Starting phenix.real_space_refine on Fri Mar 22 21:36:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nsp_12574/03_2024/7nsp_12574_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nsp_12574/03_2024/7nsp_12574.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nsp_12574/03_2024/7nsp_12574_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/7nsp_12574/03_2024/7nsp_12574_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nsp_12574/03_2024/7nsp_12574_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nsp_12574/03_2024/7nsp_12574.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nsp_12574/03_2024/7nsp_12574.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nsp_12574/03_2024/7nsp_12574_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nsp_12574/03_2024/7nsp_12574_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= 0.002 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4733 5.49 5 S 149 5.16 5 C 73220 2.51 5 N 27221 2.21 5 O 40825 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 72": "OD1" <-> "OD2" Residue "C TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 180": "OE1" <-> "OE2" Residue "C GLU 185": "OE1" <-> "OE2" Residue "C PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 13": "NH1" <-> "NH2" Residue "D ASP 18": "OD1" <-> "OD2" Residue "D GLU 28": "OE1" <-> "OE2" Residue "D GLU 30": "OE1" <-> "OE2" Residue "D ARG 33": "NH1" <-> "NH2" Residue "D ASP 39": "OD1" <-> "OD2" Residue "D TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 59": "NH1" <-> "NH2" Residue "D ARG 77": "NH1" <-> "NH2" Residue "D ARG 83": "NH1" <-> "NH2" Residue "D GLU 89": "OE1" <-> "OE2" Residue "D PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 169": "NH1" <-> "NH2" Residue "D ASP 181": "OD1" <-> "OD2" Residue "D ARG 184": "NH1" <-> "NH2" Residue "E GLU 2": "OE1" <-> "OE2" Residue "E ASP 7": "OD1" <-> "OD2" Residue "E ARG 21": "NH1" <-> "NH2" Residue "E ASP 22": "OD1" <-> "OD2" Residue "E TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 ASP 145": "OD1" <-> "OD2" Residue "E GLU 155": "OE1" <-> "OE2" Residue "E ARG 162": "NH1" <-> "NH2" Residue "E ASP 168": "OD1" <-> "OD2" Residue "E ARG 170": "NH1" <-> "NH2" Residue "F GLU 42": "OE1" <-> "OE2" Residue "F ARG 71": "NH1" <-> "NH2" Residue "F ARG 80": "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 ASP 113": "OD1" <-> "OD2" Residue "F ARG 133": "NH1" <-> "NH2" Residue "F GLU 140": "OE1" <-> "OE2" Residue "F ASP 142": "OD1" <-> "OD2" Residue "F PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 3": "NH1" <-> "NH2" Residue "G GLU 42": "OE1" <-> "OE2" Residue "G ASP 47": "OD1" <-> "OD2" Residue "G PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 60": "OD1" <-> "OD2" Residue "G ASP 114": "OD1" <-> "OD2" Residue "G ASP 147": "OD1" <-> "OD2" Residue "G ARG 153": "NH1" <-> "NH2" Residue "G ARG 163": "NH1" <-> "NH2" Residue "G ASP 166": "OD1" <-> "OD2" Residue "G ARG 170": "NH1" <-> "NH2" Residue "H ASP 7": "OD1" <-> "OD2" Residue "H ASP 17": "OD1" <-> "OD2" Residue "H GLU 55": "OE1" <-> "OE2" Residue "H GLU 60": "OE1" <-> "OE2" Residue "H ASP 98": "OD1" <-> "OD2" Residue "J GLU 9": "OE1" <-> "OE2" Residue "J ARG 13": "NH1" <-> "NH2" Residue "J ARG 37": "NH1" <-> "NH2" Residue "J TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 71": "OD1" <-> "OD2" Residue "J TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 95": "NH1" <-> "NH2" Residue "J ARG 96": "NH1" <-> "NH2" Residue "J ARG 120": "NH1" <-> "NH2" Residue "J TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 10": "OE1" <-> "OE2" Residue "L ARG 21": "NH1" <-> "NH2" Residue "L ARG 33": "NH1" <-> "NH2" Residue "L ARG 41": "NH1" <-> "NH2" Residue "L ARG 47": "NH1" <-> "NH2" Residue "L ARG 60": "NH1" <-> "NH2" Residue "L PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 78": "NH1" <-> "NH2" Residue "L ASP 81": "OD1" <-> "OD2" Residue "L GLU 86": "OE1" <-> "OE2" Residue "L PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 115": "OE1" <-> "OE2" Residue "L ARG 126": "NH1" <-> "NH2" Residue "M ARG 10": "NH1" <-> "NH2" Residue "M ARG 18": "NH1" <-> "NH2" Residue "M ASP 25": "OD1" <-> "OD2" Residue "M ARG 40": "NH1" <-> "NH2" Residue "M ARG 44": "NH1" <-> "NH2" Residue "M GLU 47": "OE1" <-> "OE2" Residue "M ARG 50": "NH1" <-> "NH2" Residue "M ARG 55": "NH1" <-> "NH2" Residue "M ARG 59": "NH1" <-> "NH2" Residue "M ASP 70": "OD1" <-> "OD2" Residue "M GLU 75": "OE1" <-> "OE2" Residue "M TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 110": "OE1" <-> "OE2" Residue "M ARG 114": "NH1" <-> "NH2" Residue "M GLU 115": "OE1" <-> "OE2" Residue "N ARG 8": "NH1" <-> "NH2" Residue "N ARG 12": "NH1" <-> "NH2" Residue "N ARG 17": "NH1" <-> "NH2" Residue "N ARG 22": "NH1" <-> "NH2" Residue "N GLU 32": "OE1" <-> "OE2" Residue "N GLU 43": "OE1" <-> "OE2" Residue "N ARG 46": "NH1" <-> "NH2" Residue "N ASP 58": "OD1" <-> "OD2" Residue "N ARG 63": "NH1" <-> "NH2" Residue "N ARG 64": "NH1" <-> "NH2" Residue "N ARG 69": "NH1" <-> "NH2" Residue "N ARG 71": "NH1" <-> "NH2" Residue "N GLU 74": "OE1" <-> "OE2" Residue "N PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 96": "NH1" <-> "NH2" Residue "N ASP 106": "OD1" <-> "OD2" Residue "N ARG 118": "NH1" <-> "NH2" Residue "O ARG 10": "NH1" <-> "NH2" Residue "O ARG 16": "NH1" <-> "NH2" Residue "O TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 81": "NH1" <-> "NH2" Residue "O ASP 89": "OD1" <-> "OD2" Residue "O ARG 94": "NH1" <-> "NH2" Residue "O ARG 102": "NH1" <-> "NH2" Residue "O ARG 111": "NH1" <-> "NH2" Residue "O GLU 112": "OE1" <-> "OE2" Residue "P GLU 11": "OE1" <-> "OE2" Residue "P ASP 16": "OD1" <-> "OD2" Residue "P ARG 21": "NH1" <-> "NH2" Residue "P ASP 24": "OD1" <-> "OD2" Residue "P GLU 34": "OE1" <-> "OE2" Residue "P ARG 39": "NH1" <-> "NH2" Residue "P PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 62": "NH1" <-> "NH2" Residue "P GLU 71": "OE1" <-> "OE2" Residue "P ARG 89": "NH1" <-> "NH2" Residue "P ARG 101": "NH1" <-> "NH2" Residue "P ARG 109": "NH1" <-> "NH2" Residue "P GLU 112": "OE1" <-> "OE2" Residue "Q ARG 3": "NH1" <-> "NH2" Residue "Q ARG 6": "NH1" <-> "NH2" Residue "Q ARG 13": "NH1" <-> "NH2" Residue "Q ARG 33": "NH1" <-> "NH2" Residue "Q ARG 48": "NH1" <-> "NH2" Residue "Q ASP 49": "OD1" <-> "OD2" Residue "Q PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 70": "NH1" <-> "NH2" Residue "R TYR 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 21": "NH1" <-> "NH2" Residue "R ARG 68": "NH1" <-> "NH2" Residue "R ARG 78": "NH1" <-> "NH2" Residue "R ARG 79": "NH1" <-> "NH2" Residue "R ARG 84": "NH1" <-> "NH2" Residue "S GLU 2": "OE1" <-> "OE2" Residue "S ASP 22": "OD1" <-> "OD2" Residue "S ASP 34": "OD1" <-> "OD2" Residue "S ASP 68": "OD1" <-> "OD2" Residue "S ARG 84": "NH1" <-> "NH2" Residue "S ARG 88": "NH1" <-> "NH2" Residue "S ASP 94": "OD1" <-> "OD2" Residue "S ARG 95": "NH1" <-> "NH2" Residue "S ARG 110": "NH1" <-> "NH2" Residue "T GLU 5": "OE1" <-> "OE2" Residue "T GLU 18": "OE1" <-> "OE2" Residue "T ASP 37": "OD1" <-> "OD2" Residue "T ARG 69": "NH1" <-> "NH2" Residue "T ARG 73": "NH1" <-> "NH2" Residue "T TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 6": "NH1" <-> "NH2" Residue "U ARG 7": "NH1" <-> "NH2" Residue "U ASP 9": "OD1" <-> "OD2" Residue "U GLU 37": "OE1" <-> "OE2" Residue "U ARG 82": "NH1" <-> "NH2" Residue "U PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 86": "NH1" <-> "NH2" Residue "U ARG 94": "NH1" <-> "NH2" Residue "U PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 69": "OE1" <-> "OE2" Residue "V TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 90": "OD1" <-> "OD2" Residue "W GLU 17": "OE1" <-> "OE2" Residue "W PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 64": "OD1" <-> "OD2" Residue "W PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 43": "OE1" <-> "OE2" Residue "X PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 60": "OD1" <-> "OD2" Residue "X GLU 70": "OE1" <-> "OE2" Residue "X TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 5": "OE1" <-> "OE2" Residue "Y GLU 12": "OE1" <-> "OE2" Residue "Y ARG 29": "NH1" <-> "NH2" Residue "Y ARG 47": "NH1" <-> "NH2" Residue "Y ARG 52": "NH1" <-> "NH2" Residue "Z ARG 11": "NH1" <-> "NH2" Residue "Z ARG 30": "NH1" <-> "NH2" Residue "Z GLU 39": "OE1" <-> "OE2" Residue "Z ARG 45": "NH1" <-> "NH2" Residue "Z PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 ARG 10": "NH1" <-> "NH2" Residue "0 ARG 16": "NH1" <-> "NH2" Residue "0 ASP 20": "OD1" <-> "OD2" Residue "0 GLU 36": "OE1" <-> "OE2" Residue "0 ARG 40": "NH1" <-> "NH2" Residue "0 ARG 52": "NH1" <-> "NH2" Residue "1 GLU 7": "OE1" <-> "OE2" Residue "1 PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 35": "OE1" <-> "OE2" Residue "1 ARG 44": "NH1" <-> "NH2" Residue "1 TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 51": "OE1" <-> "OE2" Residue "2 ARG 3": "NH1" <-> "NH2" Residue "2 ARG 12": "NH1" <-> "NH2" Residue "2 ARG 14": "NH1" <-> "NH2" Residue "2 ARG 19": "NH1" <-> "NH2" Residue "2 ARG 21": "NH1" <-> "NH2" Residue "2 ARG 33": "NH1" <-> "NH2" Residue "2 ARG 41": "NH1" <-> "NH2" Residue "3 ARG 13": "NH1" <-> "NH2" Residue "3 ARG 30": "NH1" <-> "NH2" Residue "3 ARG 40": "NH1" <-> "NH2" Residue "3 ARG 42": "NH1" <-> "NH2" Residue "3 ASP 54": "OD1" <-> "OD2" Residue "4 ARG 24": "NH1" <-> "NH2" Residue "5 ASP 4": "OD1" <-> "OD2" Residue "5 ASP 31": "OD1" <-> "OD2" Residue "5 ASP 35": "OD1" <-> "OD2" Residue "5 PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ARG 56": "NH1" <-> "NH2" Residue "5 PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 8": "OD1" <-> "OD2" Residue "b TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 44": "OE1" <-> "OE2" Residue "b GLU 56": "OE1" <-> "OE2" Residue "b ARG 63": "NH1" <-> "NH2" Residue "b PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 82": "OD1" <-> "OD2" Residue "b ARG 113": "NH1" <-> "NH2" Residue "b ASP 123": "OD1" <-> "OD2" Residue "b PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 208": "NH1" <-> "NH2" Residue "b ARG 222": "NH1" <-> "NH2" Residue "b GLU 223": "OE1" <-> "OE2" Residue "c PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ASP 36": "OD1" <-> "OD2" Residue "c GLU 85": "OE1" <-> "OE2" Residue "c GLU 105": "OE1" <-> "OE2" Residue "c ARG 107": "NH1" <-> "NH2" Residue "c GLU 110": "OE1" <-> "OE2" Residue "c ASP 118": "OD1" <-> "OD2" Residue "c PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 131": "NH1" <-> "NH2" Residue "c GLU 166": "OE1" <-> "OE2" Residue "c GLU 170": "OE1" <-> "OE2" Residue "c ASP 183": "OD1" <-> "OD2" Residue "c GLU 188": "OE1" <-> "OE2" Residue "d GLU 15": "OE1" <-> "OE2" Residue "d ASP 18": "OD1" <-> "OD2" Residue "d ASP 29": "OD1" <-> "OD2" Residue "d ASP 50": "OD1" <-> "OD2" Residue "d GLU 57": "OE1" <-> "OE2" Residue "d PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 78": "OE1" <-> "OE2" Residue "d GLU 147": "OE1" <-> "OE2" Residue "d GLU 172": "OE1" <-> "OE2" Residue "d GLU 179": "OE1" <-> "OE2" Residue "d ARG 184": "NH1" <-> "NH2" Residue "d GLU 187": "OE1" <-> "OE2" Residue "d ASP 194": "OD1" <-> "OD2" Residue "e ARG 20": "NH1" <-> "NH2" Residue "e ASP 41": "OD1" <-> "OD2" Residue "e PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 55": "OE1" <-> "OE2" Residue "e ARG 68": "NH1" <-> "NH2" Residue "e ARG 93": "NH1" <-> "NH2" Residue "e GLU 116": "OE1" <-> "OE2" Residue "e ARG 157": "NH1" <-> "NH2" Residue "f TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ASP 13": "OD1" <-> "OD2" Residue "f GLU 69": "OE1" <-> "OE2" Residue "f ASP 72": "OD1" <-> "OD2" Residue "f ARG 91": "NH1" <-> "NH2" Residue "g GLU 74": "OE1" <-> "OE2" Residue "g ARG 78": "NH1" <-> "NH2" Residue "g TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 139": "OE1" <-> "OE2" Residue "h GLU 43": "OE1" <-> "OE2" Residue "h GLU 47": "OE1" <-> "OE2" Residue "h ASP 48": "OD1" <-> "OD2" Residue "h PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 52": "OE1" <-> "OE2" Residue "h TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i GLU 36": "OE1" <-> "OE2" Residue "i ARG 45": "NH1" <-> "NH2" Residue "i ARG 49": "NH1" <-> "NH2" Residue "i GLU 59": "OE1" <-> "OE2" Residue "i ASP 91": "OD1" <-> "OD2" Residue "i ARG 99": "NH1" <-> "NH2" Residue "i ARG 124": "NH1" <-> "NH2" Residue "j GLU 27": "OE1" <-> "OE2" Residue "j ASP 60": "OD1" <-> "OD2" Residue "j TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ARG 