Starting phenix.real_space_refine on Mon Mar 25 21:07:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u4i_8505/03_2024/5u4i_8505_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u4i_8505/03_2024/5u4i_8505.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u4i_8505/03_2024/5u4i_8505_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u4i_8505/03_2024/5u4i_8505_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u4i_8505/03_2024/5u4i_8505_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u4i_8505/03_2024/5u4i_8505.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u4i_8505/03_2024/5u4i_8505.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u4i_8505/03_2024/5u4i_8505_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u4i_8505/03_2024/5u4i_8505_updated.pdb" } resolution = 3.5 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 1 6.06 5 P 4713 5.49 5 Mg 124 5.21 5 S 157 5.16 5 C 75286 2.51 5 N 27806 2.21 5 O 41408 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ARG 52": "NH1" <-> "NH2" Residue "C ARG 63": "NH1" <-> "NH2" Residue "C ASP 72": "OD1" <-> "OD2" Residue "C ARG 80": "NH1" <-> "NH2" Residue "C TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 100": "OE1" <-> "OE2" Residue "C ASP 114": "OD1" <-> "OD2" Residue "C ARG 133": "NH1" <-> "NH2" Residue "C GLU 145": "OE1" <-> "OE2" Residue "C ARG 167": "NH1" <-> "NH2" Residue "C TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 177": "NH1" <-> "NH2" Residue "C ARG 182": "NH1" <-> "NH2" Residue "C ARG 189": "NH1" <-> "NH2" Residue "C GLU 194": "OE1" <-> "OE2" Residue "C ARG 212": "NH1" <-> "NH2" Residue "C GLU 236": "OE1" <-> "OE2" Residue "D ARG 13": "NH1" <-> "NH2" Residue "D GLU 17": "OE1" <-> "OE2" Residue "D GLU 28": "OE1" <-> "OE2" Residue "D GLU 30": "OE1" <-> "OE2" Residue "D ARG 33": "NH1" <-> "NH2" Residue "D ASP 43": "OD1" <-> "OD2" Residue "D ARG 59": "NH1" <-> "NH2" Residue "D GLU 64": "OE1" <-> "OE2" Residue "D GLU 74": "OE1" <-> "OE2" Residue "D ARG 77": "NH1" <-> "NH2" Residue "D GLU 81": "OE1" <-> "OE2" Residue "D ARG 83": "NH1" <-> "NH2" Residue "D GLU 88": "OE1" <-> "OE2" Residue "D GLU 89": "OE1" <-> "OE2" Residue "D ARG 169": "NH1" <-> "NH2" Residue "D GLU 183": "OE1" <-> "OE2" Residue "D ARG 184": "NH1" <-> "NH2" Residue "E GLU 2": "OE1" <-> "OE2" Residue "E ARG 21": "NH1" <-> "NH2" Residue "E ASP 22": "OD1" <-> "OD2" Residue "E ARG 44": "NH1" <-> "NH2" Residue "E ARG 49": "NH1" <-> "NH2" Residue "E ARG 61": "NH1" <-> "NH2" Residue "E ARG 88": "NH1" <-> "NH2" Residue "E ARG 102": "NH1" <-> "NH2" Residue "E GLU 122": "OE1" <-> "OE2" Residue "E GLU 152": "OE1" <-> "OE2" Residue "E GLU 155": "OE1" <-> "OE2" Residue "E ARG 162": "NH1" <-> "NH2" Residue "E ARG 170": "NH1" <-> "NH2" Residue "F ASP 6": "OD1" <-> "OD2" Residue "F GLU 11": "OE1" <-> "OE2" Residue "F TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 32": "OE1" <-> "OE2" Residue "F ARG 71": "NH1" <-> "NH2" Residue "F ARG 92": "NH1" <-> "NH2" Residue "F GLU 94": "OE1" <-> "OE2" Residue "F GLU 98": "OE1" <-> "OE2" Residue "F ARG 102": "NH1" <-> "NH2" Residue "F ARG 110": "NH1" <-> "NH2" Residue "F ARG 112": "NH1" <-> "NH2" Residue "F ARG 115": "NH1" <-> "NH2" Residue "F ARG 133": "NH1" <-> "NH2" Residue "F GLU 134": "OE1" <-> "OE2" Residue "F GLU 140": "OE1" <-> "OE2" Residue "F ASP 147": "OD1" <-> "OD2" Residue "F ARG 148": "NH1" <-> "NH2" Residue "F ASP 163": "OD1" <-> "OD2" Residue "F GLU 164": "OE1" <-> "OE2" Residue "F GLU 165": "OE1" <-> "OE2" Residue "F PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 178": "NH1" <-> "NH2" Residue "G ARG 3": "NH1" <-> "NH2" Residue "G GLU 32": "OE1" <-> "OE2" Residue "G ASP 114": "OD1" <-> "OD2" Residue "G GLU 124": "OE1" <-> "OE2" Residue "G GLU 130": "OE1" <-> "OE2" Residue "G ARG 153": "NH1" <-> "NH2" Residue "G ARG 163": "NH1" <-> "NH2" Residue "G ARG 170": "NH1" <-> "NH2" Residue "G GLU 173": "OE1" <-> "OE2" Residue "H GLU 53": "OE1" <-> "OE2" Residue "H GLU 137": "OE1" <-> "OE2" Residue "J TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 95": "OD1" <-> "OD2" Residue "J GLU 122": "OE1" <-> "OE2" Residue "K GLU 9": "OE1" <-> "OE2" Residue "K ARG 13": "NH1" <-> "NH2" Residue "K ASP 14": "OD1" <-> "OD2" Residue "K TYR 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 31": "OE1" <-> "OE2" Residue "K ARG 37": "NH1" <-> "NH2" Residue "K TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 91": "OE1" <-> "OE2" Residue "K ARG 96": "NH1" <-> "NH2" Residue "K GLU 102": "OE1" <-> "OE2" Residue "K ARG 120": "NH1" <-> "NH2" Residue "K ASP 141": "OD1" <-> "OD2" Residue "L ARG 17": "NH1" <-> "NH2" Residue "L ARG 18": "NH1" <-> "NH2" Residue "L ASP 37": "OD1" <-> "OD2" Residue "L ASP 56": "OD1" <-> "OD2" Residue "L GLU 92": "OE1" <-> "OE2" Residue "M GLU 10": "OE1" <-> "OE2" Residue "M ARG 21": "NH1" <-> "NH2" Residue "M ARG 33": "NH1" <-> "NH2" Residue "M ARG 41": "NH1" <-> "NH2" Residue "M ARG 47": "NH1" <-> "NH2" Residue "M GLU 51": "OE1" <-> "OE2" Residue "M ARG 60": "NH1" <-> "NH2" Residue "M GLU 76": "OE1" <-> "OE2" Residue "M ARG 78": "NH1" <-> "NH2" Residue "M ASP 91": "OD1" <-> "OD2" Residue "M GLU 106": "OE1" <-> "OE2" Residue "M ARG 126": "NH1" <-> "NH2" Residue "N ARG 10": "NH1" <-> "NH2" Residue "N ARG 18": "NH1" <-> "NH2" Residue "N ARG 40": "NH1" <-> "NH2" Residue "N ARG 44": "NH1" <-> "NH2" Residue "N GLU 47": "OE1" <-> "OE2" Residue "N ARG 50": "NH1" <-> "NH2" Residue "N ARG 55": "NH1" <-> "NH2" Residue "N GLU 75": "OE1" <-> "OE2" Residue "N GLU 90": "OE1" <-> "OE2" Residue "N GLU 104": "OE1" <-> "OE2" Residue "N ARG 114": "NH1" <-> "NH2" Residue "O ARG 8": "NH1" <-> "NH2" Residue "O ARG 12": "NH1" <-> "NH2" Residue "O ARG 17": "NH1" <-> "NH2" Residue "O ARG 22": "NH1" <-> "NH2" Residue "O GLU 32": "OE1" <-> "OE2" Residue "O GLU 43": "OE1" <-> "OE2" Residue "O ARG 46": "NH1" <-> "NH2" Residue "O GLU 49": "OE1" <-> "OE2" Residue "O ARG 63": "NH1" <-> "NH2" Residue "O ARG 64": "NH1" <-> "NH2" Residue "O ARG 69": "NH1" <-> "NH2" Residue "O GLU 74": "OE1" <-> "OE2" Residue "O PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 82": "OE1" <-> "OE2" Residue "O ARG 96": "NH1" <-> "NH2" Residue "O PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 114": "OE1" <-> "OE2" Residue "O ARG 118": "NH1" <-> "NH2" Residue "O GLU 120": "OE1" <-> "OE2" Residue "P ARG 10": "NH1" <-> "NH2" Residue "P ARG 16": "NH1" <-> "NH2" Residue "P ARG 25": "NH1" <-> "NH2" Residue "P TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 46": "OE1" <-> "OE2" Residue "P GLU 55": "OE1" <-> "OE2" Residue "P ARG 81": "NH1" <-> "NH2" Residue "P ARG 94": "NH1" <-> "NH2" Residue "P ARG 102": "NH1" <-> "NH2" Residue "P ARG 111": "NH1" <-> "NH2" Residue "Q GLU 11": "OE1" <-> "OE2" Residue "Q ARG 21": "NH1" <-> "NH2" Residue "Q GLU 27": "OE1" <-> "OE2" Residue "Q ARG 39": "NH1" <-> "NH2" Residue "Q GLU 44": "OE1" <-> "OE2" Residue "Q ARG 62": "NH1" <-> "NH2" Residue "Q GLU 68": "OE1" <-> "OE2" Residue "Q GLU 71": "OE1" <-> "OE2" Residue "Q ARG 89": "NH1" <-> "NH2" Residue "Q ARG 101": "NH1" <-> "NH2" Residue "Q GLU 102": "OE1" <-> "OE2" Residue "Q ARG 109": "NH1" <-> "NH2" Residue "R ARG 3": "NH1" <-> "NH2" Residue "R ARG 6": "NH1" <-> "NH2" Residue "R ARG 13": "NH1" <-> "NH2" Residue "R TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 33": "NH1" <-> "NH2" Residue "R ARG 48": "NH1" <-> "NH2" Residue "R ARG 70": "NH1" <-> "NH2" Residue "R GLU 89": "OE1" <-> "OE2" Residue "R GLU 111": "OE1" <-> "OE2" Residue "S TYR 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 21": "NH1" <-> "NH2" Residue "S GLU 23": "OE1" <-> "OE2" Residue "S PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 62": "OE1" <-> "OE2" Residue "S ARG 68": "NH1" <-> "NH2" Residue "S GLU 70": "OE1" <-> "OE2" Residue "S ARG 78": "NH1" <-> "NH2" Residue "S ARG 79": "NH1" <-> "NH2" Residue "S ARG 84": "NH1" <-> "NH2" Residue "S PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 2": "OE1" <-> "OE2" Residue "T GLU 52": "OE1" <-> "OE2" Residue "T GLU 59": "OE1" <-> "OE2" Residue "T GLU 78": "OE1" <-> "OE2" Residue "T ARG 84": "NH1" <-> "NH2" Residue "T ARG 88": "NH1" <-> "NH2" Residue "T ARG 95": "NH1" <-> "NH2" Residue "T ASP 109": "OD1" <-> "OD2" Residue "T ARG 110": "NH1" <-> "NH2" Residue "U GLU 4": "OE1" <-> "OE2" Residue "U GLU 5": "OE1" <-> "OE2" Residue "U GLU 25": "OE1" <-> "OE2" Residue "U ASP 37": "OD1" <-> "OD2" Residue "U GLU 52": "OE1" <-> "OE2" Residue "U GLU 56": "OE1" <-> "OE2" Residue "U ARG 69": "NH1" <-> "NH2" Residue "V ARG 6": "NH1" <-> "NH2" Residue "V GLU 37": "OE1" <-> "OE2" Residue "V ARG 82": "NH1" <-> "NH2" Residue "V ARG 86": "NH1" <-> "NH2" Residue "V GLU 88": "OE1" <-> "OE2" Residue "V ASP 89": "OD1" <-> "OD2" Residue "V ARG 94": "NH1" <-> "NH2" Residue "V GLU 101": "OE1" <-> "OE2" Residue "W GLU 7": "OE1" <-> "OE2" Residue "W ASP 43": "OD1" <-> "OD2" Residue "W GLU 55": "OE1" <-> "OE2" Residue "W GLU 59": "OE1" <-> "OE2" Residue "W GLU 69": "OE1" <-> "OE2" Residue "X ARG 11": "NH1" <-> "NH2" Residue "X GLU 17": "OE1" <-> "OE2" Residue "X GLU 29": "OE1" <-> "OE2" Residue "X PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 64": "OD1" <-> "OD2" Residue "X GLU 70": "OE1" <-> "OE2" Residue "X GLU 83": "OE1" <-> "OE2" Residue "Y ARG 3": "NH1" <-> "NH2" Residue "Y ARG 11": "NH1" <-> "NH2" Residue "Y ARG 18": "NH1" <-> "NH2" Residue "Y ARG 37": "NH1" <-> "NH2" Residue "Y GLU 41": "OE1" <-> "OE2" Residue "Y GLU 43": "OE1" <-> "OE2" Residue "Y ARG 50": "NH1" <-> "NH2" Residue "Y ARG 57": "NH1" <-> "NH2" Residue "Y ASP 60": "OD1" <-> "OD2" Residue "Y ARG 74": "NH1" <-> "NH2" Residue "Y GLU 76": "OE1" <-> "OE2" Residue "Z GLU 5": "OE1" <-> "OE2" Residue "Z GLU 12": "OE1" <-> "OE2" Residue "Z ARG 29": "NH1" <-> "NH2" Residue "Z ARG 47": "NH1" <-> "NH2" Residue "Z ARG 52": "NH1" <-> "NH2" Residue "0 ARG 11": "NH1" <-> "NH2" Residue "0 ARG 30": "NH1" <-> "NH2" Residue "0 GLU 37": "OE1" <-> "OE2" Residue "0 ARG 45": "NH1" <-> "NH2" Residue "0 GLU 59": "OE1" <-> "OE2" Residue "1 ARG 10": "NH1" <-> "NH2" Residue "1 ARG 16": "NH1" <-> "NH2" Residue "1 ARG 52": "NH1" <-> "NH2" Residue "2 TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 35": "OE1" <-> "OE2" Residue "2 ARG 44": "NH1" <-> "NH2" Residue "3 ARG 3": "NH1" <-> "NH2" Residue "3 ARG 12": "NH1" <-> "NH2" Residue "3 ARG 14": "NH1" <-> "NH2" Residue "3 ARG 19": "NH1" <-> "NH2" Residue "3 ARG 21": "NH1" <-> "NH2" Residue "3 ARG 33": "NH1" <-> "NH2" Residue "3 ARG 41": "NH1" <-> "NH2" Residue "4 ARG 13": "NH1" <-> "NH2" Residue "4 PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 30": "NH1" <-> "NH2" Residue "4 ARG 40": "NH1" <-> "NH2" Residue "4 ARG 42": "NH1" <-> "NH2" Residue "5 ARG 24": "NH1" <-> "NH2" Residue "b ARG 74": "NH1" <-> "NH2" Residue "b GLU 78": "OE1" <-> "OE2" Residue "b ASP 88": "OD1" <-> "OD2" Residue "b ASP 116": "OD1" <-> "OD2" Residue "b GLU 133": "OE1" <-> "OE2" Residue "b ARG 139": "NH1" <-> "NH2" Residue "b GLU 142": "OE1" <-> "OE2" Residue "b GLU 145": "OE1" <-> "OE2" Residue "b ASP 153": "OD1" <-> "OD2" Residue "b ASP 167": "OD1" <-> "OD2" Residue "b PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 188": "OD1" <-> "OD2" Residue "b ASP 194": "OD1" <-> "OD2" Residue "b ARG 225": "NH1" <-> "NH2" Residue "c PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ASP 31": "OD1" <-> "OD2" Residue "c GLU 58": "OE1" <-> "OE2" Residue "c GLU 82": "OE1" <-> "OE2" Residue "c ASP 83": "OD1" <-> "OD2" Residue "c GLU 85": "OE1" <-> "OE2" Residue "c ASP 93": "OD1" <-> "OD2" Residue "c GLU 105": "OE1" <-> "OE2" Residue "c GLU 110": "OE1" <-> "OE2" Residue "c GLU 125": "OE1" <-> "OE2" Residue "c ARG 127": "NH1" <-> "NH2" Residue "c ARG 131": "NH1" <-> "NH2" Residue "c ARG 143": "NH1" <-> "NH2" Residue "c GLU 152": "OE1" <-> "OE2" Residue "c GLU 188": "OE1" <-> "OE2" Residue "c GLU 206": "OE1" <-> "OE2" Residue "d GLU 35": "OE1" <-> "OE2" Residue "d GLU 57": "OE1" <-> "OE2" Residue "d GLU 69": "OE1" <-> "OE2" Residue "d ARG 81": "NH1" <-> "NH2" Residue "d GLU 147": "OE1" <-> "OE2" Residue "d GLU 160": "OE1" <-> "OE2" Residue "d GLU 163": "OE1" <-> "OE2" Residue "d GLU 166": "OE1" <-> "OE2" Residue "d GLU 202": "OE1" <-> "OE2" Residue "e GLU 10": "OE1" <-> "OE2" Residue "e ASP 41": "OD1" <-> "OD2" Residue "e GLU 55": "OE1" <-> "OE2" Residue "e GLU 101": "OE1" <-> "OE2" Residue "e GLU 116": "OE1" <-> "OE2" Residue "e ASP 142": "OD1" <-> "OD2" Residue "e GLU 145": "OE1" <-> "OE2" Residue "e GLU 151": "OE1" <-> "OE2" Residue "e ARG 157": "NH1" <-> "NH2" Residue "f GLU 5": "OE1" <-> "OE2" Residue "f GLU 33": "OE1" <-> "OE2" Residue "f ARG 45": "NH1" <-> "NH2" Residue "f TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 69": "OE1" <-> "OE2" Residue "f ASP 82": "OD1" <-> "OD2" Residue "f GLU 98": "OE1" <-> "OE2" Residue "g GLU 21": "OE1" <-> "OE2" Residue "g GLU 40": "OE1" <-> "OE2" Residue "g GLU 58": "OE1" <-> "OE2" Residue "g GLU 63": "OE1" <-> "OE2" Residue "g GLU 67": "OE1" <-> "OE2" Residue "g GLU 90": "OE1" <-> "OE2" Residue "g GLU 106": "OE1" <-> "OE2" Residue "g ASP 113": "OD1" <-> "OD2" Residue "g GLU 123": "OE1" <-> "OE2" Residue "g ASP 126": "OD1" <-> "OD2" Residue "g GLU 146": "OE1" <-> "OE2" Residue "h GLU 42": "OE1" <-> "OE2" Residue "h GLU 43": "OE1" <-> "OE2" Residue "h ASP 48": "OD1" <-> "OD2" Residue "h GLU 52": "OE1" <-> "OE2" Residue "h GLU 60": "OE1" <-> "OE2" Residue "h GLU 73": "OE1" <-> "OE2" Residue "h ASP 90": "OD1" <-> "OD2" Residue "h GLU 91": "OE1" <-> "OE2" Residue "h ASP 113": "OD1" <-> "OD2" Residue "h GLU 124": "OE1" <-> "OE2" Residue "i ARG 11": "NH1" <-> "NH2" Residue "i GLU 42": "OE1" <-> "OE2" Residue "i GLU 53": "OE1" <-> "OE2" Residue "i ASP 91": "OD1" <-> "OD2" Residue "i GLU 97": "OE1" <-> "OE2" Residue "i ARG 119": "NH1" <-> "NH2" Residue "i ARG 124": "NH1" <-> "NH2" Residue "i PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ASP 14": "OD1" <-> "OD2" Residue "j ASP 19": "OD1" <-> "OD2" Residue "j GLU 27": "OE1" <-> "OE2" Residue "j ARG 45": "NH1" <-> "NH2" Residue "j GLU 47": "OE1" <-> "OE2" Residue "j ASP 60": "OD1" <-> "OD2" Residue "j TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ASP 75": "OD1" <-> "OD2" Residue "j GLU 78": "OE1" <-> "OE2" Residue "k GLU 68": "OE1" <-> "OE2" Residue "k ARG 69": "NH1" <-> "NH2" Residue "k TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k GLU 83": "OE1" <-> "OE2" Residue "k ARG 93": "NH1" <-> "NH2" Residue "l GLU 25": "OE1" <-> "OE2" Residue "l TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ARG 56": "NH1" <-> "NH2" Residue "l GLU 62": "OE1" <-> "OE2" Residue "l GLU 70": "OE1" <-> "OE2" Residue "l GLU 76": "OE1" <-> "OE2" Residue "m ASP 11": "OD1" <-> "OD2" Residue "m TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ARG 29": "NH1" <-> "NH2" Residue "m ASP 42": "OD1" <-> "OD2" Residue "m GLU 50": "OE1" <-> "OE2" Residue "m ARG 70": "NH1" <-> "NH2" Residue "m ASP 82": "OD1" <-> "OD2" Residue "m TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ARG 87": "NH1" <-> "NH2" Residue "n ASP 18": "OD1" <-> "OD2" Residue "n GLU 26": "OE1" <-> "OE2" Residue "n ASP 33": "OD1" <-> "OD2" Residue "n ASP 38": "OD1" <-> "OD2" Residue "n GLU 39": "OE1" <-> "OE2" Residue "n ASP 40": "OD1" <-> "OD2" Residue "n ASP 54": "OD1" <-> "OD2" Residue "n ARG 65": "NH1" <-> "NH2" Residue "n ARG 85": "NH1" <-> "NH2" Residue "n GLU 86": "OE1" <-> "OE2" Residue "o GLU 6": "OE1" <-> "OE2" Residue "o GLU 14": "OE1" <-> "OE2" Residue "o ARG 17": "NH1" <-> "NH2" Residue "o ARG 77": "NH1" <-> "NH2" Residue "o GLU 83": "OE1" <-> "OE2" Residue "o ARG 89": "NH1" <-> "NH2" Residue "p ARG 28": "NH1" <-> "NH2" Residue "p PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p GLU 34": "OE1" <-> "OE2" Residue "p ASP 55": "OD1" <-> "OD2" Residue "p ASP 69": "OD1" <-> "OD2" Residue "q GLU 18": "OE1" <-> "OE2" Residue "q GLU 49": "OE1" <-> "OE2" Residue "q GLU 52": "OE1" <-> "OE2" Residue "q GLU 63": "OE1" <-> "OE2" Residue "q ARG 65": "NH1" <-> "NH2" Residue "q GLU 80": "OE1" <-> "OE2" Residue "r GLU 15": "OE1" <-> "OE2" Residue "r GLU 20": "OE1" <-> "OE2" Residue "r TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ASP 25": "OD1" <-> "OD2" Residue "r TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s GLU 20": "OE1" <-> "OE2" Residue "s GLU 24": "OE1" <-> "OE2" Residue "s ASP 64": "OD1" <-> "OD2" Residue "s GLU 65": "OE1" <-> "OE2" Residue "s GLU 73": "OE1" <-> "OE2" Residue "t GLU 40": "OE1" <-> "OE2" Residue "t PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u GLU 8": "OE1" <-> "OE2" Residue "u GLU 31": "OE1" <-> "OE2" Residue "u GLU 39": "OE1" <-> "OE2" Residue "v ASP 26": "OD1" <-> "OD2" Residue "v ASP 28": "OD1" <-> "OD2" Residue "v GLU 32": "OE1" <-> "OE2" Residue "v GLU 35": "OE1" <-> "OE2" Residue "v GLU 36": "OE1" <-> "OE2" Residue "v GLU 40": "OE1" <-> "OE2" Residue "v GLU 42": "OE1" <-> "OE2" Residue "v ASP 45": "OD1" <-> "OD2" Residue "v GLU 51": "OE1" <-> "OE2" Residue "v ASP 92": "OD1" <-> "OD2" Residue "v GLU 93": "OE1" <-> "OE2" Residue "v GLU 94": "OE1" <-> "OE2" Residue "v GLU 102": "OE1" <-> "OE2" Residue "v GLU 107": "OE1" <-> "OE2" Residue "v PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v ASP 131": "OD1" <-> "OD2" Residue "v ARG 150": "NH1" <-> "NH2" Residue "v TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v ARG 154": "NH1" <-> "NH2" Residue "v GLU 157": "OE1" <-> "OE2" Residue "v GLU 164": "OE1" <-> "OE2" Residue "v GLU 167": "OE1" <-> "OE2" Residue "v GLU 168": "OE1" <-> "OE2" Residue "v GLU 170": "OE1" <-> "OE2" Residue "v GLU 172": "OE1" <-> "OE2" Residue "v TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v GLU 195": "OE1" <-> "OE2" Residue "v ARG 200": "NH1" <-> "NH2" Residue "v ASP 208": "OD1" <-> "OD2" Residue "v ARG 213": "NH1" <-> "NH2" Residue "v PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v GLU 225": "OE1" <-> "OE2" Residue "v ASP 227": "OD1" <-> "OD2" Residue "v ASP 229": "OD1" <-> "OD2" Residue "v GLU 233": "OE1" <-> "OE2" Residue "v GLU 258": "OE1" <-> "OE2" Residue "v ARG 262": "NH1" <-> "NH2" Residue "v ASP 277": "OD1" <-> "OD2" Residue "v GLU 311": "OE1" <-> "OE2" Residue "v TYR 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v ARG 332": "NH1" <-> "NH2" Residue "v ASP 335": "OD1" <-> "OD2" Residue "v ASP 354": "OD1" <-> "OD2" Residue "v GLU 358": "OE1" <-> "OE2" Residue "w ARG 26": "NH1" <-> "NH2" Residue "w GLU 30": "OE1" <-> "OE2" Residue "w ARG 41": "NH1" <-> "NH2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 149495 Number of models: 1 Model: "" Number of chains: 61 Chain: "A" Number of atoms: 62351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2904, 62351 Classifications: {'RNA': 2904} Modifications used: {'rna2p': 3, 'rna2p_pur': 283, 'rna2p_pyr': 159, 'rna3p': 14, 'rna3p_pur': 1388, 'rna3p_pyr': 1057} Link IDs: {'rna2p': 445, 'rna3p': 2458} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 7 Chain: "B" Number of atoms: 2529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 2529 Classifications: {'RNA': 118} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 57, 'rna3p_pyr': 48} Link IDs: {'rna2p': 13, 'rna3p': 104} Chain: "C" 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: "D" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1565 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 202} Chain: "E" 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: "F" 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: "G" Number of atoms: 1323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1323 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "H" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1111 Classifications: {'peptide': 149} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 145} Chain: "J" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1032 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 131} Chain: "K" 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: "L" 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: "M" 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: "N" 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: "O" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 960 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "P" 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: "Q" 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: "R" 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: "S" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "T" 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: "U" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 738 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 1, 'TRANS': 91} Chain: "V" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 779 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "W" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 753 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "X" Number of atoms: 588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 588 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 75} Chain: "Y" 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: "Z" 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: "0" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 449 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "1" 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: "2" Number of atoms: 409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 409 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "3" 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: "4" 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: "5" 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: "a" Number of atoms: 32906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1533, 32906 Classifications: {'RNA': 1533} Modifications used: {'rna2p': 1, 'rna2p_pur': 117, 'rna2p_pyr': 87, 'rna3p': 9, 'rna3p_pur': 752, 'rna3p_pyr': 567} Link IDs: {'rna2p': 204, 'rna3p': 1328} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 7 Chain: "b" Number of atoms: 1753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1753 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 7, 'TRANS': 216} Chain: "c" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1624 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain: "d" Number of atoms: 1633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1633 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 6, 'TRANS': 197} Chain: "e" Number of atoms: 1156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1156 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 5, 'TRANS': 151} Chain: "f" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 817 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "g" 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: "h" 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: "i" 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: "j" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 786 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "k" 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: "l" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 955 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "m" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 883 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "n" 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: "o" 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: "p" 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: "q" 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: "r" Number of atoms: 539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 539 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "s" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 658 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 5, 'TRANS': 76} Chain: "t" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 670 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "u" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 465 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 2, 'TRANS': 53} Chain: "v" Number of atoms: 2836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2836 Classifications: {'peptide': 357} Link IDs: {'PTRANS': 6, 'TRANS': 350} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MEQ:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "w" Number of atoms: 388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 388 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "x" 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': 6, 'rna2p_pyr': 4, 'rna3p_pur': 33, 'rna3p_pyr': 34} Link IDs: {'rna2p': 9, 'rna3p': 67} Chain: "y" 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': 6, 'rna2p_pyr': 3, 'rna3p_pur': 33, 'rna3p_pyr': 35} Link IDs: {'rna2p': 9, 'rna3p': 67} Chain: "z" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 131 Classifications: {'RNA': 6} Modifications used: {'rna3p_pur': 5, 'rna3p_pyr': 1} Link IDs: {'rna3p': 5} Chain: "A" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 100 Unusual residues: {' MG': 100} Classifications: {'undetermined': 100} Link IDs: {None: 99} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "5" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Unusual residues: {' MG': 20} Classifications: {'undetermined': 20} Link IDs: {None: 19} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 90798 SG CYS 5 11 110.974 147.941 49.932 1.00330.17 S ATOM 90926 SG CYS 5 27 114.378 146.841 48.909 1.00378.49 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb="MG MG A3071 " occ=0.50 Time building chain proxies: 59.36, per 1000 atoms: 0.40 Number of scatterers: 149495 At special positions: 0 Unit cell: (262.46, 280.355, 226.67, 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 1 29.99 S 157 16.00 P 4713 15.00 Mg 124 11.99 O 41408 8.00 N 27806 7.00 C 75286 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: 68.68 Conformation dependent library (CDL) restraints added in 8.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 5 101 " pdb="ZN ZN 5 101 " - pdb=" SG CYS 5 27 " pdb="ZN ZN 5 101 " - pdb=" SG CYS 5 11 " 12108 Ramachandran restraints generated. 6054 Oldfield, 0 Emsley, 6054 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11318 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: 190 helices and 70 sheets defined 40.6% alpha, 18.3% beta 1437 base pairs and 2339 stacking pairs defined. Time for finding SS restraints: 85.69 Creating SS restraints... Processing helix chain 'C' and resid 10 through 15 removed outlier: 5.109A pdb=" N HIS C 15 " --> pdb=" O PRO C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 136 removed outlier: 3.638A pdb=" N ILE C 135 " --> pdb=" O PRO C 131 " (cutoff:3.500A) Proline residue: C 136 - end of helix No H-bonds generated for 'chain 'C' and resid 131 through 136' Processing helix chain 'C' and resid 207 through 215 Processing helix chain 'C' and resid 221 through 226 removed outlier: 5.000A pdb=" N ASN C 226 " --> pdb=" O GLY C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 268 removed outlier: 6.219A pdb=" N ASP C 264 " --> pdb=" O ASN C 260 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N LYS C 265 " --> pdb=" O LYS C 261 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N PHE C 266 " --> pdb=" O ARG C 262 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N VAL C 268 " --> pdb=" O ASP C 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 72 Processing helix chain 'D' and resid 98 through 103 removed outlier: 3.613A pdb=" N ALA D 102 " --> pdb=" O VAL D 98 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N ASP D 103 " --> pdb=" O GLU D 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 98 through 103' Processing helix chain 'D' and resid 120 through 125 Processing helix chain 'E' and resid 15 through 20 Processing helix chain 'E' and resid 24 through 41 removed outlier: 3.802A pdb=" N VAL E 28 " --> pdb=" O ASN E 24 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N GLN E 41 " --> pdb=" O ALA E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 53 removed outlier: 7.299A pdb=" N THR E 53 " --> pdb=" O ARG E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 116 Processing helix chain 'E' and resid 130 through 142 removed outlier: 3.582A pdb=" N LEU E 134 " --> pdb=" O LYS E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 163 removed outlier: 4.629A pdb=" N ASN E 163 " --> pdb=" O LEU E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 184 removed outlier: 5.072A pdb=" N ASP E 184 " --> pdb=" O LEU E 180 " (cutoff:3.500A) Processing helix chain 'E' and resid 189 through 201 Processing helix chain 'F' and resid 2 through 20 removed outlier: 5.409A pdb=" N VAL F 13 " --> pdb=" O LYS F 9 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LYS F 14 " --> pdb=" O ASP F 10 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 62 removed outlier: 4.151A pdb=" N LEU F 50 " --> pdb=" O ASP F 46 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY F 62 " --> pdb=" O ALA F 58 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 111 removed outlier: 4.132A pdb=" N ALA F 107 " --> pdb=" O LEU F 103 " (cutoff:3.500A) Proline residue: F 109 - end of helix Processing helix chain 'F' and resid 162 through 174 Processing helix chain 'F' and resid 134 through 139 removed outlier: 4.648A pdb=" N ILE F 137 " --> pdb=" O GLU F 134 " (cutoff:3.500A) Proline residue: F 139 - end of helix Processing helix chain 'G' and resid 2 through 8 removed outlier: 3.622A pdb=" N ALA G 7 " --> pdb=" O ARG G 3 " (cutoff:3.500A) Proline residue: G 8 - end of helix Processing helix chain 'G' and resid 60 through 81 removed outlier: 3.902A pdb=" N GLN G 64 " --> pdb=" O ASP G 60 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 153 removed outlier: 3.590A pdb=" N ILE G 141 " --> pdb=" O ASP G 137 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ARG G 152 " --> pdb=" O LEU G 148 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 28 removed outlier: 3.590A pdb=" N ALA H 26 " --> pdb=" O LYS H 22 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG H 27 " --> pdb=" O ALA H 23 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ASN H 28 " --> pdb=" O GLY H 24 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 22 through 28' Processing helix chain 'H' and resid 29 through 34 removed outlier: 3.681A pdb=" N GLN H 33 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 40 through 50 Processing helix chain 'H' and resid 51 through 73 removed outlier: 4.028A pdb=" N GLU H 55 " --> pdb=" O ARG H 51 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ALA H 56 " --> pdb=" O ALA H 52 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N LYS H 57 " --> pdb=" O GLU H 53 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ASN H 73 " --> pdb=" O ALA H 69 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 107 removed outlier: 3.922A pdb=" N ILE H 99 " --> pdb=" O GLY H 95 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 116 removed outlier: 3.713A pdb=" N VAL H 115 " --> pdb=" O ALA H 111 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N ARG H 116 " --> pdb=" O LYS H 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 111 through 116' Processing helix chain 'J' and resid 23 through 29 removed outlier: 5.726A pdb=" N LEU J 27 " --> pdb=" O VAL J 23 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N GLY J 28 " --> pdb=" O GLY J 24 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN J 29 " --> pdb=" O PRO J 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 23 through 29' Processing helix chain 'J' and resid 39 through 49 removed outlier: 3.904A pdb=" N ALA J 43 " --> pdb=" O LYS J 39 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LYS J 44 " --> pdb=" O ALA J 40 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N THR J 45 " --> pdb=" O PHE J 41 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASP J 46 " --> pdb=" O ASN J 42 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N SER J 47 " --> pdb=" O ALA J 43 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ILE J 48 " --> pdb=" O LYS J 44 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU J 49 " --> pdb=" O THR J 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 39 through 49' Processing helix chain 'J' and resid 74 through 83 removed outlier: 5.152A pdb=" N LYS J 80 " --> pdb=" O ALA J 76 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N LYS J 81 " --> pdb=" O VAL J 77 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ALA J 82 " --> pdb=" O LEU J 78 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N ALA J 83 " --> pdb=" O LEU J 79 " (cutoff:3.500A) Processing helix chain 'J' and resid 101 through 113 removed outlier: 4.221A pdb=" N THR J 111 " --> pdb=" O GLU J 107 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N LYS J 112 " --> pdb=" O ILE J 108 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ALA J 113 " --> pdb=" O ALA J 109 " (cutoff:3.500A) Processing helix chain 'J' and resid 120 through 136 removed outlier: 3.622A pdb=" N MET J 124 " --> pdb=" O ASP J 120 " (cutoff:3.500A) Processing helix chain 'J' and resid 33 through 38 removed outlier: 3.615A pdb=" N GLU J 36 " --> pdb=" O ASN J 33 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE J 37 " --> pdb=" O ILE J 34 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N CYS J 38 " --> pdb=" O MET J 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 33 through 38' Processing helix chain 'K' and resid 24 through 38 removed outlier: 3.685A pdb=" N LEU K 28 " --> pdb=" O THR K 24 " (cutoff:3.500A) Processing helix chain 'K' and resid 88 through 96 Processing helix chain 'K' and resid 97 through 110 removed outlier: 4.093A pdb=" N ILE K 101 " --> pdb=" O PRO K 97 " (cutoff:3.500A) Proline residue: K 110 - end of helix Processing helix chain 'K' and resid 112 through 123 removed outlier: 3.637A pdb=" N LEU K 122 " --> pdb=" O MET K 118 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N LYS K 123 " --> pdb=" O PHE K 119 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 72 removed outlier: 4.633A pdb=" N LYS K 72 " --> pdb=" O ASN K 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 67 through 72' Processing helix chain 'L' and resid 112 through 120 Proline residue: L 120 - end of helix Processing helix chain 'M' and resid 2 through 7 removed outlier: 3.814A pdb=" N LEU M 6 " --> pdb=" O ARG M 2 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N SER M 7 " --> pdb=" O LEU M 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 2 through 7' Processing helix chain 'M' and resid 37 through 42 removed outlier: 5.658A pdb=" N SER M 42 " --> pdb=" O GLN M 38 " (cutoff:3.500A) Processing helix chain 'M' and resid 56 through 62 Proline residue: M 62 - end of helix Processing helix chain 'M' and resid 68 through 75 removed outlier: 4.128A pdb=" N ALA M 72 " --> pdb=" O SER M 68 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ILE M 73 " --> pdb=" O ARG M 69 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N ALA M 75 " --> pdb=" O ALA M 71 " (cutoff:3.500A) Processing helix chain 'M' and resid 78 through 86 removed outlier: 4.073A pdb=" N LEU M 82 " --> pdb=" O ARG M 78 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N ALA M 83 " --> pdb=" O LEU M 79 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N LYS M 84 " --> pdb=" O SER M 80 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N VAL M 85 " --> pdb=" O ASP M 81 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N GLU M 86 " --> pdb=" O LEU M 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 78 through 86' Processing helix chain 'M' and resid 91 through 99 removed outlier: 3.739A pdb=" N ALA M 98 " --> pdb=" O THR M 94 " (cutoff:3.500A) Processing helix chain 'M' and resid 128 through 139 Processing helix chain 'N' and resid 42 through 58 Processing helix chain 'N' and resid 109 through 125 Proline residue: N 125 - end of helix Processing helix chain 'O' and resid 13 through 32 Processing helix chain 'O' and resid 38 through 57 removed outlier: 3.966A pdb=" N ARG O 46 " --> pdb=" O LYS O 42 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N VAL O 47 " --> pdb=" O GLU O 43 " (cutoff:3.500A) Proline residue: O 50 - end of helix removed outlier: 3.508A pdb=" N THR O 57 " --> pdb=" O THR O 53 " (cutoff:3.500A) Processing helix chain 'O' and resid 59 through 70 removed outlier: 3.977A pdb=" N ALA O 68 " --> pdb=" O ARG O 64 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ARG O 69 " --> pdb=" O LEU O 65 " (cutoff:3.500A) Processing helix chain 'O' and resid 72 through 88 removed outlier: 3.828A pdb=" N ALA O 77 " --> pdb=" O ASN O 73 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY O 84 " --> pdb=" O PHE O 80 " (cutoff:3.500A) Proline residue: O 85 - end of helix removed outlier: 4.109A pdb=" N ALA O 88 " --> pdb=" O GLY O 84 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 22 removed outlier: 3.614A pdb=" N THR P 12 " --> pdb=" O ILE P 8 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N ARG P 13 " --> pdb=" O ARG P 9 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N ALA P 14 " --> pdb=" O ARG P 10 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N ARG P 15 " --> pdb=" O ALA P 11 " (cutoff:3.500A) Processing helix chain 'P' and resid 55 through 63 removed outlier: 4.556A pdb=" N GLN P 61 " --> pdb=" O ALA P 57 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N LYS P 63 " --> pdb=" O ALA P 59 " (cutoff:3.500A) Processing helix chain 'P' and resid 67 through 86 Processing helix chain 'P' and resid 101 through 114 Processing helix chain 'Q' and resid 2 through 13 removed outlier: 3.614A pdb=" N GLU Q 11 " --> pdb=" O GLN Q 7 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN Q 12 " --> pdb=" O LEU Q 8 " (cutoff:3.500A) Processing helix chain 'Q' and resid 97 through 104 removed outlier: 4.835A pdb=" N ARG Q 101 " --> pdb=" O LEU Q 97 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N GLU Q 102 " --> pdb=" O TYR Q 98 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N THR Q 104 " --> pdb=" O LEU Q 100 " (cutoff:3.500A) Processing helix chain 'Q' and resid 105 through 110 removed outlier: 3.568A pdb=" N ARG Q 109 " --> pdb=" O GLY Q 105 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N ILE Q 110 " --> pdb=" O LYS Q 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 105 through 110' Processing helix chain 'R' and resid 6 through 22 removed outlier: 4.696A pdb=" N ALA R 10 " --> pdb=" O ARG R 6 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE R 17 " --> pdb=" O ARG R 13 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LYS R 22 " --> pdb=" O LEU R 18 " (cutoff:3.500A) Processing helix chain 'R' and resid 26 through 31 removed outlier: 4.407A pdb=" N ARG R 30 " --> pdb=" O GLY R 26 " (cutoff:3.500A) Processing helix chain 'R' and resid 39 through 73 removed outlier: 4.525A pdb=" N LYS R 54 " --> pdb=" O ARG R 50 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N ARG R 55 " --> pdb=" O ARG R 51 " (cutoff:3.500A) Processing helix chain 'R' and resid 75 through 87 Processing helix chain 'R' and resid 91 through 102 Processing helix chain 'R' and resid 103 through 118 Processing helix chain 'T' and resid 13 through 25 removed outlier: 3.885A pdb=" N LEU T 19 " --> pdb=" O GLN T 15 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N VAL T 20 " --> pdb=" O LYS T 16 " (cutoff:3.500A) Processing helix chain 'T' and resid 28 through 39 Processing helix chain 'T' and resid 41 through 61 removed outlier: 4.196A pdb=" N VAL T 45 " --> pdb=" O LYS T 41 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU T 46 " --> pdb=" O LYS T 42 " (cutoff:3.500A) Processing helix chain 'U' and resid 3 through 11 removed outlier: 4.460A pdb=" N LEU U 11 " --> pdb=" O LEU U 7 " (cutoff:3.500A) Processing helix chain 'U' and resid 17 through 26 Processing helix chain 'U' and resid 39 through 51 Processing helix chain 'V' and resid 66 through 71 removed outlier: 3.860A pdb=" N VAL V 70 " --> pdb=" O GLN V 66 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N ALA V 71 " --> pdb=" O VAL V 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 66 through 71' Processing helix chain 'W' and resid 13 through 24 removed outlier: 4.174A pdb=" N SER W 17 " --> pdb=" O GLY W 13 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASN W 24 " --> pdb=" O LEU W 20 " (cutoff:3.500A) Processing helix chain 'W' and resid 43 through 53 removed outlier: 4.890A pdb=" N LYS W 53 " --> pdb=" O ASN W 49 " (cutoff:3.500A) Processing helix chain 'W' and resid 54 through 59 Processing helix chain 'Y' and resid 52 through 63 Processing helix chain 'Y' and resid 64 through 75 Processing helix chain 'Z' and resid 2 through 9 removed outlier: 5.928A pdb=" N LEU Z 6 " --> pdb=" O LYS Z 2 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG Z 7 " --> pdb=" O ALA Z 3 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU Z 8 " --> pdb=" O LYS Z 4 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N LYS Z 9 " --> pdb=" O GLU Z 5 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 2 through 9' Processing helix chain 'Z' and resid 10 through 35 Processing helix chain 'Z' and resid 40 through 63 removed outlier: 4.877A pdb=" N LYS Z 44 " --> pdb=" O SER Z 40 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLN Z 45 " --> pdb=" O HIS Z 41 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N GLY Z 62 " --> pdb=" O ASN Z 58 " (cutoff:3.500A) Processing helix chain '0' and resid 17 through 28 Processing helix chain '0' and resid 41 through 52 Processing helix chain '1' and resid 9 through 21 removed outlier: 4.671A pdb=" N HIS 1 19 " --> pdb=" O MET 1 15 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ASP 1 20 " --> pdb=" O ARG 1 16 " (cutoff:3.500A) Processing helix chain '2' and resid 26 through 31 removed outlier: 3.676A pdb=" N LYS 2 30 " --> pdb=" O ASN 2 26 " (cutoff:3.500A) Proline residue: 2 31 - end of helix No H-bonds generated for 'chain '2' and resid 26 through 31' Processing helix chain '3' and resid 8 through 16 Processing helix chain '3' and resid 17 through 25 removed outlier: 3.725A pdb=" N THR 3 24 " --> pdb=" O ALA 3 20 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N LYS 3 25 " --> pdb=" O ARG 3 21 " (cutoff:3.500A) Processing helix chain '3' and resid 26 through 38 Processing helix chain '4' and resid 7 through 14 Processing helix chain '4' and resid 32 through 37 removed outlier: 4.407A pdb=" N LYS 4 36 " --> pdb=" O ILE 4 32 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N ALA 4 37 " --> pdb=" O LEU 4 33 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 32 through 37' Processing helix chain '4' and resid 38 through 46 Proline residue: 4 46 - end of helix Processing helix chain '4' and resid 52 through 63 removed outlier: 4.518A pdb=" N GLY 4 56 " --> pdb=" O LYS 4 52 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N LEU 4 57 " --> pdb=" O GLY 4 53 " (cutoff:3.500A) Proline residue: 4 63 - end of helix Processing helix chain 'b' and resid 5 through 13 Processing helix chain 'b' and resid 43 through 64 Proline residue: b 48 - end of helix Processing helix chain 'b' and resid 74 through 88 removed outlier: 4.355A pdb=" N GLU b 78 " --> pdb=" O ARG b 74 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N ALA b 79 " --> pdb=" O ALA b 75 " (cutoff:3.500A) Processing helix chain 'b' and resid 103 through 123 removed outlier: 4.289A pdb=" N GLN b 109 " --> pdb=" O LYS b 105 " (cutoff:3.500A) Processing helix chain 'b' and resid 130 through 149 Processing helix chain 'b' and resid 150 through 155 removed outlier: 4.277A pdb=" N MET b 154 " --> pdb=" O GLY b 150 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N