residue 53 SER Chi-restraints excluded: chain h residue 162 ILE Chi-restraints excluded: chain h residue 185 ASN Chi-restraints excluded: chain h residue 187 SER Chi-restraints excluded: chain i residue 78 GLU Chi-restraints excluded: chain i residue 143 VAL Chi-restraints excluded: chain i residue 156 LYS Chi-restraints excluded: chain i residue 166 GLU Chi-restraints excluded: chain j residue 61 GLN Chi-restraints excluded: chain j residue 114 VAL Chi-restraints excluded: chain j residue 164 ILE Chi-restraints excluded: chain k residue 2 ARG Chi-restraints excluded: chain k residue 44 ARG Chi-restraints excluded: chain k residue 52 ASN Chi-restraints excluded: chain k residue 54 LEU Chi-restraints excluded: chain k residue 92 THR Chi-restraints excluded: chain l residue 23 LEU Chi-restraints excluded: chain l residue 58 GLU Chi-restraints excluded: chain l residue 118 LEU Chi-restraints excluded: chain l residue 133 THR Chi-restraints excluded: chain m residue 11 LEU Chi-restraints excluded: chain m residue 60 GLU Chi-restraints excluded: chain m residue 74 SER Chi-restraints excluded: chain m residue 83 LEU Chi-restraints excluded: chain m residue 94 LYS Chi-restraints excluded: chain n residue 15 SER Chi-restraints excluded: chain n residue 61 LEU Chi-restraints excluded: chain n residue 85 ARG Chi-restraints excluded: chain o residue 7 ARG Chi-restraints excluded: chain o residue 17 LEU Chi-restraints excluded: chain o residue 80 THR Chi-restraints excluded: chain p residue 15 GLN Chi-restraints excluded: chain p residue 35 THR Chi-restraints excluded: chain p residue 79 ILE Chi-restraints excluded: chain q residue 30 LYS Chi-restraints excluded: chain q residue 35 THR Chi-restraints excluded: chain q residue 65 SER Chi-restraints excluded: chain q residue 112 GLN Chi-restraints excluded: chain r residue 25 VAL Chi-restraints excluded: chain r residue 30 SER Chi-restraints excluded: chain r residue 78 LYS Chi-restraints excluded: chain r residue 113 ARG Chi-restraints excluded: chain s residue 19 LYS Chi-restraints excluded: chain s residue 47 LYS Chi-restraints excluded: chain s residue 55 SER Chi-restraints excluded: chain s residue 92 GLU Chi-restraints excluded: chain s residue 100 SER Chi-restraints excluded: chain t residue 22 THR Chi-restraints excluded: chain t residue 75 VAL Chi-restraints excluded: chain u residue 68 SER Chi-restraints excluded: chain u residue 78 VAL Chi-restraints excluded: chain v residue 13 VAL Chi-restraints excluded: chain v residue 18 GLU Chi-restraints excluded: chain v residue 67 LEU Chi-restraints excluded: chain w residue 42 SER Chi-restraints excluded: chain w residue 43 ARG Chi-restraints excluded: chain w residue 61 ARG Chi-restraints excluded: chain x residue 21 LYS Chi-restraints excluded: chain x residue 29 LYS Chi-restraints excluded: chain x residue 56 GLN Chi-restraints excluded: chain x residue 64 ASP Chi-restraints excluded: chain x residue 79 THR Chi-restraints excluded: chain y residue 64 LYS Chi-restraints excluded: chain y residue 82 GLN Chi-restraints excluded: chain y residue 85 LYS Chi-restraints excluded: chain z residue 4 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1063 random chunks: chunk 932 optimal weight: 7.9990 chunk 981 optimal weight: 9.9990 chunk 895 optimal weight: 3.9990 chunk 954 optimal weight: 1.9990 chunk 574 optimal weight: 8.9990 chunk 415 optimal weight: 10.0000 chunk 749 optimal weight: 10.0000 chunk 292 optimal weight: 0.9990 chunk 862 optimal weight: 9.9990 chunk 903 optimal weight: 0.7980 chunk 951 optimal weight: 9.