68": "NH1" <-> "NH2" Residue "k PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ASP 72": "OD1" <-> "OD2" Residue "k GLU 83": "OE1" <-> "OE2" Residue "k ARG 93": "NH1" <-> "NH2" Residue "k ASP 112": "OD1" <-> "OD2" Residue "l ARG 9": "NH1" <-> "NH2" Residue "l ARG 14": "NH1" <-> "NH2" Residue "l ARG 50": "NH1" <-> "NH2" Residue "l ARG 56": "NH1" <-> "NH2" Residue "l PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 62": "OE1" <-> "OE2" Residue "l GLU 70": "OE1" <-> "OE2" Residue "l GLU 76": "OE1" <-> "OE2" Residue "l ARG 83": "NH1" <-> "NH2" Residue "l ASP 109": "OD1" <-> "OD2" Residue "m TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ASP 54": "OD1" <-> "OD2" Residue "m GLU 59": "OE1" <-> "OE2" Residue "m PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ASP 82": "OD1" <-> "OD2" Residue "n GLU 26": "OE1" <-> "OE2" Residue "n ASP 38": "OD1" <-> "OD2" Residue "n ARG 90": "NH1" <-> "NH2" Residue "o GLU 14": "OE1" <-> "OE2" Residue "o PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ASP 21": "OD1" <-> "OD2" Residue "o GLU 45": "OE1" <-> "OE2" Residue "o ASP 74": "OD1" <-> "OD2" Residue "o GLU 83": "OE1" <-> "OE2" Residue "p ARG 8": "NH1" <-> "NH2" Residue "p PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ARG 28": "NH1" <-> "NH2" Residue "p PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p GLU 47": "OE1" <-> "OE2" Residue "p ASP 55": "OD1" <-> "OD2" Residue "p GLU 77": "OE1" <-> "OE2" Residue "q ARG 11": "NH1" <-> "NH2" Residue "q ARG 27": "NH1" <-> "NH2" Residue "q PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ASP 48": "OD1" <-> "OD2" Residue "q ASP 57": "OD1" <-> "OD2" Residue "q GLU 80": "OE1" <-> "OE2" Residue "r ARG 12": "NH1" <-> "NH2" Residue "r TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r GLU 35": "OE1" <-> "OE2" Residue "r ARG 61": "NH1" <-> "NH2" Residue "s GLU 20": "OE1" <-> "OE2" Residue "s GLU 24": "OE1" <-> "OE2" Residue "s ARG 32": "NH1" <-> "NH2" Residue "t ARG 24": "NH1" <-> "NH2" Residue "t GLU 40": "OE1" <-> "OE2" Residue "t GLU 53": "OE1" <-> "OE2" Residue "t ARG 60": "NH1" <-> "NH2" Residue "t ARG 74": "NH1" <-> "NH2" Residue "u ASP 13": "OD1" <-> "OD2" Residue "u PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u GLU 24": "OE1" <-> "OE2" Residue "u GLU 31": "OE1" <-> "OE2" Residue "u ARG 33": "NH1" <-> "NH2" Residue "u GLU 36": "OE1" <-> "OE2" Residue "u GLU 39": "OE1" <-> "OE2" Residue "u ARG 45": "NH1" <-> "NH2" Residue "u ARG 55": "NH1" <-> "NH2" Residue "u GLU 63": "OE1" <-> "OE2" Residue "u ARG 66": "NH1" <-> "NH2" Residue "u ARG 69": "NH1" <-> "NH2" Residue "u TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 146148 Number of models: 1 Model: "" Number of chains: 57 Chain: "A" Number of atoms: 62320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2903, 62320 Classifications: {'RNA': 2903} Modifications used: {'rna2p_pur': 250, 'rna2p_pyr': 130, 'rna3p_pur': 1424, 'rna3p_pyr': 1099} Link IDs: {'rna2p': 380, 'rna3p': 2522} Chain: "B" Number of atoms: 2570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2570 Classifications: {'RNA': 120} Modifications used: {'p5*END': 1, 'rna2p_pur': 5, 'rna2p_pyr': 5, 'rna3p_pur': 59, 'rna3p_pyr': 51} Link IDs: {'rna2p': 10, 'rna3p': 109} 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: 1304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1304 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 8, 'TRANS': 165} 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: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "K" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 938 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "L" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1053 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain: "M" Number of atoms: 1074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1074 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "N" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 945 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "O" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 892 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "P" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 917 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "Q" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "R" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "S" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 857 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "T" Number of atoms: 709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 709 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 1, 'TRANS': 87} Chain: "U" 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: "V" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 753 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "W" Number of atoms: 575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 575 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "X" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "Y" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 509 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'TRANS': 62} Chain: "Z" 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: "0" Number of atoms: 434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 434 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 1, 'TRANS': 53} Chain: "1" 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: "2" 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: "3" 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: "4" 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: "5" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 514 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "6" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 123 Classifications: {'RNA': 6} Modifications used: {'rna2p_pyr': 2, 'rna3p_pur': 1, 'rna3p_pyr': 3} Link IDs: {'rna2p': 1, 'rna3p': 4} Chain: "7" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 58 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Chain: "8" Number of atoms: 1861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 1861 Classifications: {'RNA': 87} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 7, 'rna3p_pur': 39, 'rna3p_pyr': 34} Link IDs: {'rna2p': 13, 'rna3p': 73} Chain: "a" Number of atoms: 33037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1540, 33037 Classifications: {'RNA': 1540} Modifications used: {'rna2p_pur': 109, 'rna2p_pyr': 68, 'rna3p_pur': 766, 'rna3p_pyr': 597} Link IDs: {'rna2p': 177, 'rna3p': 1362} 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: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "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: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 811 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} 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: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 545 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "s" Number of atoms: 663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 663 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 5, 'TRANS': 77} Chain: "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: 590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 590 Classifications: {'peptide': 70} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "v" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1643 Classifications: {'RNA': 77} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 3, 'rna3p_pur': 34, 'rna3p_pyr': 34} Link IDs: {'rna2p': 8, 'rna3p': 68} Chain: "7" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'ERY': 1} Classifications: {'undetermined': 1} Time building chain proxies: 55.36, per 1000 atoms: 0.38 Number of scatterers: 146148 At special positions: 0 Unit cell: (268.136, 275.892, 228.248, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 149 16.00 P 4733 15.00 O 40825 8.00 N 27221 7.00 C 73220 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS 4 11 " - pdb=" SG CYS 4 14 " distance=2.04 Simple disulfide: pdb=" SG CYS 4 11 " - pdb=" SG CYS 4 27 " distance=2.03 Simple disulfide: pdb=" SG CYS 5 16 " - pdb=" SG CYS 5 37 " distance=2.04 Simple disulfide: pdb=" SG CYS 5 18 " - pdb=" SG CYS 5 40 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 58.37 Conformation dependent library (CDL) restraints added in 6.4 seconds 11182 Ramachandran restraints generated. 5591 Oldfield, 0 Emsley, 5591 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10456 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: 170 helices and 68 sheets defined 38.9% alpha, 18.7% beta 1530 base pairs and 2663 stacking pairs defined. Time for finding SS restraints: 72.08 Creating SS restraints... Processing helix chain 'C' and resid 10 through 16 removed outlier: 4.107A pdb=" N VAL C 16 " --> pdb=" O GLY C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 35 removed outlier: 3.979A pdb=" N LEU C 34 " --> pdb=" O PHE C 30 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N GLU C 35 " --> pdb=" O ALA C 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 30 through 35' Processing helix chain 'C' and resid 131 through 136 removed outlier: 4.032A 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 removed outlier: 3.981A pdb=" N ALA C 211 " --> pdb=" O LYS C 207 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLY C 215 " --> pdb=" O ALA C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 226 removed outlier: 3.987A pdb=" N MET C 225 " --> pdb=" O ARG C 221 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N ASN C 226 " --> pdb=" O GLY C 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 221 through 226' Processing helix chain 'C' and resid 263 through 268 removed outlier: 4.292A pdb=" N ILE C 267 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N VAL C 268 " --> pdb=" O ASP C 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 263 through 268' Processing helix chain 'C' and resid 197 through 202 removed outlier: 4.450A pdb=" N MET C 201 " --> pdb=" O ALA C 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 61 removed outlier: 5.802A pdb=" N THR D 61 " --> pdb=" O ALA D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 72 removed outlier: 4.485A pdb=" N ALA D 71 " --> pdb=" O HIS D 67 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLY D 72 " --> pdb=" O PHE D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 105 removed outlier: 3.746A pdb=" N VAL D 104 " --> pdb=" O LEU D 100 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N LYS D 105 " --> pdb=" O PHE D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 125 Processing helix chain 'E' and resid 15 through 20 removed outlier: 3.527A pdb=" N PHE E 19 " --> pdb=" O SER E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 41 removed outlier: 5.750A pdb=" N GLN E 41 " --> pdb=" O ALA E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 116 Processing helix chain 'E' and resid 130 through 142 removed outlier: 3.711A pdb=" N LEU E 134 " --> pdb=" O LYS E 130 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N MET E 141 " --> pdb=" O LYS E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 162 removed outlier: 3.556A pdb=" N PHE E 158 " --> pdb=" O ASP E 154 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ALA E 160 " --> pdb=" O ASN E 156 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA E 161 " --> pdb=" O LEU E 157 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ARG E 162 " --> pdb=" O PHE E 158 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 183 Processing helix chain 'E' and resid 189 through 201 Processing helix chain 'F' and resid 2 through 20 removed outlier: 5.412A pdb=" N VAL F 13 " --> pdb=" O LYS F 9 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 61 removed outlier: 4.867A pdb=" N LEU F 50 " --> pdb=" O ASP F 46 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASP F 51 " --> pdb=" O LYS F 47 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 112 removed outlier: 3.574A pdb=" N ALA F 107 " --> pdb=" O LEU F 103 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N VAL F 108 " --> pdb=" O ILE F 104 " (cutoff:3.500A) Proline residue: F 109 - end of helix removed outlier: 5.514A pdb=" N ARG F 112 " --> pdb=" O VAL F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 174 removed outlier: 3.875A pdb=" N GLY F 166 " --> pdb=" O SER F 162 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE F 173 " --> pdb=" O LEU F 169 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ASP F 174 " --> pdb=" O LEU F 170 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 removed outlier: 4.134A pdb=" N VAL F 28 " --> pdb=" O VAL F 25 " (cutoff:3.500A) Proline residue: F 29 - end of helix Processing helix chain 'F' and resid 40 through 45 removed outlier: 5.315A pdb=" N ALA F 43 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ILE F 44 " --> pdb=" O GLY F 41 " (cutoff:3.500A) Processing helix chain 'F' and resid 134 through 139 removed outlier: 4.188A pdb=" N ILE F 137 " --> pdb=" O GLU F 134 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHE F 138 " --> pdb=" O GLN F 135 " (cutoff:3.500A) Proline residue: F 139 - end of helix No H-bonds generated for 'chain 'F' and resid 134 through 139' Processing helix chain 'G' and resid 2 through 8 removed outlier: 3.883A 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: 3.538A pdb=" N GLN G 64 " --> pdb=" O ASP G 60 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 153 removed outlier: 4.110A pdb=" N ILE G 141 " --> pdb=" O ASP G 137 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ARG G 152 " --> pdb=" O LEU G 148 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ARG G 153 " --> pdb=" O ARG G 149 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 29 removed outlier: 3.717A pdb=" N PHE H 29 " --> pdb=" O TYR H 25 " (cutoff:3.500A) Processing helix chain 'H' and resid 40 through 50 removed outlier: 6.143A pdb=" N ILE H 44 " --> pdb=" O THR H 40 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N GLU H 45 " --> pdb=" O LYS H 41 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N ALA H 49 " --> pdb=" O GLU H 45 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG H 50 " --> pdb=" O PHE H 46 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 73 removed outlier: 5.091A pdb=" N LYS H 57 " --> pdb=" O GLU H 53 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU H 58 " --> pdb=" O LEU H 54 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N ASN H 73 " --> pdb=" O ALA H 69 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 107 removed outlier: 4.787A pdb=" N ALA H 106 " --> pdb=" O ALA H 102 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY H 107 " --> pdb=" O VAL H 103 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 116 removed outlier: 5.389A pdb=" N ARG H 116 " --> pdb=" O LYS H 112 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 38 removed outlier: 3.719A pdb=" N GLY J 38 " --> pdb=" O ARG J 34 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 96 Processing helix chain 'J' and resid 98 through 110 removed outlier: 4.124A pdb=" N MET J 108 " --> pdb=" O ALA J 104 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU J 109 " --> pdb=" O VAL J 105 " (cutoff:3.500A) Proline residue: J 110 - end of helix Processing helix chain 'J' and resid 112 through 122 removed outlier: 4.276A pdb=" N LEU J 122 " --> pdb=" O MET J 118 " (cutoff:3.500A) Processing helix chain 'K' and resid 110 through 120 removed outlier: 4.083A pdb=" N LEU K 118 " --> pdb=" O LYS K 114 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA K 119 " --> pdb=" O ILE K 115 " (cutoff:3.500A) Proline residue: K 120 - end of helix Processing helix chain 'L' and resid 56 through 62 removed outlier: 3.853A pdb=" N LEU L 61 " --> pdb=" O LEU L 57 " (cutoff:3.500A) Proline residue: L 62 - end of helix Processing helix chain 'L' and resid 68 through 75 removed outlier: 4.217A pdb=" N ALA L 72 " --> pdb=" O SER L 68 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ILE L 73 " --> pdb=" O ARG L 69 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N THR L 74 " --> pdb=" O LYS L 70 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N ALA L 75 " --> pdb=" O ALA L 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 68 through 75' Processing helix chain 'L' and resid 78 through 85 removed outlier: 3.705A pdb=" N ALA L 83 " --> pdb=" O LEU L 79 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N LYS L 84 " --> pdb=" O SER L 80 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N VAL L 85 " --> pdb=" O ASP L 81 " (cutoff:3.500A) Processing helix chain 'L' and resid 91 through 99 Processing helix chain 'L' and resid 128 through 139 Processing helix chain 'M' and resid 42 through 58 Processing helix chain 'M' and resid 109 through 125 removed outlier: 3.550A pdb=" N ALA M 113 " --> pdb=" O PRO M 109 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N LYS M 123 " --> pdb=" O LEU M 119 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LEU M 124 " --> pdb=" O ALA M 120 " (cutoff:3.500A) Proline residue: M 125 - end of helix Processing helix chain 'N' and resid 13 through 32 Processing helix chain 'N' and resid 38 through 57 Proline residue: N 50 - end of helix removed outlier: 3.753A pdb=" N LYS N 56 " --> pdb=" O ILE N 52 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N THR N 57 " --> pdb=" O THR N 53 " (cutoff:3.500A) Processing helix chain 'N' and resid 59 through 71 removed outlier: 3.906A pdb=" N ARG N 63 " --> pdb=" O SER N 59 " (cutoff:3.500A) Processing helix chain 'N' and resid 72 through 88 removed outlier: 3.767A pdb=" N VAL N 76 " --> pdb=" O ASP N 72 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N GLY N 84 " --> pdb=" O PHE N 80 " (cutoff:3.500A) Proline residue: N 85 - end of helix removed outlier: 3.601A pdb=" N ALA N 88 " --> pdb=" O GLY N 84 " (cutoff:3.500A) Processing helix chain 'O' and resid 2 through 20 removed outlier: 4.376A pdb=" N ILE O 8 " --> pdb=" O LYS O 4 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG O 9 " --> pdb=" O SER O 5 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ARG O 10 " --> pdb=" O ALA O 6 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N ALA O 14 " --> pdb=" O ARG O 10 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ARG O 16 " --> pdb=" O THR O 12 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LYS O 17 " --> pdb=" O ARG O 13 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 63 removed outlier: 5.420A pdb=" N GLN O 61 " --> pdb=" O ALA O 57 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LEU O 62 " --> pdb=" O ILE O 58 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N LYS O 63 " --> pdb=" O ALA O 59 " (cutoff:3.500A) Processing helix chain 'O' and resid 67 through 86 Processing helix chain 'O' and resid 101 through 114 removed outlier: 4.583A pdb=" N ALA O 105 " --> pdb=" O GLY O 101 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ALA O 113 " --> pdb=" O ALA O 109 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLY O 114 " --> pdb=" O ALA O 110 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 13 removed outlier: 4.501A pdb=" N LYS P 6 " --> pdb=" O SER P 2 " (cutoff:3.500A) Processing helix chain 'P' and resid 97 through 103 removed outlier: 3.934A pdb=" N ARG P 101 " --> pdb=" O LEU P 97 " (cutoff:3.500A) Processing helix chain 'P' and resid 105 through 110 removed outlier: 5.712A pdb=" N ILE P 110 " --> pdb=" O LYS P 106 " (cutoff:3.500A) Processing helix chain 'Q' and resid 6 through 22 removed outlier: 3.582A pdb=" N ALA Q 10 " --> pdb=" O ARG Q 6 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE Q 17 " --> pdb=" O ARG Q 13 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLN Q 20 " --> pdb=" O LYS Q 16 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS Q 22 " --> pdb=" O LEU Q 18 " (cutoff:3.500A) Processing helix chain 'Q' and resid 26 through 31 removed outlier: 4.149A pdb=" N ARG Q 30 " --> pdb=" O GLY Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 32 through 37 Processing helix chain 'Q' and resid 39 through 73 removed outlier: 4.338A pdb=" N ARG Q 58 " --> pdb=" O LYS Q 54 " (cutoff:3.500A) Processing helix chain 'Q' and resid 75 through 87 Processing helix chain 'Q' and resid 91 through 102 Processing helix chain 'Q' and resid 103 through 118 removed outlier: 3.663A pdb=" N ALA Q 118 " --> pdb=" O LYS Q 114 " (cutoff:3.500A) Processing helix chain 'S' and resid 13 through 25 removed outlier: 3.860A pdb=" N VAL S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LEU S 23 " --> pdb=" O LEU S 19 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ILE S 24 " --> pdb=" O VAL S 20 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ARG S 25 " --> pdb=" O ALA S 21 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 39 removed outlier: 3.699A pdb=" N THR S 39 " --> pdb=" O ILE S 35 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 61 removed outlier: 3.637A pdb=" N VAL S 45 " --> pdb=" O LYS S 41 " (cutoff:3.500A) Processing helix chain 'T' and resid 1 through 11 removed outlier: 4.043A pdb=" N GLU T 5 " --> pdb=" O MET T 1 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N LEU T 11 " --> pdb=" O LEU T 7 " (cutoff:3.500A) Processing helix chain 'T' and resid 17 through 27 Processing helix chain 'T' and resid 39 through 51 Processing helix chain 'U' and resid 66 through 71 removed outlier: 3.552A pdb=" N VAL U 70 " --> pdb=" O GLN U 66 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N ALA U 71 " --> pdb=" O VAL U 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 66 through 71' Processing helix chain 'V' and resid 13 through 24 removed outlier: 3.580A pdb=" N SER V 17 " --> pdb=" O GLY V 13 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ASN V 24 " --> pdb=" O LEU V 20 " (cutoff:3.500A) Processing helix chain 'V' and resid 43 through 53 removed outlier: 4.090A pdb=" N ALA V 52 " --> pdb=" O MET V 48 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N LYS V 53 " --> pdb=" O ASN V 49 " (cutoff:3.500A) Processing helix chain 'V' and resid 54 through 59 Processing helix chain 'X' and resid 52 through 62 Processing helix chain 'X' and resid 63 through 75 Processing helix chain 'Y' and resid 2 through 10 removed outlier: 4.590A pdb=" N LYS Y 9 " --> pdb=" O GLU Y 5 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N SER Y 10 " --> pdb=" O LEU Y 6 " (cutoff:3.500A) Processing helix chain 'Y' and resid 11 through 35 Processing helix chain 'Y' and resid 40 through 62 removed outlier: 4.127A pdb=" N LYS Y 44 " --> pdb=" O SER Y 40 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ALA Y 61 " --> pdb=" O LEU Y 57 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLY Y 62 " --> pdb=" O ASN Y 58 " (cutoff:3.500A) Processing helix chain 'Z' and resid 17 through 28 Processing helix chain 'Z' and resid 41 through 52 Processing helix chain '0' and resid 9 through 21 removed outlier: 3.690A pdb=" N ARG 0 16 " --> pdb=" O LYS 0 12 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N HIS 0 19 " --> pdb=" O MET 0 15 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ASP 0 20 " --> pdb=" O ARG 0 16 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N ALA 0 21 " --> pdb=" O ARG 0 17 " (cutoff:3.500A) Processing helix chain '2' and resid 8 through 16 Processing helix chain '2' and resid 17 through 25 removed outlier: 3.585A pdb=" N ARG 2 21 " --> pdb=" O GLY 2 17 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N THR 2 24 " --> pdb=" O ALA 2 20 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N LYS 2 25 " --> pdb=" O ARG 2 21 " (cutoff:3.500A) Processing helix chain '2' and resid 26 through 38 Processing helix chain '3' and resid 7 through 14 Processing helix chain '3' and resid 37 through 46 removed outlier: 3.792A pdb=" N ARG 3 45 " --> pdb=" O LYS 3 41 " (cutoff:3.500A) Proline residue: 3 46 - end of helix Processing helix chain '3' and resid 52 through 63 removed outlier: 4.216A pdb=" N ALA 3 60 " --> pdb=" O GLY 3 56 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N CYS 3 61 " --> pdb=" O LEU 3 57 " (cutoff:3.500A) Proline residue: 3 63 - end of helix Processing helix chain '5' and resid 41 through 46 removed outlier: 3.576A pdb=" N THR 5 45 " --> pdb=" O HIS 5 41 " (cutoff:3.500A) Processing helix chain '5' and resid 55 through 65 removed outlier: 4.993A pdb=" N ASN 5 65 " --> pdb=" O ASN 5 61 " (cutoff:3.500A) Processing helix chain 'b' and resid 5 through 13 removed outlier: 3.670A pdb=" N MET b 9 " --> pdb=" O SER b 5 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLY b 13 " --> pdb=" O MET b 9 " (cutoff:3.500A) Processing helix chain 'b' and resid 27 through 32 removed