GLY b 155 " --> pdb=" O ILE b 151 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 150 through 155' Processing helix chain 'b' and resid 169 through 180 removed outlier: 4.018A pdb=" N ILE b 173 " --> pdb=" O GLU b 169 " (cutoff:3.500A) Processing helix chain 'b' and resid 192 through 197 removed outlier: 4.858A pdb=" N VAL b 196 " --> pdb=" O ASP b 192 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N ASP b 197 " --> pdb=" O PRO b 193 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 192 through 197' Processing helix chain 'b' and resid 206 through 227 removed outlier: 3.844A pdb=" N VAL b 210 " --> pdb=" O ALA b 206 " (cutoff:3.500A) Processing helix chain 'c' and resid 6 through 12 removed outlier: 3.569A pdb=" N LEU c 12 " --> pdb=" O ASN c 8 " (cutoff:3.500A) Processing helix chain 'c' and resid 28 through 48 removed outlier: 4.070A pdb=" N ASN c 32 " --> pdb=" O GLU c 28 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA c 48 " --> pdb=" O THR c 44 " (cutoff:3.500A) Processing helix chain 'c' and resid 72 through 77 removed outlier: 3.748A pdb=" N VAL c 76 " --> pdb=" O ARG c 72 " (cutoff:3.500A) Processing helix chain 'c' and resid 81 through 96 Processing helix chain 'c' and resid 108 through 113 removed outlier: 3.779A pdb=" N ASP c 112 " --> pdb=" O LYS c 108 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N ALA c 113 " --> pdb=" O PRO c 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 108 through 113' Processing helix chain 'c' and resid 114 through 127 Processing helix chain 'c' and resid 129 through 145 Processing helix chain 'd' and resid 7 through 16 removed outlier: 4.551A pdb=" N LEU d 11 " --> pdb=" O PRO d 7 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N SER d 12 " --> pdb=" O LYS d 8 " (cutoff:3.500A) Processing helix chain 'd' and resid 27 through 32 removed outlier: 3.501A pdb=" N CYS d 32 " --> pdb=" O ILE d 28 " (cutoff:3.500A) Processing helix chain 'd' and resid 49 through 66 Processing helix chain 'd' and resid 68 through 83 removed outlier: 4.938A pdb=" N LYS d 83 " --> pdb=" O ALA d 79 " (cutoff:3.500A) Processing helix chain 'd' and resid 85 through 97 Processing helix chain 'd' and resid 98 through 106 Processing helix chain 'd' and resid 110 through 121 removed outlier: 3.757A pdb=" N LYS d 121 " --> pdb=" O LEU d 117 " (cutoff:3.500A) Processing helix chain 'd' and resid 146 through 151 removed outlier: 4.436A pdb=" N LYS d 151 " --> pdb=" O GLU d 147 " (cutoff:3.500A) Processing helix chain 'd' and resid 152 through 166 removed outlier: 4.070A pdb=" N LYS d 156 " --> pdb=" O GLN d 152 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N GLU d 166 " --> pdb=" O ALA d 162 " (cutoff:3.500A) Processing helix chain 'd' and resid 187 through 192 removed outlier: 3.673A pdb=" N LEU d 191 " --> pdb=" O GLU d 187 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N SER d 192 " --> pdb=" O ARG d 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 187 through 192' Processing helix chain 'd' and resid 196 through 205 removed outlier: 3.696A pdb=" N ILE d 200 " --> pdb=" O ASN d 196 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N SER d 205 " --> pdb=" O VAL d 201 " (cutoff:3.500A) Processing helix chain 'e' and resid 55 through 71 removed outlier: 3.859A pdb=" N ALA e 59 " --> pdb=" O GLU e 55 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG e 69 " --> pdb=" O GLU e 65 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ASN e 70 " --> pdb=" O LYS e 66 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N MET e 71 " --> pdb=" O ALA e 67 " (cutoff:3.500A) Processing helix chain 'e' and resid 109 through 119 removed outlier: 4.671A pdb=" N ALA e 113 " --> pdb=" O GLY e 109 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA e 118 " --> pdb=" O VAL e 114 " (cutoff:3.500A) Processing helix chain 'e' and resid 132 through 148 removed outlier: 5.092A pdb=" N ASN e 148 " --> pdb=" O LEU e 144 " (cutoff:3.500A) Processing helix chain 'e' and resid 149 through 158 removed outlier: 3.661A pdb=" N ALA e 154 " --> pdb=" O PRO e 150 " (cutoff:3.500A) Processing helix chain 'e' and resid 160 through 166 Processing helix chain 'f' and resid 14 through 33 Proline residue: f 19 - end of helix removed outlier: 3.569A pdb=" N ALA f 32 " --> pdb=" O ALA f 28 " (cutoff:3.500A) Processing helix chain 'f' and resid 67 through 82 removed outlier: 3.771A pdb=" N ILE f 71 " --> pdb=" O PRO f 67 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N ASP f 82 " --> pdb=" O PHE f 78 " (cutoff:3.500A) Processing helix chain 'g' and resid 20 through 32 removed outlier: 3.507A pdb=" N ALA g 24 " --> pdb=" O SER g 20 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N VAL g 32 " --> pdb=" O ASN g 28 " (cutoff:3.500A) Processing helix chain 'g' and resid 35 through 55 removed outlier: 3.638A pdb=" N ALA g 39 " --> pdb=" O LYS g 35 " (cutoff:3.500A) Processing helix chain 'g' and resid 57 through 70 removed outlier: 3.628A pdb=" N PHE g 62 " --> pdb=" O GLU g 58 " (cutoff:3.500A) Processing helix chain 'g' and resid 92 through 112 removed outlier: 4.059A pdb=" N ASN g 97 " --> pdb=" O PRO g 93 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ALA g 98 " --> pdb=" O VAL g 94 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N GLY g 112 " --> pdb=" O ALA g 108 " (cutoff:3.500A) Processing helix chain 'g' and resid 115 through 130 Processing helix chain 'g' and resid 132 through 149 removed outlier: 3.593A pdb=" N LYS g 136 " --> pdb=" O GLY g 132 " (cutoff:3.500A) Processing helix chain 'h' and resid 5 through 21 removed outlier: 3.513A pdb=" N ASP h 9 " --> pdb=" O ASP h 5 " (cutoff:3.500A) Processing helix chain 'h' and resid 30 through 44 Processing helix chain 'h' and resid 112 through 120 Processing helix chain 'i' and resid 34 through 39 Processing helix chain 'i' and resid 41 through 56 Proline residue: i 51 - end of helix removed outlier: 3.979A pdb=" N VAL i 55 " --> pdb=" O PRO i 51 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N ASP i 56 " --> pdb=" O LEU i 52 " (cutoff:3.500A) Processing helix chain 'i' and resid 72 through 92 Processing helix chain 'i' and resid 94 through 102 removed outlier: 4.221A pdb=" N LEU i 98 " --> pdb=" O LEU i 94 " (cutoff:3.500A) Processing helix chain 'j' and resid 14 through 33 removed outlier: 3.539A pdb=" N THR j 32 " --> pdb=" O THR j 28 " (cutoff:3.500A) Processing helix chain 'j' and resid 80 through 90 removed outlier: 3.855A pdb=" N MET j 88 " --> pdb=" O VAL j 84 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ARG j 89 " --> pdb=" O ASP j 85 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N LEU j 90 " --> pdb=" O ALA j 86 " (cutoff:3.500A) Processing helix chain 'k' and resid 46 through 51 removed outlier: 4.414A pdb=" N GLY k 51 " --> pdb=" O ALA k 47 " (cutoff:3.500A) Processing helix chain 'k' and resid 54 through 59 removed outlier: 3.688A pdb=" N SER k 58 " --> pdb=" O GLY k 54 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N THR k 59 " --> pdb=" O SER k 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 54 through 59' Processing helix chain 'k' and resid 60 through 76 removed outlier: 4.885A pdb=" N GLU k 76 " --> pdb=" O ASP k 72 " (cutoff:3.500A) Processing helix chain 'k' and resid 93 through 104 removed outlier: 5.023A pdb=" N ILE k 97 " --> pdb=" O ARG k 93 " (cutoff:3.500A) Processing helix chain 'l' and resid 3 through 10 Processing helix chain 'l' and resid 113 through 118 removed outlier: 4.329A pdb=" N TYR l 117 " --> pdb=" O ALA l 113 " (cutoff:3.500A) Processing helix chain 'm' and resid 14 through 23 removed outlier: 3.979A pdb=" N ILE m 22 " --> pdb=" O ALA m 18 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N TYR m 23 " --> pdb=" O LEU m 19 " (cutoff:3.500A) Processing helix chain 'm' and resid 26 through 38 Processing helix chain 'm' and resid 49 through 64 removed outlier: 4.717A pdb=" N VAL m 64 " --> pdb=" O VAL m 60 " (cutoff:3.500A) Processing helix chain 'm' and resid 66 through 84 Processing helix chain 'm' and resid 85 through 94 Processing helix chain 'm' and resid 106 through 111 Processing helix chain 'n' and resid 3 through 21 Processing helix chain 'n' and resid 22 through 34 removed outlier: 5.519A pdb=" N VAL n 34 " --> pdb=" O ILE n 30 " (cutoff:3.500A) Processing helix chain 'n' and resid 37 through 51 Processing helix chain 'n' and resid 52 through 57 removed outlier: 3.894A pdb=" N SER n 56 " --> pdb=" O PRO n 52 " (cutoff:3.500A) Proline residue: n 57 - end of helix No H-bonds generated for 'chain 'n' and resid 52 through 57' Processing helix chain 'n' and resid 80 through 91 Processing helix chain 'o' and resid 4 through 16 Processing helix chain 'o' and resid 24 through 47 removed outlier: 4.083A pdb=" N GLY o 41 " --> pdb=" O ASN o 37 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N HIS o 42 " --> pdb=" O HIS o 38 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS o 47 " --> pdb=" O PHE o 43 " (cutoff:3.500A) Processing helix chain 'o' and resid 49 through 74 removed outlier: 3.512A pdb=" N ARG o 72 " --> pdb=" O ASP o 68 " (cutoff:3.500A) Processing helix chain 'o' and resid 75 through 86 Processing helix chain 'p' and resid 53 through 64 Processing helix chain 'p' and resid 68 through 82 Processing helix chain 'r' and resid 11 through 17 removed outlier: 3.688A pdb=" N GLU r 15 " --> pdb=" O CYS r 11 " (cutoff:3.500A) Processing helix chain 'r' and resid 25 through 34 removed outlier: 3.700A pdb=" N LEU r 29 " --> pdb=" O ASP r 25 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ASN r 31 " --> pdb=" O ALA r 27 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N TYR r 32 " --> pdb=" O THR r 28 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE r 33 " --> pdb=" O LEU r 29 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N THR r 34 " --> pdb=" O LYS r 30 " (cutoff:3.500A) Processing helix chain 'r' and resid 41 through 46 Processing helix chain 'r' and resid 48 through 66 Processing helix chain 's' and resid 12 through 26 Processing helix chain 's' and resid 70 through 76 removed outlier: 4.109A pdb=" N PHE s 74 " --> pdb=" O LYS s 70 " (cutoff:3.500A) Proline residue: s 76 - end of helix Processing helix chain 't' and resid 4 through 42 Processing helix chain 't' and resid 43 through 65 removed outlier: 3.594A pdb=" N ALA t 47 " --> pdb=" O ASP t 43 " (cutoff:3.500A) Proline residue: t 56 - end of helix Processing helix chain 't' and resid 68 through 87 Processing helix chain 'u' and resid 11 through 27 Processing helix chain 'u' and resid 28 through 38 removed outlier: 4.347A pdb=" N PHE u 37 " --> pdb=" O ARG u 33 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N TYR u 38 " --> pdb=" O ARG u 34 " (cutoff:3.500A) Processing helix chain 'u' and resid 40 through 57 removed outlier: 5.054A pdb=" N ALA u 57 " --> pdb=" O VAL u 53 " (cutoff:3.500A) Processing helix chain 'v' and resid 6 through 26 removed outlier: 3.567A pdb=" N ARG v 10 " --> pdb=" O PRO v 6 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY v 23 " --> pdb=" O ASP v 19 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N TYR v 24 " --> pdb=" O VAL v 20 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU v 25 " --> pdb=" O LEU v 21 " (cutoff:3.500A) Processing helix chain 'v' and resid 27 through 42 removed outlier: 3.652A pdb=" N LYS v 31 " --> pdb=" O TYR v 27 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLU v 32 " --> pdb=" O ASP v 28 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU v 36 " --> pdb=" O GLU v 32 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU v 40 " --> pdb=" O GLU v 36 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU v 42 " --> pdb=" O ASN v 38 " (cutoff:3.500A) Processing helix chain 'v' and resid 50 through 91 removed outlier: 3.773A pdb=" N ALA v 55 " --> pdb=" O GLU v 51 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS v 58 " --> pdb=" O GLN v 54 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLU v 59 " --> pdb=" O ALA v 55 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA v 65 " --> pdb=" O SER v 61 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N VAL v 66 " --> pdb=" O SER v 62 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP v 68 " --> pdb=" O GLU v 64 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N THR v 69 " --> pdb=" O ALA v 65 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLU v 78 " --> pdb=" O LYS v 74 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASP v 79 " --> pdb=" O GLN v 75 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA v 87 " --> pdb=" O LEU v 83 " (cutoff:3.500A) Processing helix chain 'v' and resid 92 through 120 removed outlier: 4.554A pdb=" N PHE v 96 " --> pdb=" O ASP v 92 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLU v 102 " --> pdb=" O GLU v 98 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU v 103 " --> pdb=" O ALA v 99 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA v 105 " --> pdb=" O ALA v 101 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU v 106 " --> pdb=" O GLU v 102 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU v 108 " --> pdb=" O ASP v 104 " (cutoff:3.500A) Processing helix chain 'v' and resid 138 through 160 removed outlier: 5.244A pdb=" N GLN v 142 " --> pdb=" O GLY v 138 " (cutoff:3.500A) Processing helix chain 'v' and resid 187 through 196 removed outlier: 3.628A pdb=" N TRP v 191 " --> pdb=" O TYR v 187 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU v 192 " --> pdb=" O ALA v 188 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N THR v 194 " --> pdb=" O GLY v 190 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N GLU v 195 " --> pdb=" O TRP v 191 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N THR v 196 " --> pdb=" O LEU v 192 " (cutoff:3.500A) Processing helix chain 'v' and resid 235 through 240 removed outlier: 3.850A pdb=" N LEU v 239 " --> pdb=" O ASN v 235 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N ARG v 240 " --> pdb=" O PRO v 236 " (cutoff:3.500A) No H-bonds generated for 'chain 'v' and resid 235 through 240' Processing helix chain 'v' and resid 251 through 257 removed outlier: 4.821A pdb=" N ASN v 255 " --> pdb=" O GLY v 251 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG v 256 " --> pdb=" O MEQ v 252 " (cutoff:3.500A) Processing helix chain 'v' and resid 279 through 322 removed outlier: 3.704A pdb=" N ASN v 283 " --> pdb=" O SER v 279 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS v 314 " --> pdb=" O MET v 310 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLY v 318 " --> pdb=" O LYS v 314 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N TRP v 319 " --> pdb=" O SER v 315 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N GLY v 320 " --> pdb=" O ASP v 316 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N SER v 321 " --> pdb=" O ILE v 317 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N GLN v 322 " --> pdb=" O GLY v 318 " (cutoff:3.500A) Processing helix chain 'v' and resid 344 through 351 removed outlier: 3.538A pdb=" N GLY v 351 " --> pdb=" O ALA v 347 " (cutoff:3.500A) Processing helix chain 'v' and resid 353 through 362 removed outlier: 4.191A pdb=" N GLU v 358 " --> pdb=" O ASP v 354 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N ALA v 359 " --> pdb=" O GLN v 355 " (cutoff:3.500A) Processing helix chain 'w' and resid 14 through 23 removed outlier: 3.703A pdb=" N ASP w 22 " --> pdb=" O ALA w 18 " (cutoff:3.500A) Proline residue: w 23 - end of helix Processing sheet with id= 1, first strand: chain 'C' and resid 2 through 6 removed outlier: 5.926A pdb=" N VAL C 16 " --> pdb=" O CYS C 6 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'C' and resid 80 through 83 removed outlier: 7.050A pdb=" N LEU C 93 " --> pdb=" O GLU C 79 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ASP C 114 " --> pdb=" O VAL C 78 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'C' and resid 162 through 165 removed outlier: 6.549A pdb=" N THR C 173 " --> pdb=" O VAL C 165 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLU C 180 " --> pdb=" O LEU C 176 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'C' and resid 91 through 96 removed outlier: 3.915A pdb=" N GLU C 100 " --> pdb=" O TYR C 96 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'D' and resid 3 through 7 removed outlier: 6.682A pdb=" N ASP D 200 " --> pdb=" O THR D 112 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N THR D 112 " --> pdb=" O ASP D 200 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'D' and resid 11 through 16 removed outlier: 3.560A pdb=" N THR D 16 " --> pdb=" O VAL D 20 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N VAL D 20 " --> pdb=" O THR D 16 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'D' and resid 36 through 40 removed outlier: 3.525A pdb=" N GLN D 36 " --> pdb=" O GLN D 49 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N LEU D 40 " --> pdb=" O TYR D 45 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N TYR D 45 " --> pdb=" O LEU D 40 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N GLN D 49 " --> pdb=" O THR D 35 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N GLN D 94 " --> pdb=" O VAL D 34 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'D' and resid 46 through 51 removed outlier: 6.152A pdb=" N ARG D 46 " --> pdb=" O LEU D 84 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'D' and resid 105 through 108 removed outlier: 5.994A pdb=" N LYS D 105 " --> pdb=" O VAL D 177 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'E' and resid 1 through 4 Processing sheet with id= 11, first strand: chain 'E' and resid 117 through 120 removed outlier: 3.565A pdb=" N LEU E 147 " --> pdb=" O LYS E 185 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'F' and resid 65 through 69 removed outlier: 5.432A pdb=" N GLY F 39 " --> pdb=" O GLY F 151 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N GLY F 151 " --> pdb=" O GLY F 39 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'G' and resid 15 through 19 removed outlier: 6.062A pdb=" N GLN G 22 " --> pdb=" O LEU G 37 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLY G 31 " --> pdb=" O GLY G 28 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'G' and resid 41 through 47 removed outlier: 3.570A pdb=" N LYS G 44 " --> pdb=" O THR G 51 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N THR G 51 " --> pdb=" O LYS G 44 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ALA G 46 " --> pdb=" O THR G 49 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N THR G 49 " --> pdb=" O ALA G 46 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'G' and resid 94 through 99 removed outlier: 6.574A pdb=" N ASN G 101 " --> pdb=" O LEU G 117 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'G' and resid 121 through 125 removed outlier: 5.250A pdb=" N THR G 129 " --> pdb=" O LEU G 89 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N LYS G 86 " --> pdb=" O ALA G 165 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'H' and resid 17 through 20 removed outlier: 4.315A pdb=" N ASP H 17 " --> pdb=" O LEU H 5 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL H 3 " --> pdb=" O VAL H 19 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N GLN H 2 " --> pdb=" O ALA H 39 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'H' and resid 76 through 83 removed outlier: 6.801A pdb=" N GLU H 76 " --> pdb=" O LYS H 141 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N VAL H 78 " --> pdb=" O ILE H 143 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N PHE H 132 " --> pdb=" O ALA H 140 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'L' and resid 6 through 9 removed outlier: 3.848A pdb=" N THR L 6 " --> pdb=" O CYS L 21 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LYS L 40 " --> pdb=" O ILE L 22 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ASP L 56 " --> pdb=" O ILE L 43 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'L' and resid 63 through 66 removed outlier: 6.345A pdb=" N GLY L 81 " --> pdb=" O LYS L 66 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'L' and resid 68 through 71 removed outlier: 4.093A pdb=" N SER L 75 " --> pdb=" O ARG L 71 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'N' and resid 62 through 65 removed outlier: 4.043A pdb=" N TYR N 103 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N SER N 30 " --> pdb=" O LYS N 133 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LYS N 127 " --> pdb=" O VAL N 36 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'O' and resid 33 through 37 removed outlier: 6.949A pdb=" N MET O 110 " --> pdb=" O CYS O 100 " (cutoff:3.500A) removed outlier: 8.552A pdb=" N TYR O 94 " --> pdb=" O VAL O 116 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'P' and resid 49 through 52 removed outlier: 3.920A pdb=" N VAL P 49 " --> pdb=" O VAL P 39 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'Q' and resid 38 through 45 removed outlier: 6.795A pdb=" N THR Q 25 " --> pdb=" O LYS Q 87 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER Q 83 " --> pdb=" O LYS Q 29 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'Q' and resid 49 through 53 removed outlier: 3.795A pdb=" N ALA Q 49 " --> pdb=" O THR Q 60 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N ARG Q 53 " --> pdb=" O HIS Q 56 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N HIS Q 56 " --> pdb=" O ARG Q 53 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N SER Q 57 " --> pdb=" O THR Q 76 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'S' and resid 11 through 15 Processing sheet with id= 28, first strand: chain 'S' and resid 18 through 23 removed outlier: 4.283A pdb=" N GLN S 18 " --> pdb=" O ILE S 98 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ASP S 95 " --> pdb=" O VAL S 64 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N LYS S 60 " --> pdb=" O THR S 99 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N GLU S 31 " --> pdb=" O VAL S 63 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'S' and resid 57 through 60 Processing sheet with id= 30, first strand: chain 'S' and resid 65 through 68 removed outlier: 3.517A pdb=" N ALA S 65 " --> pdb=" O ASP S 95 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'S' and resid 71 through 78 removed outlier: 3.764A pdb=" N ARG S 78 " --> pdb=" O TYR S 83 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N TYR S 83 " --> pdb=" O ARG S 78 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'T' and resid 2 through 8 removed outlier: 4.236A pdb=" N THR T 100 " --> pdb=" O GLY T 79 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LYS T 73 " --> pdb=" O VAL T 106 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'U' and resid 28 through 33 removed outlier: 6.697A pdb=" N ASN U 28 " --> pdb=" O LEU U 87 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'V' and resid 40 through 45 No H-bonds generated for sheet with id= 34 Processing sheet with id= 35, first strand: chain 'V' and resid 83 through 86 Processing sheet with id= 36, first strand: chain 'W' and resid 2 through 6 removed outlier: 5.777A pdb=" N PHE W 2 " --> pdb=" O VAL W 60 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'W' and resid 37 through 42 removed outlier: 3.717A pdb=" N ILE W 89 " --> pdb=" O PRO W 27 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'X' and resid 45 through 48 removed outlier: 6.960A pdb=" N ILE X 82 " --> pdb=" O GLY X 48 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'X' and resid 51 through 54 removed outlier: 4.554A pdb=" N THR X 58 " --> pdb=" O GLY X 54 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'Y' and resid 12 through 18 removed outlier: 5.025A pdb=" N THR Y 25 " --> pdb=" O ASN Y 17 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain '0' and resid 33 through 39 removed outlier: 4.320A pdb=" N HIS 0 34 " --> pdb=" O GLN 0 9 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N MET 0 54 " --> pdb=" O THR 0 10 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain '2' and resid 20 through 24 Processing sheet with id= 43, first strand: chain '4' and resid 22 through 25 removed outlier: 5.896A pdb=" N PHE 4 22 " --> pdb=" O VAL 4 50 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain '5' and resid 1 through 4 removed outlier: 6.359A pdb=" N HIS 5 33 " --> pdb=" O CYS 5 27 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N CYS 5 27 " --> pdb=" O HIS 5 33 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N ILE 5 23 " --> pdb=" O GLN 5 37 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL 5 22 " --> pdb=" O ARG 5 19 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N SER 5 28 " --> pdb=" O ASN 5 13 " (cutoff:3.500A) removed outlier: 8.583A pdb=" N ASN 5 13 " --> pdb=" O SER 5 28 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'b' and resid 67 through 71 removed outlier: 3.921A pdb=" N ALA b 185 " --> pdb=" O PHE b 198 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'c' and resid 19 through 22 removed outlier: 5.833A pdb=" N ASN c 19 " --> pdb=" O ILE c 55 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ARG c 59 " --> pdb=" O THR c 21 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'c' and resid 163 through 170 removed outlier: 3.587A pdb=" N GLY c 194 " --> pdb=" O THR c 191 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ASP c 181 " --> pdb=" O LYS c 204 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'd' and resid 140 through 145 removed outlier: 3.867A pdb=" N ASP d 141 " --> pdb=" O PHE d 182 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N MET d 178 " --> pdb=" O ILE d 145 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLU d 179 " --> pdb=" O ASP d 174 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N TRP d 170 " --> pdb=" O LYS d 183 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'e' and resid 11 through 16 removed outlier: 7.022A pdb=" N LEU e 36 " --> pdb=" O ILE e 16 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL e 25 " --> pdb=" O GLY e 28 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'e' and resid 84 through 88 removed outlier: 3.840A pdb=" N ARG e 93 " --> pdb=" O TYR e 128 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ALA e 99 " --> pdb=" O ASN e 122 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N ASN e 122 " --> pdb=" O ALA e 99 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'e' and resid 33 through 40 Processing sheet with id= 52, first strand: chain 'f' and resid 38 through 42 removed outlier: 3.622A pdb=" N ARG f 38 " --> pdb=" O ASN f 63 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N TYR f 59 " --> pdb=" O TRP f 42 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N HIS f 3 " --> pdb=" O THR f 92 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ARG f 86 " --> pdb=" O MET f 9 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'f' and resid 43 through 47 removed outlier: 7.187A pdb=" N HIS f 55 " --> pdb=" O LEU f 47 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'g' and resid 72 through 78 No H-bonds generated for sheet with id= 54 Processing sheet with id= 55, first strand: chain 'h' and resid 23 through 29 removed outlier: 6.045A pdb=" N ALA h 23 " --> pdb=" O LEU h 63 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASP h 48 " --> pdb=" O THR h 62 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'h' and resid 74 through 77 Processing sheet with id= 57, first strand: chain 'i' and resid 5 through 11 Processing sheet with id= 58, first strand: chain 'j' and resid 39 through 42 removed outlier: 4.213A pdb=" N LEU j 71 " --> pdb=" O LEU j 42 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'j' and resid 44 through 52 Processing sheet with id= 60, first strand: chain 'k' and resid 30 through 35 removed outlier: 4.026A pdb=" N GLY k 19 " --> pdb=" O ASN k 81 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N VAL k 84 " --> pdb=" O THR k 108 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'k' and resid 84 through 87 removed outlier: 4.975A pdb=" N ASP k 112 " --> pdb=" O VAL k 84 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N VAL k 86 " --> pdb=" O ASP k 112 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'l' and resid 29 through 33 removed outlier: 4.933A pdb=" N LEU l 81 " --> pdb=" O VAL l 98 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'l' and resid 36 through 41 removed outlier: 5.074A pdb=" N LYS l 51 " --> pdb=" O ILE l 67 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'p' and resid 4 through 11 removed outlier: 4.711A pdb=" N PHE p 16 " --> pdb=" O HIS p 9 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG p 14 " --> pdb=" O ALA p 11 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL p 19 " --> pdb=" O GLY p 37 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N GLY p 49 " --> pdb=" O ASN p 40 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'q' and resid 7 through 11 removed outlier: 7.284A pdb=" N GLU q 60 " --> pdb=" O VAL q 76 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'q' and resid 19 through 31 No H-bonds generated for sheet with id= 66 Processing sheet with id= 67, first strand: chain 's' and resid 30 through 33 removed outlier: 4.890A pdb=" N LEU s 47 " --> pdb=" O VAL s 62 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'v' and resid 161 through 166 removed outlier: 3.510A pdb=" N LYS v 162 " --> pdb=" O SER v 184 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N THR v 180 " --> pdb=" O ILE v 166 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N LYS v 177 " --> pdb=" O ALA v 134 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N ASP v 127 " --> pdb=" O GLU v 225 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N PHE v 217 " --> pdb=" O GLY v 135 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ARG v 324 " --> pdb=" O VAL v 198 " (cutoff:3.500A) removed outlier: 8.683A pdb=" N ILE v 323 " --> pdb=" O LEU v 336 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL v 327 " --> pdb=" O ARG v 332 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG v 332 " --> pdb=" O VAL v 327 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'v' and resid 241 through 244 removed outlier: 4.178A pdb=" N ILE v 270 " --> pdb=" O HIS v 265 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'v' and resid 167 through 170 2090 hydrogen bonds defined for protein. 6186 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3670 hydrogen bonds 6148 hydrogen bond angles 0 basepair planarities 1437 basepair parallelities 2339 stacking parallelities Total time for adding SS restraints: 276.62 Time building geometry restraints manager: 74.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 18669 1.33 - 1.45: 68684 1.45 - 1.57: 65100 1.57 - 1.69: 9425 1.69 - 1.81: 283 Bond restraints: 162161 Sorted by residual: bond pdb=" C4 5MU A1939 " pdb=" C5 5MU A1939 " ideal model delta sigma weight residual 1.802 1.475 0.327 2.00e-02 2.50e+03 2.67e+02 bond pdb=" C4 5MU A 747 " pdb=" C5 5MU A 747 " ideal model delta sigma weight residual 1.802 1.492 0.310 2.00e-02 2.50e+03 2.40e+02 bond pdb=" N1 5MU A1939 " pdb=" C6 5MU A1939 " ideal model delta sigma weight residual 1.635 1.340 0.295 2.00e-02 2.50e+03 2.17e+02 bond pdb=" N1 5MU A 747 " pdb=" C6 5MU A 747 " ideal model delta sigma weight residual 1.635 1.345 0.290 2.00e-02 2.50e+03 2.11e+02 bond pdb=" CZ ARG m 90 " pdb=" NH1 ARG m 90 " ideal model delta sigma weight residual 1.323 1.499 -0.176 1.40e-02 5.10e+03 1.57e+02 ... (remaining 162156 not shown) Histogram of bond angle deviations from ideal: 99.57 - 107.11: 30610 107.11 - 114.64: 98199 114.64 - 122.18: 74994 122.18 - 129.71: 35536 129.71 - 137.25: 2942 Bond angle restraints: 242281 Sorted by residual: angle pdb=" O3' C A1730 " pdb=" C3' C A1730 " pdb=" C2' C A1730 " ideal model delta sigma weight residual 109.50 122.49 -12.99 1.50e+00 4.44e-01 7.50e+01 angle pdb=" C4' A A2225 " pdb=" C3' A A2225 " pdb=" O3' A A2225 " ideal model delta sigma weight residual 109.40 122.11 -12.71 1.50e+00 4.44e-01 7.18e+01 angle pdb=" O3' U x 17 " pdb=" C3' U x 17 " pdb=" C2' U x 17 " ideal model delta sigma weight residual 109.50 121.44 -11.94 1.50e+00 4.44e-01 6.34e+01 angle pdb=" C4' U A1344 " pdb=" C3' U A1344 " pdb=" O3' U A1344 " ideal model delta sigma weight residual 109.40 120.91 -11.51 1.50e+00 4.44e-01 5.88e+01 angle pdb=" O3' G A2193 " pdb=" C3' G A2193 " pdb=" C2' G A2193 " ideal model delta sigma weight residual 113.70 124.83 -11.13 1.50e+00 4.44e-01 5.50e+01 ... (remaining 242276 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.69: 89751 35.69 - 71.37: 12408 71.37 - 107.06: 1558 107.06 - 142.74: 36 142.74 - 178.43: 26 Dihedral angle restraints: 103779 sinusoidal: 86230 harmonic: 17549 Sorted by residual: dihedral pdb=" C5' C A1730 " pdb=" C4' C A1730 " pdb=" C3' C A1730 " pdb=" O3' C A1730 " ideal model delta sinusoidal sigma weight residual 147.00 67.39 79.61 1 8.00e+00 1.56e-02 1.23e+02 dihedral pdb=" C4' C A1730 " pdb=" C3' C A1730 " pdb=" C2' C A1730 " pdb=" C1' C A1730 " ideal model delta sinusoidal sigma weight residual -35.00 31.13 -66.13 1 8.00e+00 1.56e-02 8.93e+01 dihedral pdb=" O4' U a 365 " pdb=" C1' U a 365 " pdb=" N1 U a 365 " pdb=" C2 U a 365 " ideal model delta sinusoidal sigma weight residual 200.00 43.52 156.48 1 1.50e+01 4.44e-03 8.18e+01 ... (remaining 103776 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.180: 26227 0.180 - 0.361: 4565 0.361 - 0.541: 26 0.541 - 0.722: 6 0.722 - 0.902: 1 Chirality restraints: 30825 Sorted by residual: chirality pdb=" C3' U A1344 " pdb=" C4' U A1344 " pdb=" O3' U A1344 " pdb=" C2' U A1344 " both_signs ideal model delta sigma weight residual False -2.74 -1.84 -0.90 2.00e-01 2.50e+01 2.03e+01 chirality pdb=" C3' A a1151 " pdb=" C4' A a1151 " pdb=" O3' A a1151 " pdb=" C2' A a1151 " both_signs ideal model delta sigma weight residual False -2.74 -2.04 -0.71 2.00e-01 2.50e+01 1.24e+01 chirality pdb=" C3' U x 17 " pdb=" C4' U x 17 " pdb=" O3' U x 17 " pdb=" C2' U x 17 " both_signs ideal model delta sigma weight residual False -2.74 -2.06 -0.69 2.00e-01 2.50e+01 1.19e+01 ... (remaining 30822 not shown) Planarity restraints: 13212 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' OMC A2498 " -0.048 2.00e-02 2.50e+03 6.37e-01 9.13e+03 pdb=" C4' OMC A2498 " -0.446 2.00e-02 2.50e+03 pdb=" O4' OMC A2498 " -0.652 2.00e-02 2.50e+03 pdb=" C3' OMC A2498 " 0.609 2.00e-02 2.50e+03 pdb=" O3' OMC A2498 " 0.731 2.00e-02 2.50e+03 pdb=" C2' OMC A2498 " 0.120 2.00e-02 2.50e+03 pdb=" O2' OMC A2498 " -1.068 2.00e-02 2.50e+03 pdb=" C1' OMC A2498 " -0.207 2.00e-02 2.50e+03 pdb=" N1 OMC A2498 " 0.961 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMG A2251 " -0.007 2.00e-02 2.50e+03 5.97e-01 8.03e+03 pdb=" C4' OMG A2251 " -0.446 2.00e-02 2.50e+03 pdb=" O4' OMG A2251 " -0.708 2.00e-02 2.50e+03 pdb=" C3' OMG A2251 " 0.587 2.00e-02 2.50e+03 pdb=" O3' OMG A2251 " 0.623 2.00e-02 2.50e+03 pdb=" C2' OMG A2251 " 0.191 2.00e-02 2.50e+03 pdb=" O2' OMG A2251 " -0.932 2.00e-02 2.50e+03 pdb=" C1' OMG A2251 " -0.218 2.00e-02 2.50e+03 pdb=" N9 OMG A2251 " 0.910 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG A2445 " 0.075 2.00e-02 2.50e+03 5.59e-01 7.04e+03 pdb=" C4' 2MG A2445 " -0.447 2.00e-02 2.50e+03 pdb=" O4' 2MG A2445 " -0.801 2.00e-02 2.50e+03 pdb=" C3' 2MG A2445 " 0.584 2.00e-02 2.50e+03 pdb=" O3' 2MG A2445 " 0.417 2.00e-02 2.50e+03 pdb=" C2' 2MG A2445 " 0.274 2.00e-02 2.50e+03 pdb=" O2' 2MG A2445 " -0.723 2.00e-02 2.50e+03 pdb=" C1' 2MG A2445 " -0.266 2.00e-02 2.50e+03 pdb=" N9 2MG A2445 " 0.887 2.00e-02 2.50e+03 ... (remaining 13209 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.27: 104 2.27 - 2.93: 52856 2.93 - 3.58: 247107 3.58 - 4.24: 474246 4.24 - 4.90: 612350 Nonbonded interactions: 1386663 Sorted by model distance: nonbonded pdb=" C2 A a 523 " pdb=" N6 A a 527 " model vdw 1.610 3.420 nonbonded pdb=" N3 U A2244 " pdb=" N6 A A2435 " model vdw 1.678 2.560 nonbonded pdb=" N3 U a 13 " pdb=" N6 A a 915 " model vdw 1.693 2.560 nonbonded pdb=" OP1 A A1614 " pdb="MG MG A3010 " model vdw 1.698 2.170 nonbonded pdb=" OP2 C A2611 " pdb="MG MG A3092 " model vdw 1.732 2.170 ... (remaining 1386658 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 'x' selection = chain 'y' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.150 Extract box with map and model: 17.860 Check model and map are aligned: 1.600 Set scattering table: 1.020 Process input model: 626.350 Find NCS groups from input model: 3.230 Set up NCS constraints: 0.550 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:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 658.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.327 162161 Z= 0.440 Angle : 1.169 19.772 242281 Z= 0.784 Chirality : 0.105 0.902 30825 Planarity : 0.017 0.637 13212 Dihedral : 24.786 178.428 92461 Min Nonbonded Distance : 1.610 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.84 % Allowed : 6.43 % Favored : 92.73 % Rotamer: Outliers : 8.19 % Allowed : 13.21 % Favored : 78.60 % Cbeta Deviations : 0.72 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.09), residues: 6054 helix: 1.02 (0.10), residues: 2084 sheet: -1.34 (0.15), residues: 954 loop : -2.17 (0.09), residues: 3016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 248 HIS 0.006 0.001 HIS v 281 PHE 0.020 0.002 PHE T 75 TYR 0.020 0.002 TYR f 59 ARG 0.076 0.003 ARG m 90 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12108 Ramachandran restraints generated. 6054 Oldfield, 0 Emsley, 6054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12108 Ramachandran restraints generated. 6054 Oldfield, 0 Emsley, 6054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2565 residues out of total 5041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 413 poor density : 2152 time to evaluate : 6.