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8 179 GLN B 117 GLN C 32 ASN C 42 ASN ** C 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 GLN ** D 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 156 ASN D 195 GLN E 127 ASN F 20 ASN F 104 ASN K 3 GLN M 97 GLN P 3 ASN Q 52 GLN Q 72 ASN R 86 GLN T 28 ASN ** U 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 49 ASN ** V 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 75 GLN ** V 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 76 ASN Y 15 ASN Y 20 ASN Y 39 GLN a 61 ASN d 29 GLN g 42 ASN h 100 GLN h 139 GLN i 40 GLN ** i 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 116 GLN j 73 ASN ** k 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 50 GLN n 75 GLN o 20 GLN p 24 HIS p 28 ASN p 29 ASN p 64 GLN p 81 ASN s 60 GLN s 66 GLN t 35 GLN t 40 GLN u 26 ASN w 31 ASN w 54 GLN y 3 ASN Total number of N/Q/H flips: 47 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.1216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 162437 Z= 0.259 Angle : 0.633 19.446 242695 Z= 0.339 Chirality : 0.037 0.331 30890 Planarity : 0.006 0.134 13216 Dihedral : 23.809 178.142 80453 Min Nonbonded Distance : 1.053 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.41 % Favored : 96.57 % Rotamer: Outliers : 3.69 % Allowed : 21.76 % Favored : 74.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.11), residues: 6068 helix: 1.54 (0.11), residues: 2127 sheet: -0.54 (0.15), residues: 1128 loop : -0.43 (0.11), residues: 2813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP l 103 HIS 0.007 0.001 HIS w 74 PHE 0.021 0.002 PHE g 90 TYR 0.042 0.002 TYR g 213 ARG 0.013 0.001 ARG J 96 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12136 Ramachandran restraints generated. 6068 Oldfield, 0 Emsley, 6068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12136 Ramachandran restraints generated. 6068 Oldfield, 0 Emsley, 6068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1827 residues out of total 5041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 1641 time to evaluate : 6.557 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: 8 93 LEU cc_start: 0.7919 (OUTLIER) cc_final: 0.7679 (mm) REVERT: B 167 ARG cc_start: 0.7984 (ttp80) cc_final: 0.7749 (ttp80) REVERT: C 33 ARG cc_start: 0.8907 (OUTLIER) cc_final: 0.8346 (ptt-90) REVERT: C 105 LYS cc_start: 0.8732 (mmtm) cc_final: 0.8377 (mmtm) REVERT: D 1 MET cc_start: 0.7117 (ptp) cc_final: 0.6639 (ptp) REVERT: D 16 GLU cc_start: 0.7580 (tp30) cc_final: 0.7185 (tp30) REVERT: D 111 GLU cc_start: 0.8565 (tp30) cc_final: 0.7991 (tp30) REVERT: D 141 MET cc_start: 0.8696 (mtp) cc_final: 0.8243 (mtp) REVERT: E 38 MET cc_start: 0.8401 (mtm) cc_final: 0.8100 (ttm) REVERT: E 112 ARG cc_start: 0.7840 (ttp80) cc_final: 0.7512 (ttm-80) REVERT: F 6 LYS cc_start: 0.8067 (OUTLIER) cc_final: 0.7784 (mptt) REVERT: G 129 GLU cc_start: 0.5177 (pm20) cc_final: 0.4927 (pm20) REVERT: H 38 MET cc_start: 0.2121 (mmt) cc_final: 0.1430 (mpp) REVERT: H 86 MET cc_start: 0.2688 (mmt) cc_final: 0.2007 (mmt) REVERT: I 35 MET cc_start: 0.4914 (OUTLIER) cc_final: 0.3797 (pp-130) REVERT: J 34 ARG cc_start: 0.8381 (ttp80) cc_final: 0.8047 (ttt90) REVERT: K 17 ARG cc_start: 0.7757 (mmm-85) cc_final: 0.7496 (mmm160) REVERT: K 90 ASN cc_start: 0.8300 (OUTLIER) cc_final: 0.8020 (m110) REVERT: M 5 LYS cc_start: 0.8857 (OUTLIER) cc_final: 0.8644 (mtmm) REVERT: M 6 ARG cc_start: 0.7878 (OUTLIER) cc_final: 0.7267 (ptm160) REVERT: M 12 MET cc_start: 0.7979 (OUTLIER) cc_final: 0.7607 (ttm) REVERT: P 71 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.8020 (mt-10) REVERT: Q 18 LEU cc_start: 0.9205 (OUTLIER) cc_final: 0.8928 (mm) REVERT: Q 75 SER cc_start: 0.9100 (p) cc_final: 0.8874 (p) REVERT: R 6 GLN cc_start: 0.7947 (OUTLIER) cc_final: 0.7364 (tm-30) REVERT: R 97 LYS cc_start: 0.8817 (OUTLIER) cc_final: 0.8577 (ttmt) REVERT: S 98 LYS cc_start: 0.9106 (OUTLIER) cc_final: 