outlier: 3.572A pdb=" N ILE b 31 " --> pdb=" O MET b 27 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N PHE b 32 " --> pdb=" O LYS b 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 27 through 32' Processing helix chain 'b' and resid 44 through 64 Proline residue: b 48 - end of helix removed outlier: 4.033A pdb=" N ARG b 63 " --> pdb=" O LYS b 59 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N LYS b 64 " --> pdb=" O ILE b 60 " (cutoff:3.500A) Processing helix chain 'b' and resid 74 through 87 removed outlier: 3.593A pdb=" N GLU b 78 " --> pdb=" O ARG b 74 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA b 79 " --> pdb=" O ALA b 75 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS b 81 " --> pdb=" O SER b 77 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASP b 82 " --> pdb=" O GLU b 78 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER b 86 " --> pdb=" O ASP b 82 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N CYS b 87 " --> pdb=" O ALA b 83 " (cutoff:3.500A) Processing helix chain 'b' and resid 103 through 122 removed outlier: 3.521A pdb=" N VAL b 107 " --> pdb=" O ASN b 103 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N THR b 119 " --> pdb=" O LYS b 115 " (cutoff:3.500A) Processing helix chain 'b' and resid 130 through 148 removed outlier: 5.831A pdb=" N ALA b 134 " --> pdb=" O THR b 130 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG b 137 " --> pdb=" O GLU b 133 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ARG b 139 " --> pdb=" O LEU b 135 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N GLU b 140 " --> pdb=" O MET b 136 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER b 147 " --> pdb=" O LYS b 143 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU b 148 " --> pdb=" O LEU b 144 " (cutoff:3.500A) Processing helix chain 'b' and resid 165 through 170 removed outlier: 4.099A pdb=" N GLU b 169 " --> pdb=" O ASP b 165 " (cutoff:3.500A) Processing helix chain 'b' and resid 171 through 180 Processing helix chain 'b' and resid 206 through 227 Processing helix chain 'c' and resid 6 through 15 removed outlier: 3.921A pdb=" N ILE c 10 " --> pdb=" O HIS c 6 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N GLY c 13 " --> pdb=" O GLY c 9 " (cutoff:3.500A) Processing helix chain 'c' and resid 25 through 51 removed outlier: 4.547A pdb=" N ALA c 30 " --> pdb=" O THR c 26 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N ASP c 31 " --> pdb=" O LYS c 27 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N LYS c 45 " --> pdb=" O GLN c 41 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLU c 46 " --> pdb=" O TYR c 42 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ALA c 50 " --> pdb=" O GLU c 46 " (cutoff:3.500A) Processing helix chain 'c' and resid 72 through 78 Processing helix chain 'c' and resid 81 through 96 removed outlier: 3.550A pdb=" N GLU c 85 " --> pdb=" O GLY c 81 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ASP c 93 " --> pdb=" O LYS c 89 " (cutoff:3.500A) Processing helix chain 'c' and resid 112 through 127 Processing helix chain 'c' and resid 129 through 145 Processing helix chain 'd' and resid 7 through 16 removed outlier: 4.296A pdb=" N LEU d 11 " --> pdb=" O PRO d 7 " (cutoff:3.500A) Processing helix chain 'd' and resid 27 through 32 removed outlier: 3.554A pdb=" N CYS d 32 " --> pdb=" O ILE d 28 " (cutoff:3.500A) Processing helix chain 'd' and resid 49 through 66 removed outlier: 3.510A pdb=" N VAL d 53 " --> pdb=" O SER d 49 " (cutoff:3.500A) Processing helix chain 'd' and resid 68 through 83 removed outlier: 5.116A pdb=" N LYS d 83 " --> pdb=" O ALA d 79 " (cutoff:3.500A) Processing helix chain 'd' and resid 85 through 97 removed outlier: 4.771A pdb=" N ARG d 97 " --> pdb=" O LEU d 93 " (cutoff:3.500A) Processing helix chain 'd' and resid 98 through 106 Processing helix chain 'd' and resid 110 through 121 removed outlier: 3.711A pdb=" N HIS d 120 " --> pdb=" O GLN d 116 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N LYS d 121 " --> pdb=" O LEU d 117 " (cutoff:3.500A) Processing helix chain 'd' and resid 146 through 153 removed outlier: 3.882A pdb=" N LYS d 151 " --> pdb=" O GLU d 147 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N GLN d 152 " --> pdb=" O LYS d 148 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N SER d 153 " --> pdb=" O ALA d 149 " (cutoff:3.500A) Processing helix chain 'd' and resid 154 through 166 removed outlier: 3.649A pdb=" N ARG d 165 " --> pdb=" O LEU d 161 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N GLU d 166 " --> pdb=" O ALA d 162 " (cutoff:3.500A) Processing helix chain 'd' and resid 187 through 192 removed outlier: 3.540A pdb=" N LEU d 191 " --> pdb=" O GLU d 187 " (cutoff:3.500A) removed outlier: 5.218A 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 206 removed outlier: 4.218A pdb=" N ILE d 200 " --> pdb=" O ASN d 196 " (cutoff:3.500A) Processing helix chain 'd' and resid 40 through 45 removed outlier: 5.211A pdb=" N ALA d 43 " --> pdb=" O GLN d 40 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG d 44 " --> pdb=" O HIS d 41 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N LYS d 45 " --> pdb=" O GLY d 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 40 through 45' Processing helix chain 'e' and resid 55 through 71 removed outlier: 4.025A pdb=" N ARG e 69 " --> pdb=" O GLU e 65 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASN e 70 " --> pdb=" O LYS e 66 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N MET e 71 " --> pdb=" O ALA e 67 " (cutoff:3.500A) Processing helix chain 'e' and resid 109 through 119 Processing helix chain 'e' and resid 132 through 148 removed outlier: 3.551A pdb=" N MET e 147 " --> pdb=" O GLY e 143 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N ASN e 148 " --> pdb=" O LEU e 144 " (cutoff:3.500A) Processing helix chain 'e' and resid 149 through 158 Processing helix chain 'e' and resid 160 through 166 removed outlier: 4.136A pdb=" N GLY e 166 " --> pdb=" O GLU e 162 " (cutoff:3.500A) Processing helix chain 'f' and resid 14 through 33 Proline residue: f 19 - end of helix removed outlier: 4.116A pdb=" N GLY f 31 " --> pdb=" O ALA f 27 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N ALA f 32 " --> pdb=" O ALA f 28 " (cutoff:3.500A) Processing helix chain 'f' and resid 67 through 81 removed outlier: 3.882A pdb=" N ILE f 71 " --> pdb=" O PRO f 67 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N PHE f 80 " --> pdb=" O THR f 76 " (cutoff:3.500A) Processing helix chain 'g' and resid 20 through 31 removed outlier: 4.070A pdb=" N ALA g 24 " --> pdb=" O SER g 20 " (cutoff:3.500A) Processing helix chain 'g' and resid 35 through 55 removed outlier: 3.793A pdb=" N ALA g 39 " --> pdb=" O LYS g 35 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N THR g 49 " --> pdb=" O SER g 45 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ALA g 51 " --> pdb=" O LEU g 47 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLN g 52 " --> pdb=" O GLU g 48 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ARG g 53 " --> pdb=" O THR g 49 " (cutoff:3.500A) Processing helix chain 'g' and resid 57 through 70 removed outlier: 3.718A pdb=" N ALA g 61 " --> pdb=" O SER g 57 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ASN g 68 " --> pdb=" O VAL g 64 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N VAL g 69 " --> pdb=" O ALA g 65 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ARG g 70 " --> pdb=" O LEU g 66 " (cutoff:3.500A) Processing helix chain 'g' and resid 92 through 111 removed outlier: 4.052A pdb=" N ALA g 98 " --> pdb=" O VAL g 94 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N LYS g 110 " --> pdb=" O GLU g 106 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N ARG g 111 " --> pdb=" O ALA g 107 " (cutoff:3.500A) Processing helix chain 'g' and resid 115 through 130 removed outlier: 3.640A pdb=" N ASN g 130 " --> pdb=" O ASP g 126 " (cutoff:3.500A) Processing helix chain 'g' and resid 132 through 149 Processing helix chain 'h' and resid 5 through 21 removed outlier: 3.756A pdb=" N ASP h 9 " --> pdb=" O ASP h 5 " (cutoff:3.500A) Processing helix chain 'h' and resid 30 through 44 removed outlier: 4.017A pdb=" N VAL h 34 " --> pdb=" O SER h 30 " (cutoff:3.500A) Processing helix chain 'h' and resid 112 through 120 Processing helix chain 'i' and resid 34 through 40 removed outlier: 4.252A pdb=" N GLY i 40 " --> pdb=" O GLU i 36 " (cutoff:3.500A) Processing helix chain 'i' and resid 43 through 54 removed outlier: 6.249A pdb=" N VAL i 47 " --> pdb=" O THR i 43 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N VAL i 48 " --> pdb=" O ALA i 44 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ARG i 49 " --> pdb=" O ARG i 45 " (cutoff:3.500A) Proline residue: i 51 - end of helix Processing helix chain 'i' and resid 71 through 91 removed outlier: 3.729A pdb=" N TYR i 90 " --> pdb=" O ALA i 86 " (cutoff:3.500A) Processing helix chain 'i' and resid 92 through 102 removed outlier: 3.639A pdb=" N SER i 96 " --> pdb=" O GLU i 92 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N LYS i 100 " --> pdb=" O SER i 96 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA i 101 " --> pdb=" O GLU i 97 " (cutoff:3.500A) Processing helix chain 'j' and resid 14 through 33 removed outlier: 4.170A pdb=" N GLN j 20 " --> pdb=" O ARG j 16 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA j 21 " --> pdb=" O LEU j 17 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N THR j 32 " --> pdb=" O THR j 28 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLY j 33 " --> pdb=" O ALA j 29 " (cutoff:3.500A) Processing helix chain 'j' and resid 80 through 90 removed outlier: 3.589A pdb=" N LEU j 90 " --> pdb=" O ALA j 86 " (cutoff:3.500A) Processing helix chain 'k' and resid 54 through 59 removed outlier: 4.491A pdb=" N SER k 58 " --> pdb=" O GLY k 54 " (cutoff:3.500A) removed outlier: 4.335A 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 75 removed outlier: 4.101A pdb=" N VAL k 74 " --> pdb=" O CYS k 70 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N LYS k 75 " --> pdb=" O ALA k 71 " (cutoff:3.500A) Processing helix chain 'k' and resid 93 through 104 removed outlier: 3.954A pdb=" N ASN k 101 " --> pdb=" O ILE k 97 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA k 102 " --> pdb=" O ARG k 98 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N GLY k 104 " --> pdb=" O LEU k 100 " (cutoff:3.500A) Processing helix chain 'l' and resid 3 through 11 Proline residue: l 11 - end of helix Processing helix chain 'l' and resid 113 through 118 removed outlier: 4.118A pdb=" N TYR l 117 " --> pdb=" O ALA l 113 " (cutoff:3.500A) Processing helix chain 'm' and resid 14 through 22 removed outlier: 4.045A pdb=" N SER m 21 " --> pdb=" O ILE m 17 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ILE m 22 " --> pdb=" O ALA m 18 " (cutoff:3.500A) Processing helix chain 'm' and resid 26 through 38 Processing helix chain 'm' and resid 44 through 49 removed outlier: 4.295A pdb=" N LEU m 48 " --> pdb=" O LYS m 44 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N SER m 49 " --> pdb=" O ILE m 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 44 through 49' Processing helix chain 'm' and resid 50 through 84 removed outlier: 3.985A pdb=" N GLU m 59 " --> pdb=" O THR m 55 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE m 63 " --> pdb=" O GLU m 59 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N VAL m 64 " --> pdb=" O VAL m 60 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N VAL m 65 " --> pdb=" O ALA m 61 " (cutoff:3.500A) removed outlier: 10.489A pdb=" N GLU m 66 " --> pdb=" O LYS m 62 " (cutoff:3.500A) removed outlier: 9.064A pdb=" N GLY m 67 " --> pdb=" O PHE m 63 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N ASP m 68 " --> pdb=" O VAL m 64 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLY m 84 " --> pdb=" O LEU m 80 " (cutoff:3.500A) Processing helix chain 'm' and resid 85 through 94 removed outlier: 3.509A pdb=" N LEU m 89 " --> pdb=" O CYS m 85 " (cutoff:3.500A) Processing helix chain 'm' and resid 106 through 111 removed outlier: 4.240A pdb=" N LYS m 110 " --> pdb=" O ALA m 106 " (cutoff:3.500A) Processing helix chain 'n' and resid 3 through 25 removed outlier: 3.939A pdb=" N ALA n 15 " --> pdb=" O VAL n 11 