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 14 ARG cc_start: 0.8715 (ttm110) cc_final: 0.7818 (mtp85) REVERT: C 18 LYS cc_start: 0.9260 (mttt) cc_final: 0.9032 (mttt) REVERT: C 74 ILE cc_start: 0.6650 (OUTLIER) cc_final: 0.6370 (mt) REVERT: C 78 VAL cc_start: 0.7266 (t) cc_final: 0.7062 (t) REVERT: C 79 GLU cc_start: 0.6776 (tt0) cc_final: 0.6010 (tt0) REVERT: C 82 GLU cc_start: 0.8125 (mt-10) cc_final: 0.7815 (mp0) REVERT: C 83 TYR cc_start: 0.8550 (t80) cc_final: 0.7941 (t80) REVERT: C 87 ARG cc_start: 0.8183 (ptp-110) cc_final: 0.7460 (ptp-110) REVERT: C 91 ILE cc_start: 0.8724 (pt) cc_final: 0.8388 (pt) REVERT: C 96 TYR cc_start: 0.8039 (m-80) cc_final: 0.6264 (m-80) REVERT: C 101 ARG cc_start: 0.7284 (mpt180) cc_final: 0.6025 (mmm-85) REVERT: C 115 GLN cc_start: 0.7634 (mt0) cc_final: 0.7167 (tp40) REVERT: C 129 THR cc_start: 0.7370 (m) cc_final: 0.6685 (p) REVERT: C 130 LEU cc_start: 0.7071 (pp) cc_final: 0.6287 (tt) REVERT: C 132 MET cc_start: 0.7941 (mtt) cc_final: 0.7702 (mtt) REVERT: C 146 MET cc_start: 0.6642 (mtt) cc_final: 0.6120 (mmt) REVERT: C 175 ARG cc_start: 0.8729 (OUTLIER) cc_final: 0.8347 (ptm160) REVERT: C 184 VAL cc_start: 0.8502 (OUTLIER) cc_final: 0.8226 (t) REVERT: C 213 TRP cc_start: 0.9201 (m-10) cc_final: 0.8465 (m-10) REVERT: C 267 ILE cc_start: 0.7732 (mm) cc_final: 0.7174 (mm) REVERT: C 271 ARG cc_start: 0.7355 (ptt-90) cc_final: 0.6961 (ptt90) REVERT: D 34 VAL cc_start: 0.5633 (t) cc_final: 0.5399 (t) REVERT: D 36 GLN cc_start: 0.7279 (tt0) cc_final: 0.6451 (tm-30) REVERT: D 43 ASP cc_start: 0.4642 (m-30) cc_final: 0.3942 (m-30) REVERT: D 49 GLN cc_start: 0.7562 (tt0) cc_final: 0.7275 (tp40) REVERT: D 127 PHE cc_start: 0.9121 (m-10) cc_final: 0.8771 (m-80) REVERT: E 1 MET cc_start: 0.7175 (tpt) cc_final: 0.6788 (tpt) REVERT: E 47 LYS cc_start: 0.8896 (mttp) cc_final: 0.8274 (mttp) REVERT: E 49 ARG cc_start: 0.9162 (ptm160) cc_final: 0.8645 (ptm-80) REVERT: E 97 ASN cc_start: 0.6427 (m-40) cc_final: 0.6103 (t0) REVERT: E 99 LYS cc_start: 0.8376 (mtpt) cc_final: 0.7966 (mptt) REVERT: E 100 MET cc_start: 0.8529 (OUTLIER) cc_final: 0.8080 (mtt) REVERT: E 106 LYS cc_start: 0.8570 (mtpt) cc_final: 0.8267 (mtpt) REVERT: E 115 GLN cc_start: 0.8749 (mm-40) cc_final: 0.8513 (mm110) REVERT: E 116 ASP cc_start: 0.6973 (m-30) cc_final: 0.6744 (m-30) REVERT: E 117 ARG cc_start: 0.6197 (ptt180) cc_final: 0.5484 (ptt180) REVERT: E 123 LYS cc_start: 0.7865 (tttp) cc_final: 0.7585 (ptpp) REVERT: E 133 LEU cc_start: 0.7565 (tp) cc_final: 0.7305 (tp) REVERT: E 176 ASP cc_start: 0.5507 (p0) cc_final: 0.5293 (p0) REVERT: E 183 PHE cc_start: 0.6534 (m-80) cc_final: 0.6308 (m-10) REVERT: E 189 THR cc_start: 0.7267 (OUTLIER) cc_final: 0.6804 (p) REVERT: F 44 ILE cc_start: 0.8195 (pt) cc_final: 0.7807 (mt) REVERT: F 80 ARG cc_start: 0.8324 (mmm-85) cc_final: 0.8116 (mmm160) REVERT: F 83 TYR cc_start: 0.6746 (t80) cc_final: 0.5998 (t80) REVERT: F 110 ARG cc_start: 0.4251 (mmp-170) cc_final: 0.2729 (tmm160) REVERT: F 120 LYS cc_start: 0.8437 (tttp) cc_final: 0.8139 (tptp) REVERT: F 121 SER cc_start: -0.0508 (p) cc_final: -0.2113 (m) REVERT: F 142 ASP cc_start: 0.6970 (t70) cc_final: 0.6601 (t70) REVERT: F 174 ASP cc_start: 0.5781 (t0) cc_final: 0.5508 (p0) REVERT: G 25 THR cc_start: 0.6716 (p) cc_final: 0.6466 (t) REVERT: G 88 GLN cc_start: 0.6884 (pt0) cc_final: 0.6542 (tp40) REVERT: G 89 LEU cc_start: 0.7812 (OUTLIER) cc_final: 0.7506 (tp) REVERT: G 157 TYR cc_start: 0.5233 (m-80) cc_final: 0.5022 (m-10) REVERT: H 27 ARG cc_start: 0.7492 (OUTLIER) cc_final: 0.6718 (ptt180) REVERT: J 37 PHE cc_start: 0.2667 (OUTLIER) cc_final: 0.2340 (m-80) REVERT: J 131 THR cc_start: 0.0277 (m) cc_final: -0.0077 (p) REVERT: K 16 TYR cc_start: 0.6477 (m-80) cc_final: 0.5954 (m-10) REVERT: K 31 GLU cc_start: 0.8781 (mm-30) cc_final: 0.8490 (tm-30) REVERT: K 35 ARG cc_start: 0.7462 (mpt90) cc_final: 0.7207 (mmm-85) REVERT: K 69 ARG cc_start: 0.8092 (ttm-80) cc_final: 0.7883 (mmm160) REVERT: K 116 ARG cc_start: 0.7599 (mtm-85) cc_final: 0.7269 (mtm-85) REVERT: K 119 PHE cc_start: 0.8179 (t80) cc_final: 0.7848 (t80) REVERT: K 125 TYR cc_start: 0.5681 (m-10) cc_final: 0.5439 (m-80) REVERT: K 132 HIS cc_start: 0.5450 (m-70) cc_final: 0.5026 (m90) REVERT: K 135 GLN cc_start: 0.4795 (mp10) cc_final: 0.4257 (mp10) REVERT: K 138 GLN cc_start: 0.8009 (pt0) cc_final: 0.7736 (mp10) REVERT: L 3 GLN cc_start: 0.7380 (pt0) cc_final: 0.6743 (mp10) REVERT: L 56 ASP cc_start: 0.8259 (m-30) cc_final: 0.7885 (t0) REVERT: L 78 ARG cc_start: 0.8166 (OUTLIER) cc_final: 0.7932 (mpt180) REVERT: L 111 LYS cc_start: 0.8554 (mttt) cc_final: 0.8350 (tptp) REVERT: L 116 ILE cc_start: 0.7044 (OUTLIER) cc_final: 0.6725 (tp) REVERT: M 41 ARG cc_start: 0.7772 (mmt180) cc_final: 0.6533 (mmt180) REVERT: M 48 ARG cc_start: 0.7326 (OUTLIER) cc_final: 0.6489 (ptt180) REVERT: M 50 PHE cc_start: 0.8674 (t80) cc_final: 0.8457 (t80) REVERT: M 55 MET cc_start: 0.8897 (tpp) cc_final: 0.8465 (tpp) REVERT: N 2 LEU cc_start: 0.8598 (mt) cc_final: 0.8237 (mt) REVERT: N 8 LYS cc_start: 0.8272 (mmtt) cc_final: 0.7814 (mmtt) REVERT: N 12 MET cc_start: 0.8635 (ttm) cc_final: 0.8394 (mtm) REVERT: N 66 ARG cc_start: 0.6433 (OUTLIER) cc_final: 0.4717 (mtm-85) REVERT: N 68 PHE cc_start: 0.7964 (t80) cc_final: 0.7730 (t80) REVERT: N 92 TRP cc_start: 0.7711 (m100) cc_final: 0.7072 (m-90) REVERT: N 102 LEU cc_start: 0.9122 (mt) cc_final: 0.8794 (mt) REVERT: O 3 HIS cc_start: 0.6955 (m170) cc_final: 0.6329 (m-70) REVERT: O 9 GLN cc_start: 0.8511 (tt0) cc_final: 0.8309 (tt0) REVERT: O 12 ARG cc_start: 0.8449 (mtt90) cc_final: 0.8141 (mtt90) REVERT: O 13 ASN cc_start: 0.8321 (p0) cc_final: 0.8116 (p0) REVERT: O 17 ARG cc_start: 0.8966 (ttm-80) cc_final: 0.8227 (mtm180) REVERT: O 22 ARG cc_start: 0.8939 (ttm170) cc_final: 0.8694 (ttt180) REVERT: O 29 VAL cc_start: 0.8491 (t) cc_final: 0.7941 (t) REVERT: O 37 THR cc_start: 0.8546 (OUTLIER) cc_final: 0.8155 (t) REVERT: O 45 ARG cc_start: 0.7133 (mtm180) cc_final: 0.6567 (mtm180) REVERT: O 78 LYS cc_start: 0.8276 (tttt) cc_final: 0.7920 (tptm) REVERT: O 86 ARG cc_start: 0.6882 (ttm170) cc_final: 0.6648 (tpp80) REVERT: O 87 PHE cc_start: 0.5854 (m-80) cc_final: 0.4675 (m-10) REVERT: O 103 ARG cc_start: 0.8447 (ttp-170) cc_final: 0.8203 (ttm170) REVERT: P 7 ARG cc_start: 0.8269 (OUTLIER) cc_final: 0.7908 (ttt90) REVERT: P 16 ARG cc_start: 0.8428 (mmt-90) cc_final: 0.8042 (mtt-85) REVERT: P 32 PRO cc_start: 0.7100 (Cg_exo) cc_final: 0.6827 (Cg_endo) REVERT: P 36 TYR cc_start: 0.8145 (OUTLIER) cc_final: 0.7595 (m-80) REVERT: P 76 LYS cc_start: 0.7657 (tttt) cc_final: 0.7320 (mttm) REVERT: P 102 ARG cc_start: 0.6958 (mtm180) cc_final: 0.6682 (mmm-85) REVERT: Q 21 ARG cc_start: 0.6249 (mmm-85) cc_final: 0.5942 (mmm160) REVERT: Q 52 ASN cc_start: 0.8177 (t0) cc_final: 0.7950 (m-40) REVERT: Q 110 ILE cc_start: 0.7368 (pt) cc_final: 0.6912 (tt) REVERT: R 50 ARG cc_start: 0.8298 (mtm-85) cc_final: 0.7915 (mtm-85) REVERT: R 53 ARG cc_start: 0.7501 (OUTLIER) cc_final: 0.6937 (ttp80) REVERT: R 74 ILE cc_start: 0.6560 (OUTLIER) cc_final: 0.6204 (tp) REVERT: S 37 GLU cc_start: 0.7384 (mt-10) cc_final: 0.6833 (mp0) REVERT: S 47 VAL cc_start: 0.5265 (OUTLIER) cc_final: 0.5020 (p) REVERT: S 80 ARG cc_start: 0.8187 (OUTLIER) cc_final: 0.7516 (mtm110) REVERT: T 1 MET cc_start: 0.6234 (tpt) cc_final: 0.6010 (tpt) REVERT: T 7 HIS cc_start: 0.8258 (t70) cc_final: 0.7860 (t-90) REVERT: T 16 LYS cc_start: 0.8807 (mttt) cc_final: 0.8336 (mttm) REVERT: T 33 LEU cc_start: 0.8853 (tp) cc_final: 0.8325 (tp) REVERT: T 38 TYR cc_start: 0.7876 (m-80) cc_final: 0.7632 (m-80) REVERT: T 48 LYS cc_start: 0.8630 (tttt) cc_final: 0.8048 (tptp) REVERT: T 82 MET cc_start: 0.8794 (mmt) cc_final: 0.8146 (mmt) REVERT: T 84 ARG cc_start: 0.8249 (mmt-90) cc_final: 0.7898 (mmt90) REVERT: T 90 LYS cc_start: 0.8933 (mttt) cc_final: 0.8495 (mttt) REVERT: T 98 LYS cc_start: 0.8871 (mttp) cc_final: 0.8097 (tttm) REVERT: T 107 VAL cc_start: 0.8498 (p) cc_final: 0.8267 (p) REVERT: U 1 MET cc_start: 0.6289 (ptt) cc_final: 0.5718 (mtp) REVERT: U 8 LEU cc_start: 0.7376 (OUTLIER) cc_final: 0.6617 (mt) REVERT: U 51 PHE cc_start: 0.7404 (m-80) cc_final: 0.7175 (m-80) REVERT: U 57 VAL cc_start: 0.8323 (p) cc_final: 0.8072 (p) REVERT: U 68 LYS cc_start: 0.5484 (mttp) cc_final: 0.5237 (mttt) REVERT: U 76 ARG cc_start: 0.8371 (ptm160) cc_final: 0.7867 (ptm160) REVERT: U 77 ARG cc_start: 0.7540 (mmt-90) cc_final: 0.7039 (mmt90) REVERT: U 91 GLN cc_start: 0.6863 (pm20) cc_final: 0.6571 (pm20) REVERT: V 6 ARG cc_start: 0.5557 (mpt-90) cc_final: 0.5325 (mmm-85) REVERT: V 12 ILE cc_start: 0.7667 (tt) cc_final: 0.7256 (tt) REVERT: V 24 LYS cc_start: 0.8555 (ttpt) cc_final: 0.8332 (tptt) REVERT: V 26 LYS cc_start: 0.8851 (mmmt) cc_final: 0.8539 (mmtp) REVERT: V 44 LYS cc_start: 0.8446 (tttt) cc_final: 0.7956 (tptp) REVERT: V 82 ARG cc_start: 0.6020 (mpp80) cc_final: 0.5708 (mtm-85) REVERT: W 1 MET cc_start: 0.6292 (tpt) cc_final: 0.5989 (ptm) REVERT: W 80 HIS cc_start: 0.7852 (t-90) cc_final: 0.7404 (t-90) REVERT: W 82 TYR cc_start: 0.8299 (OUTLIER) cc_final: 0.8092 (p90) REVERT: X 25 ARG cc_start: 0.7048 (OUTLIER) cc_final: 0.6815 (tpp-160) REVERT: Y 22 LEU cc_start: 0.8615 (mp) cc_final: 0.8233 (mp) REVERT: Y 27 ARG cc_start: 0.8279 (ttp80) cc_final: 0.7969 (tmm160) REVERT: Y 78 TYR cc_start: 0.6223 (OUTLIER) cc_final: 0.6011 (p90) REVERT: Z 16 THR cc_start: 0.8171 (m) cc_final: 0.7708 (p) REVERT: Z 37 LEU cc_start: 0.6778 (tp) cc_final: 0.5898 (tt) REVERT: Z 38 GLN cc_start: 0.8050 (mp10) cc_final: 0.7551 (pm20) REVERT: Z 47 ARG cc_start: 0.7413 (ttp-110) cc_final: 0.6772 (tmm160) REVERT: 0 34 HIS cc_start: 0.7674 (t-90) cc_final: 0.6995 (t70) REVERT: 0 54 MET cc_start: 0.8441 (ptm) cc_final: 0.7957 (ttm) REVERT: 1 31 ASP cc_start: 0.6135 (t70) cc_final: 0.5756 (t0) REVERT: 1 48 TYR cc_start: 0.7995 (m-80) cc_final: 0.7767 (m-80) REVERT: 3 9 VAL cc_start: 0.9183 (t) cc_final: 0.8689 (t) REVERT: 3 13 ASN cc_start: 0.9362 (m-40) cc_final: 0.9022 (m-40) REVERT: 3 14 ARG cc_start: 0.8868 (mtt180) cc_final: 0.8374 (mtt180) REVERT: 3 26 ASN cc_start: 0.9024 (m-40) cc_final: 0.8799 (m-40) REVERT: 4 17 THR cc_start: 0.5644 (p) cc_final: 0.4784 (t) REVERT: 4 24 HIS cc_start: 0.7779 (p90) cc_final: 0.7446 (p90) REVERT: 4 49 MET cc_start: 0.6191 (mmm) cc_final: 0.5619 (mmm) REVERT: 5 1 MET cc_start: 0.4099 (tpp) cc_final: 0.3855 (tpp) REVERT: 5 36 ARG cc_start: 0.8533 (ttt-90) cc_final: 0.8240 (ttt180) REVERT: b 15 HIS cc_start: 0.7166 (p-80) cc_final: 0.6911 (p-80) REVERT: b 30 PHE cc_start: 0.6803 (m-80) cc_final: 0.6551 (m-80) REVERT: b 49 MET cc_start: 0.8343 (mtt) cc_final: 0.7825 (mmm) REVERT: b 52 GLU cc_start: 0.8038 (tt0) cc_final: 0.7372 (tt0) REVERT: b 94 HIS cc_start: 0.6968 (m90) cc_final: 0.6528 (m170) REVERT: b 100 MET cc_start: 0.8085 (mtt) cc_final: 0.7742 (mtt) REVERT: b 111 ILE cc_start: 0.8265 (mt) cc_final: 0.7961 (mt) REVERT: b 183 VAL cc_start: 0.6100 (t) cc_final: 0.5791 (t) REVERT: b 187 VAL cc_start: 0.6577 (t) cc_final: 0.6330 (m) REVERT: c 14 ILE cc_start: 0.7450 (mm) cc_final: 0.6851 (mm) REVERT: c 22 TRP cc_start: 0.7372 (p-90) cc_final: 0.5794 (p-90) REVERT: c 86 LYS cc_start: 0.8641 (tttt) cc_final: 0.8429 (mttt) REVERT: c 103 ILE cc_start: 0.8332 (OUTLIER) cc_final: 0.8082 (mm) REVERT: c 129 MET cc_start: 0.8954 (mmm) cc_final: 0.8729 (tpp) REVERT: c 130 PHE cc_start: 0.8887 (p90) cc_final: 0.8377 (p90) REVERT: c 134 MET cc_start: 0.8905 (OUTLIER) cc_final: 0.8035 (ttp) REVERT: c 135 LYS cc_start: 0.8705 (ttpp) cc_final: 0.8492 (mmmm) REVERT: c 139 GLN cc_start: 0.9384 (mt0) cc_final: 0.9118 (mp10) REVERT: c 144 LEU cc_start: 0.8034 (mm) cc_final: 0.6734 (mm) REVERT: c 149 ILE cc_start: 0.8574 (tt) cc_final: 0.8102 (pt) REVERT: c 166 GLU cc_start: 0.7350 (tt0) cc_final: 0.6419 (tt0) REVERT: c 168 TYR cc_start: 0.7460 (m-80) cc_final: 0.6666 (m-80) REVERT: c 184 TYR cc_start: 0.7853 (t80) cc_final: 0.7042 (t80) REVERT: c 199 LYS cc_start: 0.8635 (mttt) cc_final: 0.8282 (mmtt) REVERT: d 3 ARG cc_start: 0.3777 (OUTLIER) cc_final: 0.2174 (ptp-110) REVERT: d 9 LEU cc_start: 0.6944 (mt) cc_final: 0.6667 (mt) REVERT: d 36 GLN cc_start: 0.7832 (tt0) cc_final: 0.7560 (tt0) REVERT: d 91 LEU cc_start: 0.6360 (OUTLIER) cc_final: 0.5858 (mp) REVERT: d 93 LEU cc_start: 0.5967 (OUTLIER) cc_final: 0.5680 (pp) REVERT: d 100 ASN cc_start: 0.7854 (t0) cc_final: 0.7244 (t0) REVERT: d 101 VAL cc_start: 0.8645 (t) cc_final: 0.8126 (t) REVERT: d 116 GLN cc_start: 0.6130 (OUTLIER) cc_final: 0.5015 (mm110) REVERT: d 146 ARG cc_start: 0.6449 (ttt180) cc_final: 0.6208 (ptp-170) REVERT: d 166 GLU cc_start: 0.6511 (tt0) cc_final: 0.6224 (tm-30) REVERT: d 172 GLU cc_start: 0.6481 (tt0) cc_final: 0.5956 (tm-30) REVERT: d 179 GLU cc_start: 0.8299 (tt0) cc_final: 0.7935 (tp30) REVERT: e 34 THR cc_start: 0.8137 (OUTLIER) cc_final: 0.7690 (m) REVERT: e 43 ASN cc_start: 0.7284 (t0) cc_final: 0.7020 (t0) REVERT: e 61 GLN cc_start: 0.8913 (tp40) cc_final: 0.8704 (tp40) REVERT: e 85 VAL cc_start: 0.7261 (p) cc_final: 0.6357 (m) REVERT: e 96 MET cc_start: 0.8385 (ttp) cc_final: 0.7929 (mpp) REVERT: e 105 ILE cc_start: 0.8254 (mp) cc_final: 0.8004 (pt) REVERT: e 117 VAL cc_start: 0.8240 (m) cc_final: 0.7150 (p) REVERT: e 123 VAL cc_start: 0.8736 (OUTLIER) cc_final: 0.8480 (p) REVERT: f 1 MET cc_start: 0.7151 (ttm) cc_final: 0.6919 (tmm) REVERT: f 18 VAL cc_start: 0.8504 (OUTLIER) cc_final: 0.8125 (t) REVERT: f 59 TYR cc_start: 0.7266 (m-80) cc_final: 0.6439 (m-80) REVERT: f 62 MET cc_start: 0.8509 (ttp) cc_final: 0.8200 (tpp) REVERT: f 94 HIS cc_start: 0.7709 (m90) cc_final: 0.7140 (m90) REVERT: g 56 LYS cc_start: 0.7093 (mttt) cc_final: 0.6837 (pttt) REVERT: g 59 LEU cc_start: 0.7864 (tt) cc_final: 0.7650 (tp) REVERT: g 89 VAL cc_start: 0.8207 (p) cc_final: 0.7817 (p) REVERT: g 92 ARG cc_start: 0.7885 (OUTLIER) cc_final: 0.7651 (ttp-110) REVERT: g 148 ASN cc_start: 0.7602 (m110) cc_final: 0.7032 (m-40) REVERT: h 66 PHE cc_start: 0.7880 (t80) cc_final: 0.7600 (t80) REVERT: h 67 GLN cc_start: 0.8295 (mm-40) cc_final: 0.7572 (mt0) REVERT: h 112 THR cc_start: 0.7139 (m) cc_final: 0.6905 (p) REVERT: i 6 TYR cc_start: 0.7253 (m-80) cc_final: 0.6959 (m-80) REVERT: i 64 TYR cc_start: 0.7077 (t80) cc_final: 0.6812 (t80) REVERT: i 90 TYR cc_start: 0.7745 (t80) cc_final: 0.7488 (t80) REVERT: i 91 ASP cc_start: 0.6920 (t0) cc_final: 0.6589 (t70) REVERT: i 124 ARG cc_start: 0.8440 (OUTLIER) cc_final: 0.8015 (mpt180) REVERT: j 6 ILE cc_start: 0.5803 (mt) cc_final: 0.5353 (pt) REVERT: j 77 VAL cc_start: 0.7264 (OUTLIER) cc_final: 0.7017 (m) REVERT: j 102 LEU cc_start: 0.6287 (OUTLIER) cc_final: 0.5839 (mp) REVERT: k 24 HIS cc_start: 0.7646 (t70) cc_final: 0.7184 (t70) REVERT: k 31 ILE cc_start: 0.7816 (mt) cc_final: 0.7545 (mt) REVERT: k 59 THR cc_start: 0.7703 (m) cc_final: 0.7321 (p) REVERT: k 77 TYR cc_start: 0.6664 (m-80) cc_final: 0.6390 (m-10) REVERT: k 94 GLU cc_start: 0.8808 (pt0) cc_final: 0.8604 (tm-30) REVERT: k 123 PRO cc_start: 0.8090 (Cg_exo) cc_final: 0.7871 (Cg_endo) REVERT: l 29 GLN cc_start: 0.9040 (mp10) cc_final: 0.8690 (mp10) REVERT: l 30 LYS cc_start: 0.8296 (mttt) cc_final: 0.7913 (mmmm) REVERT: l 33 VAL cc_start: 0.8808 (t) cc_final: 0.8540 (p) REVERT: l 67 ILE cc_start: 0.8657 (mt) cc_final: 0.8165 (mm) REVERT: l 75 GLN cc_start: 0.8797 (tt0) cc_final: 0.8413 (pm20) REVERT: l 97 THR cc_start: 0.8461 (p) cc_final: 0.8171 (p) REVERT: l 99 ARG cc_start: 0.5835 (mmm-85) cc_final: 0.5004 (ttt180) REVERT: l 107 VAL cc_start: 0.6830 (OUTLIER) cc_final: 0.5841 (p) REVERT: m 22 ILE cc_start: 0.5965 (OUTLIER) cc_final: 0.5656 (mt) REVERT: m 71 ARG cc_start: 0.6277 (ttm110) cc_final: 0.5906 (ttp80) REVERT: m 98 ARG cc_start: 0.7216 (mmt90) cc_final: 0.6746 (ttm110) REVERT: m 102 THR cc_start: 0.7811 (OUTLIER) cc_final: 0.7581 (m) REVERT: m 107 ARG cc_start: 0.7565 (mmp80) cc_final: 0.7358 (tpp80) REVERT: n 19 LYS cc_start: 0.7753 (tttm) cc_final: 0.7517 (tttm) REVERT: n 20 TYR cc_start: 0.8276 (OUTLIER) cc_final: 0.7448 (m-80) REVERT: n 33 ASP cc_start: 0.5878 (OUTLIER) cc_final: 0.5670 (t0) REVERT: n 51 LEU cc_start: 0.5755 (mt) cc_final: 0.5275 (mp) REVERT: n 69 ARG cc_start: 0.7852 (ttt-90) cc_final: 0.7253 (ttt-90) REVERT: n 83 LYS cc_start: 0.8788 (mmtt) cc_final: 0.8537 (tmtt) REVERT: n 85 ARG cc_start: 0.8347 (ttt-90) cc_final: 0.7805 (ttt180) REVERT: n 89 MET cc_start: 0.9019 (mmt) cc_final: 0.8647 (mmm) REVERT: o 57 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8753 (mp) REVERT: o 60 VAL cc_start: 0.8971 (t) cc_final: 0.8567 (t) REVERT: o 63 ARG cc_start: 0.8570 (ttt180) cc_final: 0.8355 (ptt180) REVERT: o 84 ARG cc_start: 0.7897 (OUTLIER) cc_final: 0.7217 (ttt-90) REVERT: p 36 VAL cc_start: 0.5183 (OUTLIER) cc_final: 0.4435 (t) REVERT: q 9 GLN cc_start: 0.7162 (mt0) cc_final: 0.6839 (tp-100) REVERT: q 18 GLU cc_start: 0.8832 (mt-10) cc_final: 0.8511 (pm20) REVERT: q 59 VAL cc_start: 0.5661 (p) cc_final: 0.5430 (t) REVERT: r 13 PHE cc_start: 0.6962 (m-80) cc_final: 0.6609 (m-80) REVERT: r 54 GLN cc_start: 0.8434 (mt0) cc_final: 0.8188 (tm-30) REVERT: s 11 ILE cc_start: 0.5451 (OUTLIER) cc_final: 0.5060 (tp) REVERT: s 18 LYS cc_start: 0.6141 (mtpt) cc_final: 0.5698 (mttp) REVERT: s 20 GLU cc_start: 0.6035 (tt0) cc_final: 0.5776 (mt-10) REVERT: s 24 GLU cc_start: 0.4485 (OUTLIER) cc_final: 0.4059 (mm-30) REVERT: s 36 ARG cc_start: 0.5336 (OUTLIER) cc_final: 0.4789 (ptt-90) REVERT: s 37 ARG cc_start: 0.7751 (mtm-85) cc_final: 0.7287 (mtm-85) REVERT: u 5 LYS cc_start: 0.8755 (pttm) cc_final: 0.8438 (tmtt) REVERT: u 18 ARG cc_start: 0.8068 (tmm-80) cc_final: 0.7857 (ttt-90) REVERT: u 44 GLU cc_start: 0.8944 (OUTLIER) cc_final: 0.8655 (tm-30) REVERT: v 80 VAL cc_start: 0.3821 (OUTLIER) cc_final: 0.3446 (m) REVERT: v 81 SER cc_start: 0.6123 (t) cc_final: 0.5884 (p) REVERT: v 114 GLU cc_start: 0.8816 (tm-30) cc_final: 0.8613 (mm-30) REVERT: v 115 PHE cc_start: 0.8601 (m-80) cc_final: 0.8355 (m-80) REVERT: v 128 CYS cc_start: 0.7792 (t) cc_final: 0.7418 (t) REVERT: v 133 GLN cc_start: 0.7538 (tp40) cc_final: 0.7270 (mm-40) REVERT: v 144 TRP cc_start: 0.8301 (t-100) cc_final: 0.7709 (t-100) REVERT: v 150 ARG cc_start: 0.7968 (OUTLIER) cc_final: 0.7673 (ptm-80) REVERT: v 178 SER cc_start: 0.6519 (t) cc_final: 0.5963 (m) REVERT: v 189 TYR cc_start: 0.7353 (t80) cc_final: 0.6925 (t80) REVERT: v 200 ARG cc_start: 0.7976 (ttt180) cc_final: 0.7564 (ttt180) REVERT: v 201 LEU cc_start: 0.8827 (tp) cc_final: 0.8214 (tp) REVERT: v 221 PHE cc_start: 0.8141 (t80) cc_final: 0.7606 (t80) REVERT: v 225 GLU cc_start: 0.7831 (tt0) cc_final: 0.7378 (tm-30) REVERT: v 234 ILE cc_start: 0.7344 (mm) cc_final: 0.7116 (mp) REVERT: v 274 CYS cc_start: 0.8545 (t) cc_final: 0.7711 (t) REVERT: v 277 ASP cc_start: 0.6751 (t70) cc_final: 0.6267 (t70) REVERT: v 279 SER cc_start: 0.8769 (t) cc_final: 0.8273 (p) REVERT: v 289 LYS cc_start: 0.9154 (tttt) cc_final: 0.8920 (tmmt) REVERT: v 296 TYR cc_start: 0.8826 (t80) cc_final: 0.8398 (t80) REVERT: v 299 GLU cc_start: 0.9140 (OUTLIER) cc_final: 0.8832 (pt0) REVERT: v 306 GLU cc_start: 0.8495 (tt0) cc_final: 0.8125 (pt0) REVERT: v 307 LYS cc_start: 0.9054 (tptt) cc_final: 0.8749 (tptt) REVERT: v 310 MET cc_start: 0.8377 (OUTLIER) cc_final: 0.8037 (mtm) REVERT: v 311 GLU cc_start: 0.8595 (mm-30) cc_final: 0.8178 (mm-30) REVERT: w 6 HIS cc_start: 0.7025 (m-70) cc_final: 0.5727 (m-70) REVERT: w 10 GLN cc_start: 0.8399 (tt0) cc_final: 0.8080 (tt0) REVERT: w 13 ASP cc_start: 0.8347 (OUTLIER) cc_final: 0.8080 (t70) REVERT: w 14 ASN cc_start: 0.8132 (m-40) cc_final: 0.7899 (t0) outliers start: 413 outliers final: 88 residues processed: 2382 average time/residue: 1.5317 time to fit residues: 6035.3608 Evaluate side-chains 1786 residues out of total 5041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 1645 time to evaluate : 6.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 156 ARG Chi-restraints excluded: chain C residue 175 ARG Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 221 ARG Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 141 ARG Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 179 ARG Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain F residue 22 TYR Chi-restraints excluded: chain F residue 135 GLN Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 27 ARG Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 37 PHE Chi-restraints excluded: chain K residue 28 LEU Chi-restraints excluded: chain K residue 95 ARG Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 31 ARG Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 78 ARG Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 116 ILE Chi-restraints excluded: chain M residue 27 LEU Chi-restraints excluded: chain M residue 48 ARG Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain N residue 66 ARG Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 101 VAL Chi-restraints excluded: chain O residue 37 THR Chi-restraints excluded: chain O residue 70 THR Chi-restraints excluded: chain P residue 7 ARG Chi-restraints excluded: chain P residue 36 TYR Chi-restraints excluded: chain P residue 53 THR Chi-restraints excluded: chain Q residue 33 VAL Chi-restraints excluded: chain Q residue 88 ARG Chi-restraints excluded: chain Q residue 100 LEU Chi-restraints excluded: chain R residue 11 ARG Chi-restraints excluded: chain R residue 30 ARG Chi-restraints excluded: chain R residue 53 ARG Chi-restraints excluded: chain R residue 74 ILE Chi-restraints excluded: chain S residue 23 GLU Chi-restraints excluded: chain S residue 47 VAL Chi-restraints excluded: chain S residue 80 ARG Chi-restraints excluded: chain U residue 8 LEU Chi-restraints excluded: chain V residue 49 VAL Chi-restraints excluded: chain W residue 82 TYR Chi-restraints excluded: chain X residue 25 ARG Chi-restraints excluded: chain X residue 69 PHE Chi-restraints excluded: chain Y residue 23 ASN Chi-restraints excluded: chain Y residue 33 LEU Chi-restraints excluded: chain Y residue 37 ARG Chi-restraints excluded: chain Y residue 40 VAL Chi-restraints excluded: chain Y residue 46 PHE Chi-restraints excluded: chain Y residue 78 TYR Chi-restraints excluded: chain 4 residue 4 ILE Chi-restraints excluded: chain 4 residue 38 THR Chi-restraints excluded: chain b residue 97 LEU Chi-restraints excluded: chain b residue 114 LEU Chi-restraints excluded: chain c residue 103 ILE Chi-restraints excluded: chain c residue 128 VAL Chi-restraints excluded: chain c residue 134 MET Chi-restraints excluded: chain c residue 140 ASN Chi-restraints excluded: chain c residue 169 ARG Chi-restraints excluded: chain d residue 3 ARG Chi-restraints excluded: chain d residue 91 LEU Chi-restraints excluded: chain d residue 93 LEU Chi-restraints excluded: chain d residue 116 GLN Chi-restraints excluded: chain d residue 195 ILE Chi-restraints excluded: chain e residue 16 ILE Chi-restraints excluded: chain e residue 31 PHE Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 56 VAL Chi-restraints excluded: chain e residue 93 ARG Chi-restraints excluded: chain e residue 123 VAL Chi-restraints excluded: chain f residue 18 VAL Chi-restraints excluded: chain f residue 86 ARG Chi-restraints excluded: chain g residue 92 ARG Chi-restraints excluded: chain g residue 105 VAL Chi-restraints excluded: chain h residue 32 LEU Chi-restraints excluded: chain h residue 76 GLN Chi-restraints excluded: chain h residue 83 LEU Chi-restraints excluded: chain h residue 106 THR Chi-restraints excluded: chain h residue 110 VAL Chi-restraints excluded: chain i residue 115 LYS Chi-restraints excluded: chain i residue 119 ARG Chi-restraints excluded: chain i residue 124 ARG Chi-restraints excluded: chain i residue 130 ARG Chi-restraints excluded: chain j residue 7 ARG Chi-restraints excluded: chain j residue 53 ILE Chi-restraints excluded: chain j residue 77 VAL Chi-restraints excluded: chain j residue 102 LEU Chi-restraints excluded: chain k residue 37 ARG Chi-restraints excluded: chain k residue 53 ARG Chi-restraints excluded: chain l residue 56 ARG Chi-restraints excluded: chain l residue 74 LEU Chi-restraints excluded: chain l residue 107 VAL Chi-restraints excluded: chain l residue 110 ARG Chi-restraints excluded: chain m residue 22 ILE Chi-restraints excluded: chain m residue 102 THR Chi-restraints excluded: chain m residue 113 ARG Chi-restraints excluded: chain n residue 20 TYR Chi-restraints excluded: chain n residue 33 ASP Chi-restraints excluded: chain o residue 57 LEU Chi-restraints excluded: chain o residue 84 ARG Chi-restraints excluded: chain o residue 89 ARG Chi-restraints excluded: chain p residue 14 ARG Chi-restraints excluded: chain p residue 25 ARG Chi-restraints excluded: chain p residue 36 VAL Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain q residue 79 VAL Chi-restraints excluded: chain r residue 18 VAL Chi-restraints excluded: chain r residue 72 ASP Chi-restraints excluded: chain s residue 11 ILE Chi-restraints excluded: chain s residue 24 GLU Chi-restraints excluded: chain s residue 36 ARG Chi-restraints excluded: chain s residue 55 ARG Chi-restraints excluded: chain t residue 18 ARG Chi-restraints excluded: chain u residue 44 GLU Chi-restraints excluded: chain v residue 80 VAL Chi-restraints excluded: chain v residue 150 ARG Chi-restraints excluded: chain v residue 163 THR Chi-restraints excluded: chain v residue 167 GLU Chi-restraints excluded: chain v residue 254 VAL Chi-restraints excluded: chain v residue 273 GLN Chi-restraints excluded: chain v residue 285 ASP Chi-restraints excluded: chain v residue 299 GLU Chi-restraints excluded: chain v residue 310 MET Chi-restraints excluded: chain v residue 361 LEU Chi-restraints excluded: chain w residue 13 ASP Chi-restraints excluded: chain w residue 17 GLU Chi-restraints excluded: chain w residue 20 LEU Chi-restraints excluded: chain w residue 22 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1061 random chunks: chunk 895 optimal weight: 9.9990 chunk 804 optimal weight: 8.9990 chunk 446 optimal weight: 6.9990 chunk 274 optimal weight: 20.0000 chunk 542 optimal weight: 5.9990 chunk 429 optimal weight: 0.3980 chunk 831 optimal weight: 3.9990 chunk 321 optimal weight: 3.9990 chunk 505 optimal weight: 6.9990 chunk 618 optimal weight: 2.9990 chunk 963 optimal weight: 9.9990 overall best weight: 3.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 58 HIS C 86 ASN ** C 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 HIS D 173 GLN E 90 GLN E 156 ASN F 5 HIS F 63 GLN G 111 HIS H 135 HIS ** K 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 138 GLN M 35 HIS M 38 GLN N 17 ASN N 97 GLN O 16 HIS ** O 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 98 GLN ** Q 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 115 ASN R 20 GLN R 56 GLN R 72 ASN R 81 ASN S 66 HIS S 91 GLN ** T 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 15 GLN T 61 ASN ** T 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 46 GLN V 74 ASN ** W 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 76 ASN Y 16 ASN Z 27 ASN Z 58 ASN 0 49 ASN 1 6 ASN ** b 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 103 ASN b 122 GLN b 177 ASN ** c 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 41 GLN c 102 ASN c 123 GLN d 36 GLN ** e 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 61 GLN e 77 ASN e 146 ASN ** f 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 52 ASN g 86 GLN g 130 ASN i 32 GLN i 50 GLN i 110 GLN i 126 GLN j 58 ASN k 28 ASN k 81 ASN ** k 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 6 GLN l 73 ASN m 105 ASN o 28 GLN ** p 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 51 ASN ** r 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 54 GLN s 53 ASN t 21 ASN v 43 GLN v 48 ASN ** v 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 214 HIS ** v 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 322 GLN w 27 GLN Total number of N/Q/H flips: 67 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 162161 Z= 0.229 Angle : 0.719 15.685 242281 Z= 0.381 Chirality : 0.039 0.472 30825 Planarity : 0.007 0.130 13212 Dihedral : 24.631 179.802 80684 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 17.94 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.82 % Favored : 94.98 % Rotamer: Outliers : 6.35 % Allowed : 21.54 % Favored : 72.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.11), residues: 6054 helix: 2.22 (0.11), residues: 2107 sheet: -1.06 (0.15), residues: 1037 loop : -1.74 (0.10), residues: 2910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 248 HIS 0.015 0.002 HIS w 6 PHE 0.034 0.003 PHE O 21 TYR 0.027 0.002 TYR d 75 ARG 0.011 0.001 ARG L 71 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12108 Ramachandran restraints generated. 6054 Oldfield, 0 Emsley, 6054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12108 Ramachandran restraints generated. 6054 Oldfield, 0 Emsley, 6054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2069 residues out of total 5041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 320 poor density : 1749 time to evaluate : 6.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 46 ASN cc_start: 0.8981 (m-40) cc_final: 0.8749 (m-40) REVERT: C 69 ARG cc_start: 0.8643 (mmm-85) cc_final: 0.8367 (mtp85) REVERT: C 82 GLU cc_start: 0.8247 (mt-10) cc_final: 0.7437 (mp0) REVERT: C 83 TYR cc_start: 0.8536 (t80) cc_final: 0.7848 (t80) REVERT: C 84 ASP cc_start: 0.7509 (t0) cc_final: 0.7076 (t0) REVERT: C 87 ARG cc_start: 0.8458 (ptp-170) cc_final: 0.8240 (ptp90) REVERT: C 91 ILE cc_start: 0.8910 (pt) cc_final: 0.8703 (pt) REVERT: C 115 GLN cc_start: 0.7778 (mt0) cc_final: 0.7365 (tp40) REVERT: C 146 MET cc_start: 0.7316 (mtt) cc_final: 0.6216 (mmp) REVERT: C 175 ARG cc_start: 0.8540 (ttt90) cc_final: 0.8210 (ptm160) REVERT: C 213 TRP cc_start: 0.8992 (m-10) cc_final: 0.8599 (m-10) REVERT: C 221 ARG cc_start: 0.9060 (mtm180) cc_final: 0.8781 (mtm110) REVERT: C 261 LYS cc_start: 0.8571 (tttt) cc_final: 0.8368 (mtpp) REVERT: C 267 ILE cc_start: 0.7168 (mm) cc_final: 0.6948 (mm) REVERT: D 2 ILE cc_start: 0.2615 (OUTLIER) cc_final: 0.2395 (mp) REVERT: D 36 GLN cc_start: 0.7023 (tt0) cc_final: 0.6522 (tm-30) REVERT: D 40 LEU cc_start: 0.7687 (mt) cc_final: 0.7386 (pt) REVERT: D 43 ASP cc_start: 0.4084 (m-30) cc_final: 0.3472 (m-30) REVERT: D 124 ARG cc_start: 0.7857 (ttt-90) cc_final: 0.6998 (ttt180) REVERT: D 125 TRP cc_start: 0.8793 (m100) cc_final: 0.8315 (m100) REVERT: D 127 PHE cc_start: 0.9144 (m-10) cc_final: 0.8736 (m-80) REVERT: D 165 MET cc_start: 0.8085 (ttt) cc_final: 0.7646 (ttt) REVERT: D 190 LYS cc_start: 0.6083 (tttp) cc_final: 0.5601 (mmmt) REVERT: E 25 GLU cc_start: 0.8554 (tt0) cc_final: 0.7836 (tp30) REVERT: E 49 ARG cc_start: 0.9158 (ptm160) cc_final: 0.8688 (ptm-80) REVERT: E 60 TRP cc_start: 0.6879 (p90) cc_final: 0.6248 (p90) REVERT: E 67 ARG cc_start: 0.7187 (mtp85) cc_final: 0.6792 (mtp85) REVERT: E 99 LYS cc_start: 0.8266 (mtpt) cc_final: 0.7640 (mptt) REVERT: E 100 MET cc_start: 0.8363 (mtp) cc_final: 0.7903 (mtp) REVERT: E 116 ASP cc_start: 0.6843 (m-30) cc_final: 0.6640 (m-30) REVERT: E 123 LYS cc_start: 0.7828 (tttp) cc_final: 0.7579 (ptpp) REVERT: E 189 THR cc_start: 0.6916 (OUTLIER) cc_final: 0.6137 (p) REVERT: F 44 ILE cc_start: 0.8261 (pt) cc_final: 0.8035 (mt) REVERT: F 80 ARG cc_start: 0.8260 (mmm-85) cc_final: 0.7988 (mmm160) REVERT: F 83 TYR cc_start: 0.6868 (t80) cc_final: 0.6232 (t80) REVERT: F 110 ARG cc_start: 0.4175 (mmp-170) cc_final: 0.2862 (tmm160) REVERT: F 120 LYS cc_start: 0.8565 (tttp) cc_final: 0.8216 (tptp) REVERT: F 174 ASP cc_start: 0.5935 (t0) cc_final: 0.5641 (t0) REVERT: G 35 ARG cc_start: 0.6331 (tpt170) cc_final: 0.5992 (tpt170) REVERT: G 89 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7842 (pp) REVERT: G 130 GLU cc_start: 0.1392 (OUTLIER) cc_final: 0.1167 (tm-30) REVERT: H 87 GLU cc_start: 0.1929 (mm-30) cc_final: 0.1669 (mp0) REVERT: J 37 PHE cc_start: 0.2915 (OUTLIER) cc_final: 0.2496 (m-80) REVERT: J 61 TYR cc_start: 0.5037 (OUTLIER) cc_final: 0.4561 (m-10) REVERT: K 1 MET cc_start: 0.5081 (tmm) cc_final: 0.4818 (tmm) REVERT: K 16 TYR cc_start: 0.6398 (m-80) cc_final: 0.5968 (m-10) REVERT: K 35 ARG cc_start: 0.7507 (mpt90) cc_final: 0.7298 (ttm-80) REVERT: K 116 ARG cc_start: 0.7711 (mtm-85) cc_final: 0.7408 (mtm-85) REVERT: K 119 PHE cc_start: 0.8027 (t80) cc_final: 0.7631 (t80) REVERT: K 138 GLN cc_start: 0.7875 (pt0) cc_final: 0.7589 (mp10) REVERT: L 18 ARG cc_start: 0.8747 (mmt180) cc_final: 0.8493 (mmm-85) REVERT: L 45 GLU cc_start: 0.8537 (tt0) cc_final: 0.8046 (tt0) REVERT: L 56 ASP cc_start: 0.8110 (m-30) cc_final: 0.7768 (t0) REVERT: L 64 ARG cc_start: 0.6249 (mtm180) cc_final: 0.5952 (mtm-85) REVERT: L 116 ILE cc_start: 0.6846 (OUTLIER) cc_final: 0.6298 (tp) REVERT: M 55 MET cc_start: 0.8922 (tpp) cc_final: 0.8612 (tpp) REVERT: N 8 LYS cc_start: 0.8269 (mmtt) cc_final: 0.7856 (mmtm) REVERT: N 12 MET cc_start: 0.8360 (ttm) cc_final: 0.8115 (mtm) REVERT: N 13 HIS cc_start: 0.8090 (m-70) cc_final: 0.7597 (m-70) REVERT: N 68 PHE cc_start: 0.8231 (t80) cc_final: 0.7776 (t80) REVERT: N 92 TRP cc_start: 0.7699 (m100) cc_final: 0.7158 (m100) REVERT: O 21 PHE cc_start: 0.8948 (m-80) cc_final: 0.8636 (m-80) REVERT: O 29 VAL cc_start: 0.8617 (t) cc_final: 0.8016 (t) REVERT: O 37 THR cc_start: 0.8110 (m) cc_final: 0.7646 (t) REVERT: O 78 LYS cc_start: 0.8378 (tttt) cc_final: 0.7897 (tptp) REVERT: O 86 ARG cc_start: 0.6957 (ttm170) cc_final: 0.6578 (tpp80) REVERT: O 87 PHE cc_start: 0.5320 (m-80) cc_final: 0.4960 (m-10) REVERT: O 110 MET cc_start: 0.7409 (mmm) cc_final: 0.7205 (mmm) REVERT: P 7 ARG cc_start: 0.7996 (OUTLIER) cc_final: 0.7604 (ttt90) REVERT: P 16 ARG cc_start: 0.8443 (mmt-90) cc_final: 0.8134 (mtt-85) REVERT: P 34 HIS cc_start: 0.4964 (m90) cc_final: 0.4746 (m-70) REVERT: Q 84 ILE cc_start: 0.4485 (OUTLIER) cc_final: 0.4064 (mt) REVERT: Q 110 ILE cc_start: 0.7267 (pt) cc_final: 0.6901 (tt) REVERT: R 16 LYS cc_start: 0.8475 (pttt) cc_final: 0.8157 (pttt) REVERT: R 20 GLN cc_start: 0.8829 (mt0) cc_final: 0.8470 (mt0) REVERT: R 22 LYS cc_start: 0.8472 (tttt) cc_final: 0.8212 (tppp) REVERT: S 6 GLN cc_start: 0.8918 (tm-30) cc_final: 0.8639 (tm-30) REVERT: S 53 PHE cc_start: 0.8039 (p90) cc_final: 0.7427 (m-10) REVERT: T 1 MET cc_start: 0.6682 (tpt) cc_final: 0.6337 (tpt) REVERT: T 13 SER cc_start: 0.5256 (p) cc_final: 0.4508 (p) REVERT: T 16 LYS cc_start: 0.8887 (mttt) cc_final: 0.8453 (mttp) REVERT: T 82 MET cc_start: 0.8881 (mmt) cc_final: 0.8328 (mmt) REVERT: T 84 ARG cc_start: 0.8260 (mmt-90) cc_final: 0.8034 (mmt90) REVERT: T 90 LYS cc_start: 0.8749 (mttt) cc_final: 0.8234 (mttt) REVERT: T 98 LYS cc_start: 0.8690 (mttp) cc_final: 0.8170 (tttp) REVERT: U 2 ILE cc_start: 0.4580 (mt) cc_final: 0.3865 (mt) REVERT: U 44 LYS cc_start: 0.9116 (tttm) cc_final: 0.8891 (tttp) REVERT: U 51 PHE cc_start: 0.7345 (m-80) cc_final: 0.7087 (m-80) REVERT: U 59 ASN cc_start: 0.7239 (m-40) cc_final: 0.7001 (t0) REVERT: U 69 ARG cc_start: 0.7300 (ttm-80) cc_final: 0.6977 (tpp80) REVERT: U 76 ARG cc_start: 0.8392 (ptm160) cc_final: 0.7924 (ptm160) REVERT: U 77 ARG cc_start: 0.7577 (OUTLIER) cc_final: 0.7315 (mmt90) REVERT: V 62 GLU cc_start: 0.7235 (mp0) cc_final: 0.6874 (mt-10) REVERT: V 82 ARG cc_start: 0.6106 (mpp80) cc_final: 0.5859 (mtm-85) REVERT: W 1 MET cc_start: 0.6231 (tpt) cc_final: 0.5975 (ptt) REVERT: W 80 HIS cc_start: 0.7382 (t-90) cc_final: 0.7175 (t-90) REVERT: X 68 LYS cc_start: 0.8235 (tptp) cc_final: 0.7817 (ptpt) REVERT: X 70 GLU cc_start: 0.7947 (mp0) cc_final: 0.7644 (mp0) REVERT: Y 27 ARG cc_start: 0.8425 (ttp80) cc_final: 0.7995 (ttp80) REVERT: Z 4 LYS cc_start: 0.7325 (ttpp) cc_final: 0.6812 (mmtp) REVERT: Z 31 GLN cc_start: 0.7791 (mt0) cc_final: 0.7525 (tt0) REVERT: Z 37 LEU cc_start: 0.6801 (tp) cc_final: 0.6564 (tp) REVERT: Z 38 GLN cc_start: 0.8098 (mp10) cc_final: 0.7580 (pp30) REVERT: Z 47 ARG cc_start: 0.7453 (ttp-110) cc_final: 0.7084 (ttp80) REVERT: 0 36 VAL cc_start: 0.6076 (m) cc_final: 0.5685 (m) REVERT: 0 54 MET cc_start: 0.8434 (ptm) cc_final: 0.8223 (ttm) REVERT: 1 16 ARG cc_start: 0.8115 (ttp-170) cc_final: 0.7855 (ttp-170) REVERT: 1 38 HIS cc_start: 0.7211 (p90) cc_final: 0.6750 (p-80) REVERT: 1 50 ARG cc_start: 0.6232 (mtt180) cc_final: 0.5942 (mtt180) REVERT: 2 49 TYR cc_start: 0.3315 (m-80) cc_final: 0.2405 (m-80) REVERT: 3 9 VAL cc_start: 0.9215 (t) cc_final: 0.8732 (t) REVERT: 3 13 ASN cc_start: 0.9313 (m-40) cc_final: 0.9002 (m-40) REVERT: 4 3 LYS cc_start: 0.7473 (mtmm) cc_final: 0.7179 (ttmt) REVERT: 4 4 ILE cc_start: 0.8642 (mt) cc_final: 0.8209 (pt) REVERT: 4 24 HIS cc_start: 0.7771 (p90) cc_final: 0.7384 (p90) REVERT: 4 49 MET cc_start: 0.6033 (mmm) cc_final: 0.5528 (mmm) REVERT: b 28 LYS cc_start: 0.7990 (tttt) cc_final: 0.7746 (mmmt) REVERT: b 30 PHE cc_start: 0.6955 (m-80) cc_final: 0.6465 (m-10) REVERT: b 49 MET cc_start: 0.8324 (mtt) cc_final: 0.7985 (mmm) REVERT: b 94 HIS cc_start: 0.6862 (m90) cc_final: 0.6446 (m170) REVERT: b 103 ASN cc_start: 0.7260 (OUTLIER) cc_final: 0.6870 (m-40) REVERT: c 6 HIS cc_start: 0.8582 (t-90) cc_final: 0.8217 (t-90) REVERT: c 18 TRP cc_start: 0.5318 (OUTLIER) cc_final: 0.4969 (m-10) REVERT: c 22 TRP cc_start: 0.7025 (p-90) cc_final: 0.6197 (p-90) REVERT: c 49 LYS cc_start: 0.7269 (OUTLIER) cc_final: 0.6909 (tttp) REVERT: c 82 GLU cc_start: 0.7984 (mt-10) cc_final: 0.7749 (pm20) REVERT: c 83 ASP cc_start: 0.8164 (p0) cc_final: 0.7375 (p0) REVERT: c 86 LYS cc_start: 0.8717 (tttt) cc_final: 0.8371 (mtmt) REVERT: c 103 ILE cc_start: 0.8308 (OUTLIER) cc_final: 0.8005 (mm) REVERT: c 129 MET cc_start: 0.8840 (mmm) cc_final: 0.8390 (tpp) REVERT: c 130 PHE cc_start: 0.8930 (p90) cc_final: 0.8595 (p90) REVERT: c 149 ILE cc_start: 0.8422 (OUTLIER) cc_final: 0.8072 (pt) REVERT: c 166 GLU cc_start: 0.7626 (tt0) cc_final: 0.6945 (tt0) REVERT: c 199 LYS cc_start: 0.8412 (mttt) cc_final: 0.8148 (mmtt) REVERT: c 202 ILE cc_start: 0.8073 (mt) cc_final: 0.7675 (tt) REVERT: d 3 ARG cc_start: 0.3952 (OUTLIER) cc_final: 0.2233 (ptp-110) REVERT: d 9 LEU cc_start: 0.6853 (mt) cc_final: 0.6476 (mt) REVERT: d 36 GLN cc_start: 0.7774 (OUTLIER) cc_final: 0.7420 (tt0) REVERT: d 44 ARG cc_start: 0.7376 (ttt-90) cc_final: 0.7118 (mtt90) REVERT: d 172 GLU cc_start: 0.6467 (tt0) cc_final: 0.6162 (tm-30) REVERT: d 179 GLU cc_start: 0.8232 (tt0) cc_final: 0.7914 (tp30) REVERT: d 196 ASN cc_start: 0.7972 (t0) cc_final: 0.7719 (t0) REVERT: e 12 GLN cc_start: 0.6927 (tm-30) cc_final: 0.6718 (pt0) REVERT: e 61 GLN cc_start: 0.8848 (tp-100) cc_final: 0.8569 (tp40) REVERT: e 64 MET cc_start: 0.8596 (ttp) cc_final: 0.8360 (tpt) REVERT: e 105 ILE cc_start: 0.8073 (mp) cc_final: 0.7672 (pt) REVERT: e 120 VAL cc_start: 0.7747 (OUTLIER) cc_final: 0.7396 (p) REVERT: f 78 PHE cc_start: 0.8359 (m-10) cc_final: 0.8063 (m-10) REVERT: g 25 LYS cc_start: 0.6660 (mtmm) cc_final: 0.6140 (mmmt) REVERT: g 95 ARG cc_start: 0.7560 (ptm-80) cc_final: 0.6940 (ttt90) REVERT: g 139 GLU cc_start: 0.8223 (mt-10) cc_final: 0.7944 (mm-30) REVERT: h 10 MET cc_start: 0.8252 (tmm) cc_final: 0.7998 (ptp) REVERT: h 15 ARG cc_start: 0.6983 (ttp-110) cc_final: 0.6744 (ttm170) REVERT: h 33 LYS cc_start: 0.8777 (tttt) cc_final: 0.8497 (mttt) REVERT: h 49 PHE cc_start: 0.7505 (p90) cc_final: 0.7281 (p90) REVERT: h 71 VAL cc_start: 0.6537 (t) cc_final: 0.6247 (m) REVERT: h 76 GLN cc_start: 0.8625 (OUTLIER) cc_final: 0.8180 (mm110) REVERT: h 127 CYS cc_start: 0.8605 (m) cc_final: 0.8355 (m) REVERT: i 6 TYR cc_start: 0.7258 (m-80) cc_final: 0.7036 (m-80) REVERT: i 20 PHE cc_start: 0.6090 (m-80) cc_final: 0.5879 (m-10) REVERT: i 88 MET cc_start: 0.8235 (mmp) cc_final: 0.7701 (mmm) REVERT: i 109 ARG cc_start: 0.6386 (mmm-85) cc_final: 0.5971 (mtp180) REVERT: j 6 ILE cc_start: 0.5536 (mt) cc_final: 0.5094 (pt) REVERT: j 68 ARG cc_start: 0.8573 (OUTLIER) cc_final: 0.8354 (mpt180) REVERT: j 102 LEU cc_start: 0.6367 (OUTLIER) cc_final: 0.5861 (mp) REVERT: k 24 HIS cc_start: 0.7362 (t70) cc_final: 0.6945 (t70) REVERT: k 28 ASN cc_start: 0.7127 (m-40) cc_final: 0.6829 (m-40) REVERT: k 59 THR cc_start: 0.7642 (m) cc_final: 0.7104 (p) REVERT: l 29 GLN cc_start: 0.9022 (mp10) cc_final: 0.8516 (mp10) REVERT: l 30 LYS cc_start: 0.8376 (mttt) cc_final: 0.7975 (mmmt) REVERT: l 33 VAL cc_start: 0.8717 (t) cc_final: 0.8504 (p) REVERT: l 75 GLN cc_start: 0.8620 (tt0) cc_final: 0.8287 (pm20) REVERT: l 99 ARG cc_start: 0.5785 (mmm-85) cc_final: 0.4790 (ttt180) REVERT: l 107 VAL cc_start: 0.7076 (t) cc_final: 0.6393 (p) REVERT: l 111 LYS cc_start: 0.6410 (mmtm) cc_final: 0.5962 (mptt) REVERT: l 112 GLN cc_start: 0.7490 (mt0) cc_final: 0.7279 (mt0) REVERT: m 71 ARG cc_start: 0.6404 (ttm110) cc_final: 0.5959 (ttp80) REVERT: m 87 ARG cc_start: 0.8342 (mtp85) cc_final: 0.8138 (mtp-110) REVERT: m 98 ARG cc_start: 0.7117 (mmt90) cc_final: 0.6361 (ttm110) REVERT: n 69 ARG cc_start: 0.8073 (ttt-90) cc_final: 0.7434 (ttt180) REVERT: n 75 ARG cc_start: 0.7425 (mtt90) cc_final: 0.6981 (mtt-85) REVERT: n 85 ARG cc_start: 0.8078 (ttt-90) cc_final: 0.7623 (ttt180) REVERT: n 89 MET cc_start: 0.8954 (mmt) cc_final: 0.8491 (mmm) REVERT: n 97 LYS cc_start: 0.8317 (tptt) cc_final: 0.8052 (tptt) REVERT: o 17 ARG cc_start: 0.6492 (mtm180) cc_final: 0.6266 (pmt-80) REVERT: o 26 GLU cc_start: 0.8021 (pt0) cc_final: 0.7769 (pp20) REVERT: o 57 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8662 (mp) REVERT: o 60 VAL cc_start: 0.9009 (t) cc_final: 0.8579 (t) REVERT: o 63 ARG cc_start: 0.8676 (ttt180) cc_final: 0.8426 (ptt180) REVERT: o 84 ARG cc_start: 0.8209 (OUTLIER) cc_final: 0.7807 (ttt180) REVERT: p 36 VAL cc_start: 0.3462 (OUTLIER) cc_final: 0.3137 (t) REVERT: q 9 GLN cc_start: 0.6849 (mt0) cc_final: 0.6627 (tp-100) REVERT: s 18 LYS cc_start: 0.5925 (mtpt) cc_final: 0.5693 (mttp) REVERT: s 24 GLU cc_start: 0.4389 (OUTLIER) cc_final: 0.3977 (mm-30) REVERT: t 43 ASP cc_start: 0.7046 (t0) cc_final: 0.6732 (p0) REVERT: t 83 ILE cc_start: 0.6607 (pp) cc_final: 0.6116 (pt) REVERT: u 5 LYS cc_start: 0.8749 (pttm) cc_final: 0.8442 (tmtt) REVERT: v 14 LEU cc_start: 0.5502 (mm) cc_final: 0.5236 (mm) REVERT: v 80 VAL cc_start: 0.2660 (OUTLIER) cc_final: 0.2324 (p) REVERT: v 108 GLU cc_start: 0.7309 (tm-30) cc_final: 0.6928 (mt-10) REVERT: v 178 SER cc_start: 0.6179 (t) cc_final: 0.5597 (m) REVERT: v 201 LEU cc_start: 0.8956 (tp) cc_final: 0.8539 (tp) REVERT: v 244 TYR cc_start: 0.7533 (p90) cc_final: 0.7303 (p90) REVERT: v 258 GLU cc_start: 0.8771 (mm-30) cc_final: 0.8116 (mm-30) REVERT: v 277 ASP cc_start: 0.7037 (t70) cc_final: 0.6515 (t70) REVERT: v 279 SER cc_start: 0.8669 (t) cc_final: 0.8057 (p) REVERT: v 296 TYR cc_start: 0.8840 (t80) cc_final: 0.8364 (t80) REVERT: v 299 GLU cc_start: 0.9147 (mm-30) cc_final: 0.8812 (pt0) REVERT: v 300 MET cc_start: 0.8907 (tpp) cc_final: 0.8593 (mmp) REVERT: v 311 GLU cc_start: 0.8379 (mm-30) cc_final: 0.7941 (pp20) REVERT: v 326 TYR cc_start: 0.8464 (m-80) cc_final: 0.8199 (m-80) REVERT: v 329 ASP cc_start: 0.7577 (OUTLIER) cc_final: 0.7357 (t0) REVERT: w 3 ARG cc_start: 0.7160 (tpt-90) cc_final: 0.6840 (tpt-90) REVERT: w 10 GLN cc_start: 0.8461 (tt0) cc_final: 0.8177 (tt0) REVERT: w 11 ILE cc_start: 0.8915 (mp) cc_final: 0.8471 (mp) REVERT: w 14 ASN cc_start: 0.7911 (m-40) cc_final: 0.7459 (t0) REVERT: w 30 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7002 (mp0) REVERT: w 41 ARG cc_start: 0.4208 (OUTLIER) cc_final: 0.3991 (ptp-170) outliers start: 320 outliers final: 161 residues processed: 1915 average time/residue: 1.6085 time to fit residues: 5157.2231 Evaluate side-chains 1722 residues out of total 5041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 1532 time to evaluate : 5.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 111 LYS Chi-restraints excluded: chain C residue 114 ASP Chi-restraints excluded: chain C residue 133 ARG Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 103 ILE Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain G residue 130 GLU Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 37 PHE Chi-restraints excluded: chain J residue 61 TYR Chi-restraints excluded: chain J residue 121 ILE Chi-restraints excluded: chain K residue 19 ASP Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 29 HIS Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 87 LEU Chi-restraints excluded: chain L residue 99 ILE Chi-restraints excluded: chain L residue 116 ILE Chi-restraints excluded: chain M residue 27 LEU Chi-restraints excluded: chain M residue 85 VAL Chi-restraints excluded: chain M residue 121 THR Chi-restraints excluded: chain M residue 122 VAL Chi-restraints excluded: chain M residue 125 LEU Chi-restraints excluded: chain N residue 73 ILE Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 126 ILE Chi-restraints excluded: chain N residue 135 VAL Chi-restraints excluded: chain O residue 16 HIS Chi-restraints excluded: chain O residue 17 ARG Chi-restraints excluded: chain O residue 70 THR Chi-restraints excluded: chain P residue 7 ARG Chi-restraints excluded: chain P residue 53 THR Chi-restraints excluded: chain P residue 97 PHE Chi-restraints excluded: chain Q residue 56 HIS Chi-restraints excluded: chain Q residue 61 VAL Chi-restraints excluded: chain Q residue 84 ILE Chi-restraints excluded: chain Q residue 88 ARG Chi-restraints excluded: chain Q residue 97 LEU Chi-restraints excluded: chain R residue 30 ARG Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain S residue 64 VAL Chi-restraints excluded: chain S residue 72 VAL Chi-restraints excluded: chain S residue 99 THR Chi-restraints excluded: chain T residue 3 THR Chi-restraints excluded: chain T residue 15 GLN Chi-restraints excluded: chain T residue 77 ASP Chi-restraints excluded: chain U residue 53 VAL Chi-restraints excluded: chain U residue 55 VAL Chi-restraints excluded: chain U residue 77 ARG Chi-restraints excluded: chain V residue 18 ASP Chi-restraints excluded: chain V residue 28 VAL Chi-restraints excluded: chain V residue 59 VAL Chi-restraints excluded: chain V residue 70 VAL Chi-restraints excluded: chain V residue 77 THR Chi-restraints excluded: chain W residue 2 PHE Chi-restraints excluded: chain W residue 4 ILE Chi-restraints excluded: chain W residue 30 ILE Chi-restraints excluded: chain W residue 40 ILE Chi-restraints excluded: chain W residue 64 VAL Chi-restraints excluded: chain W residue 91 PHE Chi-restraints excluded: chain Y residue 23 ASN Chi-restraints excluded: chain Y residue 66 THR Chi-restraints excluded: chain Y residue 68 LEU Chi-restraints excluded: chain Z residue 11 VAL Chi-restraints excluded: chain 0 residue 41 THR Chi-restraints excluded: chain 1 residue 27 SER Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 2 residue 47 VAL Chi-restraints excluded: chain 3 residue 1 MET Chi-restraints excluded: chain 3 residue 4 THR Chi-restraints excluded: chain 4 residue 30 ARG Chi-restraints excluded: chain 5 residue 17 VAL Chi-restraints excluded: chain b residue 18 HIS Chi-restraints excluded: chain b residue 27 MET Chi-restraints excluded: chain b residue 97 LEU Chi-restraints excluded: chain b residue 103 ASN Chi-restraints excluded: chain b residue 114 LEU Chi-restraints excluded: chain c residue 18 TRP Chi-restraints excluded: chain c residue 19 ASN Chi-restraints excluded: chain c residue 49 LYS Chi-restraints excluded: chain c residue 67 THR Chi-restraints excluded: chain c residue 103 ILE Chi-restraints excluded: chain c residue 138 VAL Chi-restraints excluded: chain c residue 149 ILE Chi-restraints excluded: chain c residue 152 GLU Chi-restraints excluded: chain c residue 169 ARG Chi-restraints excluded: chain c residue 195 VAL Chi-restraints excluded: chain d residue 3 ARG Chi-restraints excluded: chain d residue 25 VAL Chi-restraints excluded: chain d residue 36 GLN Chi-restraints excluded: chain d residue 91 LEU Chi-restraints excluded: chain d residue 142 VAL Chi-restraints excluded: chain e residue 16 ILE Chi-restraints excluded: chain e residue 56 VAL Chi-restraints excluded: chain e residue 76 LEU Chi-restraints excluded: chain e residue 83 HIS Chi-restraints excluded: chain e residue 88 VAL Chi-restraints excluded: chain e residue 120 VAL Chi-restraints excluded: chain e residue 137 VAL Chi-restraints excluded: chain e residue 148 ASN Chi-restraints excluded: chain f residue 8 PHE Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 60 VAL Chi-restraints excluded: chain f residue 92 THR Chi-restraints excluded: chain g residue 92 ARG Chi-restraints excluded: chain g residue 120 LEU Chi-restraints excluded: chain g residue 141 VAL Chi-restraints excluded: chain h residue 3 MET Chi-restraints excluded: chain h residue 76 GLN Chi-restraints excluded: chain h residue 106 THR Chi-restraints excluded: chain h residue 110 VAL Chi-restraints excluded: chain h residue 126 ILE Chi-restraints excluded: chain i residue 104 VAL Chi-restraints excluded: chain i residue 115 LYS Chi-restraints excluded: chain i residue 130 ARG Chi-restraints excluded: chain j residue 7 ARG Chi-restraints excluded: chain j residue 53 ILE Chi-restraints excluded: chain j residue 68 ARG Chi-restraints excluded: chain j residue 76 ILE Chi-restraints excluded: chain j residue 102 LEU Chi-restraints excluded: chain k residue 82 LEU Chi-restraints excluded: chain k residue 111 THR Chi-restraints excluded: chain l residue 16 VAL Chi-restraints excluded: chain l residue 40 THR Chi-restraints excluded: chain l residue 57 LEU Chi-restraints excluded: chain l residue 64 THR Chi-restraints excluded: chain l residue 74 LEU Chi-restraints excluded: chain l residue 79 VAL Chi-restraints excluded: chain l residue 98 VAL Chi-restraints excluded: chain n residue 14 VAL Chi-restraints excluded: chain n residue 79 LEU Chi-restraints excluded: chain o residue 33 THR Chi-restraints excluded: chain o residue 57 LEU Chi-restraints excluded: chain o residue 84 ARG Chi-restraints excluded: chain o residue 89 ARG Chi-restraints excluded: chain p residue 14 ARG Chi-restraints excluded: chain p residue 20 VAL Chi-restraints excluded: chain p residue 36 VAL Chi-restraints excluded: chain p residue 50 THR Chi-restraints excluded: chain q residue 68 SER Chi-restraints excluded: chain q residue 74 THR Chi-restraints excluded: chain q residue 79 VAL Chi-restraints excluded: chain r residue 72 ASP Chi-restraints excluded: chain s residue 24 GLU Chi-restraints excluded: chain s residue 55 ARG Chi-restraints excluded: chain u residue 53 VAL Chi-restraints excluded: chain v residue 12 GLN Chi-restraints excluded: chain v residue 80 VAL Chi-restraints excluded: chain v residue 163 THR Chi-restraints excluded: chain v residue 165 ILE Chi-restraints excluded: chain v residue 180 THR Chi-restraints excluded: chain v residue 222 VAL Chi-restraints excluded: chain v residue 226 VAL Chi-restraints excluded: chain v residue 254 VAL Chi-restraints excluded: chain v residue 264 THR Chi-restraints excluded: chain v residue 266 ILE Chi-restraints excluded: chain v residue 285 ASP Chi-restraints excluded: chain v residue 304 ASN Chi-restraints excluded: chain v residue 310 MET Chi-restraints excluded: chain v residue 329 ASP Chi-restraints excluded: chain v residue 332 ARG Chi-restraints excluded: chain w residue 30 GLU Chi-restraints excluded: chain w residue 41 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1061 random chunks: chunk 535 optimal weight: 9.9990 chunk 299 optimal weight: 20.0000 chunk 801 optimal weight: 20.0000 chunk 656 optimal weight: 20.0000 chunk 265 optimal weight: 30.0000 chunk 965 optimal weight: 10.0000 chunk 1042 optimal weight: 0.0670 chunk 859 optimal weight: 0.0870 chunk 957 optimal weight: 6.9990 chunk 329 optimal weight: 7.9990 chunk 774 optimal weight: 10.0000 overall best weight: 5.0302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 HIS D 94 GLN ** E 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 30 GLN E 41 GLN E 90 GLN F 21 ASN H 2 GLN H 33 GLN H 128 HIS ** H 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 GLN O 16 HIS ** O 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 19 GLN ** Q 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 56 HIS R 59 GLN S 91 GLN ** T 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 44 HIS W 51 GLN X 12 ASN Z 38 GLN Z 58 ASN 2 45 GLN 3 26 ASN ** b 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 54 GLN ** d 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 152 GLN ** d 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 77 ASN ** f 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 4 ASN ** k 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 73 ASN ** o 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 53 ASN v 12 GLN v 54 GLN ** v 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 346 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.4068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 162161 Z= 0.285 Angle : 0.756 13.835 242281 Z= 0.395 Chirality : 0.040 0.457 30825 Planarity : 0.007 0.136 13212 Dihedral : 24.812 178.751 80459 Min Nonbonded Distance : 1.749 Molprobity Statistics. All-atom Clashscore : 26.52 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.38 % Favored : 94.42 % Rotamer: Outliers : 8.33 % Allowed : 23.59 % Favored : 68.