0.8711 (mttm) REVERT: T 9 LYS cc_start: 0.8893 (OUTLIER) cc_final: 0.8536 (mmtp) REVERT: T 33 LYS cc_start: 0.8620 (mttp) cc_final: 0.8389 (mttp) REVERT: W 68 LYS cc_start: 0.9047 (OUTLIER) cc_final: 0.8613 (ttmm) REVERT: X 11 ARG cc_start: 0.8698 (OUTLIER) cc_final: 0.8438 (mtp85) REVERT: Y 31 GLN cc_start: 0.8403 (mt0) cc_final: 0.8023 (mt0) REVERT: d 1 MET cc_start: 0.7806 (OUTLIER) cc_final: 0.7506 (mtm) REVERT: g 10 LEU cc_start: 0.8237 (mt) cc_final: 0.8001 (tm) REVERT: g 27 MET cc_start: 0.8566 (mmm) cc_final: 0.8260 (mmm) REVERT: g 139 ARG cc_start: 0.7419 (mmt90) cc_final: 0.7199 (mtt-85) REVERT: g 173 ILE cc_start: 0.9110 (OUTLIER) cc_final: 0.8799 (mm) REVERT: i 47 ARG cc_start: 0.6786 (ptp90) cc_final: 0.6455 (mtt90) REVERT: i 65 TYR cc_start: 0.9240 (m-80) cc_final: 0.8758 (m-80) REVERT: i 78 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7645 (tm-30) REVERT: i 156 LYS cc_start: 0.8201 (OUTLIER) cc_final: 0.7768 (ttmt) REVERT: k 2 ARG cc_start: 0.7732 (OUTLIER) cc_final: 0.7461 (ttp-170) REVERT: k 44 ARG cc_start: 0.8301 (OUTLIER) cc_final: 0.8073 (tpp80) REVERT: k 54 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8263 (pp) REVERT: l 139 GLU cc_start: 0.7586 (pt0) cc_final: 0.7342 (pt0) REVERT: l 143 ARG cc_start: 0.7449 (mtm-85) cc_final: 0.7095 (mtm-85) REVERT: m 60 GLU cc_start: 0.7524 (OUTLIER) cc_final: 0.6903 (tp30) REVERT: n 27 LYS cc_start: 0.8760 (ptpp) cc_final: 0.8476 (ptpp) REVERT: o 5 ARG cc_start: 0.6351 (tmm-80) cc_final: 0.5962 (tmm-80) REVERT: o 7 ARG cc_start: 0.8186 (OUTLIER) cc_final: 0.6582 (mpt-90) REVERT: p 15 GLN cc_start: 0.7343 (OUTLIER) cc_final: 0.7129 (tt0) REVERT: p 105 PHE cc_start: 0.8832 (m-80) cc_final: 0.8555 (m-80) REVERT: s 92 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7104 (mt-10) REVERT: t 63 ARG cc_start: 0.9411 (ttp-170) cc_final: 0.9070 (ttp-170) REVERT: w 61 ARG cc_start: 0.8773 (OUTLIER) cc_final: 0.7979 (mpt180) REVERT: x 56 GLN cc_start: 0.8242 (OUTLIER) cc_final: 0.7963 (pm20) REVERT: y 82 GLN cc_start: 0.8181 (OUTLIER) cc_final: 0.7225 (mp10) REVERT: z 4 ILE cc_start: 0.7024 (OUTLIER) cc_final: 0.6578 (mt) outliers start: 186 outliers final: 113 residues processed: 1700 average time/residue: 2.3187 time to fit residues: 5590.9860 Evaluate side-chains 1772 residues out of total 5041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 1628 time to evaluate : 6.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 8 residue 48 SER Chi-restraints excluded: chain 8 residue 93 LEU Chi-restraints excluded: chain 8 residue 109 ILE Chi-restraints excluded: chain 8 residue 161 ILE Chi-restraints excluded: chain 8 residue 201 PHE Chi-restraints excluded: chain 8 residue 202 ILE Chi-restraints excluded: chain B residue 125 LYS Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 194 GLU Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain C residue 33 ARG Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 139 LYS Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 198 GLU Chi-restraints excluded: chain E residue 32 GLU Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 142 ASP Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain F residue 6 LYS Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain H residue 87 GLU Chi-restraints excluded: chain H residue 116 GLU Chi-restraints excluded: chain H residue 128 THR Chi-restraints excluded: chain I residue 35 MET Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 90 ASN Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain M residue 5 LYS Chi-restraints excluded: chain M residue 6 ARG Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain M residue 95 LEU Chi-restraints excluded: chain M residue 126 ILE Chi-restraints excluded: chain M