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU n 16 " --> pdb=" O LYS n 12 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N LYS n 19 " --> pdb=" O ALA n 15 " (cutoff:3.500A) Processing helix chain 'n' and resid 37 through 51 removed outlier: 4.008A pdb=" N ARG n 41 " --> pdb=" O SER n 37 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU n 46 " --> pdb=" O TRP n 42 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N LEU n 51 " --> pdb=" O LYS n 47 " (cutoff:3.500A) 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 44 Processing helix chain 'o' and resid 49 through 74 Processing helix chain 'o' and resid 75 through 86 removed outlier: 3.545A pdb=" N GLN o 80 " --> pdb=" O ALA o 76 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLY o 86 " --> pdb=" O ILE o 82 " (cutoff:3.500A) Processing helix chain 'p' and resid 53 through 64 removed outlier: 4.594A pdb=" N ILE p 57 " --> pdb=" O ASP p 53 " (cutoff:3.500A) Processing helix chain 'p' and resid 68 through 82 removed outlier: 3.955A pdb=" N ALA p 82 " --> pdb=" O VAL p 78 " (cutoff:3.500A) Processing helix chain 'r' and resid 11 through 17 removed outlier: 4.045A pdb=" N ALA r 15 " --> pdb=" O CYS r 11 " (cutoff:3.500A) Processing helix chain 'r' and resid 25 through 34 removed outlier: 4.747A pdb=" N ILE r 33 " --> pdb=" O LEU r 29 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N THR r 34 " --> pdb=" O LYS r 30 " (cutoff:3.500A) Processing helix chain 'r' and resid 41 through 46 removed outlier: 3.632A pdb=" N THR r 45 " --> pdb=" O PRO r 41 " (cutoff:3.500A) Processing helix chain 'r' and resid 48 through 66 removed outlier: 3.556A pdb=" N LEU r 65 " --> pdb=" O ARG r 61 " (cutoff:3.500A) Processing helix chain 's' and resid 12 through 26 Processing helix chain 's' and resid 70 through 76 removed outlier: 4.901A pdb=" N PHE s 74 " --> pdb=" O LYS s 70 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N ALA s 75 " --> pdb=" O LEU s 71 " (cutoff:3.500A) Proline residue: s 76 - end of helix No H-bonds generated for 'chain 's' and resid 70 through 76' Processing helix chain 't' and resid 4 through 41 removed outlier: 3.542A pdb=" N LYS t 8 " --> pdb=" O ILE t 4 " (cutoff:3.500A) Processing helix chain 't' and resid 44 through 65 Proline residue: t 56 - end of helix removed outlier: 3.709A pdb=" N GLY t 65 " --> pdb=" O GLN t 61 " (cutoff:3.500A) Processing helix chain 't' and resid 68 through 87 removed outlier: 3.602A pdb=" N ALA t 72 " --> pdb=" O HIS t 68 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA t 87 " --> pdb=" O ILE t 83 " (cutoff:3.500A) Processing helix chain 'u' and resid 11 through 27 removed outlier: 3.641A pdb=" N ALA u 15 " --> pdb=" O PRO u 11 " (cutoff:3.500A) Processing helix chain 'u' and resid 28 through 36 Processing helix chain 'u' and resid 40 through 68 removed outlier: 4.483A pdb=" N ALA u 61 " --> pdb=" O ALA u 57 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ARG u 66 " --> pdb=" O ARG u 62 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ARG u 67 " --> pdb=" O GLU u 63 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N THR u 68 " --> pdb=" O ASN u 64 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'C' and resid 2 through 5 Processing sheet with id= 2, first strand: chain 'C' and resid 80 through 83 removed outlier: 3.642A pdb=" N ARG C 80 " --> pdb=" O LEU C 93 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N LEU C 93 " --> pdb=" O GLU C 79 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N ILE C 74 " --> pdb=" O SER C 118 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N SER C 118 " --> pdb=" O ILE C 74 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ASP C 114 " --> pdb=" O VAL C 78 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'C' and resid 138 through 142 removed outlier: 3.923A pdb=" N SER C 139 " --> pdb=" O ILE C 164 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE C 164 " --> pdb=" O SER C 139 " (cutoff:3.500A) removed outlier: 4.594A 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 97 removed outlier: 4.444A 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 8 removed outlier: 4.135A pdb=" N SER D 199 " --> pdb=" O LYS D 8 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ASP D 200 " --> pdb=" O THR D 112 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N THR D 112 " --> pdb=" O ASP D 200 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N GLU D 168 " --> pdb=" O SER D 113 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'D' and resid 11 through 16 removed outlier: 4.828A pdb=" N VAL D 20 " --> pdb=" O THR D 16 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU D 186 " --> pdb=" O ASP D 181 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ARG D 179 " --> pdb=" O LEU D 188 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'D' and resid 32 through 35 removed outlier: 6.706A pdb=" N GLN D 49 " --> pdb=" O THR D 35 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA D 47 " --> pdb=" O LYS D 38 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'D' and resid 47 through 51 Processing sheet with id= 9, first strand: chain 'E' and resid 117 through 120 removed outlier: 6.434A pdb=" N ARG E 117 " --> pdb=" O ASP E 184 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'F' and resid 65 through 69 removed outlier: 5.250A pdb=" N GLY F 39 " --> pdb=" O GLY F 151 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N GLY F 151 " --> pdb=" O GLY F 39 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU F 152 " --> pdb=" O VAL F 132 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N GLY F 126 " --> pdb=" O THR F 158 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'G' and resid 16 through 19 removed outlier: 5.031A pdb=" N ASP G 16 " --> pdb=" O LYS G 27 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N LYS G 27 " --> pdb=" O ASP G 16 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS G 18 " --> pdb=" O THR G 25 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLY G 31 " --> pdb=" O GLY G 28 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'G' and resid 41 through 45 Processing sheet with id= 13, first strand: chain 'G' and resid 94 through 99 removed outlier: 3.942A pdb=" N ARG G 95 " --> pdb=" O SER G 106 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA G 97 " --> pdb=" O ASN G 104 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ASN G 101 " --> pdb=" O LEU G 117 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'G' and resid 121 through 125 removed outlier: 5.567A pdb=" N THR G 129 " --> pdb=" O LEU G 89 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'H' and resid 3 through 6 removed outlier: 7.442A pdb=" N LYS H 35 " --> pdb=" O LEU H 6 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'H' and resid 76 through 81 removed outlier: 5.838A pdb=" N GLU H 76 " --> pdb=" O LYS H 141 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASN H 145 " --> pdb=" O VAL H 78 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ILE H 80 " --> pdb=" O ASN H 145 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N PHE H 132 " --> pdb=" O ALA H 140 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'J' and resid 14 through 19 Processing sheet with id= 18, first strand: chain 'J' and resid 74 through 77 removed outlier: 3.651A pdb=" N ALA J 87 " --> pdb=" O TYR J 74 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'K' and resid 56 through 60 removed outlier: 4.839A pdb=" N ASP K 56 " --> pdb=" O ILE K 43 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LYS K 40 " --> pdb=" O ILE K 22 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N THR K 6 " --> pdb=" O CYS K 21 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N ASN K 82 " --> pdb=" O MET K 7 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'K' and resid 68 through 71 removed outlier: 3.861A pdb=" N VAL K 69 " --> pdb=" O ILE K 77 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N SER K 75 " --> pdb=" O ARG K 71 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'M' and resid 62 through 66 removed outlier: 3.547A pdb=" N ARG M 66 " --> pdb=" O LEU M 102 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N LEU M 102 " --> pdb=" O ARG M 66 " (cutoff:3.500A) removed outlier: 8.407A pdb=" N SER M 30 " --> pdb=" O LYS M 133 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'M' and resid 71 through 74 removed outlier: 3.618A pdb=" N LYS M 71 " --> pdb=" O VAL M 93 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'N' and resid 33 through 37 removed outlier: 5.048A pdb=" N MET N 110 " --> pdb=" O CYS N 100 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N TYR N 94 " --> pdb=" O VAL N 116 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'O' and resid 49 through 52 removed outlier: 3.753A pdb=" N VAL O 49 " --> pdb=" O VAL O 39 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG O 25 " --> pdb=" O ILE O 40 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL O 28 " --> pdb=" O ASP O 93 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'P' and resid 38 through 45 removed outlier: 6.676A pdb=" N THR P 25 " --> pdb=" O LYS P 87 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER P 83 " --> pdb=" O LYS P 29 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'P' and resid 49 through 53 removed outlier: 3.933A pdb=" N ALA P 49 " --> pdb=" O THR P 60 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ARG P 53 " --> pdb=" O HIS P 56 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N HIS P 56 " --> pdb=" O ARG P 53 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N SER P 57 " --> pdb=" O THR P 76 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'R' and resid 11 through 15 Processing sheet with id= 28, first strand: chain 'R' and resid 18 through 21 removed outlier: 4.156A pdb=" N GLN R 18 " --> pdb=" O ILE R 98 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ASP R 95 " --> pdb=" O VAL R 64 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N LYS R 60 " --> pdb=" O THR R 99 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'R' and resid 65 through 69 removed outlier: 3.756A pdb=" N ALA R 65 " --> pdb=" O ASP R 95 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLY R 67 " --> pdb=" O PHE R 93 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N GLN R 91 " --> pdb=" O GLY R 69 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'R' and resid 71 through 78 removed outlier: 4.540A pdb=" N TYR R 83 " --> pdb=" O ARG R 78 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'S' and resid 2 through 8 removed outlier: 4.377A pdb=" N THR S 3 " --> pdb=" O VAL S 107 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N VAL S 107 " --> pdb=" O THR S 3 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N VAL S 106 " --> pdb=" O THR S 72 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'S' and resid 80 through 88 removed outlier: 4.212A pdb=" N THR S 100 " --> pdb=" O PRO S 80 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE S 96 " --> pdb=" O ARG S 84 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ARG S 92 " --> pdb=" O ARG S 88 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'T' and resid 12 through 15 removed outlier: 5.103A pdb=" N VAL T 31 " --> pdb=" O HIS T 15 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N ASN T 28 " --> pdb=" O LEU T 87 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N LYS T 81 " --> pdb=" O VAL T 34 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N LYS T 66 " --> pdb=" O ARG T 77 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N ASP T 79 " --> pdb=" O LYS T 64 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N LYS T 64 " --> pdb=" O ASP T 79 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N LYS T 81 " --> pdb=" O VAL T 62 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N VAL T 62 " --> pdb=" O LYS T 81 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ALA T 83 " --> pdb=" O THR T 60 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N THR T 60 " --> pdb=" O ALA T 83 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N VAL T 85 " --> pdb=" O VAL T 58 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N VAL T 58 " --> pdb=" O VAL T 85 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'U' 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 75 through 78 