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.10), residues: 6054 helix: 1.09 (0.11), residues: 2147 sheet: -1.12 (0.15), residues: 1023 loop : -1.74 (0.10), residues: 2884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.004 TRP q 73 HIS 0.014 0.002 HIS u 56 PHE 0.031 0.003 PHE T 75 TYR 0.060 0.003 TYR d 75 ARG 0.025 0.001 ARG K 35 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12108 Ramachandran restraints generated. 6054 Oldfield, 0 Emsley, 6054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12108 Ramachandran restraints generated. 6054 Oldfield, 0 Emsley, 6054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2076 residues out of total 5041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 420 poor density : 1656 time to evaluate : 6.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 21 ASN cc_start: 0.8342 (t0) cc_final: 0.7951 (t0) REVERT: C 82 GLU cc_start: 0.8070 (mt-10) cc_final: 0.7313 (mp0) REVERT: C 115 GLN cc_start: 0.7641 (mt0) cc_final: 0.7197 (tp40) REVERT: C 146 MET cc_start: 0.6948 (mtt) cc_final: 0.5755 (mmp) REVERT: C 175 ARG cc_start: 0.8717 (ttt90) cc_final: 0.8135 (ptp-170) REVERT: C 194 GLU cc_start: 0.8022 (mp0) cc_final: 0.7754 (mp0) REVERT: C 266 PHE cc_start: 0.7434 (OUTLIER) cc_final: 0.7053 (m-80) REVERT: C 267 ILE cc_start: 0.7854 (mm) cc_final: 0.7653 (mm) REVERT: D 2 ILE cc_start: 0.2316 (OUTLIER) cc_final: 0.1980 (mp) REVERT: D 40 LEU cc_start: 0.8265 (mt) cc_final: 0.7857 (pt) REVERT: D 64 GLU cc_start: 0.8405 (tp30) cc_final: 0.8199 (mm-30) REVERT: D 124 ARG cc_start: 0.7853 (ttt-90) cc_final: 0.7326 (ttt180) REVERT: D 154 LYS cc_start: 0.8749 (pttm) cc_final: 0.8314 (pttm) REVERT: E 46 GLN cc_start: 0.8579 (mp10) cc_final: 0.8305 (mp10) REVERT: E 67 ARG cc_start: 0.7165 (mtp85) cc_final: 0.6888 (mtp85) REVERT: E 88 ARG cc_start: 0.8049 (mmp80) cc_final: 0.7732 (mmp80) REVERT: E 123 LYS cc_start: 0.7914 (tttp) cc_final: 0.7667 (mttp) REVERT: E 189 THR cc_start: 0.6262 (OUTLIER) cc_final: 0.5685 (p) REVERT: F 40 VAL cc_start: 0.6856 (OUTLIER) cc_final: 0.6653 (m) REVERT: F 120 LYS cc_start: 0.8548 (tttp) cc_final: 0.8319 (tptp) REVERT: F 174 ASP cc_start: 0.5968 (t0) cc_final: 0.5756 (t0) REVERT: J 61 TYR cc_start: 0.4999 (OUTLIER) cc_final: 0.4541 (m-10) REVERT: K 16 TYR cc_start: 0.6248 (m-80) cc_final: 0.5977 (m-10) REVERT: K 52 ASP cc_start: 0.5870 (m-30) cc_final: 0.5658 (m-30) REVERT: K 119 PHE cc_start: 0.8209 (t80) cc_final: 0.7708 (t80) REVERT: K 138 GLN cc_start: 0.7880 (pt0) cc_final: 0.7586 (mp10) REVERT: L 45 GLU cc_start: 0.8547 (tt0) cc_final: 0.8076 (tt0) REVERT: L 58 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8168 (mp) REVERT: L 59 LYS cc_start: 0.7986 (mttp) cc_final: 0.7706 (mppt) REVERT: L 98 ARG cc_start: 0.7366 (mmm160) cc_final: 0.7039 (mmm160) REVERT: L 111 LYS cc_start: 0.7235 (tptp) cc_final: 0.6906 (tptp) REVERT: L 112 PHE cc_start: 0.7906 (m-80) cc_final: 0.7222 (t80) REVERT: L 116 ILE cc_start: 0.6504 (OUTLIER) cc_final: 0.5295 (tp) REVERT: M 1 MET cc_start: 0.7015 (mmp) cc_final: 0.6600 (mmp) REVERT: M 55 MET cc_start: 0.8995 (tpp) cc_final: 0.8709 (tpp) REVERT: N 8 LYS cc_start: 0.7991 (mmtt) cc_final: 0.7664 (mmtm) REVERT: N 13 HIS cc_start: 0.7882 (m-70) cc_final: 0.7205 (m-70) REVERT: N 40 ARG cc_start: 0.7688 (ptp-170) cc_final: 0.7444 (ptp-170) REVERT: N 68 PHE cc_start: 0.8335 (t80) cc_final: 0.8046 (t80) REVERT: N 92 TRP cc_start: 0.7889 (m100) cc_final: 0.7535 (m100) REVERT: O 18 GLN cc_start: 0.8801 (tp-100) cc_final: 0.8572 (tp-100) REVERT: O 21 PHE cc_start: 0.8919 (m-80) cc_final: 0.8640 (m-80) REVERT: O 37 THR cc_start: 0.8129 (OUTLIER) cc_final: 0.7611 (t) REVERT: O 78 LYS cc_start: 0.8344 (tttt) cc_final: 0.7855 (tptp) REVERT: O 86 ARG cc_start: 0.6653 (ttm170) cc_final: 0.6017 (tpp80) REVERT: O 87 PHE cc_start: 0.5511 (m-80) cc_final: 0.4606 (m-10) REVERT: P 16 ARG cc_start: 0.8385 (mmt-90) cc_final: 0.7849 (mtt-85) REVERT: Q 72 ARG cc_start: 0.8367 (ttt180) cc_final: 0.8106 (mmm160) REVERT: R 14 HIS cc_start: 0.8238 (m-70) cc_final: 0.8010 (m-70) REVERT: R 20 GLN cc_start: 0.8786 (mt0) cc_final: 0.8360 (mt0) REVERT: R 28 ARG cc_start: 0.8539 (OUTLIER) cc_final: 0.8048 (mtt-85) REVERT: R 33 ARG cc_start: 0.8398 (OUTLIER) cc_final: 0.7311 (mtt-85) REVERT: R 94 ILE cc_start: 0.6117 (mp) cc_final: 0.5874 (mp) REVERT: S 1 MET cc_start: 0.6809 (tpp) cc_final: 0.5706 (ppp) REVERT: S 38 VAL cc_start: 0.5249 (OUTLIER) cc_final: 0.4994 (p) REVERT: S 40 MET cc_start: 0.8049 (tmm) cc_final: 0.7562 (ppp) REVERT: T 48 LYS cc_start: 0.8787 (tttt) cc_final: 0.8166 (tptm) REVERT: T 73 LYS cc_start: 0.8630 (mttp) cc_final: 0.8372 (mttm) REVERT: T 75 PHE cc_start: 0.8615 (OUTLIER) cc_final: 0.7476 (p90) REVERT: T 90 LYS cc_start: 0.8618 (mttt) cc_final: 0.7952 (mttt) REVERT: T 98 LYS cc_start: 0.8664 (mttp) cc_final: 0.8295 (tttp) REVERT: U 12 ARG cc_start: 0.8317 (mtt-85) cc_final: 0.8030 (mmp80) REVERT: U 44 LYS cc_start: 0.8959 (tttm) cc_final: 0.8629 (ttmt) REVERT: U 51 PHE cc_start: 0.7718 (m-80) cc_final: 0.7436 (m-80) REVERT: U 69 ARG cc_start: 0.7655 (ttm-80) cc_final: 0.7262 (tpp80) REVERT: U 76 ARG cc_start: 0.8326 (ptm160) cc_final: 0.7851 (ptm160) REVERT: U 77 ARG cc_start: 0.7637 (OUTLIER) cc_final: 0.7386 (mmt90) REVERT: U 88 LYS cc_start: 0.8465 (tppt) cc_final: 0.8137 (mmmm) REVERT: V 7 ARG cc_start: 0.6468 (ptt-90) cc_final: 0.6030 (ptt-90) REVERT: V 58 ILE cc_start: 0.7979 (mp) cc_final: 0.7773 (tp) REVERT: V 62 GLU cc_start: 0.7121 (mp0) cc_final: 0.6708 (mt-10) REVERT: W 1 MET cc_start: 0.6196 (tpt) cc_final: 0.5812 (ptp) REVERT: W 80 HIS cc_start: 0.7509 (t-90) cc_final: 0.7244 (t-90) REVERT: X 60 PHE cc_start: 0.7451 (p90) cc_final: 0.7247 (p90) REVERT: X 70 GLU cc_start: 0.7889 (mp0) cc_final: 0.7597 (pm20) REVERT: X 77 ARG cc_start: 0.8359 (mmt-90) cc_final: 0.7970 (mmt-90) REVERT: Y 56 MET cc_start: 0.8209 (tpp) cc_final: 0.7786 (mtt) REVERT: Z 19 LEU cc_start: 0.8784 (tp) cc_final: 0.8554 (tp) REVERT: 0 31 ARG cc_start: 0.7036 (OUTLIER) cc_final: 0.6717 (ptt-90) REVERT: 0 54 MET cc_start: 0.8372 (ptm) cc_final: 0.8160 (ttm) REVERT: 1 16 ARG cc_start: 0.8024 (ttp-170) cc_final: 0.7740 (ttp-110) REVERT: 3 22 MET cc_start: 0.8160 (tpt) cc_final: 0.7900 (tpt) REVERT: 4 4 ILE cc_start: 0.8689 (OUTLIER) cc_final: 0.8378 (pt) REVERT: 4 17 THR cc_start: 0.4307 (p) cc_final: 0.3734 (m) REVERT: 4 24 HIS cc_start: 0.7409 (p90) cc_final: 0.7108 (p90) REVERT: 4 49 MET cc_start: 0.5880 (mmm) cc_final: 0.5357 (mmm) REVERT: b 30 PHE cc_start: 0.6680 (m-80) cc_final: 0.6202 (m-10) REVERT: b 49 MET cc_start: 0.8464 (mtt) cc_final: 0.8173 (tmm) REVERT: b 94 HIS cc_start: 0.6573 (m90) cc_final: 0.6358 (m90) REVERT: b 97 LEU cc_start: 0.5595 (OUTLIER) cc_final: 0.5331 (pp) REVERT: c 6 HIS cc_start: 0.8614 (t-90) cc_final: 0.8209 (t-90) REVERT: c 18 TRP cc_start: 0.4909 (OUTLIER) cc_final: 0.4654 (m-10) REVERT: c 22 TRP cc_start: 0.6785 (p-90) cc_final: 0.6418 (p-90) REVERT: c 49 LYS cc_start: 0.7435 (OUTLIER) cc_final: 0.7170 (tttp) REVERT: c 103 ILE cc_start: 0.8439 (OUTLIER) cc_final: 0.8027 (mm) REVERT: c 130 PHE cc_start: 0.8966 (p90) cc_final: 0.8551 (p90) REVERT: c 135 LYS cc_start: 0.8452 (mmmm) cc_final: 0.8206 (mmtm) REVERT: c 166 GLU cc_start: 0.7124 (tt0) cc_final: 0.5861 (tt0) REVERT: c 169 ARG cc_start: 0.8394 (OUTLIER) cc_final: 0.8021 (ttm110) REVERT: c 202 ILE cc_start: 0.8009 (mt) cc_final: 0.7635 (pt) REVERT: d 9 LEU cc_start: 0.6756 (mt) cc_final: 0.6492 (mt) REVERT: d 36 GLN cc_start: 0.7762 (tt0) cc_final: 0.7245 (tt0) REVERT: d 62 ARG cc_start: 0.7327 (mtp-110) cc_final: 0.7125 (mtm180) REVERT: d 172 GLU cc_start: 0.6850 (tt0) cc_final: 0.6532 (tm-30) REVERT: d 179 GLU cc_start: 0.7988 (tt0) cc_final: 0.7543 (tp30) REVERT: e 61 GLN cc_start: 0.8691 (tp-100) cc_final: 0.8438 (tp40) REVERT: e 64 MET cc_start: 0.8554 (ttp) cc_final: 0.8330 (tpt) REVERT: e 96 MET cc_start: 0.8505 (ttp) cc_final: 0.8002 (tpt) REVERT: e 105 ILE cc_start: 0.8147 (mp) cc_final: 0.7697 (pt) REVERT: e 126 LYS cc_start: 0.7849 (tttt) cc_final: 0.7518 (tttt) REVERT: e 157 ARG cc_start: 0.7558 (mtp85) cc_final: 0.6140 (mtp-110) REVERT: e 164 ILE cc_start: 0.6760 (mt) cc_final: 0.6398 (mt) REVERT: f 21 MET cc_start: 0.8046 (mtt) cc_final: 0.7793 (mtt) REVERT: f 24 ARG cc_start: 0.7916 (ttp80) cc_final: 0.7670 (ptt90) REVERT: f 46 GLN cc_start: 0.8248 (mm-40) cc_final: 0.8013 (tp40) REVERT: f 61 LEU cc_start: 0.7502 (OUTLIER) cc_final: 0.7265 (mt) REVERT: g 25 LYS cc_start: 0.6878 (mtmm) cc_final: 0.6426 (mmmt) REVERT: g 59 LEU cc_start: 0.8378 (tp) cc_final: 0.8102 (mp) REVERT: g 131 LYS cc_start: 0.8116 (tptp) cc_final: 0.7820 (tmtt) REVERT: g 139 GLU cc_start: 0.8278 (mt-10) cc_final: 0.7977 (mm-30) REVERT: h 10 MET cc_start: 0.8066 (tmm) cc_final: 0.7615 (ptp) REVERT: h 31 LYS cc_start: 0.7606 (mmmt) cc_final: 0.7356 (mmtp) REVERT: h 43 GLU cc_start: 0.8694 (tp30) cc_final: 0.8219 (tp30) REVERT: h 71 VAL cc_start: 0.6449 (t) cc_final: 0.6225 (m) REVERT: h 89 LYS cc_start: 0.7767 (tptp) cc_final: 0.7097 (ttmt) REVERT: i 6 TYR cc_start: 0.6820 (m-80) cc_final: 0.6618 (m-80) REVERT: i 109 ARG cc_start: 0.6387 (mmm-85) cc_final: 0.5804 (mtp180) REVERT: j 49 PHE cc_start: 0.7962 (m-80) cc_final: 0.7514 (m-80) REVERT: j 68 ARG cc_start: 0.8562 (OUTLIER) cc_final: 0.8100 (mpt180) REVERT: j 97 ASP cc_start: 0.6210 (m-30) cc_final: 0.5796 (p0) REVERT: j 102 LEU cc_start: 0.5986 (OUTLIER) cc_final: 0.5747 (mm) REVERT: k 24 HIS cc_start: 0.7045 (t70) cc_final: 0.6762 (t70) REVERT: k 44 TRP cc_start: 0.7571 (p-90) cc_final: 0.7034 (p90) REVERT: k 59 THR cc_start: 0.7320 (m) cc_final: 0.6869 (p) REVERT: k 61 PHE cc_start: 0.8017 (t80) cc_final: 0.7742 (t80) REVERT: l 29 GLN cc_start: 0.8471 (mp10) cc_final: 0.8192 (mp10) REVERT: l 30 LYS cc_start: 0.8474 (mttt) cc_final: 0.8067 (mmmt) REVERT: l 50 ARG cc_start: 0.7505 (mmt-90) cc_final: 0.7108 (mmt180) REVERT: l 54 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.8127 (ttp-110) REVERT: l 74 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8211 (tp) REVERT: l 75 GLN cc_start: 0.8025 (tt0) cc_final: 0.7626 (pm20) REVERT: l 112 GLN cc_start: 0.7544 (mt0) cc_final: 0.7327 (mt0) REVERT: m 29 ARG cc_start: 0.7565 (mtt-85) cc_final: 0.7051 (ttm110) REVERT: m 71 ARG cc_start: 0.6213 (ttm110) cc_final: 0.5741 (ptm-80) REVERT: n 65 ARG cc_start: 0.8625 (mtp85) cc_final: 0.8424 (mtm110) REVERT: n 75 ARG cc_start: 0.7153 (mtt90) cc_final: 0.6659 (mtt-85) REVERT: n 89 MET cc_start: 0.8921 (mmt) cc_final: 0.8603 (mmm) REVERT: n 97 LYS cc_start: 0.7983 (tptt) cc_final: 0.7351 (tptt) REVERT: o 43 PHE cc_start: 0.8691 (m-80) cc_final: 0.8353 (m-80) REVERT: o 60 VAL cc_start: 0.9081 (t) cc_final: 0.8871 (t) REVERT: o 84 ARG cc_start: 0.8233 (ttm110) cc_final: 0.7756 (ttt-90) REVERT: q 9 GLN cc_start: 0.6838 (mt0) cc_final: 0.6615 (tp-100) REVERT: q 30 LYS cc_start: 0.8418 (tttt) cc_final: 0.7887 (mmtt) REVERT: r 32 TYR cc_start: 0.8023 (m-80) cc_final: 0.7391 (m-80) REVERT: r 74 HIS cc_start: 0.4119 (OUTLIER) cc_final: 0.3667 (m90) REVERT: s 24 GLU cc_start: 0.4191 (OUTLIER) cc_final: 0.3621 (mt-10) REVERT: t 39 ILE cc_start: 0.6235 (mt) cc_final: 0.5650 (mt) REVERT: t 51 PHE cc_start: 0.7850 (t80) cc_final: 0.7421 (m-80) REVERT: u 5 LYS cc_start: 0.8832 (pttm) cc_final: 0.8546 (tmtt) REVERT: u 18 ARG cc_start: 0.6573 (ptm-80) cc_final: 0.6356 (ptm160) REVERT: v 108 GLU cc_start: 0.7331 (tm-30) cc_final: 0.6973 (mt-10) REVERT: v 213 ARG cc_start: 0.7543 (mtp-110) cc_final: 0.7003 (mtm110) REVERT: v 221 PHE cc_start: 0.8531 (t80) cc_final: 0.8203 (t80) REVERT: v 258 GLU cc_start: 0.8827 (mm-30) cc_final: 0.8117 (mm-30) REVERT: v 277 ASP cc_start: 0.7623 (t70) cc_final: 0.7234 (t70) REVERT: v 300 MET cc_start: 0.8825 (tpp) cc_final: 0.8478 (mmp) REVERT: v 311 GLU cc_start: 0.8236 (mm-30) cc_final: 0.7835 (pp20) REVERT: v 356 PHE cc_start: 0.8126 (m-80) cc_final: 0.7237 (m-10) REVERT: w 3 ARG cc_start: 0.6976 (tpt-90) cc_final: 0.6675 (tpt-90) REVERT: w 4 TYR cc_start: 0.8018 (t80) cc_final: 0.7816 (t80) REVERT: w 10 GLN cc_start: 0.8345 (tt0) cc_final: 0.8041 (tt0) REVERT: w 11 ILE cc_start: 0.8975 (mp) cc_final: 0.8509 (mp) REVERT: w 14 ASN cc_start: 0.8120 (m-40) cc_final: 0.7208 (m-40) REVERT: w 30 GLU cc_start: 0.8121 (mp0) cc_final: 0.7407 (mp0) REVERT: w 45 HIS cc_start: 0.5832 (m-70) cc_final: 0.5597 (m-70) outliers start: 420 outliers final: 268 residues processed: 1892 average time/residue: 1.4640 time to fit residues: 4590.2352 Evaluate side-chains 1808 residues out of total 5041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 295 poor density : 1513 time to evaluate : 6.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 111 LYS Chi-restraints excluded: chain C residue 114 ASP Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 133 ARG Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 266 PHE Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 67 HIS Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain E residue 14 VAL Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 41 GLN Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 22 TYR Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain F residue 136 ILE Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 81 GLU Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 2 GLN Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 35 MET Chi-restraints excluded: chain J residue 61 TYR Chi-restraints excluded: chain J residue 121 ILE Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 19 ASP Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 56 VAL Chi-restraints excluded: chain K residue 81 ILE Chi-restraints excluded: chain K residue 93 ILE Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 87 LEU Chi-restraints excluded: chain L residue 99 ILE Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain L residue 116 ILE Chi-restraints excluded: chain M residue 27 LEU Chi-restraints excluded: chain M residue 85 VAL Chi-restraints excluded: chain M residue 122 VAL Chi-restraints excluded: chain M residue 125 LEU Chi-restraints excluded: chain M residue 141 LYS Chi-restraints excluded: chain N residue 6 ARG Chi-restraints excluded: chain N residue 73 ILE Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 126 ILE Chi-restraints excluded: chain O residue 13 ASN Chi-restraints excluded: chain O residue 37 THR Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain O residue 70 THR Chi-restraints excluded: chain P residue 7 ARG Chi-restraints excluded: chain P residue 35 ILE Chi-restraints excluded: chain P residue 53 THR Chi-restraints excluded: chain P residue 87 ILE Chi-restraints excluded: chain P residue 97 PHE Chi-restraints excluded: chain P residue 106 LEU Chi-restraints excluded: chain Q residue 28 VAL Chi-restraints excluded: chain Q residue 30 VAL Chi-restraints excluded: chain Q residue 46 VAL Chi-restraints excluded: chain Q residue 56 HIS Chi-restraints excluded: chain Q residue 70 VAL Chi-restraints excluded: chain Q residue 78 SER Chi-restraints excluded: chain Q residue 104 THR Chi-restraints excluded: chain R residue 28 ARG Chi-restraints excluded: chain R residue 30 ARG Chi-restraints excluded: chain R residue 33 ARG Chi-restraints excluded: chain S residue 25 LEU Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 41 ILE Chi-restraints excluded: chain S residue 59 ILE Chi-restraints excluded: chain S residue 64 VAL Chi-restraints excluded: chain S residue 72 VAL Chi-restraints excluded: chain S residue 93 PHE Chi-restraints excluded: chain T residue 3 THR Chi-restraints excluded: chain T residue 20 VAL Chi-restraints excluded: chain T residue 30 SER Chi-restraints excluded: chain T residue 45 VAL Chi-restraints excluded: chain T residue 71 VAL Chi-restraints excluded: chain T residue 75 PHE Chi-restraints excluded: chain T residue 77 ASP Chi-restraints excluded: chain T residue 107 VAL Chi-restraints excluded: chain U residue 16 VAL Chi-restraints excluded: chain U residue 53 VAL Chi-restraints excluded: chain U residue 55 VAL Chi-restraints excluded: chain U residue 77 ARG Chi-restraints excluded: chain V residue 12 ILE Chi-restraints excluded: chain V residue 15 THR Chi-restraints excluded: chain V residue 18 ASP Chi-restraints excluded: chain V residue 28 VAL Chi-restraints excluded: chain V residue 34 VAL Chi-restraints excluded: chain V residue 59 VAL Chi-restraints excluded: chain V residue 70 VAL Chi-restraints excluded: chain V residue 77 THR Chi-restraints excluded: chain W residue 2 PHE Chi-restraints excluded: chain W residue 4 ILE Chi-restraints excluded: chain W residue 30 ILE Chi-restraints excluded: chain W residue 40 ILE Chi-restraints excluded: chain W residue 64 VAL Chi-restraints excluded: chain W residue 91 PHE Chi-restraints excluded: chain X residue 43 THR Chi-restraints excluded: chain Y residue 18 ARG Chi-restraints excluded: chain Y residue 23 ASN Chi-restraints excluded: chain Y residue 40 VAL Chi-restraints excluded: chain Y residue 71 LEU Chi-restraints excluded: chain Z residue 11 VAL Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 31 ARG Chi-restraints excluded: chain 0 residue 41 THR Chi-restraints excluded: chain 1 residue 9 THR Chi-restraints excluded: chain 1 residue 39 LEU Chi-restraints excluded: chain 2 residue 23 THR Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 2 residue 47 VAL Chi-restraints excluded: chain 3 residue 1 MET Chi-restraints excluded: chain 3 residue 4 THR Chi-restraints excluded: chain 4 residue 4 ILE Chi-restraints excluded: chain 4 residue 30 ARG Chi-restraints excluded: chain 4 residue 57 LEU Chi-restraints excluded: chain 5 residue 7 VAL Chi-restraints excluded: chain 5 residue 17 VAL Chi-restraints excluded: chain 5 residue 23 ILE Chi-restraints excluded: chain b residue 4 VAL Chi-restraints excluded: chain b residue 18 HIS Chi-restraints excluded: chain b residue 52 GLU Chi-restraints excluded: chain b residue 97 LEU Chi-restraints excluded: chain b residue 114 LEU Chi-restraints excluded: chain b residue 116 ASP Chi-restraints excluded: chain b residue 188 ASP Chi-restraints excluded: chain b residue 208 ARG Chi-restraints excluded: chain c residue 18 TRP Chi-restraints excluded: chain c residue 19 ASN Chi-restraints excluded: chain c residue 33 LEU Chi-restraints excluded: chain c residue 49 LYS Chi-restraints excluded: chain c residue 52 VAL Chi-restraints excluded: chain c residue 67 THR Chi-restraints excluded: chain c residue 102 ASN Chi-restraints excluded: chain c residue 103 ILE Chi-restraints excluded: chain c residue 149 ILE Chi-restraints excluded: chain c residue 162 ILE Chi-restraints excluded: chain c residue 169 ARG Chi-restraints excluded: chain c residue 195 VAL Chi-restraints excluded: chain c residue 200 VAL Chi-restraints excluded: chain d residue 3 ARG Chi-restraints excluded: chain d residue 78 GLU Chi-restraints excluded: chain d residue 91 LEU Chi-restraints excluded: chain d residue 97 ARG Chi-restraints excluded: chain d residue 116 GLN Chi-restraints excluded: chain d residue 137 VAL Chi-restraints excluded: chain d residue 169 THR Chi-restraints excluded: chain e residue 46 VAL Chi-restraints excluded: chain e residue 56 VAL Chi-restraints excluded: chain e residue 76 LEU Chi-restraints excluded: chain e residue 83 HIS Chi-restraints excluded: chain e residue 88 VAL Chi-restraints excluded: chain e residue 131 THR Chi-restraints excluded: chain e residue 137 VAL Chi-restraints excluded: chain e residue 148 ASN Chi-restraints excluded: chain f residue 8 PHE Chi-restraints excluded: chain f residue 9 MET Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 58 HIS Chi-restraints excluded: chain f residue 60 VAL Chi-restraints excluded: chain f residue 61 LEU Chi-restraints excluded: chain f residue 85 ILE Chi-restraints excluded: chain f residue 92 THR Chi-restraints excluded: chain g residue 6 VAL Chi-restraints excluded: chain g residue 21 GLU Chi-restraints excluded: chain g residue 27 VAL Chi-restraints excluded: chain g residue 56 LYS Chi-restraints excluded: chain g residue 87 VAL Chi-restraints excluded: chain g residue 92 ARG Chi-restraints excluded: chain g residue 120 LEU Chi-restraints excluded: chain g residue 141 VAL Chi-restraints excluded: chain h residue 3 MET Chi-restraints excluded: chain h residue 42 GLU Chi-restraints excluded: chain h residue 112 THR Chi-restraints excluded: chain h residue 126 ILE Chi-restraints excluded: chain i residue 104 VAL Chi-restraints excluded: chain i residue 111 VAL Chi-restraints excluded: chain i residue 115 LYS Chi-restraints excluded: chain i residue 130 ARG Chi-restraints excluded: chain j residue 7 ARG Chi-restraints excluded: chain j residue 53 ILE Chi-restraints excluded: chain j residue 62 ARG Chi-restraints excluded: chain j residue 68 ARG Chi-restraints excluded: chain j residue 76 ILE Chi-restraints excluded: chain j residue 88 MET Chi-restraints excluded: chain j residue 102 LEU Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 31 ILE Chi-restraints excluded: chain k residue 35 THR Chi-restraints excluded: chain k residue 82 LEU Chi-restraints excluded: chain k residue 96 THR Chi-restraints excluded: chain k residue 110 ILE Chi-restraints excluded: chain k residue 111 THR Chi-restraints excluded: chain l residue 35 THR Chi-restraints excluded: chain l residue 54 ARG Chi-restraints excluded: chain l residue 57 LEU Chi-restraints excluded: chain l residue 64 THR Chi-restraints excluded: chain l residue 73 ASN Chi-restraints excluded: chain l residue 74 LEU Chi-restraints excluded: chain l residue 79 VAL Chi-restraints excluded: chain l residue 97 THR Chi-restraints excluded: chain l residue 98 VAL Chi-restraints excluded: chain m residue 4 ILE Chi-restraints excluded: chain m residue 39 ILE Chi-restraints excluded: chain m residue 80 LEU Chi-restraints excluded: chain n residue 14 VAL Chi-restraints excluded: chain n residue 30 ILE Chi-restraints excluded: chain n residue 43 ASN Chi-restraints excluded: chain n residue 64 CYS Chi-restraints excluded: chain n residue 79 LEU Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 89 ARG Chi-restraints excluded: chain p residue 1 MET Chi-restraints excluded: chain p residue 6 LEU Chi-restraints excluded: chain p residue 20 VAL Chi-restraints excluded: chain p residue 25 ARG Chi-restraints excluded: chain p residue 50 THR Chi-restraints excluded: chain q residue 18 GLU Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain q residue 68 SER Chi-restraints excluded: chain q residue 76 VAL Chi-restraints excluded: chain q residue 79 VAL Chi-restraints excluded: chain r residue 39 ILE Chi-restraints excluded: chain r residue 52 GLN Chi-restraints excluded: chain r residue 74 HIS Chi-restraints excluded: chain s residue 24 GLU Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain s residue 79 THR Chi-restraints excluded: chain u residue 53 VAL Chi-restraints excluded: chain v residue 12 GLN Chi-restraints excluded: chain v residue 69 THR Chi-restraints excluded: chain v residue 80 VAL Chi-restraints excluded: chain v residue 103 LEU Chi-restraints excluded: chain v residue 163 THR Chi-restraints excluded: chain v residue 165 ILE Chi-restraints excluded: chain v residue 180 THR Chi-restraints excluded: chain v residue 219 SER Chi-restraints excluded: chain v residue 226 VAL Chi-restraints excluded: chain v residue 239 LEU Chi-restraints excluded: chain v residue 254 VAL Chi-restraints excluded: chain v residue 264 THR Chi-restraints excluded: chain v residue 266 ILE Chi-restraints excluded: chain v residue 268 THR Chi-restraints excluded: chain v residue 285 ASP Chi-restraints excluded: chain v residue 304 ASN Chi-restraints excluded: chain v residue 308 GLN Chi-restraints excluded: chain v residue 345 THR Chi-restraints excluded: chain v residue 354 ASP Chi-restraints excluded: chain w residue 6 HIS Chi-restraints excluded: chain w residue 19 LEU Chi-restraints excluded: chain w residue 22 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1061 random chunks: chunk 953 optimal weight: 6.9990 chunk 725 optimal weight: 20.0000 chunk 500 optimal weight: 6.9990 chunk 106 optimal weight: 30.0000 chunk 460 optimal weight: 9.9990 chunk 648 optimal weight: 20.0000 chunk 968 optimal weight: 10.0000 chunk 1025 optimal weight: 1.9990 chunk 506 optimal weight: 10.0000 chunk 918 optimal weight: 2.9990 chunk 276 optimal weight: 20.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 90 ASN ** C 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 ASN ** C 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 GLN ** E 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 30 GLN F 5 HIS F 37 ASN G 73 ASN H 2 GLN H 11 ASN ** K 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 80 HIS ** K 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 136 GLN ** O 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 18 GLN ** O 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 7 GLN Q 15 GLN ** T 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 44 HIS ** W 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 26 ASN ** b 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 177 ASN ** c 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 139 GLN c 190 HIS ** d 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 77 ASN ** f 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 64 GLN k 28 ASN ** k 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 72 HIS ** l 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 50 HIS ** p 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 45 HIS ** q 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 69 HIS ** v 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 273 GLN ** v 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.4915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 162161 Z= 0.309 Angle : 0.771 16.370 242281 Z= 0.399 Chirality : 0.040 0.451 30825 Planarity : 0.007 0.132 13212 Dihedral : 24.934 179.279 80424 Min Nonbonded Distance : 1.737 Molprobity Statistics. All-atom Clashscore : 28.59 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.72 % Favored : 94.10 % Rotamer: Outliers : 9.48 % Allowed : 24.82 % Favored : 65.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.10), residues: 6054 helix: 0.80 (0.11), residues: 2135 sheet: -1.24 (0.15), residues: 1037 loop : -1.78 (0.10), residues: 2882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP q 73 HIS 0.032 0.002 HIS Q 56 PHE 0.027 0.003 PHE v 96 TYR 0.047 0.003 TYR d 75 ARG 0.015 0.001 ARG c 131 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12108 Ramachandran restraints generated. 6054 Oldfield, 0 Emsley, 6054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12108 Ramachandran restraints generated. 6054 Oldfield, 0 Emsley, 6054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2104 residues out of total 5041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 478 poor density : 1626 time to evaluate : 6.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 21 ASN cc_start: 0.8278 (t0) cc_final: 0.7995 (t0) REVERT: C 69 ARG cc_start: 0.8368 (mmm-85) cc_final: 0.8150 (mmm-85) REVERT: C 74 ILE cc_start: 0.4579 (mp) cc_final: 0.4071 (mt) REVERT: C 82 GLU cc_start: 0.8216 (mt-10) cc_final: 0.7625 (mp0) REVERT: C 83 TYR cc_start: 0.8034 (t80) cc_final: 0.7274 (t80) REVERT: C 115 GLN cc_start: 0.7828 (mt0) cc_final: 0.7441 (tp40) REVERT: C 146 MET cc_start: 0.7184 (mtt) cc_final: 0.6008 (mmp) REVERT: C 175 ARG cc_start: 0.8645 (ttt90) cc_final: 0.8079 (ptp-170) REVERT: C 266 PHE cc_start: 0.7341 (OUTLIER) cc_final: 0.6937 (m-80) REVERT: C 267 ILE cc_start: 0.7862 (mm) cc_final: 0.7641 (mm) REVERT: D 2 ILE cc_start: 0.2363 (OUTLIER) cc_final: 0.2126 (mp) REVERT: D 36 GLN cc_start: 0.6949 (mt0) cc_final: 0.6600 (tm-30) REVERT: D 67 HIS cc_start: 0.7012 (OUTLIER) cc_final: 0.6715 (t-170) REVERT: D 124 ARG cc_start: 0.7957 (ttt-90) cc_final: 0.7511 (ttt180) REVERT: E 67 ARG cc_start: 0.7095 (mtp85) cc_final: 0.6841 (mtp85) REVERT: E 122 GLU cc_start: 0.7562 (mt-10) cc_final: 0.7320 (mt-10) REVERT: E 189 THR cc_start: 0.6204 (OUTLIER) cc_final: 0.5829 (p) REVERT: F 47 LYS cc_start: 0.8680 (mmmt) cc_final: 0.8452 (mmmt) REVERT: F 57 LEU cc_start: 0.7729 (mp) cc_final: 0.7513 (mp) REVERT: F 83 TYR cc_start: 0.7397 (t80) cc_final: 0.7050 (t80) REVERT: F 87 CYS cc_start: 0.7124 (m) cc_final: 0.6380 (p) REVERT: F 174 ASP cc_start: 0.6313 (t0) cc_final: 0.5967 (p0) REVERT: F 178 ARG cc_start: -0.4342 (OUTLIER) cc_final: -0.4746 (ptt-90) REVERT: J 61 TYR cc_start: 0.5177 (OUTLIER) cc_final: 0.4739 (m-10) REVERT: K 119 PHE cc_start: 0.8312 (t80) cc_final: 0.7840 (t80) REVERT: K 129 GLU cc_start: 0.6443 (tp30) cc_final: 0.6225 (tp30) REVERT: K 138 GLN cc_start: 0.7683 (pt0) cc_final: 0.7429 (mp10) REVERT: L 53 LYS cc_start: 0.8923 (tttt) cc_final: 0.8673 (mptt) REVERT: L 98 ARG cc_start: 0.7367 (mmm160) cc_final: 0.7071 (mmm160) REVERT: L 106 GLU cc_start: 0.6589 (OUTLIER) cc_final: 0.6209 (mp0) REVERT: L 111 LYS cc_start: 0.6891 (tptp) cc_final: 0.6564 (tptp) REVERT: L 112 PHE cc_start: 0.7926 (m-80) cc_final: 0.7247 (t80) REVERT: M 55 MET cc_start: 0.8971 (tpp) cc_final: 0.8729 (tpp) REVERT: M 70 LYS cc_start: 0.6536 (tptp) cc_final: 0.5920 (ptpt) REVERT: M 81 ASP cc_start: 0.6615 (m-30) cc_final: 0.6256 (p0) REVERT: N 8 LYS cc_start: 0.7975 (mmtt) cc_final: 0.7629 (mmtm) REVERT: N 13 HIS cc_start: 0.7827 (m-70) cc_final: 0.7202 (m-70) REVERT: N 20 LEU cc_start: 0.4755 (OUTLIER) cc_final: 0.4498 (mm) REVERT: N 68 PHE cc_start: 0.8421 (t80) cc_final: 0.8145 (t80) REVERT: N 92 TRP cc_start: 0.7909 (m100) cc_final: 0.7646 (m-90) REVERT: N 105 MET cc_start: 0.6685 (mmm) cc_final: 0.6413 (tmm) REVERT: O 17 ARG cc_start: 0.8380 (ttm-80) cc_final: 0.7473 (mtm180) REVERT: O 18 GLN cc_start: 0.8640 (tp40) cc_final: 0.8404 (tp-100) REVERT: O 37 THR cc_start: 0.7852 (OUTLIER) cc_final: 0.7465 (t) REVERT: O 45 ARG cc_start: 0.6429 (mtp180) cc_final: 0.5906 (tpp-160) REVERT: O 78 LYS cc_start: 0.8347 (tttt) cc_final: 0.7885 (tptp) REVERT: P 36 TYR cc_start: 0.7646 (OUTLIER) cc_final: 0.6976 (m-80) REVERT: Q 13 MET cc_start: 0.7023 (mmp) cc_final: 0.6813 (tpp) REVERT: Q 72 ARG cc_start: 0.8136 (ttt180) cc_final: 0.7872 (mmm160) REVERT: R 20 GLN cc_start: 0.8826 (mt0) cc_final: 0.8405 (mt0) REVERT: R 28 ARG cc_start: 0.8585 (OUTLIER) cc_final: 0.8218 (mtt-85) REVERT: R 33 ARG cc_start: 0.8472 (OUTLIER) cc_final: 0.7527 (mtt-85) REVERT: R 50 ARG cc_start: 0.8510 (mtm-85) cc_final: 0.8015 (ttm110) REVERT: T 16 LYS cc_start: 0.8862 (mttp) cc_final: 0.8561 (mttp) REVERT: T 48 LYS cc_start: 0.8904 (tttt) cc_final: 0.8310 (tptm) REVERT: T 98 LYS cc_start: 0.8740 (mttp) cc_final: 0.8400 (tttp) REVERT: U 44 LYS cc_start: 0.9050 (tttm) cc_final: 0.8720 (ttmt) REVERT: U 69 ARG cc_start: 0.8056 (ttm-80) cc_final: 0.7710 (tpp80) REVERT: U 76 ARG cc_start: 0.8411 (ptm160) cc_final: 0.7920 (ptm160) REVERT: U 77 ARG cc_start: 0.7810 (OUTLIER) cc_final: 0.7508 (mmt90) REVERT: V 7 ARG cc_start: 0.6323 (ptt-90) cc_final: 0.5860 (ptt-90) REVERT: V 43 LYS cc_start: 0.8054 (OUTLIER) cc_final: 0.7841 (mtpt) REVERT: W 1 MET cc_start: 0.6209 (tpt) cc_final: 0.5635 (mtt) REVERT: X 60 PHE cc_start: 0.7566 (p90) cc_final: 0.7245 (p90) REVERT: X 77 ARG cc_start: 0.8222 (mmt-90) cc_final: 0.8021 (mpt-90) REVERT: Y 37 ARG cc_start: 0.8032 (OUTLIER) cc_final: 0.7675 (ppt170) REVERT: Y 46 PHE cc_start: 0.8140 (OUTLIER) cc_final: 0.7394 (m-80) REVERT: Z 7 ARG cc_start: 0.6865 (mmm160) cc_final: 0.6567 (mmp80) REVERT: Z 8 GLU cc_start: 0.6700 (mm-30) cc_final: 0.6292 (pm20) REVERT: 0 34 HIS cc_start: 0.7949 (t-90) cc_final: 0.7630 (m-70) REVERT: 0 54 MET cc_start: 0.8447 (ptm) cc_final: 0.7853 (ttm) REVERT: 1 16 ARG cc_start: 0.7911 (ttp-170) cc_final: 0.7675 (ttp-110) REVERT: 4 4 ILE cc_start: 0.8691 (OUTLIER) cc_final: 0.8335 (pt) REVERT: 4 24 HIS cc_start: 0.7331 (p90) cc_final: 0.7068 (p90) REVERT: 4 49 MET cc_start: 0.5633 (mmm) cc_final: 0.4907 (mmm) REVERT: b 26 LYS cc_start: 0.7968 (mmtt) cc_final: 0.7717 (mmtt) REVERT: b 49 MET cc_start: 0.8396 (mtt) cc_final: 0.8069 (tpp) REVERT: b 94 HIS cc_start: 0.6637 (m90) cc_final: 0.6362 (m-70) REVERT: b 100 MET cc_start: 0.7495 (mtp) cc_final: 0.7028 (mtt) REVERT: b 175 GLU cc_start: 0.8791 (mt-10) cc_final: 0.8436 (mt-10) REVERT: c 6 HIS cc_start: 0.8680 (t-90) cc_final: 0.8313 (t-90) REVERT: c 18 TRP cc_start: 0.4971 (OUTLIER) cc_final: 0.4679 (m-10) REVERT: c 49 LYS cc_start: 0.7379 (OUTLIER) cc_final: 0.7125 (tttp) REVERT: c 130 PHE cc_start: 0.8906 (p90) cc_final: 0.8447 (p90) REVERT: c 131 ARG cc_start: 0.8713 (ttp80) cc_final: 0.8471 (ptm-80) REVERT: c 152 GLU cc_start: 0.8364 (tm-30) cc_final: 0.8052 (tm-30) REVERT: c 166 GLU cc_start: 0.7457 (tt0) cc_final: 0.6746 (mt-10) REVERT: c 168 TYR cc_start: 0.7657 (m-80) cc_final: 0.7280 (m-80) REVERT: c 202 ILE cc_start: 0.7990 (mt) cc_final: 0.7714 (pt) REVERT: d 9 LEU cc_start: 0.6651 (mt) cc_final: 0.6433 (mt) REVERT: d 19 LEU cc_start: 0.3735 (OUTLIER) cc_final: 0.3331 (mt) REVERT: d 36 GLN cc_start: 0.8126 (tt0) cc_final: 0.7708 (tt0) REVERT: d 115 ARG cc_start: 0.6542 (tmm-80) cc_final: 0.6291 (tmm-80) REVERT: d 116 GLN cc_start: 0.5790 (OUTLIER) cc_final: 0.4431 (mm110) REVERT: d 152 GLN cc_start: 0.3216 (mm-40) cc_final: 0.2986 (mm-40) REVERT: d 179 GLU cc_start: 0.8019 (tt0) cc_final: 0.7587 (pp20) REVERT: e 71 MET cc_start: 0.6795 (ptp) cc_final: 0.6579 (ptp) REVERT: e 105 ILE cc_start: 0.8211 (mp) cc_final: 0.7962 (mm) REVERT: e 126 LYS cc_start: 0.7851 (tttt) cc_final: 0.7496 (tptt) REVERT: e 157 ARG cc_start: 0.7128 (mtp85) cc_final: 0.6510 (mtp-110) REVERT: f 46 GLN cc_start: 0.8462 (mm-40) cc_final: 0.8221 (tp40) REVERT: f 78 PHE cc_start: 0.8295 (m-10) cc_final: 0.8016 (m-10) REVERT: f 88 MET cc_start: 0.7353 (ttt) cc_final: 0.6926 (ttt) REVERT: f 90 MET cc_start: 0.7833 (mtm) cc_final: 0.7612 (mtm) REVERT: g 25 LYS cc_start: 0.7080 (mtmm) cc_final: 0.6491 (tptp) REVERT: g 131 LYS cc_start: 0.8160 (tptp) cc_final: 0.7863 (tmtt) REVERT: g 139 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7807 (mm-30) REVERT: h 13 ARG cc_start: 0.7021 (mtt90) cc_final: 0.6503 (tpp80) REVERT: h 15 ARG cc_start: 0.7057 (OUTLIER) cc_final: 0.6747 (ttp-170) REVERT: h 43 GLU cc_start: 0.8710 (tp30) cc_final: 0.8509 (tp30) REVERT: h 71 VAL cc_start: 0.6400 (t) cc_final: 0.6141 (m) REVERT: j 49 PHE cc_start: 0.7788 (m-80) cc_final: 0.7227 (m-80) REVERT: j 102 LEU cc_start: 0.5748 (OUTLIER) cc_final: 0.5533 (mm) REVERT: k 24 HIS cc_start: 0.6959 (t70) cc_final: 0.6710 (t70) REVERT: l 29 GLN cc_start: 0.8444 (mp10) cc_final: 0.8152 (mp10) REVERT: l 30 LYS cc_start: 0.8542 (mttt) cc_final: 0.8187 (mmtt) REVERT: l 36 ARG cc_start: 0.8140 (mtp85) cc_final: 0.7655 (mtp85) REVERT: l 50 ARG cc_start: 0.7522 (mmt-90) cc_final: 0.7067 (mmt180) REVERT: l 54 ARG cc_start: 0.8512 (ttp-110) cc_final: 0.7580 (tmm-80) REVERT: l 56 ARG cc_start: 0.8323 (tpp-160) cc_final: 0.8015 (tpp-160) REVERT: l 66 TYR cc_start: 0.8838 (t80) cc_final: 0.8638 (t80) REVERT: l 74 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8228 (tt) REVERT: l 75 GLN cc_start: 0.8221 (tt0) cc_final: 0.7850 (pm20) REVERT: l 76 GLU cc_start: 0.8321 (mm-30) cc_final: 0.8015 (mm-30) REVERT: l 81 LEU cc_start: 0.8291 (tp) cc_final: 0.7815 (tt) REVERT: l 99 ARG cc_start: 0.4951 (mmm-85) cc_final: 0.4477 (mmm-85) REVERT: l 112 GLN cc_start: 0.7439 (mt0) cc_final: 0.7221 (mt0) REVERT: m 29 ARG cc_start: 0.7629 (mtt-85) cc_final: 0.6997 (ttm110) REVERT: m 71 ARG cc_start: 0.6266 (ttm110) cc_final: 0.5713 (ptm-80) REVERT: m 98 ARG cc_start: 0.7348 (mmt180) cc_final: 0.7148 (mmt180) REVERT: n 65 ARG cc_start: 0.8568 (mtp85) cc_final: 0.8332 (mtp85) REVERT: n 74 LEU cc_start: 0.8563 (mp) cc_final: 0.8361 (mp) REVERT: n 75 ARG cc_start: 0.7300 (mtt90) cc_final: 0.6683 (mtt-85) REVERT: n 89 MET cc_start: 0.8781 (mmt) cc_final: 0.8552 (mmm) REVERT: o 43 PHE cc_start: 0.8743 (m-10) cc_final: 0.8423 (m-80) REVERT: o 74 ASP cc_start: 0.6704 (t70) cc_final: 0.6433 (t70) REVERT: o 89 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.7962 (ppt90) REVERT: p 51 ARG cc_start: 0.6231 (ttp80) cc_final: 0.5882 (ttp80) REVERT: q 30 LYS cc_start: 0.8637 (tttt) cc_final: 0.8008 (mmtt) REVERT: r 32 TYR cc_start: 0.7911 (m-80) cc_final: 0.7240 (m-80) REVERT: r 74 HIS cc_start: 0.3929 (OUTLIER) cc_final: 0.3622 (m90) REVERT: s 34 TRP cc_start: 0.6511 (m-90) cc_final: 0.6298 (m-90) REVERT: s 70 LYS cc_start: 0.5467 (OUTLIER) cc_final: 0.5244 (ttmt) REVERT: t 35 VAL cc_start: 0.2395 (t) cc_final: 0.1723 (m) REVERT: t 39 ILE cc_start: 0.6155 (mt) cc_final: 0.5832 (mt) REVERT: t 51 PHE cc_start: 0.7669 (t80) cc_final: 0.7372 (m-10) REVERT: t 83 ILE cc_start: 0.6928 (pp) cc_final: 0.5896 (pt) REVERT: u 5 LYS cc_start: 0.8736 (pttm) cc_final: 0.8429 (tmtt) REVERT: u 38 TYR cc_start: 0.7780 (t80) cc_final: 0.7498 (t80) REVERT: v 12 GLN cc_start: 0.6404 (OUTLIER) cc_final: 0.6105 (pp30) REVERT: v 109 LYS cc_start: 0.6821 (tmtt) cc_final: 0.6415 (mtpt) REVERT: v 201 LEU cc_start: 0.8567 (tp) cc_final: 0.8302 (tp) REVERT: v 213 ARG cc_start: 0.7703 (mtp-110) cc_final: 0.7145 (mtm110) REVERT: v 221 PHE cc_start: 0.8238 (t80) cc_final: 0.7870 (t80) REVERT: v 258 GLU cc_start: 0.8795 (mm-30) cc_final: 0.8373 (mm-30) REVERT: v 278 ARG cc_start: 0.7494 (ttm-80) cc_final: 0.7044 (ttm-80) REVERT: v 285 ASP cc_start: 0.9281 (OUTLIER) cc_final: 0.8954 (p0) REVERT: v 300 MET cc_start: 0.8744 (tpp) cc_final: 0.8408 (mmp) REVERT: v 311 GLU cc_start: 0.8074 (mm-30) cc_final: 0.7736 (pp20) REVERT: v 356 PHE cc_start: 0.7996 (m-80) cc_final: 0.7350 (m-10) REVERT: w 3 ARG cc_start: 0.7170 (tpt-90) cc_final: 0.6937 (tpt-90) REVERT: w 10 GLN cc_start: 0.8284 (tt0) cc_final: 0.8019 (tt0) REVERT: w 11 ILE cc_start: 0.9069 (mp) cc_final: 0.8602 (mp) REVERT: w 14 ASN cc_start: 0.8112 (m-40) cc_final: 0.7379 (m-40) REVERT: w 30 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7366 (mp0) outliers start: 478 outliers final: 301 residues processed: 1876 average time/residue: 1.4570 time to fit residues: 4539.9005 Evaluate side-chains 1860 residues out of total 5041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 331 poor density : 1529 time to evaluate : 6.