residue 135 VAL Chi-restraints excluded: chain N residue 89 SER Chi-restraints excluded: chain O residue 24 THR Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain O residue 68 LYS Chi-restraints excluded: chain P residue 71 GLU Chi-restraints excluded: chain P residue 110 ILE Chi-restraints excluded: chain P residue 111 LYS Chi-restraints excluded: chain Q residue 18 LEU Chi-restraints excluded: chain R residue 6 GLN Chi-restraints excluded: chain R residue 37 GLU Chi-restraints excluded: chain R residue 48 LYS Chi-restraints excluded: chain R residue 97 LYS Chi-restraints excluded: chain S residue 96 ILE Chi-restraints excluded: chain S residue 98 LYS Chi-restraints excluded: chain T residue 9 LYS Chi-restraints excluded: chain T residue 10 VAL Chi-restraints excluded: chain T residue 16 VAL Chi-restraints excluded: chain T residue 27 SER Chi-restraints excluded: chain T residue 32 LEU Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain W residue 32 LEU Chi-restraints excluded: chain W residue 68 LYS Chi-restraints excluded: chain X residue 2 SER Chi-restraints excluded: chain X residue 11 ARG Chi-restraints excluded: chain X residue 43 GLU Chi-restraints excluded: chain X residue 71 LEU Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain Y residue 24 GLU Chi-restraints excluded: chain Z residue 21 LYS Chi-restraints excluded: chain Z residue 39 GLU Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain e residue 32 ILE Chi-restraints excluded: chain f residue 8 LYS Chi-restraints excluded: chain g residue 35 ARG Chi-restraints excluded: chain g residue 110 SER Chi-restraints excluded: chain g residue 161 LEU Chi-restraints excluded: chain g residue 167 ASP Chi-restraints excluded: chain g residue 173 ILE Chi-restraints excluded: chain g residue 199 VAL Chi-restraints excluded: chain h residue 53 SER Chi-restraints excluded: chain h residue 185 ASN Chi-restraints excluded: chain h residue 187 SER Chi-restraints excluded: chain i residue 64 ILE Chi-restraints excluded: chain i residue 78 GLU Chi-restraints excluded: chain i residue 143 VAL Chi-restraints excluded: chain i residue 156 LYS Chi-restraints excluded: chain j residue 61 GLN Chi-restraints excluded: chain j residue 114 VAL Chi-restraints excluded: chain j residue 164 ILE Chi-restraints excluded: chain k residue 2 ARG Chi-restraints excluded: chain k residue 44 ARG Chi-restraints excluded: chain k residue 52 ASN Chi-restraints excluded: chain k residue 54 LEU Chi-restraints excluded: chain k residue 92 THR Chi-restraints excluded: chain l residue 23 LEU Chi-restraints excluded: chain l residue 133 THR Chi-restraints excluded: chain m residue 11 LEU Chi-restraints excluded: chain m residue 60 GLU Chi-restraints excluded: chain m residue 74 SER Chi-restraints excluded: chain n residue 15 SER Chi-restraints excluded: chain n residue 85 ARG Chi-restraints excluded: chain o residue 7 ARG Chi-restraints excluded: chain o residue 17 LEU Chi-restraints excluded: chain o residue 80 THR Chi-restraints excluded: chain p residue 15 GLN Chi-restraints excluded: chain p residue 35 THR Chi-restraints excluded: chain p residue 79 ILE Chi-restraints excluded: chain q residue 30 LYS Chi-restraints excluded: chain q residue 65 SER Chi-restraints excluded: chain q residue 112 GLN Chi-restraints excluded: chain r residue 25 VAL Chi-restraints excluded: chain r residue 30 SER Chi-restraints excluded: chain r residue 113 ARG Chi-restraints excluded: chain s residue 47 LYS Chi-restraints excluded: chain s residue 55 SER Chi-restraints excluded: chain s residue 92 GLU Chi-restraints excluded: chain s residue 100 SER Chi-restraints excluded: chain t residue 75 VAL Chi-restraints excluded: chain u residue 66 THR Chi-restraints excluded: chain v residue 13 VAL Chi-restraints excluded: chain v residue 18 GLU Chi-restraints excluded: chain v residue 67 LEU Chi-restraints excluded: chain w residue 42 SER Chi-restraints excluded: chain w residue 43 ARG Chi-restraints excluded: chain w residue 61 ARG Chi-restraints excluded: chain x residue 21 LYS Chi-restraints excluded: chain x residue 56 GLN Chi-restraints excluded: chain x residue 64 ASP Chi-restraints excluded: chain x residue 79 THR Chi-restraints excluded: chain y residue 64 LYS Chi-restraints excluded: chain y residue 82 GLN Chi-restraints excluded: chain z residue 4 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1063 random chunks: chunk 626 optimal weight: 0.0980 chunk 1009 optimal weight: 3.9990 chunk 616 optimal weight: 0.0470 chunk 478 optimal weight: 10.0000 chunk 701 optimal weight: 5.9990 chunk 1059 optimal weight: 10.0000 chunk 974 optimal weight: 0.9990 chunk 843 optimal weight: 4.9990 chunk 87 optimal weight: 10.0000 chunk 651 optimal weight: 9.9990 chunk 517 optimal weight: 10.0000 overall best weight: 2.0284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8 179 GLN B 117 GLN C 42 ASN C 94 GLN D 41 GLN ** D 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 156 ASN D 195 GLN E 127 ASN P 3 ASN Q 52 GLN S 40 ASN T 28 ASN U 69 ASN ** U 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 49 ASN ** V 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 75 GLN ** V 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 76 ASN Y 15 ASN Y 20 ASN Y 39 GLN a 61 ASN d 29 GLN g 24 ASN g 42 ASN h 8 ASN h 100 GLN h 123 GLN h 139 GLN i 40 GLN ** i 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 116 GLN i 152 GLN j 73 ASN j 132 ASN ** k 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 50 GLN n 75 GLN n 126 GLN o 20 GLN p 24 HIS p 28 ASN s 60 GLN s 66 GLN t 35 GLN t 40 GLN u 26 ASN w 31 ASN w 54 GLN y 3 ASN ** y 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.1379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 162437 Z= 0.196 Angle : 0.610 19.008 242695 Z= 0.328 Chirality : 0.035 0.345 30890 Planarity : 0.006 0.131 13216 Dihedral : 23.762 179.214 80453 Min Nonbonded Distance : 1.092 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.38 % Favored : 96.61 % Rotamer: Outliers : 3.07 % Allowed : 22.77 % Favored : 74.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.11), residues: 6068 helix: 1.65 (0.11), residues: 2123 sheet: -0.51 (0.15), residues: 1133 loop : -0.39 (0.11), residues: 2812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP l 103 HIS 0.006 0.001 HIS w 74 PHE 0.021 0.002 PHE g 90 TYR 0.042 0.002 TYR g 213 ARG 0.018 0.001 ARG J 96 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12136 Ramachandran restraints generated. 6068 Oldfield, 0 Emsley, 6068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12136 Ramachandran restraints generated. 6068 Oldfield, 0 Emsley, 6068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1805 residues out of total 5041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 1650 time to evaluate : 6.442 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: 8 93 LEU cc_start: 0.7906 (OUTLIER) cc_final: 0.7620 (mm) REVERT: 8 201 PHE cc_start: 0.8412 (OUTLIER) cc_final: 0.7926 (t80) REVERT: B 167 ARG cc_start: 0.7964 (ttp80) cc_final: 0.7734 (ttp80) REVERT: C 33 ARG cc_start: 0.8899 (OUTLIER) cc_final: 0.8375 (ptt-90) REVERT: D 1 MET cc_start: 0.7037 (ptp) cc_final: 0.6588 (ptp) REVERT: D 16 GLU cc_start: 0.7534 (tp30) cc_final: 0.7143 (tp30) REVERT: D 111 GLU cc_start: 0.8588 (tp30) cc_final: 0.7933 (tp30) REVERT: D 141 MET cc_start: 0.8677 (mtp) cc_final: 0.8259 (mtp) REVERT: E 38 MET cc_start: 0.8403 (mtm) cc_final: 0.8107 (ttm) REVERT: E 112 ARG cc_start: 0.7841 (ttp80) cc_final: 0.7483 (ttm-80) REVERT: F 6 LYS cc_start: 0.8070 (OUTLIER) cc_final: 0.7833 (mptt) REVERT: G 129 GLU cc_start: 0.5040 (pm20) cc_final: 0.4733 (pm20) REVERT: H 38 MET cc_start: 0.2120 (mmt) cc_final: 0.1424 (mpp) REVERT: H 86 MET cc_start: 0.2806 (mmt) cc_final: 0.2062 (mmt) REVERT: I 35 MET cc_start: 0.4900 (OUTLIER) cc_final: 0.3805 (pp-130) REVERT: I 124 MET cc_start: 0.3275 (tmm) cc_final: 0.2930 (tpt) REVERT: J 34 ARG cc_start: 0.8369 (ttp80) cc_final: 0.8039 (ttt90) REVERT: M 6 ARG cc_start: 0.7860 (OUTLIER) cc_final: 0.7264 (ptm160) REVERT: M 12 MET cc_start: 0.7908 (OUTLIER) cc_final: 0.7598 (ttm) REVERT: P 71 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7986 (mt-10) REVERT: Q 18 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8939 (mm) REVERT: Q 75 SER cc_start: 0.9053 (p) cc_final: 0.8822 (p) REVERT: R 6 GLN cc_start: 0.7927 (OUTLIER) cc_final: 0.7359 (tm-30) REVERT: R 97 LYS cc_start: 0.8806 (OUTLIER) cc_final: 0.8584 (ttmt) REVERT: S 98 LYS cc_start: 0.9092 (OUTLIER) cc_final: 0.8672 (mttm) REVERT: T 9 LYS cc_start: 0.8881 (OUTLIER) cc_final: 0.8521 (mmtp) REVERT: T 33 LYS cc_start: 0.8586 (mttp) cc_final: 0.8356 (mttp) REVERT: W 68 LYS cc_start: 0.9037 (OUTLIER) cc_final: 0.8597 (ttmm) REVERT: X 11 ARG cc_start: 0.8655 (OUTLIER) cc_final: 0.8411 (mtp85) REVERT: Y 31 GLN cc_start: 0.8384 (mt0) cc_final: 0.7965 (mt0) REVERT: d 1 MET cc_start: 0.7822 (OUTLIER) cc_final: 0.7526 (mtm) REVERT: g 10 LEU cc_start: 0.8230 (mt) cc_final: 0.7992 (tm) REVERT: g 27 MET cc_start: 0.8569 (mmm) cc_final: 0.8265 (mmm) REVERT: g 139 ARG cc_start: 0.7415 (mmt90) cc_final: 0.7190 (mtt-85) REVERT: g 173 ILE cc_start: 0.9101 (OUTLIER) cc_final: 0.8773 (mm) REVERT: i 47 ARG cc_start: 0.6751 (ptp90) cc_final: 0.6412 (mtt90) REVERT: i 78 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7564 (tm-30) REVERT: i 156 LYS cc_start: 0.8180 (OUTLIER) cc_final: 0.7769 (ttmt) REVERT: k 44 ARG cc_start: 0.8254 (OUTLIER) cc_final: 0.8025 (mpt-90) REVERT: k 54 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8251 (pp) REVERT: l 58 GLU cc_start: 0.6974 (mm-30) cc_final: 0.6605 (mm-30) REVERT: l 139 GLU cc_start: 0.7566 (pt0) cc_final: 0.7275 (pt0) REVERT: l 143 ARG cc_start: 0.7471 (mtm-85) cc_final: 0.7120 (mtm-85) REVERT: m 60 GLU cc_start: 0.7510 (OUTLIER) cc_final: 0.7115 (tp30) REVERT: n 27 LYS cc_start: 0.8733 (ptpp) cc_final: 0.8460 (ptpp) REVERT: n 88 MET cc_start: 0.7596 (mtm) cc_final: 0.7374 (mtm) REVERT: o 5 ARG cc_start: 0.6332 (tmm-80) cc_final: 0.5968 (tmm-80) REVERT: o 7 ARG cc_start: 0.8147 (OUTLIER) cc_final: 0.6560 (mpt-90) REVERT: p 15 GLN cc_start: 0.7354 (OUTLIER) cc_final: 0.7153 (tt0) REVERT: p 20 VAL cc_start: 0.8861 (t) cc_final: 0.8386 (m) REVERT: p 105 PHE cc_start: 0.8819 (m-80) cc_final: 0.8535 (m-80) REVERT: s 92 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7067 (mt-10) REVERT: t 63 ARG cc_start: 0.9403 (ttp-170) cc_final: 0.9080 (ttp-170) REVERT: w 61 ARG cc_start: 0.8754 (OUTLIER) cc_final: 0.7918 (mpt180) REVERT: x 56 GLN cc_start: 0.8221 (OUTLIER) cc_final: 0.7947 (pm20) REVERT: y 82 GLN cc_start: 0.8209 (OUTLIER) cc_final: 0.7231 (mp10) outliers start: 155 outliers final: 103 residues processed: 1695 average time/residue: 2.2910 time to fit residues: 5513.3127 Evaluate side-chains 1766 residues out of total 5041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 1635 time to evaluate : 6.