removed outlier: 3.817A pdb=" N ASP V 76 " --> pdb=" O ASP V 90 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N HIS V 88 " --> pdb=" O GLN V 78 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ILE V 89 " --> pdb=" O PRO V 27 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU V 38 " --> pdb=" O ILE V 30 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N ALA V 39 " --> pdb=" O ARG V 9 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N PHE V 2 " --> pdb=" O VAL V 60 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N THR V 62 " --> pdb=" O PHE V 2 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ALA V 6 " --> pdb=" O VAL V 64 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'V' and resid 71 through 74 removed outlier: 6.206A pdb=" N LYS V 71 " --> pdb=" O ALA V 94 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'W' and resid 51 through 54 removed outlier: 6.308A pdb=" N GLY W 52 " --> pdb=" O LEU W 59 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N LEU W 59 " --> pdb=" O GLY W 52 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N GLY W 54 " --> pdb=" O HIS W 57 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'W' and resid 65 through 71 Processing sheet with id= 39, first strand: chain 'X' and resid 12 through 19 removed outlier: 3.620A pdb=" N SER X 19 " --> pdb=" O ASN X 23 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ASN X 23 " --> pdb=" O SER X 19 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'X' and resid 35 through 41 Processing sheet with id= 41, first strand: chain 'Z' and resid 35 through 39 removed outlier: 6.245A pdb=" N LYS Z 6 " --> pdb=" O GLU Z 58 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N MET Z 54 " --> pdb=" O THR Z 10 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain '0' and resid 28 through 31 No H-bonds generated for sheet with id= 42 Processing sheet with id= 43, first strand: chain '1' and resid 7 through 13 No H-bonds generated for sheet with id= 43 Processing sheet with id= 44, first strand: chain '1' and resid 34 through 37 No H-bonds generated for sheet with id= 44 Processing sheet with id= 45, first strand: chain '4' and resid 13 through 19 removed outlier: 8.538A pdb=" N ASN 4 13 " --> pdb=" O SER 4 28 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N SER 4 28 " --> pdb=" O ASN 4 13 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain '5' and resid 11 through 16 removed outlier: 4.135A pdb=" N ASN 5 20 " --> pdb=" O CYS 5 16 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'b' and resid 89 through 93 removed outlier: 3.545A pdb=" N PHE b 198 " --> pdb=" O VAL b 183 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA b 185 " --> pdb=" O PHE b 198 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'c' and resid 19 through 22 removed outlier: 6.095A pdb=" N ASN c 19 " --> pdb=" O ILE c 55 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ARG c 54 " --> pdb=" O HIS c 69 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'c' and resid 165 through 169 removed outlier: 7.237A pdb=" N ASP c 181 " --> pdb=" O LYS c 204 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'd' and resid 141 through 144 removed outlier: 3.987A pdb=" N ASP d 141 " --> pdb=" O PHE d 182 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N GLU d 179 " --> pdb=" O ASP d 174 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'e' and resid 11 through 16 removed outlier: 6.802A pdb=" N LEU e 36 " --> pdb=" O ILE e 16 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'e' and resid 84 through 88 removed outlier: 4.399A pdb=" N TYR e 128 " --> pdb=" O ARG e 93 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N ALA e 99 " --> pdb=" O ASN e 122 " (cutoff:3.500A) removed outlier: 8.926A pdb=" N ASN e 122 " --> pdb=" O ALA e 99 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'e' and resid 32 through 41 removed outlier: 3.508A pdb=" N ASP e 41 " --> pdb=" O ARG e 45 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ARG e 45 " --> pdb=" O ASP e 41 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'f' and resid 38 through 42 removed outlier: 3.754A pdb=" N ARG f 38 " --> pdb=" O ASN f 63 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASN f 63 " --> pdb=" O ARG f 38 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU f 40 " --> pdb=" O LEU f 61 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N TYR f 59 " --> pdb=" O TRP f 42 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N HIS f 3 " --> pdb=" O THR f 92 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ARG f 86 " --> pdb=" O MET f 9 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'f' and resid 43 through 46 Processing sheet with id= 56, first strand: chain 'g' and resid 72 through 77 removed outlier: 6.220A pdb=" N THR g 72 " --> pdb=" O VAL g 91 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'h' and resid 23 through 29 removed outlier: 5.628A pdb=" N ALA h 23 " --> pdb=" O LEU h 63 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N GLU h 58 " --> pdb=" O GLU h 52 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLU h 52 " --> pdb=" O GLU h 58 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR h 62 " --> pdb=" O ASP h 48 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ASP h 48 " --> pdb=" O THR h 62 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'h' and resid 74 through 77 removed outlier: 4.515A pdb=" N SER h 74 " --> pdb=" O ALA h 130 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N CYS h 127 " --> pdb=" O VAL h 103 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N VAL h 103 " --> pdb=" O ILE h 126 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLU h 124 " --> pdb=" O SER h 105 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'i' and resid 5 through 11 Processing sheet with id= 60, first strand: chain 'j' and resid 39 through 42 removed outlier: 3.736A pdb=" N LEU j 42 " --> pdb=" O LEU j 71 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N LEU j 71 " --> pdb=" O LEU j 42 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'j' and resid 44 through 52 Processing sheet with id= 62, first strand: chain 'k' and resid 29 through 36 removed outlier: 3.963A pdb=" N ASN k 29 " --> pdb=" O SER k 26 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER k 26 " --> pdb=" O ASN k 29 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'l' and resid 29 through 32 removed outlier: 5.109A pdb=" N LEU l 81 " --> pdb=" O VAL l 98 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N HIS l 96 " --> pdb=" O ARG l 83 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'l' and resid 36 through 41 removed outlier: 5.525A pdb=" N LYS l 51 " --> pdb=" O ILE l 67 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'p' and resid 4 through 10 removed outlier: 5.771A pdb=" N GLY p 49 " --> pdb=" O ASN p 40 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'q' and resid 7 through 11 removed outlier: 6.847A pdb=" N GLU q 60 " --> pdb=" O VAL q 76 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'q' and resid 19 through 30 removed outlier: 4.882A pdb=" N LYS q 19 " --> pdb=" O ASP q 48 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 's' and resid 47 through 52 removed outlier: 4.530A pdb=" N LEU s 47 " --> pdb=" O VAL s 62 " (cutoff:3.500A) 1809 hydrogen bonds defined for protein. 5358 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3838 hydrogen bonds 6030 hydrogen bond angles 0 basepair planarities 1530 basepair parallelities 2663 stacking parallelities Total time for adding SS restraints: 262.12 Time building geometry restraints manager: 63.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 17063 1.32 - 1.45: 73655 1.45 - 1.58: 59311 1.58 - 1.72: 8636 1.72 - 1.85: 266 Bond restraints: 158931 Sorted by residual: bond pdb=" CA MET 7 5 " pdb=" C MET 7 5 " ideal model delta sigma weight residual 1.524 1.412 0.111 1.26e-02 6.30e+03 7.81e+01 bond pdb=" C1 ERY 7 101 " pdb=" C2 ERY 7 101 " ideal model delta sigma weight residual 1.558 1.385 0.173 2.00e-02 2.50e+03 7.46e+01 bond pdb=" C10 ERY 7 101 " pdb=" C9 ERY 7 101 " ideal model delta sigma weight residual 1.542 1.406 0.136 2.00e-02 2.50e+03 4.61e+01 bond pdb=" C MET J 108 " pdb=" N LEU J 109 " ideal model delta sigma weight residual 1.325 1.245 0.080 1.25e-02 6.40e+03 4.11e+01 bond pdb=" N MET 7 5 " pdb=" CA MET 7 5 " ideal model delta sigma weight residual 1.456 1.383 0.073 1.23e-02 6.61e+03 3.51e+01 ... (remaining 158926 not shown) Histogram of bond angle deviations from ideal: 98.13 - 106.50: 29659 106.50 - 114.87: 102501 114.87 - 123.25: 80003 123.25 - 131.62: 24716 131.62 - 139.99: 1153 Bond angle restraints: 238032 Sorted by residual: angle pdb=" N ALA g 65 " pdb=" CA ALA g 65 " pdb=" C ALA g 65 " ideal model delta sigma weight residual 114.75 104.63 10.12 1.26e+00 6.30e-01 6.45e+01 angle pdb=" C THR l 40 " pdb=" N THR l 41 " pdb=" CA THR l 41 " ideal model delta sigma weight residual 120.94 135.90 -14.96 1.90e+00 2.77e-01 6.20e+01 angle pdb=" N THR 7 2 " pdb=" CA THR 7 2 " pdb=" C THR 7 2 " ideal model delta sigma weight residual 110.80 127.20 -16.40 2.13e+00 2.20e-01 5.93e+01 angle pdb=" N SER 2 45 " pdb=" CA SER 2 45 " pdb=" C SER 2 45 " ideal model delta sigma weight residual 113.43 104.70 8.73 1.26e+00 6.30e-01 4.80e+01 angle pdb=" C SER 7 4 " pdb=" CA SER 7 4 " pdb=" CB SER 7 4 " ideal model delta sigma weight residual 110.90 100.47 10.43 1.58e+00 4.01e-01 4.36e+01 ... (remaining 238027 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 89405 35.98 - 71.96: 11201 71.96 - 107.94: 1208 107.94 - 143.92: 45 143.92 - 179.89: 49 Dihedral angle restraints: 101908 sinusoidal: 85701 harmonic: 16207 Sorted by residual: dihedral pdb=" CA LYS d 31 " pdb=" C LYS d 31 " pdb=" N CYS d 32 " pdb=" CA CYS d 32 " ideal model delta harmonic sigma weight residual 180.00 125.04 54.96 0 5.00e+00 4.00e-02 1.21e+02 dihedral pdb=" CA LYS H 8 " pdb=" C LYS H 8 " pdb=" N VAL H 9 " pdb=" CA VAL H 9 " ideal model delta harmonic sigma weight residual 180.00 130.19 49.81 0 5.00e+00 4.00e-02 9.92e+01 dihedral pdb=" CA ASP U 89 " pdb=" C ASP U 89 " pdb=" N GLY U 90 " pdb=" CA GLY U 90 " ideal model delta harmonic sigma weight residual -180.00 -131.95 -48.05 0 5.00e+00 4.00e-02 9.24e+01 ... (remaining 101905 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.121: 30460 1.121 - 2.242: 0 2.242 - 3.363: 0 3.363 - 4.484: 0 4.484 - 5.604: 4 Chirality restraints: 30464 Sorted by residual: chirality pdb=" C16 ERY 7 101 " pdb=" C15 ERY 7 101 " pdb=" C17 ERY 7 101 " pdb=" C19 ERY 7 101 " both_signs ideal model delta sigma weight residual False 2.68 -2.93 5.60 2.00e-01 2.50e+01 7.85e+02 chirality pdb=" C12 ERY 7 101 " pdb=" C11 ERY 7 101 " pdb=" C13 ERY 7 101 " pdb=" C35 ERY 7 101 " both_signs ideal model delta sigma weight residual False -2.75 2.84 -5.59 2.00e-01 2.50e+01 7.80e+02 chirality pdb=" C6 ERY 7 101 " pdb=" C32 ERY 7 101 " pdb=" C5 ERY 7 101 " pdb=" C7 ERY 7 101 " both_signs ideal model delta sigma weight residual False -2.75 2.77 -5.52 2.00e-01 2.50e+01 7.63e+02 ... (remaining 30461 not shown) Planarity restraints: 12558 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A v 20 " 0.057 2.00e-02 2.50e+03 2.60e-02 1.86e+01 pdb=" N9 A v 20 " -0.060 2.00e-02 2.50e+03 pdb=" C8 A v 20 " -0.006 2.00e-02 2.50e+03 pdb=" N7 A v 20 " 0.006 2.00e-02 2.50e+03 pdb=" C5 A v 20 " -0.005 2.00e-02 2.50e+03 pdb=" C6 A v 20 " 0.010 2.00e-02 2.50e+03 pdb=" N6 A v 20 " 0.013 2.00e-02 2.50e+03 pdb=" N1 A v 20 " 0.003 2.00e-02 2.50e+03 pdb=" C2 A v 20 " -0.004 2.00e-02 2.50e+03 pdb=" N3 A v 20 " -0.010 2.00e-02 2.50e+03 pdb=" C4 A v 20 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C a1284 " 0.050 2.00e-02 2.50e+03 2.58e-02 1.49e+01 pdb=" N1 C a1284 " -0.053 2.00e-02 2.50e+03 pdb=" C2 C a1284 " -0.005 2.00e-02 2.50e+03 pdb=" O2 C a1284 " -0.007 2.00e-02 2.50e+03 pdb=" N3 C a1284 " 0.003 2.00e-02 2.50e+03 pdb=" C4 C a1284 " 0.017 2.00e-02 2.50e+03 pdb=" N4 C a1284 " 0.007 2.00e-02 2.50e+03 pdb=" C5 C a1284 " 0.003 2.00e-02 2.50e+03 pdb=" C6 C a1284 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU 1 34 " -0.019 2.00e-02 2.50e+03 3.79e-02 1.44e+01 pdb=" C LEU 1 34 " 0.066 2.00e-02 2.50e+03 pdb=" O LEU 1 34 " -0.024 2.00e-02 2.50e+03 pdb=" N GLU 1 35 " -0.022 2.00e-02 2.50e+03 ... (remaining 12555 not shown) Histogram of nonbonded interaction distances: 1.43 - 2.13: 4 2.13 - 2.82: 41030 2.82 - 3.51: 194673 3.51 - 4.21: 456802 4.21 - 4.90: 622588 Nonbonded interactions: 1315097 Sorted by model distance: nonbonded pdb=" C LEU 7 7 " pdb=" O3' A 8 87 " model vdw 1.432 3.270 nonbonded pdb=" N2 G v 1 " pdb=" O2 C v 73 " model vdw 2.069 2.496 nonbonded pdb=" C LEU 7 7 " pdb=" C3' A 8 87 " model vdw 2.087 3.700 nonbonded pdb=" O4 U A2584 " pdb=" NE2 HIS 7 3 " model vdw 2.119 2.520 nonbonded pdb=" OE1 GLU H 87 " pdb=" CG MET f 21 " model vdw 2.153 3.440 ... (remaining 1315092 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.110 Extract box with map and model: 14.640 Check model and map are aligned: 1.620 Set scattering table: 1.000 Process input model: 547.790 Find NCS groups from input model: 2.900 Set up NCS constraints: 0.400 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: 0.030 Load rotamer database and sin/cos tables:2.