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 111 LYS Chi-restraints excluded: chain C residue 114 ASP Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 133 ARG Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 189 ARG Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 256 LYS Chi-restraints excluded: chain C residue 266 PHE Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 67 HIS Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain E residue 5 LEU Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 19 PHE Chi-restraints excluded: chain E residue 25 GLU Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 44 ARG Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain F residue 5 HIS Chi-restraints excluded: chain F residue 22 TYR Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 136 ILE Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 147 ASP Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 178 ARG Chi-restraints excluded: chain G residue 19 ILE Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 81 GLU Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 53 GLU Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 61 TYR Chi-restraints excluded: chain J residue 121 ILE Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 19 ASP Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 56 VAL Chi-restraints excluded: chain K residue 81 ILE Chi-restraints excluded: chain K residue 93 ILE Chi-restraints excluded: chain L residue 9 ASN Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 87 LEU Chi-restraints excluded: chain L residue 99 ILE Chi-restraints excluded: chain L residue 106 GLU Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain L residue 114 LYS Chi-restraints excluded: chain L residue 116 ILE Chi-restraints excluded: chain M residue 10 GLU Chi-restraints excluded: chain M residue 23 ILE Chi-restraints excluded: chain M residue 27 LEU Chi-restraints excluded: chain M residue 122 VAL Chi-restraints excluded: chain M residue 125 LEU Chi-restraints excluded: chain N residue 2 LEU Chi-restraints excluded: chain N residue 6 ARG Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 73 ILE Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 88 ASN Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain O residue 13 ASN Chi-restraints excluded: chain O residue 37 THR Chi-restraints excluded: chain O residue 53 THR Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain O residue 70 THR Chi-restraints excluded: chain P residue 36 TYR Chi-restraints excluded: chain P residue 53 THR Chi-restraints excluded: chain P residue 87 ILE Chi-restraints excluded: chain P residue 97 PHE Chi-restraints excluded: chain Q residue 30 VAL Chi-restraints excluded: chain Q residue 46 VAL Chi-restraints excluded: chain Q residue 52 ASN Chi-restraints excluded: chain Q residue 56 HIS Chi-restraints excluded: chain Q residue 78 SER Chi-restraints excluded: chain Q residue 104 THR Chi-restraints excluded: chain R residue 28 ARG Chi-restraints excluded: chain R residue 30 ARG Chi-restraints excluded: chain R residue 33 ARG Chi-restraints excluded: chain R residue 74 ILE Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain S residue 29 THR Chi-restraints excluded: chain S residue 39 LEU Chi-restraints excluded: chain S residue 64 VAL Chi-restraints excluded: chain S residue 72 VAL Chi-restraints excluded: chain T residue 3 THR Chi-restraints excluded: chain T residue 17 VAL Chi-restraints excluded: chain T residue 30 SER Chi-restraints excluded: chain T residue 45 VAL Chi-restraints excluded: chain T residue 67 ASP Chi-restraints excluded: chain T residue 77 ASP Chi-restraints excluded: chain T residue 97 LEU Chi-restraints excluded: chain T residue 107 VAL Chi-restraints excluded: chain U residue 16 VAL Chi-restraints excluded: chain U residue 53 VAL Chi-restraints excluded: chain U residue 55 VAL Chi-restraints excluded: chain U residue 77 ARG Chi-restraints excluded: chain V residue 15 THR Chi-restraints excluded: chain V residue 18 ASP Chi-restraints excluded: chain V residue 28 VAL Chi-restraints excluded: chain V residue 35 ILE Chi-restraints excluded: chain V residue 43 LYS Chi-restraints excluded: chain V residue 59 VAL Chi-restraints excluded: chain V residue 70 VAL Chi-restraints excluded: chain V residue 77 THR Chi-restraints excluded: chain W residue 2 PHE Chi-restraints excluded: chain W residue 4 ILE Chi-restraints excluded: chain W residue 30 ILE Chi-restraints excluded: chain W residue 40 ILE Chi-restraints excluded: chain W residue 64 VAL Chi-restraints excluded: chain W residue 91 PHE Chi-restraints excluded: chain X residue 31 VAL Chi-restraints excluded: chain X residue 43 THR Chi-restraints excluded: chain Y residue 4 VAL Chi-restraints excluded: chain Y residue 22 LEU Chi-restraints excluded: chain Y residue 23 ASN Chi-restraints excluded: chain Y residue 37 ARG Chi-restraints excluded: chain Y residue 40 VAL Chi-restraints excluded: chain Y residue 46 PHE Chi-restraints excluded: chain Y residue 71 LEU Chi-restraints excluded: chain Z residue 9 LYS Chi-restraints excluded: chain Z residue 11 VAL Chi-restraints excluded: chain Z residue 56 LEU Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 41 THR Chi-restraints excluded: chain 0 residue 57 VAL Chi-restraints excluded: chain 1 residue 9 THR Chi-restraints excluded: chain 1 residue 39 LEU Chi-restraints excluded: chain 2 residue 47 VAL Chi-restraints excluded: chain 3 residue 1 MET Chi-restraints excluded: chain 3 residue 24 THR Chi-restraints excluded: chain 4 residue 4 ILE Chi-restraints excluded: chain 4 residue 30 ARG Chi-restraints excluded: chain 4 residue 57 LEU Chi-restraints excluded: chain 5 residue 3 VAL Chi-restraints excluded: chain 5 residue 7 VAL Chi-restraints excluded: chain 5 residue 17 VAL Chi-restraints excluded: chain b residue 4 VAL Chi-restraints excluded: chain b residue 8 ASP Chi-restraints excluded: chain b residue 15 HIS Chi-restraints excluded: chain b residue 18 HIS Chi-restraints excluded: chain b residue 52 GLU Chi-restraints excluded: chain b residue 72 THR Chi-restraints excluded: chain b residue 97 LEU Chi-restraints excluded: chain b residue 103 ASN Chi-restraints excluded: chain b residue 114 LEU Chi-restraints excluded: chain b residue 116 ASP Chi-restraints excluded: chain b residue 188 ASP Chi-restraints excluded: chain b residue 211 THR Chi-restraints excluded: chain c residue 18 TRP Chi-restraints excluded: chain c residue 33 LEU Chi-restraints excluded: chain c residue 49 LYS Chi-restraints excluded: chain c residue 67 THR Chi-restraints excluded: chain c residue 83 ASP Chi-restraints excluded: chain c residue 103 ILE Chi-restraints excluded: chain c residue 116 VAL Chi-restraints excluded: chain c residue 149 ILE Chi-restraints excluded: chain c residue 162 ILE Chi-restraints excluded: chain c residue 195 VAL Chi-restraints excluded: chain c residue 198 VAL Chi-restraints excluded: chain c residue 200 VAL Chi-restraints excluded: chain d residue 3 ARG Chi-restraints excluded: chain d residue 19 LEU Chi-restraints excluded: chain d residue 32 CYS Chi-restraints excluded: chain d residue 75 TYR Chi-restraints excluded: chain d residue 78 GLU Chi-restraints excluded: chain d residue 91 LEU Chi-restraints excluded: chain d residue 116 GLN Chi-restraints excluded: chain d residue 137 VAL Chi-restraints excluded: chain d residue 169 THR Chi-restraints excluded: chain d residue 173 VAL Chi-restraints excluded: chain d residue 200 ILE Chi-restraints excluded: chain e residue 37 THR Chi-restraints excluded: chain e residue 46 VAL Chi-restraints excluded: chain e residue 56 VAL Chi-restraints excluded: chain e residue 76 LEU Chi-restraints excluded: chain e residue 83 HIS Chi-restraints excluded: chain e residue 88 VAL Chi-restraints excluded: chain e residue 131 THR Chi-restraints excluded: chain e residue 137 VAL Chi-restraints excluded: chain e residue 144 LEU Chi-restraints excluded: chain e residue 148 ASN Chi-restraints excluded: chain f residue 8 PHE Chi-restraints excluded: chain f residue 9 MET Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 18 VAL Chi-restraints excluded: chain f residue 22 ILE Chi-restraints excluded: chain f residue 58 HIS Chi-restraints excluded: chain f residue 59 TYR Chi-restraints excluded: chain f residue 60 VAL Chi-restraints excluded: chain f residue 85 ILE Chi-restraints excluded: chain f residue 89 VAL Chi-restraints excluded: chain f residue 92 THR Chi-restraints excluded: chain g residue 6 VAL Chi-restraints excluded: chain g residue 13 LEU Chi-restraints excluded: chain g residue 21 GLU Chi-restraints excluded: chain g residue 27 VAL Chi-restraints excluded: chain g residue 43 VAL Chi-restraints excluded: chain g residue 120 LEU Chi-restraints excluded: chain g residue 141 VAL Chi-restraints excluded: chain h residue 3 MET Chi-restraints excluded: chain h residue 15 ARG Chi-restraints excluded: chain h residue 42 GLU Chi-restraints excluded: chain h residue 59 LEU Chi-restraints excluded: chain h residue 62 THR Chi-restraints excluded: chain i residue 54 LEU Chi-restraints excluded: chain i residue 96 SER Chi-restraints excluded: chain i residue 104 VAL Chi-restraints excluded: chain i residue 111 VAL Chi-restraints excluded: chain i residue 115 LYS Chi-restraints excluded: chain i residue 126 GLN Chi-restraints excluded: chain i residue 130 ARG Chi-restraints excluded: chain j residue 7 ARG Chi-restraints excluded: chain j residue 42 LEU Chi-restraints excluded: chain j residue 53 ILE Chi-restraints excluded: chain j residue 76 ILE Chi-restraints excluded: chain j residue 84 VAL Chi-restraints excluded: chain j residue 88 MET Chi-restraints excluded: chain j residue 102 LEU Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 31 ILE Chi-restraints excluded: chain k residue 35 THR Chi-restraints excluded: chain k residue 94 GLU Chi-restraints excluded: chain k residue 96 THR Chi-restraints excluded: chain k residue 111 THR Chi-restraints excluded: chain l residue 33 VAL Chi-restraints excluded: chain l residue 35 THR Chi-restraints excluded: chain l residue 44 LYS Chi-restraints excluded: chain l residue 52 VAL Chi-restraints excluded: chain l residue 57 LEU Chi-restraints excluded: chain l residue 61 PHE Chi-restraints excluded: chain l residue 64 THR Chi-restraints excluded: chain l residue 73 ASN Chi-restraints excluded: chain l residue 74 LEU Chi-restraints excluded: chain l residue 97 THR Chi-restraints excluded: chain l residue 98 VAL Chi-restraints excluded: chain m residue 4 ILE Chi-restraints excluded: chain m residue 39 ILE Chi-restraints excluded: chain m residue 82 ASP Chi-restraints excluded: chain m residue 83 LEU Chi-restraints excluded: chain n residue 30 ILE Chi-restraints excluded: chain n residue 43 ASN Chi-restraints excluded: chain o residue 22 THR Chi-restraints excluded: chain o residue 25 THR Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 31 LEU Chi-restraints excluded: chain o residue 89 ARG Chi-restraints excluded: chain p residue 17 TYR Chi-restraints excluded: chain p residue 25 ARG Chi-restraints excluded: chain p residue 50 THR Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain q residue 58 VAL Chi-restraints excluded: chain q residue 76 VAL Chi-restraints excluded: chain q residue 79 VAL Chi-restraints excluded: chain r residue 39 ILE Chi-restraints excluded: chain r residue 52 GLN Chi-restraints excluded: chain r residue 74 HIS Chi-restraints excluded: chain s residue 16 LEU Chi-restraints excluded: chain s residue 33 THR Chi-restraints excluded: chain s residue 37 ARG Chi-restraints excluded: chain s residue 70 LYS Chi-restraints excluded: chain u residue 47 ARG Chi-restraints excluded: chain u residue 53 VAL Chi-restraints excluded: chain v residue 12 GLN Chi-restraints excluded: chain v residue 20 VAL Chi-restraints excluded: chain v residue 69 THR Chi-restraints excluded: chain v residue 77 LEU Chi-restraints excluded: chain v residue 103 LEU Chi-restraints excluded: chain v residue 140 GLU Chi-restraints excluded: chain v residue 163 THR Chi-restraints excluded: chain v residue 180 THR Chi-restraints excluded: chain v residue 192 LEU Chi-restraints excluded: chain v residue 216 SER Chi-restraints excluded: chain v residue 219 SER Chi-restraints excluded: chain v residue 222 VAL Chi-restraints excluded: chain v residue 226 VAL Chi-restraints excluded: chain v residue 239 LEU Chi-restraints excluded: chain v residue 241 ILE Chi-restraints excluded: chain v residue 254 VAL Chi-restraints excluded: chain v residue 263 ILE Chi-restraints excluded: chain v residue 264 THR Chi-restraints excluded: chain v residue 266 ILE Chi-restraints excluded: chain v residue 285 ASP Chi-restraints excluded: chain v residue 304 ASN Chi-restraints excluded: chain v residue 308 GLN Chi-restraints excluded: chain v residue 345 THR Chi-restraints excluded: chain w residue 6 HIS Chi-restraints excluded: chain w residue 22 ASP Chi-restraints excluded: chain w residue 30 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1061 random chunks: chunk 854 optimal weight: 5.9990 chunk 582 optimal weight: 8.9990 chunk 14 optimal weight: 20.0000 chunk 763 optimal weight: 10.0000 chunk 423 optimal weight: 0.8980 chunk 875 optimal weight: 5.9990 chunk 708 optimal weight: 20.0000 chunk 1 optimal weight: 10.0000 chunk 523 optimal weight: 20.0000 chunk 920 optimal weight: 8.9990 chunk 258 optimal weight: 4.9990 overall best weight: 5.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 90 ASN ** C 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 HIS C 239 ASN ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 73 ASN ** K 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 11 ASN ** O 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 7 GLN Q 56 HIS ** R 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 59 ASN U 92 ASN ** W 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 87 GLN ** Z 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 26 ASN ** b 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 123 GLN ** d 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 77 ASN ** f 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 72 HIS l 73 ASN ** o 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 54 GLN ** t 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 280 GLN ** v 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.5427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.101 162161 Z= 0.295 Angle : 0.755 13.895 242281 Z= 0.391 Chirality : 0.039 0.454 30825 Planarity : 0.007 0.132 13212 Dihedral : 24.952 178.557 80407 Min Nonbonded Distance : 1.753 Molprobity Statistics. All-atom Clashscore : 29.90 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.03 % Favored : 93.79 % Rotamer: Outliers : 9.22 % Allowed : 26.07 % Favored : 64.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.10), residues: 6054 helix: 0.60 (0.11), residues: 2118 sheet: -1.32 (0.15), residues: 1042 loop : -1.76 (0.11), residues: 2894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP c 201 HIS 0.018 0.002 HIS F 5 PHE 0.038 0.003 PHE O 21 TYR 0.044 0.003 TYR d 75 ARG 0.019 0.001 ARG L 17 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12108 Ramachandran restraints generated. 6054 Oldfield, 0 Emsley, 6054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12108 Ramachandran restraints generated. 6054 Oldfield, 0 Emsley, 6054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2039 residues out of total 5041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 465 poor density : 1574 time to evaluate : 6.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 82 GLU cc_start: 0.8319 (mt-10) cc_final: 0.7616 (mp0) REVERT: C 83 TYR cc_start: 0.8113 (t80) cc_final: 0.7312 (t80) REVERT: C 115 GLN cc_start: 0.7944 (mt0) cc_final: 0.7565 (tp40) REVERT: C 146 MET cc_start: 0.7168 (mtt) cc_final: 0.6075 (mmp) REVERT: C 175 ARG cc_start: 0.8739 (ttt90) cc_final: 0.8185 (ptp-170) REVERT: C 212 ARG cc_start: 0.9164 (mmm-85) cc_final: 0.8884 (mmm-85) REVERT: C 266 PHE cc_start: 0.7420 (OUTLIER) cc_final: 0.6892 (m-80) REVERT: C 267 ILE cc_start: 0.7808 (mm) cc_final: 0.7586 (mm) REVERT: D 36 GLN cc_start: 0.6972 (mt0) cc_final: 0.6629 (tt0) REVERT: E 67 ARG cc_start: 0.7071 (mtp85) cc_final: 0.6831 (mtp85) REVERT: E 88 ARG cc_start: 0.7977 (mmp80) cc_final: 0.7744 (mmp80) REVERT: E 189 THR cc_start: 0.6214 (OUTLIER) cc_final: 0.5919 (p) REVERT: F 38 MET cc_start: 0.5375 (tpt) cc_final: 0.4886 (tpt) REVERT: F 57 LEU cc_start: 0.7664 (mp) cc_final: 0.7407 (mp) REVERT: F 83 TYR cc_start: 0.7528 (t80) cc_final: 0.7095 (t80) REVERT: F 87 CYS cc_start: 0.7155 (OUTLIER) cc_final: 0.6416 (p) REVERT: F 95 ARG cc_start: 0.7015 (mpt-90) cc_final: 0.6601 (mtt90) REVERT: G 94 TYR cc_start: 0.6891 (m-10) cc_final: 0.6669 (m-80) REVERT: G 152 ARG cc_start: 0.6333 (OUTLIER) cc_final: 0.5170 (tpp-160) REVERT: J 61 TYR cc_start: 0.5255 (m-10) cc_final: 0.4801 (m-10) REVERT: K 119 PHE cc_start: 0.8528 (t80) cc_final: 0.8128 (t80) REVERT: K 138 GLN cc_start: 0.7641 (pt0) cc_final: 0.7296 (mp10) REVERT: L 1 MET cc_start: 0.7291 (tpt) cc_final: 0.7080 (mmm) REVERT: L 30 ARG cc_start: 0.7762 (ptm160) cc_final: 0.7531 (ptm160) REVERT: L 53 LYS cc_start: 0.8899 (tttt) cc_final: 0.8656 (mmtm) REVERT: L 98 ARG cc_start: 0.7340 (mmm160) cc_final: 0.7072 (mmm160) REVERT: L 106 GLU cc_start: 0.6654 (OUTLIER) cc_final: 0.6267 (mp0) REVERT: L 111 LYS cc_start: 0.6852 (tptp) cc_final: 0.6575 (tptp) REVERT: M 55 MET cc_start: 0.8993 (tpp) cc_final: 0.8728 (tpp) REVERT: M 81 ASP cc_start: 0.6907 (m-30) cc_final: 0.6568 (p0) REVERT: N 8 LYS cc_start: 0.7945 (mmtt) cc_final: 0.7616 (mmtm) REVERT: N 13 HIS cc_start: 0.7462 (m-70) cc_final: 0.6936 (m-70) REVERT: N 40 ARG cc_start: 0.7608 (ptp-170) cc_final: 0.7309 (ptp-170) REVERT: N 45 GLN cc_start: 0.8336 (mt0) cc_final: 0.8065 (tp40) REVERT: N 51 ARG cc_start: 0.8396 (mtp85) cc_final: 0.8126 (mtm110) REVERT: N 68 PHE cc_start: 0.8427 (t80) cc_final: 0.8226 (t80) REVERT: N 91 TYR cc_start: 0.8895 (p90) cc_final: 0.8545 (p90) REVERT: N 92 TRP cc_start: 0.7852 (m100) cc_final: 0.7536 (m-90) REVERT: O 18 GLN cc_start: 0.8544 (tp40) cc_final: 0.8320 (tp-100) REVERT: O 21 PHE cc_start: 0.8726 (m-80) cc_final: 0.8483 (m-80) REVERT: O 37 THR cc_start: 0.7769 (OUTLIER) cc_final: 0.7390 (t) REVERT: O 45 ARG cc_start: 0.6467 (mtp180) cc_final: 0.5817 (tpp-160) REVERT: O 78 LYS cc_start: 0.8416 (tttt) cc_final: 0.7881 (tptp) REVERT: O 86 ARG cc_start: 0.6854 (ttm170) cc_final: 0.6202 (tpp80) REVERT: P 36 TYR cc_start: 0.7711 (OUTLIER) cc_final: 0.7028 (m-80) REVERT: Q 56 HIS cc_start: 0.7986 (OUTLIER) cc_final: 0.7766 (m170) REVERT: Q 63 LYS cc_start: 0.5544 (ptpt) cc_final: 0.5299 (mtmt) REVERT: R 20 GLN cc_start: 0.8847 (mt0) cc_final: 0.8409 (mt0) REVERT: R 28 ARG cc_start: 0.8566 (OUTLIER) cc_final: 0.8287 (mtt-85) REVERT: R 33 ARG cc_start: 0.8385 (OUTLIER) cc_final: 0.7555 (mtt-85) REVERT: R 50 ARG cc_start: 0.8591 (mtm-85) cc_final: 0.8367 (ttm110) REVERT: S 1 MET cc_start: 0.7055 (tpp) cc_final: 0.6275 (ppp) REVERT: T 3 THR cc_start: 0.6941 (OUTLIER) cc_final: 0.6556 (p) REVERT: T 16 LYS cc_start: 0.8913 (mttp) cc_final: 0.8694 (mttp) REVERT: T 48 LYS cc_start: 0.8887 (tttt) cc_final: 0.8301 (tptm) REVERT: T 98 LYS cc_start: 0.8671 (mttp) cc_final: 0.8347 (tttp) REVERT: T 99 ARG cc_start: 0.9079 (ttm-80) cc_final: 0.8764 (tpp80) REVERT: U 44 LYS cc_start: 0.8976 (tttm) cc_final: 0.8634 (ttmm) REVERT: U 76 ARG cc_start: 0.8442 (ptm160) cc_final: 0.7985 (ptm160) REVERT: U 77 ARG cc_start: 0.7772 (OUTLIER) cc_final: 0.7417 (mmt90) REVERT: V 7 ARG cc_start: 0.6419 (ptt-90) cc_final: 0.6154 (ptt-90) REVERT: W 1 MET cc_start: 0.6401 (tpt) cc_final: 0.6009 (mtm) REVERT: X 60 PHE cc_start: 0.7605 (p90) cc_final: 0.7368 (p90) REVERT: X 77 ARG cc_start: 0.8237 (mmt-90) cc_final: 0.7956 (mpt-90) REVERT: Y 41 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7622 (mp0) REVERT: Z 9 LYS cc_start: 0.7196 (OUTLIER) cc_final: 0.6911 (mmmt) REVERT: Z 30 MET cc_start: 0.7198 (ppp) cc_final: 0.6982 (ppp) REVERT: Z 31 GLN cc_start: 0.8240 (mp10) cc_final: 0.8011 (mm110) REVERT: 0 34 HIS cc_start: 0.7997 (t-90) cc_final: 0.7584 (m-70) REVERT: 0 54 MET cc_start: 0.8396 (ptm) cc_final: 0.7811 (ttm) REVERT: 1 13 ARG cc_start: 0.7931 (ttp-110) cc_final: 0.6946 (ttp-170) REVERT: 1 16 ARG cc_start: 0.7956 (ttp-170) cc_final: 0.7716 (ttp-170) REVERT: 3 21 ARG cc_start: 0.8001 (tpp-160) cc_final: 0.7622 (tpp-160) REVERT: 4 4 ILE cc_start: 0.8714 (OUTLIER) cc_final: 0.8348 (pt) REVERT: 4 24 HIS cc_start: 0.7329 (p90) cc_final: 0.7088 (p90) REVERT: 4 49 MET cc_start: 0.5299 (mmm) cc_final: 0.4577 (mmm) REVERT: 5 4 ARG cc_start: 0.7027 (mmt90) cc_final: 0.6527 (mmm-85) REVERT: b 49 MET cc_start: 0.8516 (mtt) cc_final: 0.8160 (tpp) REVERT: b 94 HIS cc_start: 0.6671 (m90) cc_final: 0.6362 (m170) REVERT: b 97 LEU cc_start: 0.4993 (OUTLIER) cc_final: 0.4747 (pp) REVERT: b 142 GLU cc_start: 0.8158 (mt-10) cc_final: 0.7628 (tm-30) REVERT: b 175 GLU cc_start: 0.8704 (mt-10) cc_final: 0.8399 (mt-10) REVERT: c 6 HIS cc_start: 0.8694 (t-90) cc_final: 0.8333 (t-90) REVERT: c 18 TRP cc_start: 0.4958 (OUTLIER) cc_final: 0.4751 (m-10) REVERT: c 22 TRP cc_start: 0.7759 (p-90) cc_final: 0.7464 (p-90) REVERT: c 29 PHE cc_start: 0.7407 (t80) cc_final: 0.7133 (t80) REVERT: c 36 ASP cc_start: 0.7428 (m-30) cc_final: 0.7136 (m-30) REVERT: c 49 LYS cc_start: 0.7396 (OUTLIER) cc_final: 0.7134 (tttp) REVERT: c 129 MET cc_start: 0.7770 (tpt) cc_final: 0.7504 (tpt) REVERT: c 152 GLU cc_start: 0.8160 (tm-30) cc_final: 0.7942 (tm-30) REVERT: c 166 GLU cc_start: 0.7550 (tt0) cc_final: 0.6986 (mt-10) REVERT: c 168 TYR cc_start: 0.8048 (m-80) cc_final: 0.7745 (m-80) REVERT: c 202 ILE cc_start: 0.7993 (mt) cc_final: 0.7691 (pt) REVERT: d 9 LEU cc_start: 0.6593 (mt) cc_final: 0.6379 (mt) REVERT: d 19 LEU cc_start: 0.3954 (OUTLIER) cc_final: 0.3570 (mt) REVERT: d 36 GLN cc_start: 0.8265 (tt0) cc_final: 0.7844 (tt0) REVERT: d 115 ARG cc_start: 0.6620 (tmm-80) cc_final: 0.5986 (tmm-80) REVERT: d 116 GLN cc_start: 0.5738 (OUTLIER) cc_final: 0.3974 (mm110) REVERT: d 179 GLU cc_start: 0.7827 (tt0) cc_final: 0.7371 (pp20) REVERT: e 105 ILE cc_start: 0.8290 (mp) cc_final: 0.7840 (pt) REVERT: e 126 LYS cc_start: 0.7834 (tttt) cc_final: 0.7450 (tptt) REVERT: e 157 ARG cc_start: 0.7267 (mtp85) cc_final: 0.7021 (mtp85) REVERT: f 46 GLN cc_start: 0.8469 (mm-40) cc_final: 0.8213 (tp40) REVERT: f 61 LEU cc_start: 0.7528 (OUTLIER) cc_final: 0.7298 (mt) REVERT: f 88 MET cc_start: 0.7400 (ttt) cc_final: 0.6866 (ttt) REVERT: f 90 MET cc_start: 0.7880 (mtm) cc_final: 0.7585 (mtm) REVERT: g 25 LYS cc_start: 0.6991 (mtmm) cc_final: 0.6489 (tptp) REVERT: g 58 GLU cc_start: 0.4331 (mt-10) cc_final: 0.4107 (mm-30) REVERT: g 131 LYS cc_start: 0.8154 (tptp) cc_final: 0.7916 (tmtt) REVERT: g 139 GLU cc_start: 0.8054 (mt-10) cc_final: 0.7742 (mm-30) REVERT: h 13 ARG cc_start: 0.6901 (mtt90) cc_final: 0.6505 (tpp80) REVERT: h 71 VAL cc_start: 0.6410 (t) cc_final: 0.6182 (m) REVERT: h 89 LYS cc_start: 0.7324 (OUTLIER) cc_final: 0.6670 (tptp) REVERT: i 39 PHE cc_start: 0.6504 (OUTLIER) cc_final: 0.6047 (t80) REVERT: j 7 ARG cc_start: 0.7963 (OUTLIER) cc_final: 0.7646 (mmp80) REVERT: j 49 PHE cc_start: 0.7914 (m-80) cc_final: 0.7152 (m-80) REVERT: j 67 ILE cc_start: 0.9162 (OUTLIER) cc_final: 0.8776 (mt) REVERT: j 76 ILE cc_start: 0.5659 (OUTLIER) cc_final: 0.4827 (mt) REVERT: k 24 HIS cc_start: 0.6714 (t70) cc_final: 0.6378 (t70) REVERT: k 59 THR cc_start: 0.7866 (OUTLIER) cc_final: 0.7553 (p) REVERT: l 29 GLN cc_start: 0.8310 (mp10) cc_final: 0.8040 (mp10) REVERT: l 30 LYS cc_start: 0.8534 (mttt) cc_final: 0.8192 (mmmt) REVERT: l 50 ARG cc_start: 0.7474 (mmt-90) cc_final: 0.7062 (mmt180) REVERT: l 54 ARG cc_start: 0.8530 (ttp-110) cc_final: 0.8265 (ttp-110) REVERT: l 56 ARG cc_start: 0.8112 (tpp-160) cc_final: 0.7847 (tpp-160) REVERT: l 74 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8285 (tp) REVERT: l 75 GLN cc_start: 0.8258 (tt0) cc_final: 0.7892 (pm20) REVERT: l 76 GLU cc_start: 0.7591 (mm-30) cc_final: 0.7250 (mm-30) REVERT: l 81 LEU cc_start: 0.8290 (tp) cc_final: 0.7833 (tt) REVERT: l 83 ARG cc_start: 0.7854 (tmm-80) cc_final: 0.6762 (tmm-80) REVERT: l 112 GLN cc_start: 0.7443 (mt0) cc_final: 0.7222 (mt0) REVERT: m 71 ARG cc_start: 0.5966 (ttm110) cc_final: 0.5432 (ptm-80) REVERT: m 109 ARG cc_start: 0.7811 (mmm160) cc_final: 0.7458 (mmm-85) REVERT: n 65 ARG cc_start: 0.8431 (mtp85) cc_final: 0.8188 (mtp-110) REVERT: o 74 ASP cc_start: 0.7018 (t70) cc_final: 0.6656 (t70) REVERT: o 84 ARG cc_start: 0.8249 (ttm110) cc_final: 0.7791 (ttt-90) REVERT: q 30 LYS cc_start: 0.8646 (tttt) cc_final: 0.8068 (mmtt) REVERT: q 67 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7768 (mt) REVERT: q 80 GLU cc_start: 0.6393 (tp30) cc_final: 0.5982 (tm-30) REVERT: r 32 TYR cc_start: 0.7882 (m-80) cc_final: 0.7553 (m-80) REVERT: r 74 HIS cc_start: 0.3969 (OUTLIER) cc_final: 0.3662 (m90) REVERT: s 34 TRP cc_start: 0.6510 (m-90) cc_final: 0.6222 (m-90) REVERT: t 35 VAL cc_start: 0.2444 (t) cc_final: 0.1811 (m) REVERT: t 39 ILE cc_start: 0.5933 (mt) cc_final: 0.5599 (mt) REVERT: t 48 GLN cc_start: 0.4318 (mm-40) cc_final: 0.3864 (mm-40) REVERT: t 51 PHE cc_start: 0.7555 (t80) cc_final: 0.7337 (m-10) REVERT: t 83 ILE cc_start: 0.6883 (pp) cc_final: 0.5906 (pt) REVERT: u 5 LYS cc_start: 0.8877 (pttm) cc_final: 0.8619 (ptmm) REVERT: v 48 ASN cc_start: 0.5407 (OUTLIER) cc_final: 0.5144 (t0) REVERT: v 213 ARG cc_start: 0.7588 (mtp-110) cc_final: 0.7173 (mtm110) REVERT: v 221 PHE cc_start: 0.8136 (t80) cc_final: 0.7826 (t80) REVERT: v 258 GLU cc_start: 0.8765 (mm-30) cc_final: 0.8327 (mm-30) REVERT: v 278 ARG cc_start: 0.7608 (ttm-80) cc_final: 0.7202 (ttm-80) REVERT: v 283 ASN cc_start: 0.8504 (OUTLIER) cc_final: 0.8007 (m110) REVERT: v 300 MET cc_start: 0.8622 (tpp) cc_final: 0.8319 (mmp) REVERT: v 311 GLU cc_start: 0.8110 (mm-30) cc_final: 0.7840 (pp20) REVERT: v 341 GLU cc_start: 0.4920 (mp0) cc_final: 0.4243 (tt0) REVERT: v 356 PHE cc_start: 0.7899 (m-80) cc_final: 0.7194 (m-10) REVERT: w 10 GLN cc_start: 0.8240 (tt0) cc_final: 0.7987 (tt0) REVERT: w 11 ILE cc_start: 0.9055 (mp) cc_final: 0.8634 (mp) REVERT: w 14 ASN cc_start: 0.7972 (m-40) cc_final: 0.7263 (m-40) REVERT: w 30 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7260 (mp0) REVERT: w 45 HIS cc_start: 0.6071 (m-70) cc_final: 0.5863 (m-70) outliers start: 465 outliers final: 317 residues processed: 1819 average time/residue: 1.4530 time to fit residues: 4387.5537 Evaluate side-chains 1845 residues out of total 5041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 350 poor density : 1495 time to evaluate : 5.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 53 HIS Chi-restraints excluded: chain C residue 103 TYR Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 111 LYS Chi-restraints excluded: chain C residue 114 ASP Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 133 ARG Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 182 ARG Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 256 LYS Chi-restraints excluded: chain C residue 266 PHE Chi-restraints excluded: chain D residue 14 ILE Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain E residue 5 LEU Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 19 PHE Chi-restraints excluded: chain E residue 25 GLU Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 44 ARG Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 123 LYS Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 22 TYR Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 71 ARG Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 87 CYS Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 136 ILE Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 147 ASP Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 81 GLU Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 152 ARG Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 53 GLU Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain J residue 121 ILE Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 55 ILE Chi-restraints excluded: chain K residue 56 VAL Chi-restraints excluded: chain K residue 81 ILE Chi-restraints excluded: chain K residue 93 ILE Chi-restraints excluded: chain K residue 130 HIS Chi-restraints excluded: chain L residue 9 ASN Chi-restraints excluded: chain L residue 22 ILE Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 87 LEU Chi-restraints excluded: chain L residue 106 GLU Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain L residue 114 LYS Chi-restraints excluded: chain L residue 116 ILE Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 23 ILE Chi-restraints excluded: chain M residue 27 LEU Chi-restraints excluded: chain M residue 103 ILE Chi-restraints excluded: chain M residue 122 VAL Chi-restraints excluded: chain M residue 125 LEU Chi-restraints excluded: chain N residue 2 LEU Chi-restraints excluded: chain N residue 6 ARG Chi-restraints excluded: chain N residue 73 ILE Chi-restraints excluded: chain N residue 88 ASN Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 135 VAL Chi-restraints excluded: chain O residue 13 ASN Chi-restraints excluded: chain O residue 33 ILE Chi-restraints excluded: chain O residue 37 THR Chi-restraints excluded: chain O residue 53 THR Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain P residue 36 TYR Chi-restraints excluded: chain P residue 53 THR Chi-restraints excluded: chain P residue 97 PHE Chi-restraints excluded: chain Q residue 7 GLN Chi-restraints excluded: chain Q residue 30 VAL Chi-restraints excluded: chain Q residue 46 VAL Chi-restraints excluded: chain Q residue 48 ILE Chi-restraints excluded: chain Q residue 52 ASN Chi-restraints excluded: chain Q residue 56 HIS Chi-restraints excluded: chain Q residue 104 THR Chi-restraints excluded: chain R residue 16 LYS Chi-restraints excluded: chain R residue 28 ARG Chi-restraints excluded: chain R residue 30 ARG Chi-restraints excluded: chain R residue 33 ARG Chi-restraints excluded: chain R residue 74 ILE Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain S residue 27 ILE Chi-restraints excluded: chain S residue 29 THR Chi-restraints excluded: chain S residue 39 LEU Chi-restraints excluded: chain S residue 41 ILE Chi-restraints excluded: chain S residue 64 VAL Chi-restraints excluded: chain S residue 72 VAL Chi-restraints excluded: chain T residue 3 THR Chi-restraints excluded: chain T residue 13 SER Chi-restraints excluded: chain T residue 17 VAL Chi-restraints excluded: chain T residue 30 SER Chi-restraints excluded: chain T residue 60 HIS Chi-restraints excluded: chain T residue 67 ASP Chi-restraints excluded: chain T residue 77 ASP Chi-restraints excluded: chain T residue 97 LEU Chi-restraints excluded: chain T residue 107 VAL Chi-restraints excluded: chain U residue 16 VAL Chi-restraints excluded: chain U residue 32 LEU Chi-restraints excluded: chain U residue 53 VAL Chi-restraints excluded: chain U residue 55 VAL Chi-restraints excluded: chain U residue 77 ARG Chi-restraints excluded: chain V residue 15 THR Chi-restraints excluded: chain V residue 18 ASP Chi-restraints excluded: chain V residue 28 VAL Chi-restraints excluded: chain V residue 43 LYS Chi-restraints excluded: chain V residue 59 VAL Chi-restraints excluded: chain V residue 70 VAL Chi-restraints excluded: chain V residue 77 THR Chi-restraints excluded: chain V residue 93 VAL Chi-restraints excluded: chain W residue 2 PHE Chi-restraints excluded: chain W residue 30 ILE Chi-restraints excluded: chain W residue 40 ILE Chi-restraints excluded: chain W residue 91 PHE Chi-restraints excluded: chain X residue 43 THR Chi-restraints excluded: chain Y residue 13 VAL Chi-restraints excluded: chain Y residue 22 LEU Chi-restraints excluded: chain Y residue 23 ASN Chi-restraints excluded: chain Y residue 41 GLU Chi-restraints excluded: chain Z residue 9 LYS Chi-restraints excluded: chain Z residue 11 VAL Chi-restraints excluded: chain Z residue 28 LEU Chi-restraints excluded: chain Z residue 50 VAL Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 25 LEU Chi-restraints excluded: chain 0 residue 41 THR Chi-restraints excluded: chain 1 residue 9 THR Chi-restraints excluded: chain 1 residue 22 LEU Chi-restraints excluded: chain 1 residue 39 LEU Chi-restraints excluded: chain 1 residue 49 TYR Chi-restraints excluded: chain 2 residue 23 THR Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 2 residue 47 VAL Chi-restraints excluded: chain 3 residue 1 MET Chi-restraints excluded: chain 3 residue 4 THR Chi-restraints excluded: chain 3 residue 8 SER Chi-restraints excluded: chain 3 residue 24 THR Chi-restraints excluded: chain 3 residue 30 VAL Chi-restraints excluded: chain 3 residue 45 SER Chi-restraints excluded: chain 4 residue 4 ILE Chi-restraints excluded: chain 4 residue 30 ARG Chi-restraints excluded: chain 4 residue 57 LEU Chi-restraints excluded: chain 5 residue 3 VAL Chi-restraints excluded: chain 5 residue 17 VAL Chi-restraints excluded: chain b residue 4 VAL Chi-restraints excluded: chain b residue 8 ASP Chi-restraints excluded: chain b residue 15 HIS Chi-restraints excluded: chain b residue 18 HIS Chi-restraints excluded: chain b residue 52 GLU Chi-restraints excluded: chain b residue 72 THR Chi-restraints excluded: chain b residue 97 LEU Chi-restraints excluded: chain b residue 103 ASN Chi-restraints excluded: chain b residue 114 LEU Chi-restraints excluded: chain b residue 116 ASP Chi-restraints excluded: chain b residue 129 LEU Chi-restraints excluded: chain b residue 130 THR Chi-restraints excluded: chain b residue 188 ASP Chi-restraints excluded: chain b residue 190 ASN Chi-restraints excluded: chain b residue 200 ILE Chi-restraints excluded: chain b residue 208 ARG Chi-restraints excluded: chain b residue 211 THR Chi-restraints excluded: chain c residue 18 TRP Chi-restraints excluded: chain c residue 19 ASN Chi-restraints excluded: chain c residue 33 LEU Chi-restraints excluded: chain c residue 37 PHE Chi-restraints excluded: chain c residue 49 LYS Chi-restraints excluded: chain c residue 67 THR Chi-restraints excluded: chain c residue 83 ASP Chi-restraints excluded: chain c residue 102 ASN Chi-restraints excluded: chain c residue 103 ILE Chi-restraints excluded: chain c residue 116 VAL Chi-restraints excluded: chain c residue 138 VAL Chi-restraints excluded: chain c residue 149 ILE Chi-restraints excluded: chain c residue 162 ILE Chi-restraints excluded: chain c residue 195 VAL Chi-restraints excluded: chain c residue 198 VAL Chi-restraints excluded: chain c residue 200 VAL Chi-restraints excluded: chain d residue 19 LEU Chi-restraints excluded: chain d residue 32 CYS Chi-restraints excluded: chain d residue 75 TYR Chi-restraints excluded: chain d residue 78 GLU Chi-restraints excluded: chain d residue 97 ARG Chi-restraints excluded: chain d residue 116 GLN Chi-restraints excluded: chain d residue 137 VAL Chi-restraints excluded: chain d residue 141 ASP Chi-restraints excluded: chain d residue 169 THR Chi-restraints excluded: chain d residue 173 VAL Chi-restraints excluded: chain d residue 195 ILE Chi-restraints excluded: chain d residue 200 ILE Chi-restraints excluded: chain e residue 11 LEU Chi-restraints excluded: chain e residue 20 ARG Chi-restraints excluded: chain e residue 46 VAL Chi-restraints excluded: chain e residue 56 VAL Chi-restraints excluded: chain e residue 76 LEU Chi-restraints excluded: chain e residue 88 VAL Chi-restraints excluded: chain e residue 94 VAL Chi-restraints excluded: chain e residue 131 THR Chi-restraints excluded: chain e residue 137 VAL Chi-restraints excluded: chain e residue 148 ASN Chi-restraints excluded: chain f residue 8 PHE Chi-restraints excluded: chain f residue 9 MET Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 18 VAL Chi-restraints excluded: chain f residue 22 ILE Chi-restraints excluded: chain f residue 58 HIS Chi-restraints excluded: chain f residue 60 VAL Chi-restraints excluded: chain f residue 61 LEU Chi-restraints excluded: chain f residue 85 ILE Chi-restraints excluded: chain f residue 89 VAL Chi-restraints excluded: chain f residue 92 THR Chi-restraints excluded: chain g residue 6 VAL Chi-restraints excluded: chain g residue 13 LEU Chi-restraints excluded: chain g residue 21 GLU Chi-restraints excluded: chain g residue 27 VAL Chi-restraints excluded: chain g residue 120 LEU Chi-restraints excluded: chain g residue 141 VAL Chi-restraints excluded: chain h residue 3 MET Chi-restraints excluded: chain h residue 15 ARG Chi-restraints excluded: chain h residue 42 GLU Chi-restraints excluded: chain h residue 54 ASP Chi-restraints excluded: chain h residue 62 THR Chi-restraints excluded: chain h residue 77 ARG Chi-restraints excluded: chain h residue 89 LYS Chi-restraints excluded: chain i residue 20 PHE Chi-restraints excluded: chain i residue 39 PHE Chi-restraints excluded: chain i residue 54 LEU Chi-restraints excluded: chain i residue 104 VAL Chi-restraints excluded: chain i residue 111 VAL Chi-restraints excluded: chain i residue 130 ARG Chi-restraints excluded: chain j residue 7 ARG Chi-restraints excluded: chain j residue 32 THR Chi-restraints excluded: chain j residue 53 ILE Chi-restraints excluded: chain j residue 67 ILE Chi-restraints excluded: chain j residue 76 ILE Chi-restraints excluded: chain j residue 84 VAL Chi-restraints excluded: chain j residue 88 MET Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 31 ILE Chi-restraints excluded: chain k residue 35 THR Chi-restraints excluded: chain k residue 59 THR Chi-restraints excluded: chain k residue 80 LYS Chi-restraints excluded: chain k residue 96 THR Chi-restraints excluded: chain k residue 108 THR Chi-restraints excluded: chain k residue 111 THR Chi-restraints excluded: chain k residue 125 LYS Chi-restraints excluded: chain l residue 35 THR Chi-restraints excluded: chain l residue 44 LYS Chi-restraints excluded: chain l residue 52 VAL Chi-restraints excluded: chain l residue 61 PHE Chi-restraints excluded: chain l residue 64 THR Chi-restraints excluded: chain l residue 72 HIS Chi-restraints excluded: chain l residue 74 LEU Chi-restraints excluded: chain l residue 90 LEU Chi-restraints excluded: chain l residue 97 THR Chi-restraints excluded: chain l residue 98 VAL Chi-restraints excluded: chain m residue 39 ILE Chi-restraints excluded: chain m residue 43 VAL Chi-restraints excluded: chain m residue 80 LEU Chi-restraints excluded: chain n residue 30 ILE Chi-restraints excluded: chain n residue 43 ASN Chi-restraints excluded: chain n residue 90 ARG Chi-restraints excluded: chain o residue 22 THR Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 48 LYS Chi-restraints excluded: chain p residue 16 PHE Chi-restraints excluded: chain p residue 17 TYR Chi-restraints excluded: chain p residue 50 THR Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain q residue 58 VAL Chi-restraints excluded: chain q residue 67 LEU Chi-restraints excluded: chain q residue 76 VAL Chi-restraints excluded: chain q residue 79 VAL Chi-restraints excluded: chain r residue 28 THR Chi-restraints excluded: chain r residue 39 ILE Chi-restraints excluded: chain r residue 52 GLN Chi-restraints excluded: chain r residue 74 HIS Chi-restraints excluded: chain s residue 29 LYS Chi-restraints excluded: chain s residue 33 THR Chi-restraints excluded: chain s residue 37 ARG Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain s residue 79 THR Chi-restraints excluded: chain u residue 47 ARG Chi-restraints excluded: chain u residue 53 VAL Chi-restraints excluded: chain v residue 20 VAL Chi-restraints excluded: chain v residue 48 ASN Chi-restraints excluded: chain v residue 69 THR Chi-restraints excluded: chain v residue 77 LEU Chi-restraints excluded: chain v residue 103 LEU Chi-restraints excluded: chain v residue 140 GLU Chi-restraints excluded: chain v residue 148 LEU Chi-restraints excluded: chain v residue 180 THR Chi-restraints excluded: chain v residue 192 LEU Chi-restraints excluded: chain v residue 219 SER Chi-restraints excluded: chain v residue 226 VAL Chi-restraints excluded: chain v residue 241 ILE Chi-restraints excluded: chain v residue 254 VAL Chi-restraints excluded: chain v residue 263 ILE Chi-restraints excluded: chain v residue 264 THR Chi-restraints excluded: chain v residue 266 ILE Chi-restraints excluded: chain v residue 283 ASN Chi-restraints excluded: chain v residue 304 ASN Chi-restraints excluded: chain v residue 308 GLN Chi-restraints excluded: chain v residue 345 THR Chi-restraints excluded: chain w residue 6 HIS Chi-restraints excluded: chain w residue 22 ASP Chi-restraints excluded: chain w residue 30 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1061 random chunks: chunk 345 optimal weight: 7.9990 chunk 923 optimal weight: 9.9990 chunk 202 optimal weight: 10.0000 chunk 602 optimal weight: 0.6980 chunk 253 optimal weight: 20.0000 chunk 1026 optimal weight: 10.0000 chunk 852 optimal weight: 0.3980 chunk 475 optimal weight: 4.9990 chunk 85 optimal weight: 20.0000 chunk 339 optimal weight: 1.9990 chunk 538 optimal weight: 9.9990 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 86 ASN ** C 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 HIS ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 134 HIS E 41 GLN F 5 HIS G 73 ASN H 2 GLN ** K 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 60 GLN O 11 ASN ** O 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 7 GLN Q 56 HIS ** R 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 34 HIS 2 46 HIS ** 3 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 26 ASN b 15 HIS ** b 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 177 ASN ** c 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 77 ASN ** f 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 126 GLN ** j 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 72 HIS l 73 ASN ** o 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 12 GLN ** v 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.5591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 162161 Z= 0.204 Angle : 0.683 17.967 242281 Z= 0.357 Chirality : 0.036 0.509 30825 Planarity : 0.006 0.128 13212 Dihedral : 24.821 178.758 80386 Min Nonbonded Distance : 1.769 Molprobity Statistics. All-atom Clashscore : 25.35 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.48 % Favored : 94.35 % Rotamer: Outliers : 7.66 % Allowed : 28.66 % Favored : 63.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.10), residues: 6054 helix: 0.78 (0.11), residues: 2108 sheet: -1.20 (0.15), residues: 1063 loop : -1.68 (0.11), residues: 2883 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP d 170 HIS 0.028 0.002 HIS Q 56 PHE 0.042 0.002 PHE c 130 TYR 0.046 0.002 TYR d 75 ARG 0.016 0.001 ARG P 15 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12108 Ramachandran restraints generated. 6054 Oldfield, 0 Emsley, 6054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12108 Ramachandran restraints generated. 6054 Oldfield, 0 Emsley, 6054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1924 residues out of total 5041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 386 poor density : 1538 time to evaluate : 6.