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 8 residue 48 SER Chi-restraints excluded: chain 8 residue 93 LEU Chi-restraints excluded: chain 8 residue 109 ILE Chi-restraints excluded: chain 8 residue 161 ILE Chi-restraints excluded: chain 8 residue 201 PHE Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 194 GLU Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain C residue 33 ARG Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 139 LYS Chi-restraints excluded: chain D residue 198 GLU Chi-restraints excluded: chain E residue 32 GLU Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 142 ASP Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain F residue 6 LYS Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain H residue 3 LEU Chi-restraints excluded: chain H residue 87 GLU Chi-restraints excluded: chain H residue 116 GLU Chi-restraints excluded: chain H residue 128 THR Chi-restraints excluded: chain I residue 35 MET Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain M residue 6 ARG Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain M residue 95 LEU Chi-restraints excluded: chain M residue 126 ILE Chi-restraints excluded: chain M residue 135 VAL Chi-restraints excluded: chain N residue 89 SER Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain O residue 68 LYS Chi-restraints excluded: chain P residue 6 LYS Chi-restraints excluded: chain P residue 71 GLU Chi-restraints excluded: chain P residue 110 ILE Chi-restraints excluded: chain P residue 111 LYS Chi-restraints excluded: chain Q residue 18 LEU Chi-restraints excluded: chain R residue 6 GLN Chi-restraints excluded: chain R residue 37 GLU Chi-restraints excluded: chain R residue 48 LYS Chi-restraints excluded: chain R residue 97 LYS Chi-restraints excluded: chain S residue 96 ILE Chi-restraints excluded: chain S residue 98 LYS Chi-restraints excluded: chain T residue 9 LYS Chi-restraints excluded: chain T residue 10 VAL Chi-restraints excluded: chain T residue 16 VAL Chi-restraints excluded: chain T residue 27 SER Chi-restraints excluded: chain T residue 32 LEU Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain V residue 8 VAL Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain W residue 32 LEU Chi-restraints excluded: chain W residue 68 LYS Chi-restraints excluded: chain X residue 2 SER Chi-restraints excluded: chain X residue 11 ARG Chi-restraints excluded: chain X residue 43 GLU Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain Y residue 24 GLU Chi-restraints excluded: chain Z residue 21 LYS Chi-restraints excluded: chain Z residue 39 GLU Chi-restraints excluded: chain b residue 46 ASP Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain e residue 32 ILE Chi-restraints excluded: chain f residue 8 LYS Chi-restraints excluded: chain g residue 35 ARG Chi-restraints excluded: chain g residue 161 LEU Chi-restraints excluded: chain g residue 167 ASP Chi-restraints excluded: chain g residue 173 ILE Chi-restraints excluded: chain g residue 199 VAL Chi-restraints excluded: chain h residue 53 SER Chi-restraints excluded: chain h residue 185 ASN Chi-restraints excluded: chain h residue 187 SER Chi-restraints excluded: chain i residue 64 ILE Chi-restraints excluded: chain i residue 78 GLU Chi-restraints excluded: chain i residue 143 VAL Chi-restraints excluded: chain i residue 156 LYS Chi-restraints excluded: chain j residue 114 VAL Chi-restraints excluded: chain j residue 164 ILE Chi-restraints excluded: chain k residue 44 ARG Chi-restraints excluded: chain k residue 54 LEU Chi-restraints excluded: chain k residue 92 THR Chi-restraints excluded: chain l residue 23 LEU Chi-restraints excluded: chain l residue 133 THR Chi-restraints excluded: chain m residue 11 LEU Chi-restraints excluded: chain m residue 60 GLU Chi-restraints excluded: chain n residue 15 SER Chi-restraints excluded: chain n residue 85 ARG Chi-restraints excluded: chain o residue 7 ARG Chi-restraints excluded: chain o residue 17 LEU Chi-restraints excluded: chain o residue 80 THR Chi-restraints excluded: chain p residue 15 GLN Chi-restraints excluded: chain p residue 35 THR Chi-restraints excluded: chain p residue 79 ILE Chi-restraints excluded: chain q residue 30 LYS Chi-restraints excluded: chain q residue 112 GLN Chi-restraints excluded: chain r residue 25 VAL Chi-restraints excluded: chain r residue 30 SER Chi-restraints excluded: chain r residue 113 ARG Chi-restraints excluded: chain s residue 47 LYS Chi-restraints excluded: chain s residue 55 SER Chi-restraints excluded: chain s residue 92 GLU Chi-restraints excluded: chain s residue 100 SER Chi-restraints excluded: chain t residue 75 VAL Chi-restraints excluded: chain v residue 13 VAL Chi-restraints excluded: chain v residue 67 LEU Chi-restraints excluded: chain w residue 42 SER Chi-restraints excluded: chain w residue 43 ARG Chi-restraints excluded: chain w residue 61 ARG Chi-restraints excluded: chain x residue 21 LYS Chi-restraints excluded: chain x residue 56 GLN Chi-restraints excluded: chain x residue 58 VAL Chi-restraints excluded: chain x residue 64 ASP Chi-restraints excluded: chain x residue 79 THR Chi-restraints excluded: chain y residue 64 LYS Chi-restraints excluded: chain y residue 82 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1063 random chunks: chunk 669 optimal weight: 1.9990 chunk 898 optimal weight: 5.9990 chunk 258 optimal weight: 10.0000 chunk 777 optimal weight: 0.9980 chunk 124 optimal weight: 8.9990 chunk 234 optimal weight: 10.0000 chunk 844 optimal weight: 6.9990 chunk 353 optimal weight: 10.0000 chunk 867 optimal weight: 7.9990 chunk 106 optimal weight: 50.0000 chunk 155 optimal weight: 10.0000 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 42 ASN C 94 GLN D 41 GLN D 156 ASN D 195 GLN E 127 ASN F 20 ASN P 3 ASN Q 52 GLN T 28 ASN T 59 ASN U 69 ASN U 74 ASN V 49 ASN V 51 GLN V 75 GLN ** V 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 76 ASN Y 15 ASN Y 20 ASN Y 39 GLN a 61 ASN d 29 GLN g 42 ASN h 100 GLN h 139 GLN i 40 GLN i 59 GLN i 116 GLN i 152 GLN j 73 ASN j 132 ASN ** k 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 5 GLN n 50 GLN n 75 GLN n 126 GLN o 20 GLN p 24 HIS p 28 ASN s 60 GLN s 66 GLN t 35 GLN t 40 GLN u 26 ASN w 31 ASN w 54 GLN y 3 ASN ** y 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.128660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.086594 restraints weight = 179540.538| |-----------------------------------------------------------------------------| r_work (start): 0.2813 rms_B_bonded: 0.78 r_work: 0.2703 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.2610 rms_B_bonded: 2.39 restraints_weight: 0.2500 r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2605 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2605 r_free = 0.2605 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2604 r_free = 0.2604 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2604 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8860 moved from start: 0.1199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.098 162437 Z= 0.365 Angle : 0.669 19.616 242695 Z= 0.355 Chirality : 0.040 0.398 30890 Planarity : 0.006 0.141 13216 Dihedral : 23.737 179.424 80453 Min Nonbonded Distance : 1.021 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.51 % Favored : 96.47 % Rotamer: Outliers : 3.39 % Allowed : 22.83 % Favored : 73.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.11), residues: 6068 helix: 1.54 (0.11), residues: 2134 sheet: -0.53 (0.15), residues: 1126 loop : -0.42 (0.11), residues: 2808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP l 103 HIS 0.008 0.001 HIS w 74 PHE 0.022 0.002 PHE G 91 TYR 0.038 0.002 TYR g 213 ARG 0.010 0.001 ARG p 98 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 70879.86 seconds wall clock time: 1221 minutes 23.80 seconds (73283.80 seconds total)