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 573.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.173 158931 Z= 0.476 Angle : 1.053 18.007 238032 Z= 0.539 Chirality : 0.082 5.604 30464 Planarity : 0.007 0.088 12558 Dihedral : 23.831 179.894 91440 Min Nonbonded Distance : 1.432 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.30 % Allowed : 8.12 % Favored : 91.58 % Rotamer: Outliers : 0.95 % Allowed : 12.27 % Favored : 86.79 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.33 % 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: -4.02 (0.09), residues: 5591 helix: -2.81 (0.09), residues: 1801 sheet: -1.83 (0.15), residues: 1008 loop : -2.89 (0.09), residues: 2782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 213 HIS 0.018 0.002 HIS S 7 PHE 0.029 0.003 PHE R 93 TYR 0.029 0.003 TYR k 77 ARG 0.013 0.001 ARG 1 44 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11182 Ramachandran restraints generated. 5591 Oldfield, 0 Emsley, 5591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11182 Ramachandran restraints generated. 5591 Oldfield, 0 Emsley, 5591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1709 residues out of total 4655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 1665 time to evaluate : 6.285 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: C 97 LYS cc_start: 0.7703 (mmtt) cc_final: 0.7082 (tptt) REVERT: C 202 LEU cc_start: 0.8837 (mt) cc_final: 0.8635 (mp) REVERT: D 128 ARG cc_start: 0.8197 (mtm-85) cc_final: 0.7659 (mtp85) REVERT: E 123 LYS cc_start: 0.7843 (mtpp) cc_final: 0.7600 (mtpp) REVERT: E 136 GLN cc_start: 0.6505 (tp-100) cc_final: 0.6025 (mm110) REVERT: E 194 LYS cc_start: 0.8785 (tptt) cc_final: 0.8531 (tppt) REVERT: F 16 LEU cc_start: 0.8459 (mm) cc_final: 0.8252 (mm) REVERT: F 17 MET cc_start: 0.6156 (mmt) cc_final: 0.5880 (mmm) REVERT: F 77 PHE cc_start: 0.6747 (m-80) cc_final: 0.6537 (m-80) REVERT: G 71 LEU cc_start: 0.8567 (mt) cc_final: 0.7972 (mt) REVERT: J 116 ARG cc_start: 0.8358 (mtm-85) cc_final: 0.7834 (mtm-85) REVERT: J 131 ASN cc_start: 0.7449 (p0) cc_final: 0.7025 (p0) REVERT: K 44 LYS cc_start: 0.9295 (mmmt) cc_final: 0.8948 (mmtp) REVERT: K 67 LYS cc_start: 0.8940 (tptm) cc_final: 0.8679 (tptp) REVERT: L 55 MET cc_start: 0.7827 (tpp) cc_final: 0.7622 (tpt) REVERT: M 10 ARG cc_start: 0.7916 (mmm-85) cc_final: 0.7588 (mtm-85) REVERT: M 136 MET cc_start: 0.3876 (ttp) cc_final: 0.2859 (mmt) REVERT: N 11 ASN cc_start: 0.9077 (m-40) cc_final: 0.8761 (m-40) REVERT: N 37 THR cc_start: 0.9252 (m) cc_final: 0.8962 (m) REVERT: R 11 GLN cc_start: 0.7568 (mp10) cc_final: 0.7348 (mm-40) REVERT: R 101 ILE cc_start: 0.7499 (mm) cc_final: 0.7135 (mm) REVERT: S 61 ASN cc_start: 0.7365 (m110) cc_final: 0.6958 (p0) REVERT: Y 27 ASN cc_start: 0.7550 (m-40) cc_final: 0.7250 (m110) REVERT: Y 38 GLN cc_start: 0.7695 (mp10) cc_final: 0.7043 (tp40) REVERT: Z 53 PHE cc_start: 0.8509 (p90) cc_final: 0.8250 (p90) REVERT: 7 5 MET cc_start: 0.8134 (mtm) cc_final: 0.7865 (mmm) REVERT: b 27 MET cc_start: 0.7422 (mmm) cc_final: 0.7191 (mmm) REVERT: b 35 ARG cc_start: 0.6639 (ttm-80) cc_final: 0.6230 (mtt-85) REVERT: b 40 ILE cc_start: 0.7541 (OUTLIER) cc_final: 0.7146 (mp) REVERT: b 93 ASN cc_start: 0.7602 (p0) cc_final: 0.7367 (p0) REVERT: b 113 ARG cc_start: 0.7681 (mmm160) cc_final: 0.7286 (mmp-170) REVERT: b 184 PHE cc_start: 0.7637 (m-80) cc_final: 0.7407 (m-80) REVERT: d 14 ARG cc_start: 0.7904 (tpp-160) cc_final: 0.7661 (tpp80) REVERT: d 36 GLN cc_start: 0.7658 (tt0) cc_final: 0.7454 (pt0) REVERT: d 69 GLU cc_start: 0.7201 (tp30) cc_final: 0.6807 (tp30) REVERT: d 165 ARG cc_start: 0.6152 (mtm180) cc_final: 0.5680 (mtt180) REVERT: d 198 HIS cc_start: 0.6348 (p90) cc_final: 0.6079 (p90) REVERT: d 206 LYS cc_start: 0.6950 (tttt) cc_final: 0.6710 (tttt) REVERT: e 101 GLU cc_start: 0.7478 (tp30) cc_final: 0.7223 (tp30) REVERT: e 156 LYS cc_start: 0.8521 (mtmt) cc_final: 0.8250 (mttm) REVERT: g 92 ARG cc_start: 0.7315 (mmp80) cc_final: 0.6737 (ptm160) REVERT: g 118 LEU cc_start: 0.7176 (tp) cc_final: 0.6399 (mt) REVERT: g 142 HIS cc_start: 0.7602 (m90) cc_final: 0.7205 (m-70) REVERT: i 64 TYR cc_start: 0.7064 (t80) cc_final: 0.6824 (t80) REVERT: k 31 ILE cc_start: 0.9346 (mp) cc_final: 0.9079 (mt) REVERT: l 51 LYS cc_start: 0.8361 (mptt) cc_final: 0.8149 (mttp) REVERT: l 67 ILE cc_start: 0.8848 (mp) cc_final: 0.8582 (mp) REVERT: m 73 ILE cc_start: 0.8982 (OUTLIER) cc_final: 0.8717 (mp) REVERT: m 86 TYR cc_start: 0.7742 (t80) cc_final: 0.7498 (t80) REVERT: n 28 LYS cc_start: 0.8140 (tttt) cc_final: 0.7879 (tppt) REVERT: o 26 GLU cc_start: 0.8239 (mp0) cc_final: 0.8036 (mp0) REVERT: o 48 LYS cc_start: 0.8003 (mttt) cc_final: 0.7578 (ttpt) REVERT: o 89 ARG cc_start: 0.7334 (tpt170) cc_final: 0.6341 (tpp80) REVERT: p 76 LYS cc_start: 0.7908 (mtmt) cc_final: 0.7424 (mmmt) REVERT: q 12 VAL cc_start: 0.8293 (t) cc_final: 0.7964 (m) REVERT: q 19 LYS cc_start: 0.8612 (ttmm) cc_final: 0.8363 (tttp) REVERT: q 43 LYS cc_start: 0.7198 (mtpt) cc_final: 0.6881 (mtmt) REVERT: r 48 ARG cc_start: 0.8441 (mtt180) cc_final: 0.7385 (mtt90) REVERT: r 50 LYS cc_start: 0.8142 (ptmt) cc_final: 0.7648 (ptmt) REVERT: s 44 MET cc_start: 0.6573 (mtp) cc_final: 0.6269 (mtp) REVERT: s 57 HIS cc_start: 0.6925 (m-70) cc_final: 0.6435 (m-70) REVERT: t 25 ARG cc_start: 0.8552 (ttp-170) cc_final: 0.8239 (ttm110) REVERT: t 31 PHE cc_start: 0.8494 (m-80) cc_final: 0.8279 (m-80) REVERT: t 61 GLN cc_start: 0.8062 (mm-40) cc_final: 0.7760 (mp10) outliers start: 44 outliers final: 19 residues processed: 1690 average time/residue: 1.3756 time to fit residues: 3899.8843 Evaluate side-chains 1359 residues out of total 4655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 1338 time to evaluate : 6.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain O residue 90 VAL Chi-restraints excluded: chain 4 residue 14 CYS Chi-restraints excluded: chain b residue 40 ILE Chi-restraints excluded: chain b residue 196 VAL Chi-restraints excluded: chain d residue 125 VAL Chi-restraints excluded: chain d residue 191 LEU Chi-restraints excluded: chain e residue 56 VAL Chi-restraints excluded: chain f residue 55 HIS Chi-restraints excluded: chain g residue 6 VAL Chi-restraints excluded: chain g residue 7 ILE Chi-restraints excluded: chain g residue 49 THR Chi-restraints excluded: chain i residue 9 THR Chi-restraints excluded: chain l residue 104 CYS Chi-restraints excluded: chain m residue 73 ILE Chi-restraints excluded: chain n residue 58 SER Chi-restraints excluded: chain q residue 79 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1016 random chunks: chunk 857 optimal weight: 0.9990 chunk 770 optimal weight: 10.0000 chunk 427 optimal weight: 1.9990 chunk 263 optimal weight: 10.0000 chunk 519 optimal weight: 0.4980 chunk 411 optimal weight: 9.9990 chunk 796 optimal weight: 6.9990 chunk 308 optimal weight: 1.9990 chunk 484 optimal weight: 20.0000 chunk 592 optimal weight: 20.0000 chunk 922 optimal weight: 0.8980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 37 ASN C 86 ASN C 115 GLN C 142 HIS C 239 ASN E 41 GLN E 90 GLN F 52 ASN ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 2 GLN H 11 ASN H 43 ASN ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 58 ASN J 80 HIS J 128 ASN J 132 HIS ** K 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 35 HIS ** M 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 3 HIS N 31 HIS ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 20 GLN ** Q 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 59 GLN R 82 HIS S 7 HIS ** S 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 48 GLN U 69 ASN X 6 GLN X 16 ASN X 23 ASN Y 58 ASN Z 9 GLN 0 19 HIS 2 6 GLN ** 4 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 6 HIS b 15 HIS ** b 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 58 ASN b 190 ASN ** c 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 123 GLN c 190 HIS f 55 HIS h 4 GLN h 16 ASN i 50 GLN ** i 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 15 GLN k 22 HIS l 5 ASN l 77 HIS p 18 GLN r 52 GLN r 54 GLN s 43 ASN s 52 HIS s 69 HIS t 52 ASN u 64 ASN Total number of N/Q/H flips: 53 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 158931 Z= 0.148 Angle : 0.638 27.612 238032 Z= 0.326 Chirality : 0.041 2.016 30464 Planarity : 0.005 0.066 12558 Dihedral : 24.009 179.579 80255 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.15 % Favored : 93.67 % Rotamer: Outliers : 3.42 % Allowed : 19.74 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.59 (0.10), residues: 5591 helix: -0.90 (0.11), residues: 1868 sheet: -1.34 (0.15), residues: 1017 loop : -2.48 (0.10), residues: 2706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP g 103 HIS 0.008 0.001 HIS E 165 PHE 0.030 0.001 PHE b 90 TYR 0.020 0.002 TYR r 64 ARG 0.007 0.001 ARG F 148 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11182 Ramachandran restraints generated. 5591 Oldfield, 0 Emsley, 5591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11182 Ramachandran restraints generated. 5591 Oldfield, 0 Emsley, 5591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1656 residues out of total 4655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 1497 time to evaluate : 6.228 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: C 97 LYS cc_start: 0.7638 (mmtt) cc_final: 0.6812 (tptp) REVERT: C 260 ASN cc_start: 0.7867 (t0) cc_final: 0.7619 (m-40) REVERT: C 270 ARG cc_start: 0.7182 (OUTLIER) cc_final: 0.6232 (tmm-80) REVERT: D 81 GLU cc_start: 0.7224 (tm-30) cc_final: 0.6977 (tm-30) REVERT: D 128 ARG cc_start: 0.8144 (mtm-85) cc_final: 0.7680 (mtp85) REVERT: E 1 MET cc_start: 0.6439 (ptm) cc_final: 0.3906 (mmm) REVERT: E 119 ILE cc_start: 0.8507 (mp) cc_final: 0.7953 (mm) REVERT: E 136 GLN cc_start: 0.6605 (tp-100) cc_final: 0.6065 (mm-40) REVERT: E 194 LYS cc_start: 0.8679 (tptt) cc_final: 0.8457 (tppt) REVERT: F 16 LEU cc_start: 0.8229 (mm) cc_final: 0.7961 (mm) REVERT: F 77 PHE cc_start: 0.6666 (m-80) cc_final: 0.6274 (m-80) REVERT: F 153 ASP cc_start: 0.7926 (p0) cc_final: 0.7712 (p0) REVERT: K 44 LYS cc_start: 0.9148 (mmmt) cc_final: 0.8850 (mmtp) REVERT: L 55 MET cc_start: 0.7880 (tpp) cc_final: 0.7513 (tpt) REVERT: M 10 ARG cc_start: 0.7788 (mmm-85) cc_final: 0.7432 (mtm-85) REVERT: M 136 MET cc_start: 0.4076 (ttp) cc_final: 0.3404 (mmt) REVERT: N 78 LYS cc_start: 0.7391 (tttt) cc_final: 0.6783 (tttp) REVERT: R 41 ILE cc_start: 0.8634 (mp) cc_final: 0.8322 (tp) REVERT: V 20 LEU cc_start: 0.7913 (tt) cc_final: 0.7643 (mp) REVERT: W 77 ARG cc_start: 0.7647 (mtm-85) cc_final: 0.7319 (ttm-80) REVERT: Z 12 SER cc_start: 0.8150 (t) cc_final: 0.7761 (p) REVERT: 7 5 MET cc_start: 0.8296 (mtm) cc_final: 0.7953 (mmm) REVERT: b 39 HIS cc_start: 0.5019 (m90) cc_final: 0.4757 (m90) REVERT: b 113 ARG cc_start: 0.7628 (mmm160) cc_final: 0.7237 (mmp-170) REVERT: c 140 ASN cc_start: 0.7476 (t0) cc_final: 0.6935 (m-40) REVERT: d 14 ARG cc_start: 0.7611 (tpp-160) cc_final: 0.7327 (tpp80) REVERT: d 69 GLU cc_start: 0.7254 (tp30) cc_final: 0.6827 (tp30) REVERT: d 72 PHE cc_start: 0.8811 (t80) cc_final: 0.8532 (t80) REVERT: d 74 ASN cc_start: 0.7785 (m110) cc_final: 0.7173 (p0) REVERT: d 165 ARG cc_start: 0.5935 (mtm180) cc_final: 0.5671 (mtt180) REVERT: e 156 LYS cc_start: 0.8527 (mtmt) cc_final: 0.8300 (mttm) REVERT: f 45 ARG cc_start: 0.7539 (ptm-80) cc_final: 0.7190 (ptm-80) REVERT: f 93 LYS cc_start: 0.8165 (mmtm) cc_final: 0.7879 (tmtt) REVERT: g 22 