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 79 GLU cc_start: 0.6451 (tt0) cc_final: 0.5862 (tt0) REVERT: C 82 GLU cc_start: 0.8292 (mt-10) cc_final: 0.6382 (mt-10) REVERT: C 83 TYR cc_start: 0.8169 (t80) cc_final: 0.7268 (t80) REVERT: C 114 ASP cc_start: 0.6332 (OUTLIER) cc_final: 0.5727 (p0) REVERT: C 115 GLN cc_start: 0.7967 (mt0) cc_final: 0.7600 (tp40) REVERT: C 146 MET cc_start: 0.7151 (mtt) cc_final: 0.5989 (mmp) REVERT: C 175 ARG cc_start: 0.8760 (ttt90) cc_final: 0.8147 (ptp-170) REVERT: C 266 PHE cc_start: 0.7450 (OUTLIER) cc_final: 0.6967 (m-80) REVERT: C 267 ILE cc_start: 0.7739 (mm) cc_final: 0.7499 (mm) REVERT: D 2 ILE cc_start: 0.3001 (OUTLIER) cc_final: 0.2712 (mp) REVERT: D 36 GLN cc_start: 0.6993 (mt0) cc_final: 0.6533 (tm-30) REVERT: D 127 PHE cc_start: 0.8387 (m-80) cc_final: 0.8036 (m-80) REVERT: E 67 ARG cc_start: 0.7109 (mtp85) cc_final: 0.6843 (mtp85) REVERT: E 107 SER cc_start: 0.7710 (OUTLIER) cc_final: 0.7506 (m) REVERT: E 189 THR cc_start: 0.6245 (OUTLIER) cc_final: 0.5786 (p) REVERT: F 38 MET cc_start: 0.5018 (tpt) cc_final: 0.4674 (tpt) REVERT: F 44 ILE cc_start: 0.7277 (OUTLIER) cc_final: 0.6797 (mt) REVERT: F 83 TYR cc_start: 0.7583 (t80) cc_final: 0.7273 (t80) REVERT: F 87 CYS cc_start: 0.7460 (OUTLIER) cc_final: 0.6613 (p) REVERT: F 95 ARG cc_start: 0.6973 (mpt-90) cc_final: 0.6586 (mtt90) REVERT: F 174 ASP cc_start: 0.6016 (t0) cc_final: 0.5789 (p0) REVERT: F 178 ARG cc_start: -0.4183 (OUTLIER) cc_final: -0.4614 (ptt-90) REVERT: G 94 TYR cc_start: 0.6861 (m-10) cc_final: 0.6628 (m-80) REVERT: G 139 GLN cc_start: 0.6735 (tp40) cc_final: 0.6501 (tp40) REVERT: J 61 TYR cc_start: 0.5323 (m-10) cc_final: 0.4898 (m-10) REVERT: K 96 ARG cc_start: 0.7328 (mtp85) cc_final: 0.7047 (mtp85) REVERT: K 119 PHE cc_start: 0.8483 (t80) cc_final: 0.8156 (t80) REVERT: K 135 GLN cc_start: 0.5152 (OUTLIER) cc_final: 0.4221 (mp10) REVERT: K 138 GLN cc_start: 0.7703 (pt0) cc_final: 0.7244 (mp10) REVERT: L 1 MET cc_start: 0.6769 (tpt) cc_final: 0.6468 (tpt) REVERT: L 7 MET cc_start: 0.8981 (mmt) cc_final: 0.8496 (mmm) REVERT: L 53 LYS cc_start: 0.8906 (tttt) cc_final: 0.8629 (mmtm) REVERT: L 70 ARG cc_start: 0.4182 (OUTLIER) cc_final: 0.3926 (mmt90) REVERT: L 98 ARG cc_start: 0.7435 (mmm160) cc_final: 0.7186 (mmm160) REVERT: M 55 MET cc_start: 0.8961 (tpp) cc_final: 0.8674 (tpp) REVERT: M 81 ASP cc_start: 0.6943 (m-30) cc_final: 0.6591 (p0) REVERT: N 8 LYS cc_start: 0.7938 (mmtt) cc_final: 0.7725 (mttt) REVERT: N 10 ARG cc_start: 0.7461 (OUTLIER) cc_final: 0.7255 (mtp-110) REVERT: N 13 HIS cc_start: 0.7807 (m-70) cc_final: 0.7276 (m-70) REVERT: N 40 ARG cc_start: 0.7605 (ptp-170) cc_final: 0.7257 (ptp-170) REVERT: N 92 TRP cc_start: 0.7814 (m100) cc_final: 0.7543 (m-90) REVERT: N 136 MET cc_start: 0.5021 (ttp) cc_final: 0.3834 (tpp) REVERT: O 21 PHE cc_start: 0.8771 (m-80) cc_final: 0.8550 (m-80) REVERT: O 37 THR cc_start: 0.7779 (OUTLIER) cc_final: 0.7433 (t) REVERT: O 78 LYS cc_start: 0.8387 (tttt) cc_final: 0.7913 (tptp) REVERT: O 114 GLU cc_start: 0.5740 (OUTLIER) cc_final: 0.5042 (pm20) REVERT: P 36 TYR cc_start: 0.7738 (OUTLIER) cc_final: 0.6977 (m-80) REVERT: P 38 GLN cc_start: 0.7074 (OUTLIER) cc_final: 0.6834 (pt0) REVERT: Q 13 MET cc_start: 0.6704 (mmm) cc_final: 0.6357 (tpp) REVERT: Q 72 ARG cc_start: 0.7686 (mmm160) cc_final: 0.7149 (mmm160) REVERT: R 20 GLN cc_start: 0.8824 (mt0) cc_final: 0.8399 (mt0) REVERT: R 33 ARG cc_start: 0.8262 (OUTLIER) cc_final: 0.7177 (mtt-85) REVERT: S 1 MET cc_start: 0.7126 (tpp) cc_final: 0.6355 (ppp) REVERT: T 3 THR cc_start: 0.6971 (OUTLIER) cc_final: 0.6621 (p) REVERT: T 16 LYS cc_start: 0.8914 (mttp) cc_final: 0.8698 (mttp) REVERT: T 48 LYS cc_start: 0.8852 (tttt) cc_final: 0.8273 (tptm) REVERT: T 98 LYS cc_start: 0.8662 (mttp) cc_final: 0.8314 (tttm) REVERT: T 99 ARG cc_start: 0.9066 (ttm-80) cc_final: 0.8743 (tpp80) REVERT: U 44 LYS cc_start: 0.8964 (tttm) cc_final: 0.8631 (ttmt) REVERT: U 69 ARG cc_start: 0.7936 (ttm-80) cc_final: 0.7528 (tpp80) REVERT: U 76 ARG cc_start: 0.8410 (ptm160) cc_final: 0.7940 (ptm160) REVERT: U 77 ARG cc_start: 0.7682 (OUTLIER) cc_final: 0.7417 (mmt90) REVERT: V 7 ARG cc_start: 0.6458 (ptt-90) cc_final: 0.6085 (ptt-90) REVERT: V 62 GLU cc_start: 0.6743 (mp0) cc_final: 0.6121 (mt-10) REVERT: W 1 MET cc_start: 0.6277 (tpt) cc_final: 0.5884 (mtt) REVERT: X 77 ARG cc_start: 0.8287 (mmt-90) cc_final: 0.7981 (mpt-90) REVERT: Y 39 TRP cc_start: 0.7186 (t-100) cc_final: 0.5578 (t-100) REVERT: Y 41 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7409 (mp0) REVERT: Y 46 PHE cc_start: 0.7878 (m-80) cc_final: 0.7494 (m-80) REVERT: Z 9 LYS cc_start: 0.7276 (OUTLIER) cc_final: 0.6951 (mmmt) REVERT: Z 47 ARG cc_start: 0.7082 (ttp-110) cc_final: 0.6876 (ttp-110) REVERT: 0 54 MET cc_start: 0.8384 (ptm) cc_final: 0.7775 (ttm) REVERT: 1 13 ARG cc_start: 0.7840 (ttp-110) cc_final: 0.6886 (ttp-170) REVERT: 1 16 ARG cc_start: 0.7982 (ttp-170) cc_final: 0.7738 (ttp-170) REVERT: 3 5 PHE cc_start: 0.8891 (t80) cc_final: 0.8600 (t80) REVERT: 3 35 ARG cc_start: 0.8524 (ttm110) cc_final: 0.8276 (ttm110) REVERT: 4 4 ILE cc_start: 0.8701 (OUTLIER) cc_final: 0.8345 (pt) REVERT: 4 49 MET cc_start: 0.5497 (mmm) cc_final: 0.4798 (mmm) REVERT: 5 4 ARG cc_start: 0.6750 (mmt90) cc_final: 0.6301 (mmm-85) REVERT: b 49 MET cc_start: 0.8534 (mtt) cc_final: 0.8207 (tpp) REVERT: b 67 ILE cc_start: 0.7933 (mp) cc_final: 0.7545 (tp) REVERT: b 94 HIS cc_start: 0.6722 (m90) cc_final: 0.6321 (m170) REVERT: b 97 LEU cc_start: 0.4963 (OUTLIER) cc_final: 0.4481 (pp) REVERT: c 6 HIS cc_start: 0.8540 (t-90) cc_final: 0.8201 (t-90) REVERT: c 22 TRP cc_start: 0.7808 (p-90) cc_final: 0.7465 (p-90) REVERT: c 25 ASN cc_start: 0.3955 (m110) cc_final: 0.3691 (t0) REVERT: c 28 GLU cc_start: 0.5890 (pm20) cc_final: 0.5687 (pm20) REVERT: c 130 PHE cc_start: 0.8786 (p90) cc_final: 0.8349 (p90) REVERT: c 151 VAL cc_start: 0.7584 (t) cc_final: 0.7333 (m) REVERT: c 152 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7567 (tm-30) REVERT: c 166 GLU cc_start: 0.7558 (tt0) cc_final: 0.6275 (mt-10) REVERT: c 168 TYR cc_start: 0.7800 (m-80) cc_final: 0.6680 (m-80) REVERT: c 202 ILE cc_start: 0.7972 (mt) cc_final: 0.7617 (pt) REVERT: d 9 LEU cc_start: 0.6592 (mt) cc_final: 0.6377 (mt) REVERT: d 19 LEU cc_start: 0.3889 (OUTLIER) cc_final: 0.3502 (mt) REVERT: d 36 GLN cc_start: 0.8273 (tt0) cc_final: 0.7818 (tt0) REVERT: d 41 HIS cc_start: 0.6600 (OUTLIER) cc_final: 0.6378 (m90) REVERT: d 115 ARG cc_start: 0.6611 (tmm-80) cc_final: 0.6344 (tmm-80) REVERT: d 116 GLN cc_start: 0.5540 (OUTLIER) cc_final: 0.4228 (mm110) REVERT: e 96 MET cc_start: 0.8452 (ttp) cc_final: 0.7925 (tpt) REVERT: e 105 ILE cc_start: 0.8186 (mp) cc_final: 0.7766 (pt) REVERT: e 126 LYS cc_start: 0.7822 (tttt) cc_final: 0.7436 (tptt) REVERT: f 46 GLN cc_start: 0.8456 (mm-40) cc_final: 0.8174 (tp40) REVERT: f 64 VAL cc_start: 0.7213 (m) cc_final: 0.6942 (m) REVERT: f 88 MET cc_start: 0.7362 (ttt) cc_final: 0.6849 (ttt) REVERT: f 90 MET cc_start: 0.7934 (mtm) cc_final: 0.7577 (mtm) REVERT: g 25 LYS cc_start: 0.7092 (mtmm) cc_final: 0.6625 (tptp) REVERT: g 28 ASN cc_start: 0.6741 (m-40) cc_final: 0.5655 (t0) REVERT: g 31 MET cc_start: 0.6146 (ptm) cc_final: 0.5448 (ptm) REVERT: g 58 GLU cc_start: 0.4313 (mt-10) cc_final: 0.4053 (mm-30) REVERT: g 131 LYS cc_start: 0.8065 (tptp) cc_final: 0.7816 (tmtt) REVERT: g 139 GLU cc_start: 0.8055 (mt-10) cc_final: 0.7702 (mm-30) REVERT: h 13 ARG cc_start: 0.6892 (mtt90) cc_final: 0.6667 (tpp80) REVERT: h 31 LYS cc_start: 0.7624 (mmmt) cc_final: 0.7397 (mmtp) REVERT: h 71 VAL cc_start: 0.6437 (t) cc_final: 0.6196 (m) REVERT: h 89 LYS cc_start: 0.7346 (tptp) cc_final: 0.6722 (tptp) REVERT: i 85 ARG cc_start: 0.7093 (mmp80) cc_final: 0.6826 (mmp-170) REVERT: i 120 LYS cc_start: 0.8080 (mptt) cc_final: 0.7871 (mptt) REVERT: j 7 ARG cc_start: 0.7938 (OUTLIER) cc_final: 0.7593 (mmp80) REVERT: j 49 PHE cc_start: 0.7754 (m-80) cc_final: 0.7048 (m-80) REVERT: j 76 ILE cc_start: 0.5660 (OUTLIER) cc_final: 0.4827 (mt) REVERT: k 24 HIS cc_start: 0.6741 (t70) cc_final: 0.6350 (t70) REVERT: k 53 ARG cc_start: 0.7951 (mmt-90) cc_final: 0.7203 (mmm160) REVERT: k 59 THR cc_start: 0.7911 (OUTLIER) cc_final: 0.7661 (p) REVERT: k 85 MET cc_start: 0.8060 (ptp) cc_final: 0.7383 (ptm) REVERT: l 29 GLN cc_start: 0.8408 (mp10) cc_final: 0.8141 (mp10) REVERT: l 30 LYS cc_start: 0.8320 (mttt) cc_final: 0.7786 (mmmt) REVERT: l 50 ARG cc_start: 0.7473 (mmt-90) cc_final: 0.6845 (mpt90) REVERT: l 54 ARG cc_start: 0.8546 (ttp-110) cc_final: 0.8205 (ttp-110) REVERT: l 75 GLN cc_start: 0.8181 (tt0) cc_final: 0.7749 (pm20) REVERT: l 76 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7584 (mm-30) REVERT: l 81 LEU cc_start: 0.8315 (tp) cc_final: 0.7861 (tt) REVERT: l 83 ARG cc_start: 0.7860 (tmm-80) cc_final: 0.6983 (tmm-80) REVERT: l 112 GLN cc_start: 0.7452 (mt0) cc_final: 0.7225 (mt0) REVERT: m 71 ARG cc_start: 0.6028 (ttm110) cc_final: 0.5489 (ptm-80) REVERT: m 109 ARG cc_start: 0.7751 (mmm160) cc_final: 0.7426 (mmm-85) REVERT: n 65 ARG cc_start: 0.8401 (mtp85) cc_final: 0.8186 (mtp-110) REVERT: o 74 ASP cc_start: 0.7164 (t70) cc_final: 0.6842 (t70) REVERT: o 84 ARG cc_start: 0.8382 (ttm110) cc_final: 0.7860 (ttt-90) REVERT: q 17 MET cc_start: 0.7993 (mpp) cc_final: 0.7776 (mpp) REVERT: q 30 LYS cc_start: 0.8682 (tttt) cc_final: 0.8080 (mmtt) REVERT: q 67 LEU cc_start: 0.7999 (mm) cc_final: 0.7793 (mt) REVERT: q 80 GLU cc_start: 0.6394 (tp30) cc_final: 0.5999 (tm-30) REVERT: r 28 THR cc_start: 0.7888 (m) cc_final: 0.7425 (m) REVERT: r 32 TYR cc_start: 0.7833 (m-80) cc_final: 0.7114 (m-80) REVERT: r 74 HIS cc_start: 0.3909 (OUTLIER) cc_final: 0.3623 (m90) REVERT: t 39 ILE cc_start: 0.5834 (mt) cc_final: 0.5393 (mt) REVERT: t 48 GLN cc_start: 0.4555 (mm-40) cc_final: 0.4127 (mm-40) REVERT: t 83 ILE cc_start: 0.7005 (pp) cc_final: 0.5912 (pt) REVERT: u 5 LYS cc_start: 0.8905 (pttm) cc_final: 0.8628 (ptmm) REVERT: u 38 TYR cc_start: 0.7405 (t80) cc_final: 0.7093 (t80) REVERT: v 201 LEU cc_start: 0.8677 (tp) cc_final: 0.8464 (tp) REVERT: v 213 ARG cc_start: 0.7514 (mtp-110) cc_final: 0.7136 (mtm110) REVERT: v 221 PHE cc_start: 0.8086 (t80) cc_final: 0.7676 (t80) REVERT: v 258 GLU cc_start: 0.8771 (mm-30) cc_final: 0.8323 (mm-30) REVERT: v 278 ARG cc_start: 0.7609 (ttm-80) cc_final: 0.7154 (ttm-80) REVERT: v 280 GLN cc_start: 0.8599 (OUTLIER) cc_final: 0.8176 (tm130) REVERT: v 300 MET cc_start: 0.8639 (tpp) cc_final: 0.8351 (mmp) REVERT: v 311 GLU cc_start: 0.8033 (mm-30) cc_final: 0.7752 (pp20) REVERT: v 356 PHE cc_start: 0.7869 (m-80) cc_final: 0.7208 (m-10) REVERT: w 10 GLN cc_start: 0.8201 (tt0) cc_final: 0.7874 (tt0) REVERT: w 11 ILE cc_start: 0.9053 (mp) cc_final: 0.8661 (mp) REVERT: w 12 LYS cc_start: 0.8056 (mttp) cc_final: 0.7638 (mttp) REVERT: w 14 ASN cc_start: 0.8011 (m-40) cc_final: 0.7274 (m-40) REVERT: w 30 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7210 (mp0) outliers start: 386 outliers final: 264 residues processed: 1746 average time/residue: 1.4541 time to fit residues: 4204.7500 Evaluate side-chains 1753 residues out of total 5041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 296 poor density : 1457 time to evaluate : 6.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 103 TYR Chi-restraints excluded: chain C residue 108 LYS Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 111 LYS Chi-restraints excluded: chain C residue 114 ASP Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 133 ARG Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 256 LYS Chi-restraints excluded: chain C residue 266 PHE Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 14 ILE Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 67 HIS Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 19 PHE Chi-restraints excluded: chain E residue 25 GLU Chi-restraints excluded: chain E residue 41 GLN Chi-restraints excluded: chain E residue 44 ARG Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 107 SER Chi-restraints excluded: chain E residue 123 LYS Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain F residue 5 HIS Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 71 ARG Chi-restraints excluded: chain F residue 87 CYS Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 136 ILE Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 147 ASP Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 178 ARG Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 81 GLU Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 53 GLU Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 121 ILE Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 56 VAL Chi-restraints excluded: chain K residue 81 ILE Chi-restraints excluded: chain K residue 93 ILE Chi-restraints excluded: chain K residue 130 HIS Chi-restraints excluded: chain K residue 135 GLN Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 70 ARG Chi-restraints excluded: chain L residue 87 LEU Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 10 GLU Chi-restraints excluded: chain M residue 23 ILE Chi-restraints excluded: chain M residue 27 LEU Chi-restraints excluded: chain M residue 122 VAL Chi-restraints excluded: chain M residue 125 LEU Chi-restraints excluded: chain M residue 142 ILE Chi-restraints excluded: chain N residue 2 LEU Chi-restraints excluded: chain N residue 6 ARG Chi-restraints excluded: chain N residue 10 ARG Chi-restraints excluded: chain N residue 73 ILE Chi-restraints excluded: chain N residue 88 ASN Chi-restraints excluded: chain N residue 135 VAL Chi-restraints excluded: chain O residue 13 ASN Chi-restraints excluded: chain O residue 33 ILE Chi-restraints excluded: chain O residue 37 THR Chi-restraints excluded: chain O residue 53 THR Chi-restraints excluded: chain O residue 114 GLU Chi-restraints excluded: chain P residue 36 TYR Chi-restraints excluded: chain P residue 38 GLN Chi-restraints excluded: chain P residue 53 THR Chi-restraints excluded: chain P residue 97 PHE Chi-restraints excluded: chain P residue 103 VAL Chi-restraints excluded: chain Q residue 30 VAL Chi-restraints excluded: chain Q residue 46 VAL Chi-restraints excluded: chain Q residue 52 ASN Chi-restraints excluded: chain Q residue 63 LYS Chi-restraints excluded: chain Q residue 80 VAL Chi-restraints excluded: chain Q residue 97 LEU Chi-restraints excluded: chain Q residue 104 THR Chi-restraints excluded: chain R residue 16 LYS Chi-restraints excluded: chain R residue 30 ARG Chi-restraints excluded: chain R residue 33 ARG Chi-restraints excluded: chain R residue 74 ILE Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain S residue 39 LEU Chi-restraints excluded: chain S residue 41 ILE Chi-restraints excluded: chain S residue 64 VAL Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 93 PHE Chi-restraints excluded: chain T residue 3 THR Chi-restraints excluded: chain T residue 17 VAL Chi-restraints excluded: chain T residue 30 SER Chi-restraints excluded: chain T residue 45 VAL Chi-restraints excluded: chain T residue 60 HIS Chi-restraints excluded: chain T residue 67 ASP Chi-restraints excluded: chain T residue 77 ASP Chi-restraints excluded: chain T residue 97 LEU Chi-restraints excluded: chain T residue 107 VAL Chi-restraints excluded: chain T residue 108 SER Chi-restraints excluded: chain U residue 16 VAL Chi-restraints excluded: chain U residue 77 ARG Chi-restraints excluded: chain V residue 15 THR Chi-restraints excluded: chain V residue 18 ASP Chi-restraints excluded: chain V residue 28 VAL Chi-restraints excluded: chain V residue 59 VAL Chi-restraints excluded: chain V residue 70 VAL Chi-restraints excluded: chain W residue 2 PHE Chi-restraints excluded: chain W residue 30 ILE Chi-restraints excluded: chain W residue 40 ILE Chi-restraints excluded: chain W residue 91 PHE Chi-restraints excluded: chain X residue 43 THR Chi-restraints excluded: chain Y residue 4 VAL Chi-restraints excluded: chain Y residue 22 LEU Chi-restraints excluded: chain Y residue 23 ASN Chi-restraints excluded: chain Y residue 40 VAL Chi-restraints excluded: chain Y residue 41 GLU Chi-restraints excluded: chain Y residue 66 THR Chi-restraints excluded: chain Y residue 68 LEU Chi-restraints excluded: chain Z residue 9 LYS Chi-restraints excluded: chain Z residue 11 VAL Chi-restraints excluded: chain Z residue 28 LEU Chi-restraints excluded: chain Z residue 37 LEU Chi-restraints excluded: chain 0 residue 41 THR Chi-restraints excluded: chain 1 residue 9 THR Chi-restraints excluded: chain 1 residue 22 LEU Chi-restraints excluded: chain 1 residue 39 LEU Chi-restraints excluded: chain 1 residue 49 TYR Chi-restraints excluded: chain 2 residue 23 THR Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 3 residue 1 MET Chi-restraints excluded: chain 3 residue 4 THR Chi-restraints excluded: chain 3 residue 24 THR Chi-restraints excluded: chain 3 residue 45 SER Chi-restraints excluded: chain 4 residue 4 ILE Chi-restraints excluded: chain 4 residue 30 ARG Chi-restraints excluded: chain 4 residue 55 LEU Chi-restraints excluded: chain 4 residue 57 LEU Chi-restraints excluded: chain 5 residue 17 VAL Chi-restraints excluded: chain b residue 18 HIS Chi-restraints excluded: chain b residue 52 GLU Chi-restraints excluded: chain b residue 72 THR Chi-restraints excluded: chain b residue 97 LEU Chi-restraints excluded: chain b residue 103 ASN Chi-restraints excluded: chain b residue 109 GLN Chi-restraints excluded: chain b residue 114 LEU Chi-restraints excluded: chain b residue 129 LEU Chi-restraints excluded: chain b residue 130 THR Chi-restraints excluded: chain b residue 208 ARG Chi-restraints excluded: chain b residue 211 THR Chi-restraints excluded: chain c residue 15 VAL Chi-restraints excluded: chain c residue 19 ASN Chi-restraints excluded: chain c residue 33 LEU Chi-restraints excluded: chain c residue 67 THR Chi-restraints excluded: chain c residue 83 ASP Chi-restraints excluded: chain c residue 103 ILE Chi-restraints excluded: chain c residue 116 VAL Chi-restraints excluded: chain c residue 121 THR Chi-restraints excluded: chain c residue 138 VAL Chi-restraints excluded: chain c residue 152 GLU Chi-restraints excluded: chain c residue 162 ILE Chi-restraints excluded: chain c residue 195 VAL Chi-restraints excluded: chain c residue 200 VAL Chi-restraints excluded: chain d residue 19 LEU Chi-restraints excluded: chain d residue 32 CYS Chi-restraints excluded: chain d residue 41 HIS Chi-restraints excluded: chain d residue 78 GLU Chi-restraints excluded: chain d residue 116 GLN Chi-restraints excluded: chain d residue 117 LEU Chi-restraints excluded: chain d residue 137 VAL Chi-restraints excluded: chain d residue 169 THR Chi-restraints excluded: chain d residue 173 VAL Chi-restraints excluded: chain d residue 195 ILE Chi-restraints excluded: chain d residue 200 ILE Chi-restraints excluded: chain e residue 11 LEU Chi-restraints excluded: chain e residue 20 ARG Chi-restraints excluded: chain e residue 37 THR Chi-restraints excluded: chain e residue 46 VAL Chi-restraints excluded: chain e residue 56 VAL Chi-restraints excluded: chain e residue 76 LEU Chi-restraints excluded: chain e residue 88 VAL Chi-restraints excluded: chain e residue 94 VAL Chi-restraints excluded: chain e residue 131 THR Chi-restraints excluded: chain e residue 137 VAL Chi-restraints excluded: chain e residue 148 ASN Chi-restraints excluded: chain f residue 9 MET Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 54 LEU Chi-restraints excluded: chain f residue 58 HIS Chi-restraints excluded: chain f residue 60 VAL Chi-restraints excluded: chain f residue 85 ILE Chi-restraints excluded: chain f residue 89 VAL Chi-restraints excluded: chain f residue 92 THR Chi-restraints excluded: chain g residue 13 LEU Chi-restraints excluded: chain g residue 27 VAL Chi-restraints excluded: chain g residue 43 VAL Chi-restraints excluded: chain g residue 75 VAL Chi-restraints excluded: chain g residue 120 LEU Chi-restraints excluded: chain g residue 141 VAL Chi-restraints excluded: chain h residue 3 MET Chi-restraints excluded: chain h residue 42 GLU Chi-restraints excluded: chain h residue 59 LEU Chi-restraints excluded: chain h residue 62 THR Chi-restraints excluded: chain h residue 77 ARG Chi-restraints excluded: chain i residue 9 THR Chi-restraints excluded: chain i residue 20 PHE Chi-restraints excluded: chain i residue 54 LEU Chi-restraints excluded: chain i residue 96 SER Chi-restraints excluded: chain i residue 104 VAL Chi-restraints excluded: chain i residue 111 VAL Chi-restraints excluded: chain i residue 113 ARG Chi-restraints excluded: chain i residue 126 GLN Chi-restraints excluded: chain i residue 130 ARG Chi-restraints excluded: chain j residue 7 ARG Chi-restraints excluded: chain j residue 32 THR Chi-restraints excluded: chain j residue 53 ILE Chi-restraints excluded: chain j residue 76 ILE Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 35 THR Chi-restraints excluded: chain k residue 59 THR Chi-restraints excluded: chain k residue 94 GLU Chi-restraints excluded: chain k residue 96 THR Chi-restraints excluded: chain k residue 111 THR Chi-restraints excluded: chain k residue 125 LYS Chi-restraints excluded: chain l residue 44 LYS Chi-restraints excluded: chain l residue 52 VAL Chi-restraints excluded: chain l residue 61 PHE Chi-restraints excluded: chain l residue 64 THR Chi-restraints excluded: chain l residue 90 LEU Chi-restraints excluded: chain l residue 98 VAL Chi-restraints excluded: chain m residue 39 ILE Chi-restraints excluded: chain m residue 80 LEU Chi-restraints excluded: chain m residue 82 ASP Chi-restraints excluded: chain n residue 30 ILE Chi-restraints excluded: chain n residue 43 ASN Chi-restraints excluded: chain n residue 56 SER Chi-restraints excluded: chain n residue 90 ARG Chi-restraints excluded: chain o residue 22 THR Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain p residue 16 PHE Chi-restraints excluded: chain p residue 40 ASN Chi-restraints excluded: chain p residue 50 THR Chi-restraints excluded: chain q residue 58 VAL Chi-restraints excluded: chain q residue 76 VAL Chi-restraints excluded: chain q residue 79 VAL Chi-restraints excluded: chain r residue 39 ILE Chi-restraints excluded: chain r residue 74 HIS Chi-restraints excluded: chain s residue 37 ARG Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain t residue 76 LYS Chi-restraints excluded: chain u residue 13 ASP Chi-restraints excluded: chain v residue 20 VAL Chi-restraints excluded: chain v residue 69 THR Chi-restraints excluded: chain v residue 77 LEU Chi-restraints excluded: chain v residue 140 GLU Chi-restraints excluded: chain v residue 180 THR Chi-restraints excluded: chain v residue 192 LEU Chi-restraints excluded: chain v residue 226 VAL Chi-restraints excluded: chain v residue 239 LEU Chi-restraints excluded: chain v residue 254 VAL Chi-restraints excluded: chain v residue 264 THR Chi-restraints excluded: chain v residue 266 ILE Chi-restraints excluded: chain v residue 280 GLN Chi-restraints excluded: chain v residue 304 ASN Chi-restraints excluded: chain v residue 308 GLN Chi-restraints excluded: chain v residue 345 THR Chi-restraints excluded: chain w residue 6 HIS Chi-restraints excluded: chain w residue 7 THR Chi-restraints excluded: chain w residue 22 ASP Chi-restraints excluded: chain w residue 30 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1061 random chunks: chunk 989 optimal weight: 7.9990 chunk 115 optimal weight: 20.0000 chunk 584 optimal weight: 10.0000 chunk 749 optimal weight: 20.0000 chunk 580 optimal weight: 10.0000 chunk 864 optimal weight: 0.7980 chunk 573 optimal weight: 0.4980 chunk 1022 optimal weight: 8.9990 chunk 639 optimal weight: 30.0000 chunk 623 optimal weight: 5.9990 chunk 472 optimal weight: 20.0000 overall best weight: 4.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 25 HIS ** C 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 HIS D 42 ASN D 126 ASN D 134 HIS F 5 HIS G 48 ASN G 73 ASN ** K 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 177 ASN ** d 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 77 ASN ** f 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 86 GLN g 122 ASN i 25 ASN ** j 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 4 GLN ** o 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 54 GLN ** t 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 9 ASN ** v 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.5965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 162161 Z= 0.273 Angle : 0.737 13.982 242281 Z= 0.380 Chirality : 0.038 0.461 30825 Planarity : 0.007 0.131 13212 Dihedral : 24.894 179.847 80380 Min Nonbonded Distance : 1.757 Molprobity Statistics. All-atom Clashscore : 29.62 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.56 % Favored : 93.28 % Rotamer: Outliers : 8.15 % Allowed : 28.80 % Favored : 63.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.10), residues: 6054 helix: 0.55 (0.11), residues: 2106 sheet: -1.31 (0.15), residues: 1073 loop : -1.76 (0.11), residues: 2875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP k 44 HIS 0.023 0.002 HIS f 3 PHE 0.042 0.003 PHE 3 18 TYR 0.043 0.002 TYR d 75 ARG 0.014 0.001 ARG f 79 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12108 Ramachandran restraints generated. 6054 Oldfield, 0 Emsley, 6054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12108 Ramachandran restraints generated. 6054 Oldfield, 0 Emsley, 6054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1940 residues out of total 5041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 411 poor density : 1529 time to evaluate : 6.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 79 GLU cc_start: 0.6093 (tt0) cc_final: 0.5870 (tt0) REVERT: C 83 TYR cc_start: 0.8045 (t80) cc_final: 0.7273 (t80) REVERT: C 115 GLN cc_start: 0.7996 (mt0) cc_final: 0.7637 (tp40) REVERT: C 146 MET cc_start: 0.7171 (mtt) cc_final: 0.6014 (mmp) REVERT: C 175 ARG cc_start: 0.8700 (ttt90) cc_final: 0.8090 (ptp-170) REVERT: C 266 PHE cc_start: 0.7431 (OUTLIER) cc_final: 0.6902 (m-80) REVERT: C 267 ILE cc_start: 0.7755 (mm) cc_final: 0.7517 (mm) REVERT: D 2 ILE cc_start: 0.3436 (OUTLIER) cc_final: 0.3213 (mt) REVERT: D 36 GLN cc_start: 0.7101 (mt0) cc_final: 0.6676 (tt0) REVERT: E 67 ARG cc_start: 0.7131 (mtp85) cc_final: 0.6864 (mtp85) REVERT: E 107 SER cc_start: 0.7722 (OUTLIER) cc_final: 0.7481 (m) REVERT: E 189 THR cc_start: 0.5973 (OUTLIER) cc_final: 0.5547 (p) REVERT: E 195 GLN cc_start: 0.7879 (tt0) cc_final: 0.7543 (pt0) REVERT: F 38 MET cc_start: 0.5190 (tpt) cc_final: 0.4918 (mmm) REVERT: F 44 ILE cc_start: 0.7229 (OUTLIER) cc_final: 0.6758 (mt) REVERT: F 83 TYR cc_start: 0.7617 (t80) cc_final: 0.7292 (t80) REVERT: F 95 ARG cc_start: 0.7190 (mpt-90) cc_final: 0.6746 (mtt90) REVERT: F 174 ASP cc_start: 0.5909 (t0) cc_final: 0.5669 (p0) REVERT: F 178 ARG cc_start: -0.4314 (OUTLIER) cc_final: -0.4734 (ptt-90) REVERT: G 133 LEU cc_start: 0.8125 (mt) cc_final: 0.7725 (tt) REVERT: J 61 TYR cc_start: 0.5467 (m-10) cc_final: 0.5111 (m-10) REVERT: K 138 GLN cc_start: 0.7558 (pt0) cc_final: 0.7217 (mp10) REVERT: L 1 MET cc_start: 0.6909 (tpt) cc_final: 0.6556 (tpt) REVERT: L 53 LYS cc_start: 0.8925 (tttt) cc_final: 0.8672 (mmtm) REVERT: L 70 ARG cc_start: 0.4101 (OUTLIER) cc_final: 0.3719 (mmt90) REVERT: L 106 GLU cc_start: 0.6611 (OUTLIER) cc_final: 0.6260 (mp0) REVERT: M 14 LYS cc_start: 0.7652 (tttm) cc_final: 0.7427 (tttm) REVERT: M 23 ILE cc_start: 0.8548 (OUTLIER) cc_final: 0.8342 (tp) REVERT: M 55 MET cc_start: 0.8981 (tpp) cc_final: 0.8716 (tpp) REVERT: M 81 ASP cc_start: 0.7088 (m-30) cc_final: 0.6718 (p0) REVERT: N 8 LYS cc_start: 0.7945 (mmtt) cc_final: 0.7723 (mttt) REVERT: N 10 ARG cc_start: 0.7510 (OUTLIER) cc_final: 0.7288 (mtp-110) REVERT: N 13 HIS cc_start: 0.7790 (m-70) cc_final: 0.7336 (m-70) REVERT: N 40 ARG cc_start: 0.7604 (ptp-170) cc_final: 0.6791 (ptp-170) REVERT: N 92 TRP cc_start: 0.7794 (m100) cc_final: 0.7505 (m-90) REVERT: N 136 MET cc_start: 0.5231 (ttp) cc_final: 0.4262 (tpp) REVERT: O 37 THR cc_start: 0.7713 (OUTLIER) cc_final: 0.7403 (t) REVERT: O 45 ARG cc_start: 0.6510 (mtp180) cc_final: 0.5994 (tpp-160) REVERT: O 78 LYS cc_start: 0.8428 (tttt) cc_final: 0.7939 (tptp) REVERT: O 82 GLU cc_start: 0.8604 (tt0) cc_final: 0.8207 (tm-30) REVERT: O 114 GLU cc_start: 0.5591 (OUTLIER) cc_final: 0.4931 (pm20) REVERT: P 36 TYR cc_start: 0.7728 (OUTLIER) cc_final: 0.7018 (m-80) REVERT: Q 56 HIS cc_start: 0.6621 (m170) cc_final: 0.6351 (m90) REVERT: Q 72 ARG cc_start: 0.7673 (mmm160) cc_final: 0.7266 (mmm160) REVERT: R 20 GLN cc_start: 0.8890 (mt0) cc_final: 0.8467 (mt0) REVERT: R 28 ARG cc_start: 0.8566 (OUTLIER) cc_final: 0.8306 (mtt-85) REVERT: R 33 ARG cc_start: 0.8388 (OUTLIER) cc_final: 0.7568 (mtt-85) REVERT: S 1 MET cc_start: 0.7029 (tpp) cc_final: 0.6315 (ppp) REVERT: S 40 MET cc_start: 0.7657 (tmm) cc_final: 0.6962 (tmm) REVERT: T 3 THR cc_start: 0.6939 (OUTLIER) cc_final: 0.6554 (p) REVERT: T 16 LYS cc_start: 0.8900 (mttp) cc_final: 0.8676 (mtpp) REVERT: T 48 LYS cc_start: 0.8856 (tttt) cc_final: 0.8274 (tptm) REVERT: T 98 LYS cc_start: 0.8655 (mttp) cc_final: 0.8348 (tttp) REVERT: U 44 LYS cc_start: 0.8953 (tttm) cc_final: 0.8439 (mtpp) REVERT: U 76 ARG cc_start: 0.8459 (ptm160) cc_final: 0.8041 (ptm160) REVERT: U 77 ARG cc_start: 0.7714 (OUTLIER) cc_final: 0.7410 (mmt90) REVERT: V 62 GLU cc_start: 0.6857 (mp0) cc_final: 0.6258 (mt-10) REVERT: W 1 MET cc_start: 0.6698 (tpt) cc_final: 0.6332 (mtt) REVERT: Y 39 TRP cc_start: 0.6932 (t-100) cc_final: 0.5420 (t-100) REVERT: Y 41 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.7487 (mp0) REVERT: Y 46 PHE cc_start: 0.7775 (m-80) cc_final: 0.7317 (m-80) REVERT: Z 8 GLU cc_start: 0.6736 (mm-30) cc_final: 0.6258 (pm20) REVERT: Z 43 LEU cc_start: 0.8388 (mt) cc_final: 0.8092 (mt) REVERT: 0 54 MET cc_start: 0.8375 (ptm) cc_final: 0.7438 (ttp) REVERT: 1 13 ARG cc_start: 0.7854 (ttp-110) cc_final: 0.7013 (ttp-170) REVERT: 1 16 ARG cc_start: 0.7952 (ttp-170) cc_final: 0.7748 (ttp-170) REVERT: 3 5 PHE cc_start: 0.8931 (t80) cc_final: 0.8694 (t80) REVERT: 3 35 ARG cc_start: 0.8531 (ttm110) cc_final: 0.8311 (ttm110) REVERT: 4 4 ILE cc_start: 0.8725 (OUTLIER) cc_final: 0.8345 (pt) REVERT: b 37 LYS cc_start: 0.8124 (tttt) cc_final: 0.7915 (mttt) REVERT: b 49 MET cc_start: 0.8589 (mtt) cc_final: 0.8183 (tpp) REVERT: b 67 ILE cc_start: 0.7958 (mp) cc_final: 0.7561 (tp) REVERT: b 94 HIS cc_start: 0.6878 (m90) cc_final: 0.6602 (m170) REVERT: b 100 MET cc_start: 0.7160 (ttm) cc_final: 0.6482 (mtt) REVERT: b 142 GLU cc_start: 0.8091 (mt-10) cc_final: 0.7571 (tm-30) REVERT: b 175 GLU cc_start: 0.8660 (mt-10) cc_final: 0.8280 (mt-10) REVERT: c 6 HIS cc_start: 0.8538 (t-90) cc_final: 0.8315 (t-90) REVERT: c 25 ASN cc_start: 0.3548 (m110) cc_final: 0.3275 (t0) REVERT: c 130 PHE cc_start: 0.8824 (p90) cc_final: 0.8365 (p90) REVERT: c 152 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.7959 (tm-30) REVERT: c 166 GLU cc_start: 0.7287 (tt0) cc_final: 0.6811 (mt-10) REVERT: c 202 ILE cc_start: 0.7972 (mt) cc_final: 0.7690 (tt) REVERT: d 19 LEU cc_start: 0.4313 (OUTLIER) cc_final: 0.3712 (mt) REVERT: d 36 GLN cc_start: 0.8284 (tt0) cc_final: 0.7851 (tt0) REVERT: d 60 LYS cc_start: 0.7204 (OUTLIER) cc_final: 0.6793 (ptmm) REVERT: d 115 ARG cc_start: 0.6659 (tmm-80) cc_final: 0.6396 (tmm-80) REVERT: d 116 GLN cc_start: 0.5774 (OUTLIER) cc_final: 0.4508 (mm110) REVERT: e 96 MET cc_start: 0.8529 (ttp) cc_final: 0.8004 (tpt) REVERT: e 105 ILE cc_start: 0.8214 (mp) cc_final: 0.7792 (pt) REVERT: e 126 LYS cc_start: 0.7787 (tttt) cc_final: 0.7479 (tptt) REVERT: f 88 MET cc_start: 0.7563 (ttt) cc_final: 0.6968 (ttt) REVERT: f 90 MET cc_start: 0.7872 (mtm) cc_final: 0.7562 (mtm) REVERT: g 25 LYS cc_start: 0.7120 (mtmm) cc_final: 0.6666 (tptp) REVERT: g 28 ASN cc_start: 0.6561 (m-40) cc_final: 0.5548 (m-40) REVERT: g 31 MET cc_start: 0.6114 (ptm) cc_final: 0.5458 (ptm) REVERT: g 36 LYS cc_start: 0.6813 (mmtp) cc_final: 0.6559 (mmtp) REVERT: g 58 GLU cc_start: 0.4309 (mt-10) cc_final: 0.4025 (mm-30) REVERT: g 131 LYS cc_start: 0.8122 (tptp) cc_final: 0.7876 (tmtt) REVERT: g 139 GLU cc_start: 0.8095 (mt-10) cc_final: 0.7792 (mm-30) REVERT: h 13 ARG cc_start: 0.6869 (mtt90) cc_final: 0.6445 (tpp80) REVERT: h 71 VAL cc_start: 0.6487 (t) cc_final: 0.6208 (m) REVERT: h 89 LYS cc_start: 0.7321 (OUTLIER) cc_final: 0.6683 (tptp) REVERT: i 39 PHE cc_start: 0.6899 (OUTLIER) cc_final: 0.6413 (t80) REVERT: i 120 LYS cc_start: 0.8025 (mptt) cc_final: 0.7807 (mptt) REVERT: j 49 PHE cc_start: 0.7694 (m-80) cc_final: 0.7024 (m-80) REVERT: k 24 HIS cc_start: 0.6734 (t70) cc_final: 0.6378 (t70) REVERT: k 85 MET cc_start: 0.8065 (ptp) cc_final: 0.7437 (ptm) REVERT: l 25 GLU cc_start: 0.8561 (mt-10) cc_final: 0.8117 (mp0) REVERT: l 29 GLN cc_start: 0.8359 (mp10) cc_final: 0.8092 (mp10) REVERT: l 30 LYS cc_start: 0.8358 (mttt) cc_final: 0.7738 (mmmt) REVERT: l 50 ARG cc_start: 0.7700 (mmt-90) cc_final: 0.6926 (mpt90) REVERT: l 54 ARG cc_start: 0.8564 (ttp-110) cc_final: 0.8218 (tmm-80) REVERT: l 56 ARG cc_start: 0.8080 (tpp-160) cc_final: 0.7765 (tpp-160) REVERT: l 81 LEU cc_start: 0.8232 (tp) cc_final: 0.7790 (tt) REVERT: l 83 ARG cc_start: 0.7956 (tmm-80) cc_final: 0.7090 (tmm-80) REVERT: l 112 GLN cc_start: 0.7472 (mt0) cc_final: 0.7238 (mt0) REVERT: n 65 ARG cc_start: 0.8331 (mtp85) cc_final: 0.8081 (mtp-110) REVERT: o 74 ASP cc_start: 0.7372 (t70) cc_final: 0.7117 (t70) REVERT: o 84 ARG cc_start: 0.8457 (ttm110) cc_final: 0.8007 (ttt-90) REVERT: q 17 MET cc_start: 0.7986 (mpp) cc_final: 0.7781 (mpp) REVERT: q 30 LYS cc_start: 0.8526 (tttt) cc_final: 0.7971 (mmtt) REVERT: q 67 LEU cc_start: 0.8028 (OUTLIER) cc_final: 0.7793 (mt) REVERT: q 80 GLU cc_start: 0.6289 (tp30) cc_final: 0.5967 (tm-30) REVERT: r 28 THR cc_start: 0.7885 (m) cc_final: 0.7448 (m) REVERT: r 32 TYR cc_start: 0.7792 (m-80) cc_final: 0.7115 (m-80) REVERT: r 74 HIS cc_start: 0.3858 (OUTLIER) cc_final: 0.3625 (m90) REVERT: t 27 MET cc_start: 0.7133 (tpt) cc_final: 0.6926 (tpt) REVERT: t 35 VAL cc_start: 0.3852 (t) cc_final: 0.2543 (t) REVERT: u 5 LYS cc_start: 0.8954 (pttm) cc_final: 0.8702 (ptmm) REVERT: v 48 ASN cc_start: 0.5441 (OUTLIER) cc_final: 0.5214 (t0) REVERT: v 115 PHE cc_start: 0.8543 (m-80) cc_final: 0.8341 (m-80) REVERT: v 147 MET cc_start: 0.8891 (ptp) cc_final: 0.8527 (ptp) REVERT: v 161 PHE cc_start: 0.7558 (m-80) cc_final: 0.7180 (m-80) REVERT: v 213 ARG cc_start: 0.7559 (mtp-110) cc_final: 0.7167 (mtm110) REVERT: v 221 PHE cc_start: 0.7974 (t80) cc_final: 0.7662 (t80) REVERT: v 258 GLU cc_start: 0.8707 (mm-30) cc_final: 0.8277 (mm-30) REVERT: v 280 GLN cc_start: 0.8629 (OUTLIER) cc_final: 0.8169 (tm130) REVERT: v 283 ASN cc_start: 0.8557 (OUTLIER) cc_final: 0.8113 (m110) REVERT: v 288 MET cc_start: 0.9283 (ttp) cc_final: 0.9045 (tpt) REVERT: v 300 MET cc_start: 0.8609 (tpp) cc_final: 0.8331 (mmp) REVERT: v 311 GLU cc_start: 0.8123 (mm-30) cc_final: 0.7893 (pp20) REVERT: v 341 GLU cc_start: 0.4807 (mp0) cc_final: 0.4263 (tt0) REVERT: v 356 PHE cc_start: 0.7883 (m-80) cc_final: 0.7271 (m-10) REVERT: w 10 GLN cc_start: 0.8228 (tt0) cc_final: 0.7986 (tt0) REVERT: w 11 ILE cc_start: 0.9070 (mp) cc_final: 0.8717 (mp) REVERT: w 14 ASN cc_start: 0.7930 (m-40) cc_final: 0.7125 (m-40) REVERT: w 30 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7371 (mp0) outliers start: 411 outliers final: 301 residues processed: 1754 average time/residue: 1.5652 time to fit residues: 4621.8336 Evaluate side-chains 1795 residues out of total 5041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 332 poor density : 1463 time to evaluate : 6.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 53 HIS Chi-restraints excluded: chain C residue 86 ASN Chi-restraints excluded: chain C residue 103 TYR Chi-restraints excluded: chain C residue 108 LYS Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 111 LYS Chi-restraints excluded: chain C residue 114 ASP Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 133 ARG Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 182 ARG Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 256 LYS Chi-restraints excluded: chain C residue 266 PHE Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 14 ILE Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 67 HIS Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain E residue 5 LEU Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 19 PHE Chi-restraints excluded: chain E residue 25 GLU Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 41 GLN Chi-restraints excluded: chain E residue 44 ARG Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 107 SER Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain F residue 22 TYR Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 71 ARG Chi-restraints excluded: chain F residue 87 CYS Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 136 ILE Chi-restraints excluded: chain F residue 147 ASP Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain F residue 178 ARG Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 81 GLU Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 53 GLU Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 121 ILE Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 55 ILE Chi-restraints excluded: chain K residue 56 VAL Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 81 ILE Chi-restraints excluded: chain K residue 93 ILE Chi-restraints excluded: chain K residue 130 HIS Chi-restraints excluded: chain K residue 135 GLN Chi-restraints excluded: chain L residue 22 ILE Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 70 ARG Chi-restraints excluded: chain L residue 86 LEU Chi-restraints excluded: chain L residue 87 LEU Chi-restraints excluded: chain L residue 106 GLU Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 23 ILE Chi-restraints excluded: chain M residue 27 LEU Chi-restraints excluded: chain M residue 122 VAL Chi-restraints excluded: chain M residue 125 LEU Chi-restraints excluded: chain M residue 142 ILE Chi-restraints excluded: chain N residue 2 LEU Chi-restraints excluded: chain N residue 6 ARG Chi-restraints excluded: chain N residue 10 ARG Chi-restraints excluded: chain N residue 73 ILE Chi-restraints excluded: chain N residue 88 ASN Chi-restraints excluded: chain N residue 135 VAL Chi-restraints excluded: chain O residue 13 ASN Chi-restraints excluded: chain O residue 33 ILE Chi-restraints excluded: chain O residue 37 THR Chi-restraints excluded: chain O residue 53 THR Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain O residue 114 GLU Chi-restraints excluded: chain P residue 36 TYR Chi-restraints excluded: chain P residue 53 THR Chi-restraints excluded: chain P residue 97 PHE Chi-restraints excluded: chain P residue 103 VAL Chi-restraints excluded: chain Q residue 30 VAL Chi-restraints excluded: chain Q residue 46 VAL Chi-restraints excluded: chain Q residue 48 ILE Chi-restraints excluded: chain Q residue 52 ASN Chi-restraints excluded: chain Q residue 63 LYS Chi-restraints excluded: chain Q residue 80 VAL Chi-restraints excluded: chain Q residue 104 THR Chi-restraints excluded: chain R residue 16 LYS Chi-restraints excluded: chain R residue 28 ARG Chi-restraints excluded: chain R residue 30 ARG Chi-restraints excluded: chain R residue 33 ARG Chi-restraints excluded: chain R residue 74 ILE Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain S residue 19 THR Chi-restraints excluded: chain S residue 29 THR Chi-restraints excluded: chain S residue 39 LEU Chi-restraints excluded: chain S residue 41 ILE Chi-restraints excluded: chain S residue 64 VAL Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 93 PHE Chi-restraints excluded: chain T residue 3 THR Chi-restraints excluded: chain T residue 17 VAL Chi-restraints excluded: chain T residue 45 VAL Chi-restraints excluded: chain T residue 60 HIS Chi-restraints excluded: chain T residue 67 ASP Chi-restraints excluded: chain T residue 73 LYS Chi-restraints excluded: chain T residue 77 ASP Chi-restraints excluded: chain T residue 97 LEU Chi-restraints excluded: chain T residue 107 VAL Chi-restraints excluded: chain T residue 108 SER Chi-restraints excluded: chain U residue 16 VAL Chi-restraints excluded: chain U residue 32 LEU Chi-restraints excluded: chain U residue 77 ARG Chi-restraints excluded: chain V residue 15 THR Chi-restraints excluded: chain V residue 28 VAL Chi-restraints excluded: chain V residue 59 VAL Chi-restraints excluded: chain V residue 70 VAL Chi-restraints excluded: chain V residue 77 THR Chi-restraints excluded: chain V residue 93 VAL Chi-restraints excluded: chain W residue 2 PHE Chi-restraints excluded: chain W residue 30 ILE Chi-restraints excluded: chain W residue 40 ILE Chi-restraints excluded: chain W residue 53 LYS Chi-restraints excluded: chain W residue 91 PHE Chi-restraints excluded: chain X residue 10 THR Chi-restraints excluded: chain X residue 43 THR Chi-restraints excluded: chain Y residue 4 VAL Chi-restraints excluded: chain Y residue 22 LEU Chi-restraints excluded: chain Y residue 23 ASN Chi-restraints excluded: chain Y residue 41 GLU Chi-restraints excluded: chain Y residue 66 THR Chi-restraints excluded: chain Y residue 68 LEU Chi-restraints excluded: chain Z residue 9 LYS Chi-restraints excluded: chain Z residue 11 VAL Chi-restraints excluded: chain Z residue 37 LEU Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 41 THR Chi-restraints excluded: chain 1 residue 9 THR Chi-restraints excluded: chain 1 residue 22 LEU Chi-restraints excluded: chain 1 residue 39 LEU Chi-restraints excluded: chain 2 residue 23 THR Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 2 residue 47 VAL Chi-restraints excluded: chain 3 residue 1 MET Chi-restraints excluded: chain 3 residue 4 THR Chi-restraints excluded: chain 3 residue 24 THR Chi-restraints excluded: chain 3 residue 45 SER Chi-restraints excluded: chain 4 residue 4 ILE Chi-restraints excluded: chain 4 residue 30 ARG Chi-restraints excluded: chain 4 residue 55 LEU Chi-restraints excluded: chain 4 residue 57 LEU Chi-restraints excluded: chain 5 residue 3 VAL Chi-restraints excluded: chain 5 residue 17 VAL Chi-restraints excluded: chain b residue 8 ASP Chi-restraints excluded: chain b residue 18 HIS Chi-restraints excluded: chain b residue 52 GLU Chi-restraints excluded: chain b residue 72 THR Chi-restraints excluded: chain b residue 103 ASN Chi-restraints excluded: chain b residue 109 GLN Chi-restraints excluded: chain b residue 114 LEU Chi-restraints excluded: chain b residue 116 ASP Chi-restraints excluded: chain b residue 129 LEU Chi-restraints excluded: chain b residue 130 THR Chi-restraints excluded: chain b residue 190 ASN Chi-restraints excluded: chain b residue 208 ARG Chi-restraints excluded: chain b residue 211 THR Chi-restraints excluded: chain c residue 19 ASN Chi-restraints excluded: chain c residue 33 LEU Chi-restraints excluded: chain c residue 67 THR Chi-restraints excluded: chain c residue 83 ASP Chi-restraints excluded: chain c residue 102 ASN Chi-restraints excluded: chain c residue 116 VAL Chi-restraints excluded: chain c residue 121 THR Chi-restraints excluded: chain c residue 138 VAL Chi-restraints excluded: chain c residue 149 ILE Chi-restraints excluded: chain c residue 152 GLU Chi-restraints excluded: chain c residue 162 ILE Chi-restraints excluded: chain c residue 195 VAL Chi-restraints excluded: chain c residue 200 VAL Chi-restraints excluded: chain d residue 19 LEU Chi-restraints excluded: chain d residue 32 CYS Chi-restraints excluded: chain d residue 60 LYS Chi-restraints excluded: chain d residue 78 GLU Chi-restraints excluded: chain d residue 116 GLN Chi-restraints excluded: chain d residue 117 LEU Chi-restraints excluded: chain d residue 137 VAL Chi-restraints excluded: chain d residue 169 THR Chi-restraints excluded: chain d residue 181 THR Chi-restraints excluded: chain d residue 195 ILE Chi-restraints excluded: chain d residue 200 ILE Chi-restraints excluded: chain e residue 20 ARG Chi-restraints excluded: chain e residue 37 THR Chi-restraints excluded: chain e residue 46 VAL Chi-restraints excluded: chain e residue 56 VAL Chi-restraints excluded: chain e residue 76 LEU Chi-restraints excluded: chain e residue 88 VAL Chi-restraints excluded: chain e residue 94 VAL Chi-restraints excluded: chain e residue 131 THR Chi-restraints excluded: chain e residue 137 VAL Chi-restraints excluded: chain e residue 148 ASN Chi-restraints excluded: chain f residue 8 PHE Chi-restraints excluded: chain f residue 9 MET Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 54 LEU Chi-restraints excluded: chain f residue 58 HIS Chi-restraints excluded: chain f residue 60 VAL Chi-restraints excluded: chain f residue 75 GLU Chi-restraints excluded: chain f residue 85 ILE Chi-restraints excluded: chain f residue 89 VAL Chi-restraints excluded: chain f residue 92 THR Chi-restraints excluded: chain g residue 6 VAL Chi-restraints excluded: chain g residue 13 LEU Chi-restraints excluded: chain g residue 21 GLU Chi-restraints excluded: chain g residue 27 VAL Chi-restraints excluded: chain g residue 43 VAL Chi-restraints excluded: chain g residue 75 VAL Chi-restraints excluded: chain g residue 141 VAL Chi-restraints excluded: chain h residue 14 ILE Chi-restraints excluded: chain h residue 42 GLU Chi-restraints excluded: chain h residue 59 LEU Chi-restraints excluded: chain h residue 62 THR Chi-restraints excluded: chain h residue 77 ARG Chi-restraints excluded: chain h residue 89 LYS Chi-restraints excluded: chain i residue 20 PHE Chi-restraints excluded: chain i residue 39 PHE Chi-restraints excluded: chain i residue 54 LEU Chi-restraints excluded: chain i residue 104 VAL Chi-restraints excluded: chain i residue 111 VAL Chi-restraints excluded: chain i residue 113 ARG Chi-restraints excluded: chain i residue 115 LYS Chi-restraints excluded: chain i residue 130 ARG Chi-restraints excluded: chain j residue 7 ARG Chi-restraints excluded: chain j residue 32 THR Chi-restraints excluded: chain j residue 42 LEU Chi-restraints excluded: chain j residue 53 ILE Chi-restraints excluded: chain j residue 67 ILE Chi-restraints excluded: chain j residue 76 ILE Chi-restraints excluded: chain j residue 88 MET Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 31 ILE Chi-restraints excluded: chain k residue 35 THR Chi-restraints excluded: chain k residue 59 THR Chi-restraints excluded: chain k residue 94 GLU Chi-restraints excluded: chain k residue 96 THR Chi-restraints excluded: chain k residue 97 ILE Chi-restraints excluded: chain k residue 125 LYS Chi-restraints excluded: chain l residue 33 VAL Chi-restraints excluded: chain l residue 44 LYS Chi-restraints excluded: chain l residue 52 VAL Chi-restraints excluded: chain l residue 61 PHE Chi-restraints excluded: chain l residue 64 THR Chi-restraints excluded: chain l residue 79 VAL Chi-restraints excluded: chain l residue 90 LEU Chi-restraints excluded: chain l residue 98 VAL Chi-restraints excluded: chain m residue 39 ILE Chi-restraints excluded: chain m residue 80 LEU Chi-restraints excluded: chain m residue 82 ASP Chi-restraints excluded: chain n residue 6 MET Chi-restraints excluded: chain n residue 30 ILE Chi-restraints excluded: chain n residue 43 ASN Chi-restraints excluded: chain n residue 56 SER Chi-restraints excluded: chain n residue 90 ARG Chi-restraints excluded: chain o residue 22 THR Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain p residue 16 PHE Chi-restraints excluded: chain p residue 50 THR Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain q residue 58 VAL Chi-restraints excluded: chain q residue 67 LEU Chi-restraints excluded: chain q residue 68 SER Chi-restraints excluded: chain q residue 76 VAL Chi-restraints excluded: chain r residue 39 ILE Chi-restraints excluded: chain r residue 52 GLN Chi-restraints excluded: chain r residue 74 HIS Chi-restraints excluded: chain s residue 33 THR Chi-restraints excluded: chain s residue 37 ARG Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain s residue 79 THR Chi-restraints excluded: chain u residue 13 ASP Chi-restraints excluded: chain v residue 48 ASN Chi-restraints excluded: chain v residue 69 THR Chi-restraints excluded: chain v residue 77 LEU Chi-restraints excluded: chain v residue 140 GLU Chi-restraints excluded: chain v residue 148 LEU Chi-restraints excluded: chain v residue 180 THR Chi-restraints excluded: chain v residue 192 LEU Chi-restraints excluded: chain v residue 196 THR Chi-restraints excluded: chain v residue 216 SER Chi-restraints excluded: chain v residue 226 VAL Chi-restraints excluded: chain v residue 239 LEU Chi-restraints excluded: chain v residue 254 VAL Chi-restraints excluded: chain v residue 264 THR Chi-restraints excluded: chain v residue 266 ILE Chi-restraints excluded: chain v residue 280 GLN Chi-restraints excluded: chain v residue 283 ASN Chi-restraints excluded: chain v residue 295 LEU Chi-restraints excluded: chain v residue 304 ASN Chi-restraints excluded: chain v residue 308 GLN Chi-restraints excluded: chain v residue 345 THR Chi-restraints excluded: chain w residue 6 HIS Chi-restraints excluded: chain w residue 16 ILE Chi-restraints excluded: chain w residue 22 ASP Chi-restraints excluded: chain w residue 30 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1061 random chunks: chunk 632 optimal weight: 30.0000 chunk 408 optimal weight: 3.9990 chunk 610 optimal weight: 9.9990 chunk 308 optimal weight: 50.0000 chunk 200 optimal weight: 10.0000 chunk 198 optimal weight: 6.9990 chunk 650 optimal weight: 20.0000 chunk 696 optimal weight: 10.0000 chunk 505 optimal weight: 0.9980 chunk 95 optimal weight: 10.0000 chunk 803 optimal weight: 3.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 90 ASN ** C 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 HIS D 150 GLN ** E 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 5 HIS G 73 ASN ** H 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 62 ASN ** P 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 69 ASN ** Z 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 31 GLN ** 3 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 36 ASN ** b 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 73 ASN e 77 ASN ** e 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 122 ASN i 25 ASN i 126 GLN ** j 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 72 HIS l 75 GLN ** o 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 80 GLN ** p 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 63 GLN ** q 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 54 GLN ** t 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.6313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 162161 Z= 0.285 Angle : 0.757 13.901 242281 Z= 0.390 Chirality : 0.039 0.501 30825 Planarity : 0.007 0.131 13212 Dihedral : 24.962 179.716 80375 Min Nonbonded Distance : 1.757 Molprobity Statistics. All-atom Clashscore : 30.08 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.48 % Favored : 93.38 % Rotamer: Outliers : 8.29 % Allowed : 29.52 % Favored : 62.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.10), residues: 6054 helix: 0.29 (0.11), residues: 2099 sheet: -1.40 (0.15), residues: 1058 loop : -1.80 (0.11), residues: 2897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP K 15 HIS 0.023 0.002 HIS f 3 PHE 0.054 0.003 PHE 3 18 TYR 0.046 0.003 TYR d 75 ARG 0.013 0.001 ARG s 78 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12108 Ramachandran restraints generated. 6054 Oldfield, 0 Emsley, 6054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12108 Ramachandran restraints generated. 6054 Oldfield, 0 Emsley, 6054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1908 residues out of total 5041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 418 poor density : 1490 time to evaluate : 6.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 79 GLU cc_start: 0.5765 (tt0) cc_final: 0.5464 (tt0) REVERT: C 82 GLU cc_start: 0.7587 (mt-10) cc_final: 0.7165 (mt-10) REVERT: C 83 TYR cc_start: 0.7979 (t80) cc_final: 0.7293 (t80) REVERT: C 96 TYR cc_start: 0.7096 (OUTLIER) cc_final: 0.5424 (m-80) REVERT: C 101 ARG cc_start: 0.6934 (mpt180) cc_final: 0.6621 (mpt180) REVERT: C 115 GLN cc_start: 0.8021 (mt0) cc_final: 0.7686 (tp40) REVERT: C 146 MET cc_start: 0.7153 (mtt) cc_final: 0.5942 (mmp) REVERT: C 175 ARG cc_start: 0.8698 (ttt90) cc_final: 0.8072 (ptp-170) REVERT: C 194 GLU cc_start: 0.8081 (tp30) cc_final: 0.7772 (tp30) REVERT: C 266 PHE cc_start: 0.7372 (OUTLIER) cc_final: 0.6779 (m-80) REVERT: C 267 ILE cc_start: 0.7742 (mm) cc_final: 0.7513 (mm) REVERT: D 2 ILE cc_start: 0.3633 (OUTLIER) cc_final: 0.3337 (mt) REVERT: D 11 MET cc_start: 0.4292 (OUTLIER) cc_final: 0.4030 (tmm) REVERT: D 36 GLN cc_start: 0.7103 (mt0) cc_final: 0.6575 (tm-30) REVERT: D 89 GLU cc_start: 0.5282 (mt-10) cc_final: 0.4809 (tm-30) REVERT: E 63 LYS cc_start: 0.3500 (tmtt) cc_final: 0.2985 (tmtt) REVERT: E 67 ARG cc_start: 0.7102 (mtp85) cc_final: 0.6836 (mtp85) REVERT: E 189 THR cc_start: 0.5534 (OUTLIER) cc_final: 0.5173 (p) REVERT: E 195 GLN cc_start: 0.7969 (tt0) cc_final: 0.7620 (pt0) REVERT: F 38 MET cc_start: 0.5141 (tpt) cc_final: 0.4896 (mmm) REVERT: F 44 ILE cc_start: 0.7118 (OUTLIER) cc_final: 0.6511 (mt) REVERT: F 47 LYS cc_start: 0.8469 (mmmt) cc_final: 0.8207 (mmmt) REVERT: F 83 TYR cc_start: 0.7477 (t80) cc_final: 0.7195 (t80) REVERT: F 95 ARG cc_start: 0.7381 (mpt-90) cc_final: 0.6921 (mtt90) REVERT: F 178 ARG cc_start: -0.4416 (OUTLIER) cc_final: -0.4796 (ptt-90) REVERT: G 133 LEU cc_start: 0.8129 (mt) cc_final: 0.7758 (tp) REVERT: J 61 TYR cc_start: 0.5435 (m-10) cc_final: 0.5114 (m-10) REVERT: K 138 GLN cc_start: 0.7553 (pt0) cc_final: 0.7196 (mp10) REVERT: L 1 MET cc_start: 0.6379 (tpt) cc_final: 0.5928 (tpt) REVERT: L 53 LYS cc_start: 0.8926 (tttt) cc_final: 0.8671 (mmtm) REVERT: L 70 ARG cc_start: 0.4174 (OUTLIER) cc_final: 0.3747 (mmt90) REVERT: L 98 ARG cc_start: 0.7342 (tpp-160) cc_final: 0.7142 (mmm160) REVERT: L 106 GLU cc_start: 0.6599 (OUTLIER) cc_final: 0.6276 (mp0) REVERT: L 114 LYS cc_start: 0.7759 (OUTLIER) cc_final: 0.7232 (ptmt) REVERT: M 23 ILE cc_start: 0.8483 (OUTLIER) cc_final: 0.8275 (tp) REVERT: M 55 MET cc_start: 0.8990 (tpp) cc_final: 0.8719 (tpp) REVERT: M 81 ASP cc_start: 0.7118 (m-30) cc_final: 0.6720 (p0) REVERT: M 82 LEU cc_start: 0.5014 (OUTLIER) cc_final: 0.4704 (pp) REVERT: N 8 LYS cc_start: 0.7924 (mmtt) cc_final: 0.7699 (mttt) REVERT: N 10 ARG cc_start: 0.7486 (OUTLIER) cc_final: 0.7214 (mtp-110) REVERT: N 13 HIS cc_start: 0.7449 (m-70) cc_final: 0.6990 (m-70) REVERT: N 45 GLN cc_start: 0.8390 (mt0) cc_final: 0.8129 (tp40) REVERT: N 51 ARG cc_start: 0.8503 (mtp85) cc_final: 0.8247 (mtm110) REVERT: N 92 TRP cc_start: 0.7823 (m100) cc_final: 0.7318 (m100) REVERT: N 136 MET cc_start: 0.5028 (ttp) cc_final: 0.4128 (tpp) REVERT: O 17 ARG cc_start: 0.8026 (ttm-80) cc_final: 0.6606 (mtm180) REVERT: O 37 THR cc_start: 0.7717 (OUTLIER) cc_final: 0.7442 (t) REVERT: O 45 ARG cc_start: 0.6529 (mtp180) cc_final: 0.6005 (tpp-160) REVERT: O 74 GLU cc_start: 0.8642 (tm-30) cc_final: 0.8426 (tm-30) REVERT: O 78 LYS cc_start: 0.8471 (tttt) cc_final: 0.7899 (tptp) REVERT: O 82 GLU cc_start: 0.8641 (tt0) cc_final: 0.8235 (tm-30) REVERT: O 114 GLU cc_start: 0.5591 (OUTLIER) cc_final: 0.4979 (pm20) REVERT: P 36 TYR cc_start: 0.7520 (OUTLIER) cc_final: 0.6820 (m-80) REVERT: P 46 GLU cc_start: 0.6819 (pt0) cc_final: 0.6456 (mm-30) REVERT: Q 72 ARG cc_start: 0.7623 (mmm160) cc_final: 0.7082 (mmm160) REVERT: R 20 GLN cc_start: 0.8861 (mt0) cc_final: 0.8422 (mt0) REVERT: R 28 ARG cc_start: 0.8540 (OUTLIER) cc_final: 0.8258 (mtt-85) REVERT: R 33 ARG cc_start: 0.8392 (OUTLIER) cc_final: 0.7410 (mtt-85) REVERT: S 1 MET cc_start: 0.6855 (tpp) cc_final: 0.6216 (ppp) REVERT: T 3 THR cc_start: 0.6872 (OUTLIER) cc_final: 0.6515 (p) REVERT: T 16 LYS cc_start: 0.8899 (mttp) cc_final: 0.8670 (mtpp) REVERT: T 48 LYS cc_start: 0.8865 (tttt) cc_final: 0.8284 (tptm) REVERT: T 98 LYS cc_start: 0.8651 (mttp) cc_final: 0.8345 (tttp) REVERT: U 44 LYS cc_start: 0.8935 (tttm) cc_final: 0.8589 (ttmt) REVERT: U 76 ARG cc_start: 0.8432 (ptm160) cc_final: 0.8039 (ptm160) REVERT: U 77 ARG cc_start: 0.7699 (OUTLIER) cc_final: 0.7392 (mmt90) REVERT: V 43 LYS cc_start: 0.7760 (ptpt) cc_final: 0.7558 (pttt) REVERT: V 62 GLU cc_start: 0.6813 (mp0) cc_final: 0.6224 (mt-10) REVERT: W 1 MET cc_start: 0.6234 (tpt) cc_final: 0.5739 (mtt) REVERT: Y 41 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7405 (mp0) REVERT: Z 8 GLU cc_start: 0.6788 (mm-30) cc_final: 0.6265 (pm20) REVERT: 0 54 MET cc_start: 0.8395 (ptm) cc_final: 0.7545 (ttm) REVERT: 1 13 ARG cc_start: 0.7884 (ttp-110) cc_final: 0.7027 (ttp-170) REVERT: 1 16 ARG cc_start: 0.7974 (ttp-170) cc_final: 0.7760 (ttp-170) REVERT: 3 5 PHE cc_start: 0.8956 (t80) cc_final: 0.8739 (t80) REVERT: 3 35 ARG cc_start: 0.8504 (ttm110) cc_final: 0.8302 (ttm110) REVERT: 4 4 ILE cc_start: 0.8671 (OUTLIER) cc_final: 0.8267 (pt) REVERT: b 21 ARG cc_start: 0.7405 (mmm-85) cc_final: 0.7203 (mmm-85) REVERT: b 49 MET cc_start: 0.8610 (mtt) cc_final: 0.8227 (tpp) REVERT: b 67 ILE cc_start: 0.8007 (mp) cc_final: 0.7619 (tp) REVERT: b 90 PHE cc_start: 0.6829 (m-80) cc_final: 0.6575 (m-80) REVERT: b 94 HIS cc_start: 0.6810 (m90) cc_final: 0.6549 (m170) REVERT: b 142 GLU cc_start: 0.8174 (mt-10) cc_final: 0.7590 (tm-30) REVERT: b 175 GLU cc_start: 0.8697 (mt-10) cc_final: 0.8283 (mt-10) REVERT: c 6 HIS cc_start: 0.8533 (t-90) cc_final: 0.8111 (t-90) REVERT: c 130 PHE cc_start: 0.8715 (p90) cc_final: 0.8247 (p90) REVERT: c 151 VAL cc_start: 0.7693 (t) cc_final: 0.7306 (m) REVERT: c 152 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.7881 (tm-30) REVERT: c 166 GLU cc_start: 0.7391 (tt0) cc_final: 0.6919 (mt-10) REVERT: c 202 ILE cc_start: 0.7997 (mt) cc_final: 0.7684 (tt) REVERT: d 19 LEU cc_start: 0.4292 (OUTLIER) cc_final: 0.3473 (mt) REVERT: d 36 GLN cc_start: 0.8274 (tt0) cc_final: 0.7829 (tt0) REVERT: d 60 LYS cc_start: 0.7207 (OUTLIER) cc_final: 0.6777 (ptmm) REVERT: d 115 ARG cc_start: 0.6699 (tmm-80) cc_final: 0.6362 (tmm-80) REVERT: d 116 GLN cc_start: 0.5599 (OUTLIER) cc_final: 0.4164 (mm110) REVERT: e 96 MET cc_start: 0.8492 (ttp) cc_final: 0.7997 (tpt) REVERT: e 105 ILE cc_start: 0.8279 (mp) cc_final: 0.7840 (pt) REVERT: e 126 LYS cc_start: 0.7671 (tttt) cc_final: 0.7446 (tptt) REVERT: f 88 MET cc_start: 0.7496 (ttt) cc_final: 0.6940 (ttt) REVERT: f 90 MET cc_start: 0.7842 (mtm) cc_final: 0.7552 (mtm) REVERT: g 25 LYS cc_start: 0.7141 (mtmm) cc_final: 0.6701 (tptp) REVERT: g 28 ASN cc_start: 0.6579 (m-40) cc_final: 0.5986 (m110) REVERT: g 36 LYS cc_start: 0.6771 (mmtp) cc_final: 0.6547 (mmtp) REVERT: g 58 GLU cc_start: 0.4216 (mt-10) cc_final: 0.4009 (mm-30) REVERT: g 86 GLN cc_start: 0.6921 (tp40) cc_final: 0.6718 (tp40) REVERT: g 131 LYS cc_start: 0.8136 (tptp) cc_final: 0.7868 (tmtt) REVERT: g 139 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7795 (mm-30) REVERT: g 148 ASN cc_start: 0.7322 (m110) cc_final: 0.7031 (m110) REVERT: h 13 ARG cc_start: 0.6754 (mtt90) cc_final: 0.6319 (tpp80) REVERT: h 31 LYS cc_start: 0.7514 (mmmt) cc_final: 0.7248 (mmtp) REVERT: h 71 VAL cc_start: 0.6449 (t) cc_final: 0.6182 (m) REVERT: h 89 LYS cc_start: 0.7319 (OUTLIER) cc_final: 0.6647 (tptp) REVERT: h 114 ARG cc_start: 0.4904 (ttp80) cc_final: 0.4392 (tpt170) REVERT: i 39 PHE cc_start: 0.6946 (OUTLIER) cc_final: 0.6494 (t80) REVERT: i 120 LYS cc_start: 0.8067 (mptt) cc_final: 0.7819 (mptt) REVERT: j 49 PHE cc_start: 0.7557 (m-80) cc_final: 0.6949 (m-80) REVERT: k 24 HIS cc_start: 0.6823 (t70) cc_final: 0.6488 (t70) REVERT: k 85 MET cc_start: 0.8047 (ptp) cc_final: 0.7373 (ptm) REVERT: l 25 GLU cc_start: 0.8549 (mt-10) cc_final: 0.8097 (mp0) REVERT: l 29 GLN cc_start: 0.8298 (mp10) cc_final: 0.8050 (mp10) REVERT: l 30 LYS cc_start: 0.8327 (mttt) cc_final: 0.7725 (mmmt) REVERT: l 50 ARG cc_start: 0.7709 (mmt-90) cc_final: 0.6978 (mpt90) REVERT: l 54 ARG cc_start: 0.8517 (ttp-110) cc_final: 0.8204 (ttp-110) REVERT: l 56 ARG cc_start: 0.8074 (tpp-160) cc_final: 0.7778 (tpp-160) REVERT: l 66 TYR cc_start: 0.8732 (t80) cc_final: 0.8507 (t80) REVERT: l 81 LEU cc_start: 0.8107 (tp) cc_final: 0.7653 (tt) REVERT: l 83 ARG cc_start: 0.8029 (tmm-80) cc_final: 0.7129 (tmm-80) REVERT: l 112 GLN cc_start: 0.7377 (mt0) cc_final: 0.7121 (mt0) REVERT: m 71 ARG cc_start: 0.4936 (ptp-170) cc_final: 0.4031 (ptm-80) REVERT: n 26 GLU cc_start: 0.7036 (tp30) cc_final: 0.6833 (tp30) REVERT: n 65 ARG cc_start: 0.8257 (mtp85) cc_final: 0.8031 (mtp-110) REVERT: n 75 ARG cc_start: 0.7193 (mtt90) cc_final: 0.6534 (mtt-85) REVERT: o 40 GLN cc_start: 0.9178 (tp-100) cc_final: 0.8936 (mp10) REVERT: o 74 ASP cc_start: 0.7142 (t70) cc_final: 0.6849 (t0) REVERT: o 84 ARG cc_start: 0.8564 (ttm110) cc_final: 0.8178 (ttt-90) REVERT: q 12 VAL cc_start: 0.8528 (m) cc_final: 0.8240 (t) REVERT: q 30 LYS cc_start: 0.8459 (tttt) cc_final: 0.7943 (mmtt) REVERT: q 67 LEU cc_start: 0.7930 (OUTLIER) cc_final: 0.7600 (mt) REVERT: q 80 GLU cc_start: 0.6361 (tp30) cc_final: 0.6113 (tm-30) REVERT: r 28 THR cc_start: 0.7892 (m) cc_final: 0.7471 (m) REVERT: r 32 TYR cc_start: 0.7677 (m-80) cc_final: 0.6987 (m-80) REVERT: r 74 HIS cc_start: 0.3928 (OUTLIER) cc_final: 0.3714 (m90) REVERT: t 83 ILE cc_start: 0.6218 (OUTLIER) cc_final: 0.6016 (pt) REVERT: u 5 LYS cc_start: 0.8924 (pttm) cc_final: 0.8667 (ptmm) REVERT: v 48 ASN cc_start: 0.5557 (OUTLIER) cc_final: 0.5329 (t0) REVERT: v 213 ARG cc_start: 0.7515 (mtp-110) cc_final: 0.7167 (mtm110) REVERT: v 221 PHE cc_start: 0.8007 (t80) cc_final: 0.7684 (t80) REVERT: v 258 GLU cc_start: 0.8679 (mm-30) cc_final: 0.8280 (mm-30) REVERT: v 280 GLN cc_start: 0.8612 (OUTLIER) cc_final: 0.8125 (tm130) REVERT: v 283 ASN cc_start: 0.8568 (OUTLIER) cc_final: 0.8125 (m110) REVERT: v 288 MET cc_start: 0.9277 (ttp) cc_final: 0.9046 (tpt) REVERT: v 300 MET cc_start: 0.8591 (tpp) cc_final: 0.8312 (mmp) REVERT: v 341 GLU cc_start: 0.4720 (mp0) cc_final: 0.4155 (tt0) REVERT: v 356 PHE cc_start: 0.7841 (m-80) cc_final: 0.7218 (m-10) REVERT: w 10 GLN cc_start: 0.8116 (tt0) cc_final: 0.7884 (tt0) REVERT: w 11 ILE cc_start: 0.9063 (mp) cc_final: 0.8787 (mp) REVERT: w 30 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.7274 (mp0) outliers start: 418 outliers final: 327 residues processed: 1726 average time/residue: 1.5262 time to fit residues: 4397.0420 Evaluate side-chains 1810 residues out of total 5041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 362 poor density : 1448 time to evaluate : 6.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 86 ASN Chi-restraints excluded: chain C residue 96 TYR Chi-restraints excluded: chain C residue 103 TYR Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 111 LYS Chi-restraints excluded: chain C residue 114 ASP Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 133 ARG Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 182 ARG Chi-restraints excluded: chain C residue 189 ARG Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 256 LYS Chi-restraints excluded: chain C residue 266 PHE Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 11 MET Chi-restraints excluded: chain D residue 14 ILE Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 67 HIS Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 169 ARG Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain E residue 5 LEU Chi-restraints excluded: chain E residue 19 PHE Chi-restraints excluded: chain E residue 25 GLU Chi-restraints excluded: chain E residue 44 ARG Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain E residue 122 GLU Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain F residue 5 HIS Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 71 ARG Chi-restraints excluded: chain F residue 87 CYS Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 136 ILE Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain F residue 178 ARG Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 81 GLU Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 53 GLU Chi-restraints excluded: chain H residue 66 ASN Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain J residue 121 ILE Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 28 LEU Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 55 ILE Chi-restraints excluded: chain K residue 56 VAL Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 81 ILE Chi-restraints excluded: chain K residue 93 ILE Chi-restraints excluded: chain K residue 130 HIS Chi-restraints excluded: chain K residue 135 GLN Chi-restraints excluded: chain L residue 9 ASN Chi-restraints excluded: chain L residue 22 ILE Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 70 ARG Chi-restraints excluded: chain L residue 73 ASP Chi-restraints excluded: chain L residue 84 CYS Chi-restraints excluded: chain L residue 86 LEU Chi-restraints excluded: chain L residue 87 LEU Chi-restraints excluded: chain L residue 106 GLU Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain L residue 114 LYS Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 23 ILE Chi-restraints excluded: chain M residue 27 LEU Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 103 ILE Chi-restraints excluded: chain M residue 122 VAL Chi-restraints excluded: chain M residue 125 LEU Chi-restraints excluded: chain M residue 142 ILE Chi-restraints excluded: chain N residue 2 LEU Chi-restraints excluded: chain N residue 6 ARG Chi-restraints excluded: chain N residue 10 ARG Chi-restraints excluded: chain N residue 73 ILE Chi-restraints excluded: chain N residue 88 ASN Chi-restraints excluded: chain N residue 132 THR Chi-restraints excluded: chain N residue 135 VAL Chi-restraints excluded: chain O residue 13 ASN Chi-restraints excluded: chain O residue 33 ILE Chi-restraints excluded: chain O residue 37 THR Chi-restraints excluded: chain O residue 53 THR Chi-restraints excluded: chain O residue 54 LEU Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain O residue 114 GLU Chi-restraints excluded: chain P residue 26 LEU Chi-restraints excluded: chain P residue 36 TYR Chi-restraints excluded: chain P residue 49 VAL Chi-restraints excluded: chain P residue 53 THR Chi-restraints excluded: chain P residue 97 PHE Chi-restraints excluded: chain Q residue 30 VAL Chi-restraints excluded: chain Q residue 46 VAL Chi-restraints excluded: chain Q residue 48 ILE Chi-restraints excluded: chain Q residue 52 ASN Chi-restraints excluded: chain Q residue 63 LYS Chi-restraints excluded: chain Q residue 100 LEU Chi-restraints excluded: chain Q residue 104 THR Chi-restraints excluded: chain R residue 16 LYS Chi-restraints excluded: chain R residue 28 ARG Chi-restraints excluded: chain R residue 30 ARG Chi-restraints excluded: chain R residue 33 ARG Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain S residue 13 ARG Chi-restraints excluded: chain S residue 19 THR Chi-restraints excluded: chain S residue 29 THR Chi-restraints excluded: chain S residue 39 LEU Chi-restraints excluded: chain S residue 64 VAL Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 93 PHE Chi-restraints excluded: chain T residue 3 THR Chi-restraints excluded: chain T residue 15 GLN Chi-restraints excluded: chain T residue 17 VAL Chi-restraints excluded: chain T residue 30 SER Chi-restraints excluded: chain T residue 45 VAL Chi-restraints excluded: chain T residue 46 LEU Chi-restraints excluded: chain T residue 73 LYS Chi-restraints excluded: chain T residue 77 ASP Chi-restraints excluded: chain T residue 97 LEU Chi-restraints excluded: chain T residue 107 VAL Chi-restraints excluded: chain T residue 108 SER Chi-restraints excluded: chain U residue 16 VAL Chi-restraints excluded: chain U residue 34 VAL Chi-restraints excluded: chain U residue 77 ARG Chi-restraints excluded: chain V residue 15 THR Chi-restraints excluded: chain V residue 28 VAL Chi-restraints excluded: chain V residue 59 VAL Chi-restraints excluded: chain V residue 70 VAL Chi-restraints excluded: chain V residue 77 THR Chi-restraints excluded: chain V residue 93 VAL Chi-restraints excluded: chain W residue 2 PHE Chi-restraints excluded: chain W residue 30 ILE Chi-restraints excluded: chain W residue 40 ILE Chi-restraints excluded: chain W residue 91 PHE Chi-restraints excluded: chain X residue 10 THR Chi-restraints excluded: chain X residue 43 THR Chi-restraints excluded: chain Y residue 4 VAL Chi-restraints excluded: chain Y residue 22 LEU Chi-restraints excluded: chain Y residue 23 ASN Chi-restraints excluded: chain Y residue 41 GLU Chi-restraints excluded: chain Y residue 66 THR Chi-restraints excluded: chain Y residue 68 LEU Chi-restraints excluded: chain Z residue 9 LYS Chi-restraints excluded: chain Z residue 11 VAL Chi-restraints excluded: chain Z residue 37 LEU Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 41 THR Chi-restraints excluded: chain 1 residue 9 THR Chi-restraints excluded: chain 1 residue 22 LEU Chi-restraints excluded: chain 1 residue 39 LEU Chi-restraints excluded: chain 2 residue 23 THR Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 2 residue 47 VAL Chi-restraints excluded: chain 3 residue 1 MET Chi-restraints excluded: chain 3 residue 4 THR Chi-restraints excluded: chain 3 residue 8 SER Chi-restraints excluded: chain 3 residue 24 THR Chi-restraints excluded: chain 3 residue 45 SER Chi-restraints excluded: chain 4 residue 4 ILE Chi-restraints excluded: chain 4 residue 30 ARG Chi-restraints excluded: chain 4 residue 55 LEU Chi-restraints excluded: chain 4 residue 57 LEU Chi-restraints excluded: chain 5 residue 3 VAL Chi-restraints excluded: chain 5 residue 17 VAL Chi-restraints excluded: chain b residue 8 ASP Chi-restraints excluded: chain b residue 18 HIS Chi-restraints excluded: chain b residue 47 VAL Chi-restraints excluded: chain b residue 52 GLU Chi-restraints excluded: chain b residue 72 THR Chi-restraints excluded: chain b residue 103 ASN Chi-restraints excluded: chain b residue 109 GLN Chi-restraints excluded: chain b residue 114 LEU Chi-restraints excluded: chain b residue 116 ASP Chi-restraints excluded: chain b residue 129 LEU Chi-restraints excluded: chain b residue 130 THR Chi-restraints excluded: chain b residue 208 ARG Chi-restraints excluded: chain c residue 19 ASN Chi-restraints excluded: chain c residue 33 LEU Chi-restraints excluded: chain c residue 67 THR Chi-restraints excluded: chain c residue 83 ASP Chi-restraints excluded: chain c residue 102 ASN Chi-restraints excluded: chain c residue 103 ILE Chi-restraints excluded: chain c residue 116 VAL Chi-restraints excluded: chain c residue 121 THR Chi-restraints excluded: chain c residue 138 VAL Chi-restraints excluded: chain c residue 149 ILE Chi-restraints excluded: chain c residue 152 GLU Chi-restraints excluded: chain c residue 162 ILE Chi-restraints excluded: chain c residue 195 VAL Chi-restraints excluded: chain c residue 200 VAL Chi-restraints excluded: chain d residue 19 LEU Chi-restraints excluded: chain d residue 32 CYS Chi-restraints excluded: chain d residue 41 HIS Chi-restraints excluded: chain d residue 60 LYS Chi-restraints excluded: chain d residue 75 TYR Chi-restraints excluded: chain d residue 78 GLU Chi-restraints excluded: chain d residue 116 GLN Chi-restraints excluded: chain d residue 117 LEU Chi-restraints excluded: chain d residue 137 VAL Chi-restraints excluded: chain d residue 169 THR Chi-restraints excluded: chain d residue 181 THR Chi-restraints excluded: chain d residue 200 ILE Chi-restraints excluded: chain e residue 37 THR Chi-restraints excluded: chain e residue 46 VAL Chi-restraints excluded: chain e residue 76 LEU Chi-restraints excluded: chain e residue 77 ASN Chi-restraints excluded: chain e residue 88 VAL Chi-restraints excluded: chain e residue 94 VAL Chi-restraints excluded: chain e residue 131 THR Chi-restraints excluded: chain e residue 137 VAL Chi-restraints excluded: chain e residue 148 ASN Chi-restraints excluded: chain f residue 8 PHE Chi-restraints excluded: chain f residue 9 MET Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 55 HIS Chi-restraints excluded: chain f residue 58 HIS Chi-restraints excluded: chain f residue 60 VAL Chi-restraints excluded: chain f residue 75 GLU Chi-restraints excluded: chain f residue 85 ILE Chi-restraints excluded: chain f residue 89 VAL Chi-restraints excluded: chain f residue 92 THR Chi-restraints excluded: chain g residue 4 ARG Chi-restraints excluded: chain g residue 6 VAL Chi-restraints excluded: chain g residue 13 LEU Chi-restraints excluded: chain g residue 21 GLU Chi-restraints excluded: chain g residue 27 VAL Chi-restraints excluded: chain g residue 43 VAL Chi-restraints excluded: chain g residue 73 VAL Chi-restraints excluded: chain g residue 75 VAL Chi-restraints excluded: chain g residue 141 VAL Chi-restraints excluded: chain h residue 14 ILE Chi-restraints excluded: chain h residue 42 GLU Chi-restraints excluded: chain h residue 54 ASP Chi-restraints excluded: chain h residue 59 LEU Chi-restraints excluded: chain h residue 62 THR Chi-restraints excluded: chain h residue 77 ARG Chi-restraints excluded: chain h residue 89 LYS Chi-restraints excluded: chain i residue 9 THR Chi-restraints excluded: chain i residue 20 PHE Chi-restraints excluded: chain i residue 25 ASN Chi-restraints excluded: chain i residue 28 ILE Chi-restraints excluded: chain i residue 39 PHE Chi-restraints excluded: chain i residue 54 LEU Chi-restraints excluded: chain i residue 90 TYR Chi-restraints excluded: chain i residue 104 VAL Chi-restraints excluded: chain i residue 111 VAL Chi-restraints excluded: chain i residue 113 ARG Chi-restraints excluded: chain i residue 126 GLN Chi-restraints excluded: chain i residue 130 ARG Chi-restraints excluded: chain j residue 7 ARG Chi-restraints excluded: chain j residue 8 ILE Chi-restraints excluded: chain j residue 32 THR Chi-restraints excluded: chain j residue 42 LEU Chi-restraints excluded: chain j residue 53 ILE Chi-restraints excluded: chain j residue 67 ILE Chi-restraints excluded: chain j residue 76 ILE Chi-restraints excluded: chain j residue 88 MET Chi-restraints excluded: chain k residue 28 ASN Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 31 ILE Chi-restraints excluded: chain k residue 35 THR Chi-restraints excluded: chain k residue 59 THR Chi-restraints excluded: chain k residue 82 LEU Chi-restraints excluded: chain k residue 94 GLU Chi-restraints excluded: chain k residue 96 THR Chi-restraints excluded: chain k residue 108 THR Chi-restraints excluded: chain k residue 125 LYS Chi-restraints excluded: chain l residue 44 LYS Chi-restraints excluded: chain l residue 52 VAL Chi-restraints excluded: chain l residue 61 PHE Chi-restraints excluded: chain l residue 64 THR Chi-restraints excluded: chain l residue 72 HIS Chi-restraints excluded: chain l residue 79 VAL Chi-restraints excluded: chain l residue 90 LEU Chi-restraints excluded: chain l residue 97 THR Chi-restraints excluded: chain l residue 98 VAL Chi-restraints excluded: chain m residue 39 ILE Chi-restraints excluded: chain m residue 80 LEU Chi-restraints excluded: chain n residue 6 MET Chi-restraints excluded: chain n residue 30 ILE Chi-restraints excluded: chain n residue 43 ASN Chi-restraints excluded: chain n residue 56 SER Chi-restraints excluded: chain n residue 90 ARG Chi-restraints excluded: chain o residue 22 THR Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain p residue 16 PHE Chi-restraints excluded: chain p residue 40 ASN Chi-restraints excluded: chain p residue 50 THR Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain q residue 67 LEU Chi-restraints excluded: chain q residue 68 SER Chi-restraints excluded: chain q residue 76 VAL Chi-restraints excluded: chain q residue 79 VAL Chi-restraints excluded: chain r residue 11 CYS Chi-restraints excluded: chain r residue 39 ILE Chi-restraints excluded: chain r residue 74 HIS Chi-restraints excluded: chain s residue 29 LYS Chi-restraints excluded: chain s residue 33 THR Chi-restraints excluded: chain s residue 37 ARG Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain t residue 71 LYS Chi-restraints excluded: chain t residue 83 ILE Chi-restraints excluded: chain u residue 12 PHE Chi-restraints excluded: chain u residue 13 ASP Chi-restraints excluded: chain v residue 20 VAL Chi-restraints excluded: chain v residue 48 ASN Chi-restraints excluded: chain v residue 69 THR Chi-restraints excluded: chain v residue 103 LEU Chi-restraints excluded: chain v residue 140 GLU Chi-restraints excluded: chain v residue 148 LEU Chi-restraints excluded: chain v residue 180 THR Chi-restraints excluded: chain v residue 192 LEU Chi-restraints excluded: chain v residue 196 THR Chi-restraints excluded: chain v residue 219 SER Chi-restraints excluded: chain v residue 226 VAL Chi-restraints excluded: chain v residue 239 LEU Chi-restraints excluded: chain v residue 254 VAL Chi-restraints excluded: chain v residue 264 THR Chi-restraints excluded: chain v residue 266 ILE Chi-restraints excluded: chain v residue 280 GLN Chi-restraints excluded: chain v residue 283 ASN Chi-restraints excluded: chain v residue 304 ASN Chi-restraints excluded: chain v residue 308 GLN Chi-restraints excluded: chain v residue 345 THR Chi-restraints excluded: chain w residue 6 HIS Chi-restraints excluded: chain w residue 22 ASP Chi-restraints excluded: chain w residue 30 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1061 random chunks: chunk 930 optimal weight: 2.9990 chunk 979 optimal weight: 0.0980 chunk 893 optimal weight: 6.9990 chunk 952 optimal weight: 20.0000 chunk 573 optimal weight: 10.0000 chunk 415 optimal weight: 9.9990 chunk 748 optimal weight: 20.0000 chunk 292 optimal weight: 30.0000 chunk 861 optimal weight: 4.9990 chunk 901 optimal weight: 10.0000 chunk 949 optimal weight: 9.9990 overall best weight: 5.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 HIS D 150 GLN ** E 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN ** G 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 28 ASN ** K 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 99 ASN ** O 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 31 GLN ** 3 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 8 ASN c 41 GLN ** d 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 77 ASN ** e 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 54 GLN t 3 ASN ** t 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.6609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 162161 Z= 0.277 Angle : 0.756 13.863 242281 Z= 0.390 Chirality : 0.039 0.466 30825 Planarity : 0.007 0.131 13212 Dihedral : 24.995 178.704 80374 Min Nonbonded Distance : 1.759 Molprobity Statistics. All-atom Clashscore : 30.48 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.79 % Favored : 93.05 % Rotamer: Outliers : 7.74 % Allowed : 30.59 % Favored : 61.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.10), residues: 6054 helix: 0.16 (0.11), residues: 2096 sheet: -1.41 (0.15), residues: 1025 loop : -1.78 (0.11), residues: 2933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.003 TRP s 34 HIS 0.035 0.002 HIS l 72 PHE 0.046 0.003 PHE O 21 TYR 0.045 0.003 TYR d 75 ARG 0.014 0.001 ARG K 96 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12108 Ramachandran restraints generated. 6054 Oldfield, 0 Emsley, 6054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12108 Ramachandran restraints generated. 6054 Oldfield, 0 Emsley, 6054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1877 residues out of total 5041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 390 poor density : 1487 time to evaluate : 6.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 14 ARG cc_start: 0.8523 (ttm110) cc_final: 0.8156 (ttm-80) REVERT: C 69 ARG cc_start: 0.8112 (mmm-85) cc_final: 0.6910 (ptt180) REVERT: C 82 GLU cc_start: 0.7526 (mt-10) cc_final: 0.7052 (mt-10) REVERT: C 83 TYR cc_start: 0.8046 (t80) cc_final: 0.7299 (t80) REVERT: C 96 TYR cc_start: 0.6947 (OUTLIER) cc_final: 0.5282 (m-80) REVERT: C 101 ARG cc_start: 0.6959 (mpt180) cc_final: 0.6692 (mmt-90) REVERT: C 115 GLN cc_start: 0.8011 (mt0) cc_final: 0.7609 (tp40) REVERT: C 133 ARG cc_start: 0.7815 (OUTLIER) cc_final: 0.7240 (ttp-170) REVERT: C 146 MET cc_start: 0.7145 (mtt) cc_final: 0.5885 (mmp) REVERT: C 175 ARG cc_start: 0.8686 (ttt90) cc_final: 0.8036 (ptp-170) REVERT: C 189 ARG cc_start: 0.7561 (OUTLIER) cc_final: 0.7255 (mpt90) REVERT: C 266 PHE cc_start: 0.7441 (OUTLIER) cc_final: 0.6846 (m-80) REVERT: C 267 ILE cc_start: 0.7748 (mm) cc_final: 0.7523 (mm) REVERT: D 2 ILE cc_start: 0.3629 (OUTLIER) cc_final: 0.3307 (mt) REVERT: D 11 MET cc_start: 0.4074 (tmm) cc_final: 0.3847 (tmm) REVERT: D 36 GLN cc_start: 0.7096 (mt0) cc_final: 0.6527 (tm-30) REVERT: D 89 GLU cc_start: 0.5581 (mt-10) cc_final: 0.5063 (tm-30) REVERT: D 150 GLN cc_start: 0.8757 (tt0) cc_final: 0.8554 (pt0) REVERT: E 63 LYS cc_start: 0.3757 (tmtt) cc_final: 0.3207 (tmtt) REVERT: E 67 ARG cc_start: 0.7139 (mtp85) cc_final: 0.6870 (mtp85) REVERT: E 189 THR cc_start: 0.5356 (OUTLIER) cc_final: 0.5021 (p) REVERT: F 38 MET cc_start: 0.5308 (tpt) cc_final: 0.5058 (mmm) REVERT: F 83 TYR cc_start: 0.7482 (t80) cc_final: 0.7255 (t80) REVERT: F 95 ARG cc_start: 0.7263 (mpt-90) cc_final: 0.6854 (mtt90) REVERT: F 97 TRP cc_start: 0.7506 (m100) cc_final: 0.7180 (m-10) REVERT: F 142 ASP cc_start: 0.7073 (t0) cc_final: 0.6828 (p0) REVERT: F 174 ASP cc_start: 0.6270 (t0) cc_final: 0.6039 (p0) REVERT: F 178 ARG cc_start: -0.4314 (OUTLIER) cc_final: -0.4746 (ptt-90) REVERT: K 138 GLN cc_start: 0.7505 (pt0) cc_final: 0.7149 (mp10) REVERT: L 1 MET cc_start: 0.6502 (tpt) cc_final: 0.5726 (tpt) REVERT: L 53 LYS cc_start: 0.8932 (tttt) cc_final: 0.8657 (mmtm) REVERT: L 65 THR cc_start: 0.8087 (OUTLIER) cc_final: 0.7790 (t) REVERT: L 70 ARG cc_start: 0.4088 (OUTLIER) cc_final: 0.3680 (mmt90) REVERT: L 98 ARG cc_start: 0.7393 (tpp-160) cc_final: 0.7001 (mmm160) REVERT: L 106 GLU cc_start: 0.6601 (OUTLIER) cc_final: 0.6268 (mp0) REVERT: M 55 MET cc_start: 0.8987 (tpp) cc_final: 0.8717 (tpp) REVERT: M 81 ASP cc_start: 0.7123 (m-30) cc_final: 0.6734 (p0) REVERT: M 82 LEU cc_start: 0.4961 (OUTLIER) cc_final: 0.4616 (pp) REVERT: N 8 LYS cc_start: 0.7833 (mmtt) cc_final: 0.7604 (mttt) REVERT: N 10 ARG cc_start: 0.7572 (OUTLIER) cc_final: 0.7267 (mtp-110) REVERT: N 13 HIS cc_start: 0.7444 (m-70) cc_final: 0.7034 (m-70) REVERT: N 92 TRP cc_start: 0.7836 (m100) cc_final: 0.7341 (m100) REVERT: N 136 MET cc_start: 0.4996 (ttp) cc_final: 0.3980 (tpp) REVERT: O 37 THR cc_start: 0.7630 (OUTLIER) cc_final: 0.7352 (t) REVERT: O 45 ARG cc_start: 0.6511 (mtp180) cc_final: 0.6007 (tpp-160) REVERT: O 74 GLU cc_start: 0.8645 (tm-30) cc_final: 0.8430 (tm-30) REVERT: O 78 LYS cc_start: 0.8529 (tttt) cc_final: 0.7963 (tptp) REVERT: O 82 GLU cc_start: 0.8517 (tt0) cc_final: 0.8093 (tm-30) REVERT: O 114 GLU cc_start: 0.5523 (OUTLIER) cc_final: 0.4901 (pm20) REVERT: P 36 TYR cc_start: 0.7666 (OUTLIER) cc_final: 0.6929 (m-80) REVERT: P 38 GLN cc_start: 0.7232 (OUTLIER) cc_final: 0.6877 (pt0) REVERT: P 46 GLU cc_start: 0.6870 (pt0) cc_final: 0.6515 (mm-30) REVERT: Q 56 HIS cc_start: 0.7045 (m170) cc_final: 0.6804 (m-70) REVERT: Q 72 ARG cc_start: 0.7629 (mmm160) cc_final: 0.7040 (mmm160) REVERT: R 20 GLN cc_start: 0.8865 (mt0) cc_final: 0.8421 (mt0) REVERT: R 28 ARG cc_start: 0.8529 (OUTLIER) cc_final: 0.8276 (mtt-85) REVERT: R 33 ARG cc_start: 0.8395 (OUTLIER) cc_final: 0.7427 (mtt-85) REVERT: R 45 TYR cc_start: 0.9004 (m-80) cc_final: 0.8758 (m-80) REVERT: S 1 MET cc_start: 0.6876 (tpp) cc_final: 0.6252 (ppp) REVERT: T 3 THR cc_start: 0.6836 (OUTLIER) cc_final: 0.6420 (p) REVERT: T 16 LYS cc_start: 0.8769 (mttp) cc_final: 0.8529 (mtpp) REVERT: T 48 LYS cc_start: 0.8873 (tttt) cc_final: 0.8295 (tptm) REVERT: T 98 LYS cc_start: 0.8651 (mttp) cc_final: 0.8354 (tttp) REVERT: U 44 LYS cc_start: 0.8914 (tttm) cc_final: 0.8566 (ttmm) REVERT: U 76 ARG cc_start: 0.8424 (ptm160) cc_final: 0.8016 (ptm160) REVERT: U 77 ARG cc_start: 0.7720 (OUTLIER) cc_final: 0.7411 (mmt90) REVERT: V 62 GLU cc_start: 0.6794 (mp0) cc_final: 0.6232 (mt-10) REVERT: W 1 MET cc_start: 0.6015 (tpt) cc_final: 0.5506 (mtt) REVERT: Y 27 ARG cc_start: 0.8715 (ttp80) cc_final: 0.8413 (ptt90) REVERT: Y 39 TRP cc_start: 0.7366 (t-100) cc_final: 0.6126 (t-100) REVERT: Y 41 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.7359 (mp0) REVERT: Y 46 PHE cc_start: 0.7783 (m-80) cc_final: 0.7385 (m-80) REVERT: Z 8 GLU cc_start: 0.6848 (mm-30) cc_final: 0.6323 (pm20) REVERT: 0 54 MET cc_start: 0.8309 (ptm) cc_final: 0.7245 (ttt) REVERT: 1 13 ARG cc_start: 0.7869 (ttp-110) cc_final: 0.7051 (ttp-170) REVERT: 1 16 ARG cc_start: 0.7977 (ttp-170) cc_final: 0.7725 (ttp-170) REVERT: 4 4 ILE cc_start: 0.8581 (OUTLIER) cc_final: 0.7973 (pt) REVERT: 5 4 ARG cc_start: 0.7368 (tpp80) cc_final: 0.7160 (tpp80) REVERT: b 49 MET cc_start: 0.8641 (mtt) cc_final: 0.8285 (tpp) REVERT: b 67 ILE cc_start: 0.8278 (mp) cc_final: 0.7942 (tp) REVERT: b 90 PHE cc_start: 0.6718 (m-80) cc_final: 0.6432 (m-80) REVERT: b 94 HIS cc_start: 0.6820 (m90) cc_final: 0.6512 (m170) REVERT: b 100 MET cc_start: 0.6994 (ttm) cc_final: 0.6478 (mtt) REVERT: b 142 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7540 (tm-30) REVERT: c 6 HIS cc_start: 0.8373 (t-90) cc_final: 0.8080 (t-90) REVERT: c 28 GLU cc_start: 0.5770 (pm20) cc_final: 0.5511 (pm20) REVERT: c 130 PHE cc_start: 0.8669 (p90) cc_final: 0.8154 (p90) REVERT: c 136 ARG cc_start: 0.8178 (tpm170) cc_final: 0.7798 (tpm170) REVERT: c 151 VAL cc_start: 0.7822 (t) cc_final: 0.7558 (m) REVERT: c 152 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.7826 (tm-30) REVERT: c 166 GLU cc_start: 0.7422 (tt0) cc_final: 0.6600 (mt-10) REVERT: c 202 ILE cc_start: 0.8007 (mt) cc_final: 0.7669 (tt) REVERT: d 19 LEU cc_start: 0.4631 (OUTLIER) cc_final: 0.3853 (mt) REVERT: d 36 GLN cc_start: 0.8354 (tt0) cc_final: 0.7902 (tt0) REVERT: d 60 LYS cc_start: 0.7216 (OUTLIER) cc_final: 0.6438 (ptmm) REVERT: d 63 ARG cc_start: 0.7138 (OUTLIER) cc_final: 0.6879 (mtt-85) REVERT: d 115 ARG cc_start: 0.6894 (tmm-80) cc_final: 0.6483 (tmm-80) REVERT: d 116 GLN cc_start: 0.5476 (OUTLIER) cc_final: 0.4196 (mm110) REVERT: e 96 MET cc_start: 0.8540 (ttp) cc_final: 0.7589 (tmm) REVERT: e 97 GLN cc_start: 0.8184 (tm-30) cc_final: 0.7526 (pt0) REVERT: e 105 ILE cc_start: 0.8274 (mp) cc_final: 0.7493 (pt) REVERT: f 24 ARG cc_start: 0.7892 (ttp80) cc_final: 0.7602 (ptt90) REVERT: g 25 LYS cc_start: 0.7228 (mtmm) cc_final: 0.6785 (tptp) REVERT: g 28 ASN cc_start: 0.6727 (m-40) cc_final: 0.6337 (m110) REVERT: g 58 GLU cc_start: 0.4311 (mt-10) cc_final: 0.4048 (mm-30) REVERT: g 139 GLU cc_start: 0.8112 (mt-10) cc_final: 0.7764 (mm-30) REVERT: h 13 ARG cc_start: 0.6751 (mtt90) cc_final: 0.6275 (tpp80) REVERT: h 31 LYS cc_start: 0.7599 (mmmt) cc_final: 0.7357 (mmtp) REVERT: h 71 VAL cc_start: 0.6210 (t) cc_final: 0.6009 (m) REVERT: h 89 LYS cc_start: 0.7204 (OUTLIER) cc_final: 0.6527 (tptp) REVERT: i 39 PHE cc_start: 0.6968 (OUTLIER) cc_final: 0.6568 (t80) REVERT: i 61 LEU cc_start: 0.7934 (tt) cc_final: 0.7720 (mt) REVERT: i 85 ARG cc_start: 0.6467 (mmp80) cc_final: 0.6160 (mmp-170) REVERT: i 120 LYS cc_start: 0.8228 (mptt) cc_final: 0.7984 (mptt) REVERT: j 49 PHE cc_start: 0.7297 (m-80) cc_final: 0.6801 (m-80) REVERT: k 24 HIS cc_start: 0.6878 (t70) cc_final: 0.6542 (t70) REVERT: k 85 MET cc_start: 0.7947 (ptp) cc_final: 0.7261 (ptm) REVERT: l 29 GLN cc_start: 0.8273 (mp10) cc_final: 0.8036 (mp10) REVERT: l 30 LYS cc_start: 0.8306 (mttt) cc_final: 0.7752 (mmmt) REVERT: l 50 ARG cc_start: 0.7717 (mmt-90) cc_final: 0.7261 (mmt180) REVERT: l 54 ARG cc_start: 0.8524 (ttp-110) cc_final: 0.8233 (ttp-110) REVERT: l 56 ARG cc_start: 0.8024 (tpp-160) cc_final: 0.7753 (tpp-160) REVERT: l 67 ILE cc_start: 0.8215 (mp) cc_final: 0.7858 (mp) REVERT: l 81 LEU cc_start: 0.8166 (tp) cc_final: 0.7692 (tt) REVERT: l 83 ARG cc_start: 0.8024 (tmm-80) cc_final: 0.7125 (tmm-80) REVERT: l 112 GLN cc_start: 0.7337 (mt0) cc_final: 0.7083 (mt0) REVERT: m 71 ARG cc_start: 0.4754 (ptp-170) cc_final: 0.3859 (ptm-80) REVERT: n 26 GLU cc_start: 0.7049 (tp30) cc_final: 0.6849 (tp30) REVERT: n 75 ARG cc_start: 0.6948 (mtt90) cc_final: 0.6281 (mtt-85) REVERT: o 40 GLN cc_start: 0.9129 (tp-100) cc_final: 0.8888 (mp10) REVERT: o 74 ASP cc_start: 0.7111 (t70) cc_final: 0.6895 (t70) REVERT: o 84 ARG cc_start: 0.8597 (ttm110) cc_final: 0.8227 (ttt-90) REVERT: o 89 ARG cc_start: 0.8288 (ptm-80) cc_final: 0.7726 (mpt180) REVERT: q 30 LYS cc_start: 0.8483 (tttt) cc_final: 0.8063 (mmtt) REVERT: q 80 GLU cc_start: 0.6356 (tp30) cc_final: 0.6125 (tm-30) REVERT: r 28 THR cc_start: 0.7875 (m) cc_final: 0.7476 (m) REVERT: r 32 TYR cc_start: 0.7609 (m-80) cc_final: 0.6880 (m-80) REVERT: r 74 HIS cc_start: 0.4093 (OUTLIER) cc_final: 0.3890 (m90) REVERT: t 83 ILE cc_start: 0.6299 (pp) cc_final: 0.6028 (pt) REVERT: u 18 ARG cc_start: 0.6428 (ptm-80) cc_final: 0.5962 (ptt180) REVERT: v 48 ASN cc_start: 0.5722 (OUTLIER) cc_final: 0.5467 (t0) REVERT: v 114 GLU cc_start: 0.8737 (tp30) cc_final: 0.8284 (mm-30) REVERT: v 161 PHE cc_start: 0.7488 (m-80) cc_final: 0.7137 (m-80) REVERT: v 213 ARG cc_start: 0.7510 (mtp-110) cc_final: 0.7164 (mtm110) REVERT: v 221 PHE cc_start: 0.7856 (t80) cc_final: 0.7642 (t80) REVERT: v 258 GLU cc_start: 0.8721 (mm-30) cc_final: 0.8341 (mm-30) REVERT: v 280 GLN cc_start: 0.8607 (OUTLIER) cc_final: 0.8102 (tm130) REVERT: v 283 ASN cc_start: 0.8591 (OUTLIER) cc_final: 0.8176 (m110) REVERT: v 288 MET cc_start: 0.9272 (ttp) cc_final: 0.9049 (tpt) REVERT: v 300 MET cc_start: 0.8512 (tpp) cc_final: 0.8220 (mmp) REVERT: v 356 PHE cc_start: 0.7789 (m-80) cc_final: 0.6942 (m-80) REVERT: w 5 GLN cc_start: 0.8770 (OUTLIER) cc_final: 0.8408 (mt0) REVERT: w 10 GLN cc_start: 0.8018 (tt0) cc_final: 0.7691 (tt0) REVERT: w 30 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7259 (mp0) outliers start: 390 outliers final: 309 residues processed: 1698 average time/residue: 1.4507 time to fit residues: 4082.9360 Evaluate side-chains 1796 residues out of total 5041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 344 poor density : 1452 time to evaluate : 5.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 53 HIS Chi-restraints excluded: chain C residue 86 ASN Chi-restraints excluded: chain C residue 96 TYR Chi-restraints excluded: chain C residue 103 TYR Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 111 LYS Chi-restraints excluded: chain C residue 114 ASP Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 133 ARG Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 182 ARG Chi-restraints excluded: chain C residue 189 ARG Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 225 MET Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 256 LYS Chi-restraints excluded: chain C residue 266 PHE Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 14 ILE Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 67 HIS Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 169 ARG Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain E residue 5 LEU Chi-restraints excluded: chain E residue 19 PHE Chi-restraints excluded: chain E residue 25 GLU Chi-restraints excluded: chain E residue 44 ARG Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain E residue 122 GLU Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain F residue 5 HIS Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 71 ARG Chi-restraints excluded: chain F residue 87 CYS Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 136 ILE Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain F residue 178 ARG Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 81 GLU Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 53 GLU Chi-restraints excluded: chain H residue 66 ASN Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain J residue 121 ILE Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 28 LEU Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 55 ILE Chi-restraints excluded: chain K residue 56 VAL Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 81 ILE Chi-restraints excluded: chain K residue 93 ILE Chi-restraints excluded: chain K residue 130 HIS Chi-restraints excluded: chain K residue 135 GLN Chi-restraints excluded: chain L residue 9 ASN Chi-restraints excluded: chain L residue 22 ILE Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 70 ARG Chi-restraints excluded: chain L residue 73 ASP Chi-restraints excluded: chain L residue 84 CYS Chi-restraints excluded: chain L residue 87 LEU Chi-restraints excluded: chain L residue 106 GLU Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 27 LEU Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 122 VAL Chi-restraints excluded: chain M residue 125 LEU Chi-restraints excluded: chain M residue 142 ILE Chi-restraints excluded: chain N residue 2 LEU Chi-restraints excluded: chain N residue 6 ARG Chi-restraints excluded: chain N residue 10 ARG Chi-restraints excluded: chain N residue 73 ILE Chi-restraints excluded: chain N residue 88 ASN Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 132 THR Chi-restraints excluded: chain N residue 135 VAL Chi-restraints excluded: chain O residue 13 ASN Chi-restraints excluded: chain O residue 33 ILE Chi-restraints excluded: chain O residue 37 THR Chi-restraints excluded: chain O residue 53 THR Chi-restraints excluded: chain O residue 54 LEU Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain O residue 114 GLU Chi-restraints excluded: chain P residue 36 TYR Chi-restraints excluded: chain P residue 38 GLN Chi-restraints excluded: chain P residue 53 THR Chi-restraints excluded: chain P residue 97 PHE Chi-restraints excluded: chain Q residue 30 VAL Chi-restraints excluded: chain Q residue 46 VAL Chi-restraints excluded: chain Q residue 48 ILE Chi-restraints excluded: chain Q residue 52 ASN Chi-restraints excluded: chain Q residue 63 LYS Chi-restraints excluded: chain Q residue 100 LEU Chi-restraints excluded: chain Q residue 104 THR Chi-restraints excluded: chain R residue 16 LYS Chi-restraints excluded: chain R residue 28 ARG Chi-restraints excluded: chain R residue 30 ARG Chi-restraints excluded: chain R residue 33 ARG Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain S residue 19 THR Chi-restraints excluded: chain S residue 29 THR Chi-restraints excluded: chain S residue 39 LEU Chi-restraints excluded: chain S residue 64 VAL Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain T residue 3 THR Chi-restraints excluded: chain T residue 17 VAL Chi-restraints excluded: chain T residue 45 VAL Chi-restraints excluded: chain T residue 46 LEU Chi-restraints excluded: chain T residue 73 LYS Chi-restraints excluded: chain T residue 77 ASP Chi-restraints excluded: chain T residue 97 LEU Chi-restraints excluded: chain T residue 107 VAL Chi-restraints excluded: chain T residue 108 SER Chi-restraints excluded: chain U residue 16 VAL Chi-restraints excluded: chain U residue 34 VAL Chi-restraints excluded: chain U residue 77 ARG Chi-restraints excluded: chain V residue 15 THR Chi-restraints excluded: chain V residue 28 VAL Chi-restraints excluded: chain V residue 59 VAL Chi-restraints excluded: chain V residue 70 VAL Chi-restraints excluded: chain V residue 77 THR Chi-restraints excluded: chain V residue 93 VAL Chi-restraints excluded: chain W residue 2 PHE Chi-restraints excluded: chain W residue 30 ILE Chi-restraints excluded: chain W residue 40 ILE Chi-restraints excluded: chain W residue 91 PHE Chi-restraints excluded: chain X residue 10 THR Chi-restraints excluded: chain X residue 43 THR Chi-restraints excluded: chain Y residue 4 VAL Chi-restraints excluded: chain Y residue 22 LEU Chi-restraints excluded: chain Y residue 23 ASN Chi-restraints excluded: chain Y residue 41 GLU Chi-restraints excluded: chain Y residue 66 THR Chi-restraints excluded: chain Y residue 68 LEU Chi-restraints excluded: chain Z residue 9 LYS Chi-restraints excluded: chain Z residue 11 VAL Chi-restraints excluded: chain Z residue 37 LEU Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 41 THR Chi-restraints excluded: chain 1 residue 9 THR Chi-restraints excluded: chain 1 residue 22 LEU Chi-restraints excluded: chain 1 residue 39 LEU Chi-restraints excluded: chain 2 residue 23 THR Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 2 residue 47 VAL Chi-restraints excluded: chain 3 residue 1 MET Chi-restraints excluded: chain 3 residue 4 THR Chi-restraints excluded: chain 3 residue 8 SER Chi-restraints excluded: chain 3 residue 24 THR Chi-restraints excluded: chain 3 residue 26 ASN Chi-restraints excluded: chain 3 residue 45 SER Chi-restraints excluded: chain 4 residue 4 ILE Chi-restraints excluded: chain 4 residue 30 ARG Chi-restraints excluded: chain 4 residue 38 THR Chi-restraints excluded: chain 4 residue 55 LEU Chi-restraints excluded: chain 4 residue 57 LEU Chi-restraints excluded: chain 5 residue 7 VAL Chi-restraints excluded: chain 5 residue 17 VAL Chi-restraints excluded: chain b residue 18 HIS Chi-restraints excluded: chain b residue 52 GLU Chi-restraints excluded: chain b residue 69 PHE Chi-restraints excluded: chain b residue 72 THR Chi-restraints excluded: chain b residue 103 ASN Chi-restraints excluded: chain b residue 109 GLN Chi-restraints excluded: chain b residue 114 LEU Chi-restraints excluded: chain b residue 116 ASP Chi-restraints excluded: chain b residue 129 LEU Chi-restraints excluded: chain b residue 130 THR Chi-restraints excluded: chain b residue 200 ILE Chi-restraints excluded: chain b residue 208 ARG Chi-restraints excluded: chain c residue 19 ASN Chi-restraints excluded: chain c residue 33 LEU Chi-restraints excluded: chain c residue 67 THR Chi-restraints excluded: chain c residue 83 ASP Chi-restraints excluded: chain c residue 102 ASN Chi-restraints excluded: chain c residue 103 ILE Chi-restraints excluded: chain c residue 116 VAL Chi-restraints excluded: chain c residue 121 THR Chi-restraints excluded: chain c residue 138 VAL Chi-restraints excluded: chain c residue 149 ILE Chi-restraints excluded: chain c residue 152 GLU Chi-restraints excluded: chain c residue 162 ILE Chi-restraints excluded: chain c residue 195 VAL Chi-restraints excluded: chain c residue 200 VAL Chi-restraints excluded: chain d residue 19 LEU Chi-restraints excluded: chain d residue 32 CYS Chi-restraints excluded: chain d residue 41 HIS Chi-restraints excluded: chain d residue 60 LYS Chi-restraints excluded: chain d residue 63 ARG Chi-restraints excluded: chain d residue 75 TYR Chi-restraints excluded: chain d residue 78 GLU Chi-restraints excluded: chain d residue 116 GLN Chi-restraints excluded: chain d residue 169 THR Chi-restraints excluded: chain d residue 181 THR Chi-restraints excluded: chain d residue 200 ILE Chi-restraints excluded: chain e residue 37 THR Chi-restraints excluded: chain e residue 46 VAL Chi-restraints excluded: chain e residue 88 VAL Chi-restraints excluded: chain e residue 94 VAL Chi-restraints excluded: chain e residue 137 VAL Chi-restraints excluded: chain e residue 148 ASN Chi-restraints excluded: chain f residue 8 PHE Chi-restraints excluded: chain f residue 9 MET Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 58 HIS Chi-restraints excluded: chain f residue 60 VAL Chi-restraints excluded: chain f residue 75 GLU Chi-restraints excluded: chain f residue 85 ILE Chi-restraints excluded: chain f residue 89 VAL Chi-restraints excluded: chain f residue 92 THR Chi-restraints excluded: chain g residue 4 ARG Chi-restraints excluded: chain g residue 6 VAL Chi-restraints excluded: chain g residue 13 LEU Chi-restraints excluded: chain g residue 43 VAL Chi-restraints excluded: chain g residue 73 VAL Chi-restraints excluded: chain g residue 75 VAL Chi-restraints excluded: chain g residue 106 GLU Chi-restraints excluded: chain g residue 120 LEU Chi-restraints excluded: chain g residue 141 VAL Chi-restraints excluded: chain h residue 42 GLU Chi-restraints excluded: chain h residue 54 ASP Chi-restraints excluded: chain h residue 59 LEU Chi-restraints excluded: chain h residue 62 THR Chi-restraints excluded: chain h residue 77 ARG Chi-restraints excluded: chain h residue 89 LYS Chi-restraints excluded: chain i residue 9 THR Chi-restraints excluded: chain i residue 20 PHE Chi-restraints excluded: chain i residue 25 ASN Chi-restraints excluded: chain i residue 39 PHE Chi-restraints excluded: chain i residue 54 LEU Chi-restraints excluded: chain i residue 64 TYR Chi-restraints excluded: chain i residue 90 TYR Chi-restraints excluded: chain i residue 104 VAL Chi-restraints excluded: chain i residue 111 VAL Chi-restraints excluded: chain i residue 113 ARG Chi-restraints excluded: chain i residue 126 GLN Chi-restraints excluded: chain i residue 130 ARG Chi-restraints excluded: chain j residue 7 ARG Chi-restraints excluded: chain j residue 8 ILE Chi-restraints excluded: chain j residue 32 THR Chi-restraints excluded: chain j residue 36 VAL Chi-restraints excluded: chain j residue 42 LEU Chi-restraints excluded: chain j residue 53 ILE Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 31 ILE Chi-restraints excluded: chain k residue 35 THR Chi-restraints excluded: chain k residue 59 THR Chi-restraints excluded: chain k residue 82 LEU Chi-restraints excluded: chain k residue 94 GLU Chi-restraints excluded: chain k residue 96 THR Chi-restraints excluded: chain k residue 97 ILE Chi-restraints excluded: chain k residue 125 LYS Chi-restraints excluded: chain l residue 44 LYS Chi-restraints excluded: chain l residue 52 VAL Chi-restraints excluded: chain l residue 61 PHE Chi-restraints excluded: chain l residue 64 THR Chi-restraints excluded: chain l residue 72 HIS Chi-restraints excluded: chain l residue 79 VAL Chi-restraints excluded: chain l residue 90 LEU Chi-restraints excluded: chain l residue 97 THR Chi-restraints excluded: chain l residue 98 VAL Chi-restraints excluded: chain m residue 39 ILE Chi-restraints excluded: chain m residue 80 LEU Chi-restraints excluded: chain m residue 82 ASP Chi-restraints excluded: chain n residue 6 MET Chi-restraints excluded: chain n residue 30 ILE Chi-restraints excluded: chain n residue 43 ASN Chi-restraints excluded: chain n residue 56 SER Chi-restraints excluded: chain n residue 90 ARG Chi-restraints excluded: chain o residue 22 THR Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 48 LYS Chi-restraints excluded: chain p residue 16 PHE Chi-restraints excluded: chain p residue 40 ASN Chi-restraints excluded: chain p residue 50 THR Chi-restraints excluded: chain q residue 18 GLU Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain q residue 76 VAL Chi-restraints excluded: chain q residue 79 VAL Chi-restraints excluded: chain r residue 39 ILE Chi-restraints excluded: chain r residue 52 GLN Chi-restraints excluded: chain r residue 74 HIS Chi-restraints excluded: chain s residue 29 LYS Chi-restraints excluded: chain s residue 33 THR Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain s residue 66 MET Chi-restraints excluded: chain t residue 71 LYS Chi-restraints excluded: chain u residue 12 PHE Chi-restraints excluded: chain v residue 20 VAL Chi-restraints excluded: chain v residue 48 ASN Chi-restraints excluded: chain v residue 69 THR Chi-restraints excluded: chain v residue 128 CYS Chi-restraints excluded: chain v residue 140 GLU Chi-restraints excluded: chain v residue 148 LEU Chi-restraints excluded: chain v residue 180 THR Chi-restraints excluded: chain v residue 192 LEU Chi-restraints excluded: chain v residue 196 THR Chi-restraints excluded: chain v residue 219 SER Chi-restraints excluded: chain v residue 226 VAL Chi-restraints excluded: chain v residue 239 LEU Chi-restraints excluded: chain v residue 264 THR Chi-restraints excluded: chain v residue 266 ILE Chi-restraints excluded: chain v residue 280 GLN Chi-restraints excluded: chain v residue 283 ASN Chi-restraints excluded: chain v residue 304 ASN Chi-restraints excluded: chain v residue 308 GLN Chi-restraints excluded: chain v residue 313 ASN Chi-restraints excluded: chain v residue 345 THR Chi-restraints excluded: chain w residue 5 GLN Chi-restraints excluded: chain w residue 6 HIS Chi-restraints excluded: chain w residue 16 ILE Chi-restraints excluded: chain w residue 22 ASP Chi-restraints excluded: chain w residue 30 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1061 random chunks: chunk 625 optimal weight: 20.0000 chunk 1007 optimal weight: 3.9990 chunk 615 optimal weight: 6.9990 chunk 478 optimal weight: 8.9990 chunk 700 optimal weight: 20.0000 chunk 1057 optimal weight: 20.0000 chunk 972 optimal weight: 6.9990 chunk 841 optimal weight: 9.9990 chunk 87 optimal weight: 20.0000 chunk 650 optimal weight: 10.0000 chunk 516 optimal weight: 0.0470 overall best weight: 5.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 HIS ** E 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 5 HIS ** G 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 49 ASN ** Y 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 123 GLN ** d 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 77 ASN ** e 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 73 ASN ** o 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 51 HIS ** p 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 54 GLN ** t 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.6894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 162161 Z= 0.297 Angle : 0.779 15.818 242281 Z= 0.400 Chirality : 0.040 0.449 30825 Planarity : 0.007 0.132 13212 Dihedral : 25.067 178.558 80370 Min Nonbonded Distance : 1.749 Molprobity Statistics. All-atom Clashscore : 32.20 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.14 % Favored : 92.72 % Rotamer: Outliers : 7.34 % Allowed : 31.40 % Favored : 61.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.10), residues: 6054 helix: 0.08 (0.11), residues: 2091 sheet: -1.51 (0.15), residues: 1029 loop : -1.82 (0.11), residues: 2934 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.078 0.004 TRP c 201 HIS 0.021 0.002 HIS f 3 PHE 0.046 0.003 PHE O 21 TYR 0.046 0.003 TYR d 75 ARG 0.018 0.001 ARG K 96 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12108 Ramachandran restraints generated. 6054 Oldfield, 0 Emsley, 6054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12108 Ramachandran restraints generated. 6054 Oldfield, 0 Emsley, 6054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1864 residues out of total 5041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 370 poor density : 1494 time to evaluate : 6.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 14 ARG cc_start: 0.8558 (ttm110) cc_final: 0.8193 (ttm-80) REVERT: C 82 GLU cc_start: 0.7581 (mt-10) cc_final: 0.7236 (mt-10) REVERT: C 83 TYR cc_start: 0.8046 (t80) cc_final: 0.7329 (t80) REVERT: C 96 TYR cc_start: 0.6869 (OUTLIER) cc_final: 0.5228 (m-80) REVERT: C 115 GLN cc_start: 0.7967 (mt0) cc_final: 0.7625 (tp40) REVERT: C 133 ARG cc_start: 0.7789 (OUTLIER) cc_final: 0.7175 (ttp-170) REVERT: C 146 MET cc_start: 0.7160 (mtt) cc_final: 0.6846 (mmm) REVERT: C 175 ARG cc_start: 0.8706 (ttt90) cc_final: 0.8054 (ptp-170) REVERT: C 197 ASN cc_start: 0.8741 (t0) cc_final: 0.8455 (t0) REVERT: C 266 PHE cc_start: 0.7451 (OUTLIER) cc_final: 0.6857 (m-80) REVERT: C 267 ILE cc_start: 0.7761 (mm) cc_final: 0.7541 (mm) REVERT: D 11 MET cc_start: 0.4094 (tmm) cc_final: 0.3847 (tmm) REVERT: D 36 GLN cc_start: 0.7110 (mt0) cc_final: 0.6597 (tm-30) REVERT: D 89 GLU cc_start: 0.5780 (mt-10) cc_final: 0.5210 (tm-30) REVERT: D 127 PHE cc_start: 0.8459 (m-80) cc_final: 0.7941 (m-80) REVERT: D 154 LYS cc_start: 0.8896 (pttm) cc_final: 0.8544 (pttm) REVERT: E 1 MET cc_start: 0.7658 (pmm) cc_final: 0.7114 (pmm) REVERT: E 63 LYS cc_start: 0.3683 (tmtt) cc_final: 0.3141 (tmtt) REVERT: E 67 ARG cc_start: 0.7200 (mtp85) cc_final: 0.6925 (mtp85) REVERT: E 189 THR cc_start: 0.5196 (OUTLIER) cc_final: 0.4906 (p) REVERT: F 38 MET cc_start: 0.4929 (tpt) cc_final: 0.4663 (mmm) REVERT: F 95 ARG cc_start: 0.7203 (mpt-90) cc_final: 0.6746 (mtt90) REVERT: F 142 ASP cc_start: 0.7282 (t0) cc_final: 0.6827 (p0) REVERT: F 174 ASP cc_start: 0.6120 (t0) cc_final: 0.5884 (p0) REVERT: F 178 ARG cc_start: -0.4171 (OUTLIER) cc_final: -0.4682 (ptt-90) REVERT: K 119 PHE cc_start: 0.8439 (t80) cc_final: 0.8059 (t80) REVERT: K 138 GLN cc_start: 0.7628 (pt0) cc_final: 0.7251 (mp-120) REVERT: L 1 MET cc_start: 0.6277 (tpt) cc_final: 0.5472 (tpt) REVERT: L 53 LYS cc_start: 0.8929 (tttt) cc_final: 0.8654 (mmtm) REVERT: L 65 THR cc_start: 0.8105 (OUTLIER) cc_final: 0.7854 (t) REVERT: L 70 ARG cc_start: 0.3997 (OUTLIER) cc_final: 0.3567 (mmt90) REVERT: L 106 GLU cc_start: 0.6612 (OUTLIER) cc_final: 0.6289 (mp0) REVERT: M 55 MET cc_start: 0.8990 (tpp) cc_final: 0.8720 (tpp) REVERT: M 81 ASP cc_start: 0.7131 (m-30) cc_final: 0.6737 (p0) REVERT: M 82 LEU cc_start: 0.4951 (OUTLIER) cc_final: 0.4629 (pp) REVERT: N 8 LYS cc_start: 0.7819 (mmtt) cc_final: 0.7578 (mttt) REVERT: N 10 ARG cc_start: 0.7561 (OUTLIER) cc_final: 0.7276 (mtp-110) REVERT: N 13 HIS cc_start: 0.7456 (m-70) cc_final: 0.7046 (m-70) REVERT: N 45 GLN cc_start: 0.8381 (mt0) cc_final: 0.8120 (tp40) REVERT: N 92 TRP cc_start: 0.7851 (m100) cc_final: 0.7351 (m100) REVERT: N 136 MET cc_start: 0.4630 (ttp) cc_final: 0.3655 (tpt) REVERT: O 37 THR cc_start: 0.7600 (OUTLIER) cc_final: 0.7325 (t) REVERT: O 45 ARG cc_start: 0.6498 (mtp180) cc_final: 0.5993 (tpp-160) REVERT: O 78 LYS cc_start: 0.8489 (tttt) cc_final: 0.7930 (tptp) REVERT: O 82 GLU cc_start: 0.8486 (tt0) cc_final: 0.8116 (tm-30) REVERT: O 114 GLU cc_start: 0.5888 (OUTLIER) cc_final: 0.5308 (pm20) REVERT: P 36 TYR cc_start: 0.7653 (OUTLIER) cc_final: 0.6972 (m-80) REVERT: P 46 GLU cc_start: 0.6820 (pt0) cc_final: 0.6468 (mm-30) REVERT: Q 21 ARG cc_start: 0.5977 (mmm160) cc_final: 0.5753 (mmm160) REVERT: Q 72 ARG cc_start: 0.7504 (mmm160) cc_final: 0.6918 (mmm160) REVERT: R 20 GLN cc_start: 0.8868 (mt0) cc_final: 0.8439 (mt0) REVERT: R 28 ARG cc_start: 0.8522 (OUTLIER) cc_final: 0.8270 (mtt-85) REVERT: R 33 ARG cc_start: 0.8405 (OUTLIER) cc_final: 0.7608 (mtt-85) REVERT: S 68 ARG cc_start: 0.8090 (ptp-110) cc_final: 0.7765 (ptp-110) REVERT: T 3 THR cc_start: 0.6780 (OUTLIER) cc_final: 0.6480 (p) REVERT: T 16 LYS cc_start: 0.8801 (mttp) cc_final: 0.8571 (mtpp) REVERT: T 48 LYS cc_start: 0.8878 (tttt) cc_final: 0.8301 (tptm) REVERT: T 98 LYS cc_start: 0.8689 (mttp) cc_final: 0.8372 (tttm) REVERT: U 44 LYS cc_start: 0.8963 (tttm) cc_final: 0.8612 (ttmm) REVERT: U 69 ARG cc_start: 0.7817 (ttm-80) cc_final: 0.7492 (tpp80) REVERT: U 76 ARG cc_start: 0.8502 (ptm160) cc_final: 0.8078 (ptm160) REVERT: U 77 ARG cc_start: 0.7731 (OUTLIER) cc_final: 0.7414 (mmt90) REVERT: U 81 LYS cc_start: 0.7447 (mmtp) cc_final: 0.7243 (mmmm) REVERT: V 62 GLU cc_start: 0.6775 (mp0) cc_final: 0.6225 (mt-10) REVERT: W 1 MET cc_start: 0.5955 (tpt) cc_final: 0.5448 (mtt) REVERT: Y 39 TRP cc_start: 0.7335 (t-100) cc_final: 0.6010 (t-100) REVERT: Y 41 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.7360 (mp0) REVERT: Y 46 PHE cc_start: 0.7826 (m-80) cc_final: 0.7442 (m-80) REVERT: Z 8 GLU cc_start: 0.6926 (mm-30) cc_final: 0.6385 (pm20) REVERT: 0 54 MET cc_start: 0.8360 (ptm) cc_final: 0.6765 (ttt) REVERT: 1 13 ARG cc_start: 0.7845 (ttp-110) cc_final: 0.7003 (ttp-170) REVERT: 1 16 ARG cc_start: 0.7958 (ttp-170) cc_final: 0.7707 (ttp-170) REVERT: 4 4 ILE cc_start: 0.8541 (OUTLIER) cc_final: 0.7924 (pt) REVERT: 4 45 ARG cc_start: 0.7685 (OUTLIER) cc_final: 0.6734 (ptt180) REVERT: 5 4 ARG cc_start: 0.7302 (tpp80) cc_final: 0.7028 (tpp80) REVERT: b 49 MET cc_start: 0.8584 (mtt) cc_final: 0.8240 (tpp) REVERT: b 67 ILE cc_start: 0.8229 (mp) cc_final: 0.7888 (tp) REVERT: b 90 PHE cc_start: 0.6706 (m-80) cc_final: 0.6436 (m-80) REVERT: b 94 HIS cc_start: 0.6839 (m90) cc_final: 0.6440 (m170) REVERT: c 6 HIS cc_start: 0.8161 (t-90) cc_final: 0.7895 (t-90) REVERT: c 130 PHE cc_start: 0.9062 (p90) cc_final: 0.8452 (p90) REVERT: c 152 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.8017 (tm-30) REVERT: c 166 GLU cc_start: 0.7288 (tt0) cc_final: 0.6976 (mt-10) REVERT: c 202 ILE cc_start: 0.8089 (mt) cc_final: 0.7789 (tt) REVERT: d 19 LEU cc_start: 0.4672 (OUTLIER) cc_final: 0.3791 (mt) REVERT: d 36 GLN cc_start: 0.8370 (tt0) cc_final: 0.7929 (tt0) REVERT: d 60 LYS cc_start: 0.7197 (OUTLIER) cc_final: 0.6414 (ptmm) REVERT: d 63 ARG cc_start: 0.7201 (OUTLIER) cc_final: 0.6960 (mtt-85) REVERT: d 115 ARG cc_start: 0.6967 (tmm-80) cc_final: 0.6591 (tmm-80) REVERT: d 116 GLN cc_start: 0.5737 (OUTLIER) cc_final: 0.4553 (mm110) REVERT: e 96 MET cc_start: 0.8526 (ttp) cc_final: 0.7498 (tmm) REVERT: e 105 ILE cc_start: 0.7770 (mp) cc_final: 0.7445 (pt) REVERT: e 112 ARG cc_start: 0.6979 (ttm110) cc_final: 0.6749 (ttm110) REVERT: f 24 ARG cc_start: 0.7841 (ttp80) cc_final: 0.7512 (ptt90) REVERT: g 3 ARG cc_start: 0.6873 (mmm-85) cc_final: 0.6554 (mmm-85) REVERT: g 25 LYS cc_start: 0.7186 (mtmm) cc_final: 0.6657 (tptp) REVERT: g 28 ASN cc_start: 0.6675 (m-40) cc_final: 0.6125 (m110) REVERT: g 31 MET cc_start: 0.6016 (ptm) cc_final: 0.5697 (ptm) REVERT: g 58 GLU cc_start: 0.4444 (mt-10) cc_final: 0.4237 (mm-30) REVERT: g 109 ARG cc_start: 0.8101 (mpt-90) cc_final: 0.7857 (mpt-90) REVERT: g 139 GLU cc_start: 0.8029 (mt-10) cc_final: 0.7692 (mm-30) REVERT: h 13 ARG cc_start: 0.6752 (mtt90) cc_final: 0.6259 (tpp80) REVERT: h 31 LYS cc_start: 0.7546 (mmmt) cc_final: 0.7295 (mmtp) REVERT: h 71 VAL cc_start: 0.5933 (t) cc_final: 0.5723 (m) REVERT: h 89 LYS cc_start: 0.7157 (OUTLIER) cc_final: 0.6439 (ptmm) REVERT: h 114 ARG cc_start: 0.4980 (ttp80) cc_final: 0.4453 (tpt170) REVERT: i 39 PHE cc_start: 0.7042 (OUTLIER) cc_final: 0.6661 (t80) REVERT: i 120 LYS cc_start: 0.8225 (mptt) cc_final: 0.7972 (mptt) REVERT: j 49 PHE cc_start: 0.7286 (m-80) cc_final: 0.6800 (m-80) REVERT: k 24 HIS cc_start: 0.6907 (t70) cc_final: 0.6587 (t70) REVERT: l 29 GLN cc_start: 0.8245 (mp10) cc_final: 0.8015 (mp10) REVERT: l 30 LYS cc_start: 0.8375 (mttt) cc_final: 0.8013 (mmtt) REVERT: l 50 ARG cc_start: 0.7680 (mmt-90) cc_final: 0.6980 (mpt90) REVERT: l 54 ARG cc_start: 0.8490 (ttp-110) cc_final: 0.8200 (ttp-110) REVERT: l 56 ARG cc_start: 0.8061 (tpp-160) cc_final: 0.7811 (tpp-160) REVERT: l 81 LEU cc_start: 0.8229 (tp) cc_final: 0.7791 (tt) REVERT: l 83 ARG cc_start: 0.8017 (tmm-80) cc_final: 0.7117 (tmm-80) REVERT: l 112 GLN cc_start: 0.7308 (mt0) cc_final: 0.7053 (mt0) REVERT: n 26 GLU cc_start: 0.7045 (tp30) cc_final: 0.6844 (tp30) REVERT: n 75 ARG cc_start: 0.7195 (mtt90) cc_final: 0.6517 (mtt-85) REVERT: n 85 ARG cc_start: 0.8140 (ttt-90) cc_final: 0.7808 (ttp-170) REVERT: o 83 GLU cc_start: 0.8623 (pt0) cc_final: 0.8254 (pp20) REVERT: o 84 ARG cc_start: 0.8572 (ttm110) cc_final: 0.8287 (ttt-90) REVERT: q 30 LYS cc_start: 0.8391 (tttt) cc_final: 0.7864 (mmtt) REVERT: q 80 GLU cc_start: 0.6530 (tp30) cc_final: 0.6300 (tm-30) REVERT: r 28 THR cc_start: 0.7901 (m) cc_final: 0.7531 (m) REVERT: r 32 TYR cc_start: 0.7573 (m-80) cc_final: 0.6843 (m-80) REVERT: r 74 HIS cc_start: 0.4318 (OUTLIER) cc_final: 0.4110 (m90) REVERT: t 83 ILE cc_start: 0.6525 (pp) cc_final: 0.6268 (pt) REVERT: u 12 PHE cc_start: 0.5946 (OUTLIER) cc_final: 0.5695 (t80) REVERT: u 18 ARG cc_start: 0.6544 (ptm-80) cc_final: 0.6342 (ptm-80) REVERT: u 38 TYR cc_start: 0.7656 (t80) cc_final: 0.7122 (t80) REVERT: v 48 ASN cc_start: 0.5750 (OUTLIER) cc_final: 0.5512 (t0) REVERT: v 108 GLU cc_start: 0.7537 (tm-30) cc_final: 0.7198 (mt-10) REVERT: v 161 PHE cc_start: 0.7310 (m-80) cc_final: 0.6918 (m-80) REVERT: v 213 ARG cc_start: 0.7502 (mtp-110) cc_final: 0.7136 (mtm110) REVERT: v 258 GLU cc_start: 0.8625 (mm-30) cc_final: 0.8228 (mm-30) REVERT: v 280 GLN cc_start: 0.8511 (OUTLIER) cc_final: 0.7953 (tm130) REVERT: v 283 ASN cc_start: 0.8609 (OUTLIER) cc_final: 0.8205 (m110) REVERT: v 288 MET cc_start: 0.9275 (ttp) cc_final: 0.9050 (tpt) REVERT: v 300 MET cc_start: 0.8503 (tpp) cc_final: 0.8208 (mmp) REVERT: v 356 PHE cc_start: 0.7811 (m-80) cc_final: 0.7280 (m-10) REVERT: w 5 GLN cc_start: 0.8742 (OUTLIER) cc_final: 0.8334 (mt0) REVERT: w 10 GLN cc_start: 0.8047 (tt0) cc_final: 0.7749 (tt0) REVERT: w 30 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7361 (mp0) outliers start: 370 outliers final: 301 residues processed: 1698 average time/residue: 1.4436 time to fit residues: 4059.5607 Evaluate side-chains 1789 residues out of total 5041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 335 poor density : 1454 time to evaluate : 5.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 53 HIS Chi-restraints excluded: chain C residue 86 ASN Chi-restraints excluded: chain C residue 96 TYR Chi-restraints excluded: chain C residue 103 TYR Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 111 LYS Chi-restraints excluded: chain C residue 114 ASP Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 133 ARG Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 182 ARG Chi-restraints excluded: chain C residue 189 ARG Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 225 MET Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 256 LYS Chi-restraints excluded: chain C residue 266 PHE Chi-restraints excluded: chain D residue 14 ILE Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 67 HIS Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 169 ARG Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain E residue 19 PHE Chi-restraints excluded: chain E residue 25 GLU Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 44 ARG Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain E residue 122 GLU Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain F residue 5 HIS Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 71 ARG Chi-restraints excluded: chain F residue 87 CYS Chi-restraints excluded: chain F residue 99 PHE Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 136 ILE Chi-restraints excluded: chain F residue 147 ASP Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain F residue 178 ARG Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 24 ILE Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 75 MET Chi-restraints excluded: chain G residue 81 GLU Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 53 GLU Chi-restraints excluded: chain H residue 66 ASN Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain J residue 121 ILE Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 28 LEU Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 55 ILE Chi-restraints excluded: chain K residue 56 VAL Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 81 ILE Chi-restraints excluded: chain K residue 93 ILE Chi-restraints excluded: chain K residue 130 HIS Chi-restraints excluded: chain K residue 135 GLN Chi-restraints excluded: chain L residue 9 ASN Chi-restraints excluded: chain L residue 22 ILE Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 70 ARG Chi-restraints excluded: chain L residue 73 ASP Chi-restraints excluded: chain L residue 84 CYS Chi-restraints excluded: chain L residue 87 LEU Chi-restraints excluded: chain L residue 106 GLU Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain L residue 114 LYS Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 27 LEU Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 122 VAL Chi-restraints excluded: chain M residue 125 LEU Chi-restraints excluded: chain M residue 142 ILE Chi-restraints excluded: chain N residue 2 LEU Chi-restraints excluded: chain N residue 6 ARG Chi-restraints excluded: chain N residue 10 ARG Chi-restraints excluded: chain N residue 73 ILE Chi-restraints excluded: chain N residue 88 ASN Chi-restraints excluded: chain N residue 132 THR Chi-restraints excluded: chain N residue 135 VAL Chi-restraints excluded: chain O residue 13 ASN Chi-restraints excluded: chain O residue 33 ILE Chi-restraints excluded: chain O residue 37 THR Chi-restraints excluded: chain O residue 53 THR Chi-restraints excluded: chain O residue 54 LEU Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain O residue 114 GLU Chi-restraints excluded: chain P residue 26 LEU Chi-restraints excluded: chain P residue 36 TYR Chi-restraints excluded: chain P residue 53 THR Chi-restraints excluded: chain P residue 97 PHE Chi-restraints excluded: chain Q residue 30 VAL Chi-restraints excluded: chain Q residue 46 VAL Chi-restraints excluded: chain Q residue 48 ILE Chi-restraints excluded: chain Q residue 52 ASN Chi-restraints excluded: chain Q residue 63 LYS Chi-restraints excluded: chain Q residue 100 LEU Chi-restraints excluded: chain Q residue 104 THR Chi-restraints excluded: chain R residue 16 LYS Chi-restraints excluded: chain R residue 28 ARG Chi-restraints excluded: chain R residue 30 ARG Chi-restraints excluded: chain R residue 33 ARG Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain S residue 39 LEU Chi-restraints excluded: chain S residue 64 VAL Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain T residue 3 THR Chi-restraints excluded: chain T residue 15 GLN Chi-restraints excluded: chain T residue 17 VAL Chi-restraints excluded: chain T residue 45 VAL Chi-restraints excluded: chain T residue 46 LEU Chi-restraints excluded: chain T residue 73 LYS Chi-restraints excluded: chain T residue 77 ASP Chi-restraints excluded: chain T residue 97 LEU Chi-restraints excluded: chain T residue 107 VAL Chi-restraints excluded: chain T residue 108 SER Chi-restraints excluded: chain U residue 16 VAL Chi-restraints excluded: chain U residue 34 VAL Chi-restraints excluded: chain U residue 77 ARG Chi-restraints excluded: chain V residue 15 THR Chi-restraints excluded: chain V residue 28 VAL Chi-restraints excluded: chain V residue 59 VAL Chi-restraints excluded: chain V residue 70 VAL Chi-restraints excluded: chain V residue 77 THR Chi-restraints excluded: chain V residue 93 VAL Chi-restraints excluded: chain W residue 2 PHE Chi-restraints excluded: chain W residue 30 ILE Chi-restraints excluded: chain W residue 91 PHE Chi-restraints excluded: chain X residue 10 THR Chi-restraints excluded: chain X residue 43 THR Chi-restraints excluded: chain Y residue 4 VAL Chi-restraints excluded: chain Y residue 22 LEU Chi-restraints excluded: chain Y residue 23 ASN Chi-restraints excluded: chain Y residue 41 GLU Chi-restraints excluded: chain Y residue 66 THR Chi-restraints excluded: chain Y residue 68 LEU Chi-restraints excluded: chain Z residue 9 LYS Chi-restraints excluded: chain Z residue 37 LEU Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 41 THR Chi-restraints excluded: chain 1 residue 9 THR Chi-restraints excluded: chain 1 residue 22 LEU Chi-restraints excluded: chain 1 residue 39 LEU Chi-restraints excluded: chain 2 residue 23 THR Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 2 residue 47 VAL Chi-restraints excluded: chain 3 residue 1 MET Chi-restraints excluded: chain 3 residue 4 THR Chi-restraints excluded: chain 3 residue 24 THR Chi-restraints excluded: chain 3 residue 26 ASN Chi-restraints excluded: chain 3 residue 45 SER Chi-restraints excluded: chain 4 residue 4 ILE Chi-restraints excluded: chain 4 residue 30 ARG Chi-restraints excluded: chain 4 residue 38 THR Chi-restraints excluded: chain 4 residue 45 ARG Chi-restraints excluded: chain 4 residue 55 LEU Chi-restraints excluded: chain 4 residue 57 LEU Chi-restraints excluded: chain 5 residue 7 VAL Chi-restraints excluded: chain 5 residue 17 VAL Chi-restraints excluded: chain b residue 8 ASP Chi-restraints excluded: chain b residue 18 HIS Chi-restraints excluded: chain b residue 52 GLU Chi-restraints excluded: chain b residue 69 PHE Chi-restraints excluded: chain b residue 72 THR Chi-restraints excluded: chain b residue 103 ASN Chi-restraints excluded: chain b residue 109 GLN Chi-restraints excluded: chain b residue 114 LEU Chi-restraints excluded: chain b residue 116 ASP Chi-restraints excluded: chain b residue 129 LEU Chi-restraints excluded: chain b residue 130 THR Chi-restraints excluded: chain b residue 208 ARG Chi-restraints excluded: chain c residue 19 ASN Chi-restraints excluded: chain c residue 33 LEU Chi-restraints excluded: chain c residue 37 PHE Chi-restraints excluded: chain c residue 67 THR Chi-restraints excluded: chain c residue 83 ASP Chi-restraints excluded: chain c residue 103 ILE Chi-restraints excluded: chain c residue 116 VAL Chi-restraints excluded: chain c residue 121 THR Chi-restraints excluded: chain c residue 149 ILE Chi-restraints excluded: chain c residue 152 GLU Chi-restraints excluded: chain c residue 162 ILE Chi-restraints excluded: chain c residue 195 VAL Chi-restraints excluded: chain c residue 200 VAL Chi-restraints excluded: chain d residue 19 LEU Chi-restraints excluded: chain d residue 32 CYS Chi-restraints excluded: chain d residue 41 HIS Chi-restraints excluded: chain d residue 60 LYS Chi-restraints excluded: chain d residue 63 ARG Chi-restraints excluded: chain d residue 75 TYR Chi-restraints excluded: chain d residue 78 GLU Chi-restraints excluded: chain d residue 116 GLN Chi-restraints excluded: chain d residue 169 THR Chi-restraints excluded: chain d residue 181 THR Chi-restraints excluded: chain d residue 200 ILE Chi-restraints excluded: chain e residue 46 VAL Chi-restraints excluded: chain e residue 77 ASN Chi-restraints excluded: chain e residue 88 VAL Chi-restraints excluded: chain e residue 94 VAL Chi-restraints excluded: chain e residue 137 VAL Chi-restraints excluded: chain e residue 148 ASN Chi-restraints excluded: chain f residue 9 MET Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 58 HIS Chi-restraints excluded: chain f residue 60 VAL Chi-restraints excluded: chain f residue 75 GLU Chi-restraints excluded: chain f residue 85 ILE Chi-restraints excluded: chain f residue 89 VAL Chi-restraints excluded: chain f residue 92 THR Chi-restraints excluded: chain g residue 13 LEU Chi-restraints excluded: chain g residue 22 LEU Chi-restraints excluded: chain g residue 43 VAL Chi-restraints excluded: chain g residue 73 VAL Chi-restraints excluded: chain g residue 106 GLU Chi-restraints excluded: chain g residue 120 LEU Chi-restraints excluded: chain g residue 141 VAL Chi-restraints excluded: chain h residue 14 ILE Chi-restraints excluded: chain h residue 42 GLU Chi-restraints excluded: chain h residue 54 ASP Chi-restraints excluded: chain h residue 59 LEU Chi-restraints excluded: chain h residue 62 THR Chi-restraints excluded: chain h residue 77 ARG Chi-restraints excluded: chain h residue 89 LYS Chi-restraints excluded: chain i residue 9 THR Chi-restraints excluded: chain i residue 20 PHE Chi-restraints excluded: chain i residue 28 ILE Chi-restraints excluded: chain i residue 39 PHE Chi-restraints excluded: chain i residue 54 LEU Chi-restraints excluded: chain i residue 90 TYR Chi-restraints excluded: chain i residue 104 VAL Chi-restraints excluded: chain i residue 111 VAL Chi-restraints excluded: chain i residue 113 ARG Chi-restraints excluded: chain i residue 130 ARG Chi-restraints excluded: chain j residue 7 ARG Chi-restraints excluded: chain j residue 8 ILE Chi-restraints excluded: chain j residue 32 THR Chi-restraints excluded: chain j residue 36 VAL Chi-restraints excluded: chain j residue 42 LEU Chi-restraints excluded: chain j residue 53 ILE Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 31 ILE Chi-restraints excluded: chain k residue 35 THR Chi-restraints excluded: chain k residue 59 THR Chi-restraints excluded: chain k residue 80 LYS Chi-restraints excluded: chain k residue 94 GLU Chi-restraints excluded: chain k residue 96 THR Chi-restraints excluded: chain k residue 97 ILE Chi-restraints excluded: chain k residue 125 LYS Chi-restraints excluded: chain l residue 44 LYS Chi-restraints excluded: chain l residue 52 VAL Chi-restraints excluded: chain l residue 61 PHE Chi-restraints excluded: chain l residue 64 THR Chi-restraints excluded: chain l residue 79 VAL Chi-restraints excluded: chain l residue 90 LEU Chi-restraints excluded: chain l residue 97 THR Chi-restraints excluded: chain l residue 98 VAL Chi-restraints excluded: chain m residue 39 ILE Chi-restraints excluded: chain m residue 80 LEU Chi-restraints excluded: chain n residue 30 ILE Chi-restraints excluded: chain n residue 40 ASP Chi-restraints excluded: chain n residue 43 ASN Chi-restraints excluded: chain n residue 56 SER Chi-restraints excluded: chain n residue 90 ARG Chi-restraints excluded: chain o residue 22 THR Chi-restraints excluded: chain o residue 48 LYS Chi-restraints excluded: chain p residue 16 PHE Chi-restraints excluded: chain p residue 40 ASN Chi-restraints excluded: chain p residue 50 THR Chi-restraints excluded: chain p residue 55 ASP Chi-restraints excluded: chain q residue 12 VAL Chi-restraints excluded: chain q residue 18 GLU Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain q residue 76 VAL Chi-restraints excluded: chain r residue 39 ILE Chi-restraints excluded: chain r residue 74 HIS Chi-restraints excluded: chain s residue 33 THR Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain t residue 71 LYS Chi-restraints excluded: chain u residue 12 PHE Chi-restraints excluded: chain v residue 20 VAL Chi-restraints excluded: chain v residue 48 ASN Chi-restraints excluded: chain v residue 69 THR Chi-restraints excluded: chain v residue 128 CYS Chi-restraints excluded: chain v residue 140 GLU Chi-restraints excluded: chain v residue 148 LEU Chi-restraints excluded: chain v residue 163 THR Chi-restraints excluded: chain v residue 180 THR Chi-restraints excluded: chain v residue 192 LEU Chi-restraints excluded: chain v residue 219 SER Chi-restraints excluded: chain v residue 226 VAL Chi-restraints excluded: chain v residue 239 LEU Chi-restraints excluded: chain v residue 264 THR Chi-restraints excluded: chain v residue 266 ILE Chi-restraints excluded: chain v residue 280 GLN Chi-restraints excluded: chain v residue 283 ASN Chi-restraints excluded: chain v residue 304 ASN Chi-restraints excluded: chain v residue 308 GLN Chi-restraints excluded: chain v residue 313 ASN Chi-restraints excluded: chain v residue 345 THR Chi-restraints excluded: chain w residue 5 GLN Chi-restraints excluded: chain w residue 6 HIS Chi-restraints excluded: chain w residue 22 ASP Chi-restraints excluded: chain w residue 30 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1061 random chunks: chunk 668 optimal weight: 30.0000 chunk 896 optimal weight: 20.0000 chunk 257 optimal weight: 7.9990 chunk 776 optimal weight: 6.9990 chunk 124 optimal weight: 10.0000 chunk 233 optimal weight: 30.0000 chunk 843 optimal weight: 20.0000 chunk 352 optimal weight: 1.9990 chunk 865 optimal weight: 4.9990 chunk 106 optimal weight: 30.0000 chunk 155 optimal weight: 10.0000 overall best weight: 6.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 HIS ** E 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 5 HIS ** G 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 53 ASN W 49 ASN Y 6 GLN ** 3 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 54 GLN ** d 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 19 ASN e 77 ASN ** e 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 54 GLN ** t 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.154049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.124721 restraints weight = 461145.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.127714 restraints weight = 146310.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.128958 restraints weight = 79556.672| |-----------------------------------------------------------------------------| r_work (final): 0.3912 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3912 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3912 r_free = 0.3912 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3912 r_free = 0.3912 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3912 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.7185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.124 162161 Z= 0.341 Angle : 0.829 14.274 242281 Z= 0.423 Chirality : 0.042 0.471 30825 Planarity : 0.007 0.133 13212 Dihedral : 25.188 179.583 80370 Min Nonbonded Distance : 1.732 Molprobity Statistics. All-atom Clashscore : 34.64 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.85 % Favored : 92.02 % Rotamer: Outliers : 7.38 % Allowed : 31.78 % Favored : 60.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.10), residues: 6054 helix: -0.18 (0.11), residues: 2103 sheet: -1.67 (0.15), residues: 1002 loop : -1.93 (0.11), residues: 2949 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.004 TRP c 201 HIS 0.028 0.003 HIS F 5 PHE 0.044 0.003 PHE O 21 TYR 0.046 0.003 TYR d 75 ARG 0.019 0.001 ARG q 27 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 57641.20 seconds wall clock time: 998 minutes 49.15 seconds (59929.15 seconds total)