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7976 (pp) REVERT: g 92 ARG cc_start: 0.7023 (mmp80) cc_final: 0.6519 (ptt180) REVERT: g 118 LEU cc_start: 0.7067 (tp) cc_final: 0.6302 (mt) REVERT: j 89 ARG cc_start: 0.7857 (mtp85) cc_final: 0.7141 (ttp80) REVERT: j 92 LEU cc_start: 0.7486 (OUTLIER) cc_final: 0.7156 (pp) REVERT: k 31 ILE cc_start: 0.9330 (mp) cc_final: 0.9086 (mt) REVERT: l 51 LYS cc_start: 0.8034 (mptt) cc_final: 0.7794 (mttp) REVERT: m 54 ASP cc_start: 0.6806 (p0) cc_final: 0.6543 (p0) REVERT: m 86 TYR cc_start: 0.7530 (t80) cc_final: 0.7194 (t80) REVERT: o 72 ARG cc_start: 0.8376 (ttp80) cc_final: 0.8110 (ttp80) REVERT: o 74 ASP cc_start: 0.7211 (t70) cc_final: 0.6967 (t0) REVERT: p 18 GLN cc_start: 0.8170 (OUTLIER) cc_final: 0.7502 (mm-40) REVERT: p 31 ARG cc_start: 0.8223 (ttp80) cc_final: 0.8006 (ttp-170) REVERT: p 35 ARG cc_start: 0.7976 (ptm-80) cc_final: 0.7639 (ptm160) REVERT: p 76 LYS cc_start: 0.7645 (mtmt) cc_final: 0.7325 (mmmt) REVERT: q 12 VAL cc_start: 0.8049 (t) cc_final: 0.7686 (m) REVERT: q 19 LYS cc_start: 0.8587 (ttmm) cc_final: 0.8272 (tttp) REVERT: q 43 LYS cc_start: 0.6985 (mtpt) cc_final: 0.6717 (mtmt) REVERT: r 48 ARG cc_start: 0.8539 (mtt180) cc_final: 0.7331 (mtt90) REVERT: r 50 LYS cc_start: 0.7924 (ptmt) cc_final: 0.7462 (ptmt) REVERT: t 25 ARG cc_start: 0.8426 (ttp-170) cc_final: 0.8204 (ttm110) REVERT: t 31 PHE cc_start: 0.8357 (m-80) cc_final: 0.8146 (m-80) REVERT: t 85 LYS cc_start: 0.7595 (tttt) cc_final: 0.6994 (mmmt) REVERT: u 18 ARG cc_start: 0.6746 (mtp85) cc_final: 0.6467 (mtp85) REVERT: u 45 ARG cc_start: 0.7659 (mtp-110) cc_final: 0.7411 (mtp85) outliers start: 159 outliers final: 101 residues processed: 1569 average time/residue: 1.3644 time to fit residues: 3654.8452 Evaluate side-chains 1418 residues out of total 4655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 1313 time to evaluate : 6.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 264 ASP Chi-restraints excluded: chain C residue 270 ARG Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 38 MET Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain F residue 177 PHE Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 43 GLU Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 128 ASN Chi-restraints excluded: chain L residue 40 SER Chi-restraints excluded: chain L residue 76 GLU Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain O residue 40 ILE Chi-restraints excluded: chain O residue 46 GLU Chi-restraints excluded: chain O residue 83 LEU Chi-restraints excluded: chain O residue 90 VAL Chi-restraints excluded: chain P residue 4 ILE Chi-restraints excluded: chain P residue 14 LYS Chi-restraints excluded: chain Q residue 91 ASP Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 35 ILE Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain T residue 85 VAL Chi-restraints excluded: chain U residue 41 LEU Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain V residue 92 VAL Chi-restraints excluded: chain W residue 15 ASP Chi-restraints excluded: chain W residue 71 VAL Chi-restraints excluded: chain Y residue 57 LEU Chi-restraints excluded: chain Z residue 4 THR Chi-restraints excluded: chain Z residue 35 THR Chi-restraints excluded: chain 0 residue 9 THR Chi-restraints excluded: chain 0 residue 30 VAL Chi-restraints excluded: chain 2 residue 8 SER Chi-restraints excluded: chain 2 residue 44 VAL Chi-restraints excluded: chain 3 residue 28 ASN Chi-restraints excluded: chain 4 residue 11 CYS Chi-restraints excluded: chain 4 residue 14 CYS Chi-restraints excluded: chain 4 residue 24 ARG Chi-restraints excluded: chain b residue 80 VAL Chi-restraints excluded: chain b residue 161 LEU Chi-restraints excluded: chain b residue 183 VAL Chi-restraints excluded: chain c residue 87 LEU Chi-restraints excluded: chain c residue 192 THR Chi-restraints excluded: chain d residue 30 THR Chi-restraints excluded: chain d residue 125 VAL Chi-restraints excluded: chain d residue 191 LEU Chi-restraints excluded: chain e residue 32 SER Chi-restraints excluded: chain e residue 56 VAL Chi-restraints excluded: chain e residue 122 ASN Chi-restraints excluded: chain e residue 130 SER Chi-restraints excluded: chain e residue 134 ILE Chi-restraints excluded: chain f residue 29 ILE Chi-restraints excluded: chain f residue 30 THR Chi-restraints excluded: chain f residue 55 HIS Chi-restraints excluded: chain g residue 6 VAL Chi-restraints excluded: chain g residue 7 ILE Chi-restraints excluded: chain g residue 22 LEU Chi-restraints excluded: chain g residue 49 THR Chi-restraints excluded: chain g residue 84 THR Chi-restraints excluded: chain h residue 106 THR Chi-restraints excluded: chain i residue 48 VAL Chi-restraints excluded: chain i residue 63 LEU Chi-restraints excluded: chain j residue 17 LEU Chi-restraints excluded: chain j residue 36 VAL Chi-restraints excluded: chain j residue 42 LEU Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 80 THR Chi-restraints excluded: chain j residue 92 LEU Chi-restraints excluded: chain j residue 98 VAL Chi-restraints excluded: chain k residue 81 ASN Chi-restraints excluded: chain k residue 116 ILE Chi-restraints excluded: chain l residue 3 THR Chi-restraints excluded: chain l residue 55 VAL Chi-restraints excluded: chain l residue 104 CYS Chi-restraints excluded: chain m residue 9 ILE Chi-restraints excluded: chain m residue 89 LEU Chi-restraints excluded: chain n residue 21 PHE Chi-restraints excluded: chain o residue 66 LEU Chi-restraints excluded: chain p residue 2 VAL Chi-restraints excluded: chain p residue 18 GLN Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain p residue 34 GLU Chi-restraints excluded: chain p residue 53 ASP Chi-restraints excluded: chain q residue 7 THR Chi-restraints excluded: chain q residue 20 SER Chi-restraints excluded: chain q residue 76 VAL Chi-restraints excluded: chain q residue 79 VAL Chi-restraints excluded: chain u residue 36 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1016 random chunks: chunk 512 optimal weight: 5.9990 chunk 286 optimal weight: 10.0000 chunk 767 optimal weight: 10.0000 chunk 628 optimal weight: 10.0000 chunk 254 optimal weight: 10.0000 chunk 924 optimal weight: 9.9990 chunk 998 optimal weight: 1.9990 chunk 823 optimal weight: 20.0000 chunk 916 optimal weight: 0.6980 chunk 315 optimal weight: 10.0000 chunk 741 optimal weight: 20.0000 overall best weight: 5.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 45 ASN C 90 ASN C 117 GLN C 128 ASN ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 GLN E 165 HIS ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 18 GLN ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 128 ASN ** K 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 107 ASN ** P 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 14 HIS ** Q 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 52 GLN Q 59 GLN Q 72 ASN ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 61 ASN T 15 HIS ** U 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 12 ASN ** Y 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 20 HIS ** 2 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 13 ASN ** 4 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 177 ASN c 8 ASN c 123 GLN ** e 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 46 GLN g 142 HIS i 5 GLN j 58 ASN k 15 GLN m 14 HIS p 18 GLN q 45 HIS r 52 GLN t 52 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 158931 Z= 0.353 Angle : 0.758 27.393 238032 Z= 0.380 Chirality : 0.046 2.055 30464 Planarity : 0.006 0.073 12558 Dihedral : 24.006 179.943 80247 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.66 % Favored : 91.18 % Rotamer: Outliers : 6.44 % Allowed : 22.28 % Favored : 71.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.10), residues: 5591 helix: -0.31 (0.12), residues: 1841 sheet: -1.24 (0.16), residues: 1009 loop : -2.32 (0.11), residues: 2741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP g 103 HIS 0.008 0.001 HIS G 45 PHE 0.036 0.002 PHE Z 53 TYR 0.026 0.002 TYR Q 47 ARG 0.008 0.001 ARG W 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11182 Ramachandran restraints generated. 5591 Oldfield, 0 Emsley, 5591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11182 Ramachandran restraints generated. 5591 Oldfield, 0 Emsley, 5591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1635 residues out of total 4655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 300 poor density : 1335 time to evaluate : 6.209 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: C 97 LYS cc_start: 0.7643 (mmtt) cc_final: 0.6814 (tptp) REVERT: C 270 ARG cc_start: 0.7675 (OUTLIER) cc_final: 0.6765 (tmm-80) REVERT: D 184 ARG cc_start: 0.7307 (mtt180) cc_final: 0.7001 (mtt180) REVERT: E 1 MET cc_start: 0.6367 (ptm) cc_final: 0.3810 (mmm) REVERT: E 119 ILE cc_start: 0.8430 (mp) cc_final: 0.7995 (mm) REVERT: F 77 PHE cc_start: 0.6884 (m-80) cc_final: 0.6486 (m-80) REVERT: F 96 MET cc_start: 0.8173 (ttp) cc_final: 0.7949 (tmm) REVERT: H 80 ILE cc_start: 0.3874 (OUTLIER) cc_final: 0.3465 (tp) REVERT: L 18 ARG cc_start: 0.8764 (OUTLIER) cc_final: 0.8518 (mtp85) REVERT: L 55 MET cc_start: 0.7922 (tpp) cc_final: 0.7654 (tpt) REVERT: M 10 ARG cc_start: 0.7881 (mmm-85) cc_final: 0.7487 (mtm-85) REVERT: M 136 MET cc_start: 0.4392 (ttp) cc_final: 0.3756 (mmt) REVERT: S 61 ASN cc_start: 0.7381 (m110) cc_final: 0.6849 (p0) REVERT: W 77 ARG cc_start: 0.7836 (mtm-85) cc_final: 0.7508 (ttm-80) REVERT: X 56 MET cc_start: 0.7836 (tpp) cc_final: 0.7450 (mmm) REVERT: 3 29 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.8128 (tp) REVERT: 4 26 ILE cc_start: 0.8367 (OUTLIER) cc_final: 0.8149 (pp) REVERT: 5 22 MET cc_start: 0.6771 (mpp) cc_final: 0.6494 (mpp) REVERT: 7 5 MET cc_start: 0.8319 (mtm) cc_final: 0.8065 (mmm) REVERT: b 39 HIS cc_start: 0.5113 (m90) cc_final: 0.4876 (m90) REVERT: b 113 ARG cc_start: 0.7763 (mmm160) cc_final: 0.7339 (mmp-170) REVERT: c 34 ASP cc_start: 0.7593 (OUTLIER) cc_final: 0.7046 (t70) REVERT: d 69 GLU cc_start: 0.7347 (tp30) cc_final: 0.6959 (tp30) REVERT: d 165 ARG cc_start: 0.5972 (mtm180) cc_final: 0.5651 (mtt180) REVERT: e 156 LYS cc_start: 0.8582 (mtmt) cc_final: 0.8259 (mttt) REVERT: e 159 LYS cc_start: 0.7123 (mttp) cc_final: 0.6748 (mttp) REVERT: f 75 GLU cc_start: 0.8485 (mm-30) cc_final: 0.8149 (mm-30) REVERT: f 93 LYS cc_start: 0.8154 (mmtm) cc_final: 0.7856 (tmtt) REVERT: g 22 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8138 (pp) REVERT: g 92 ARG cc_start: 0.7077 (mmp80) cc_final: 0.6684 (ptt180) REVERT: g 118 LEU cc_start: 0.6944 (tp) cc_final: 0.6243 (mt) REVERT: g 136 LYS cc_start: 0.8637 (tptm) cc_final: 0.7559 (mtmt) REVERT: h 42 GLU cc_start: 0.8334 (tp30) cc_final: 0.8082 (tp30) REVERT: j 89 ARG cc_start: 0.7852 (mtp85) cc_final: 0.7184 (ttp80) REVERT: j 92 LEU cc_start: 0.7758 (OUTLIER) cc_final: 0.7334 (pp) REVERT: k 31 ILE cc_start: 0.9376 (mp) cc_final: 0.9118 (mt) REVERT: k 111 THR cc_start: 0.6755 (OUTLIER) cc_final: 0.6494 (t) REVERT: l 43 LYS cc_start: 0.8369 (mttp) cc_final: 0.7927 (mtpt) REVERT: p 76 LYS cc_start: 0.7881 (mtmt) cc_final: 0.7368 (mmmt) REVERT: q 12 VAL cc_start: 0.8457 (t) cc_final: 0.8064 (m) REVERT: q 19 LYS cc_start: 0.8569 (ttmm) cc_final: 0.8184 (tttp) REVERT: q 43 LYS cc_start: 0.7225 (mtpt) cc_final: 0.6908 (mtmt) REVERT: r 48 ARG cc_start: 0.8556 (mtt180) cc_final: 0.7346 (mtt90) REVERT: r 50 LYS cc_start: 0.8020 (ptmt) cc_final: 0.7570 (ptmt) REVERT: t 25 ARG cc_start: 0.8498 (ttp-170) cc_final: 0.8201 (ttm110) REVERT: t 85 LYS cc_start: 0.7686 (tttt) cc_final: 0.7159 (mmmt) outliers start: 300 outliers final: 211 residues processed: 1483 average time/residue: 1.2757 time to fit residues: 3263.7113 Evaluate side-chains 1492 residues out of total 4655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 220 poor density : 1272 time to evaluate : 6.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 264 ASP Chi-restraints excluded: chain C residue 270 ARG Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 191 ASP Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 38 MET Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain F residue 177 PHE Chi-restraints excluded: chain G residue 24 ILE Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 110 SER Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 80 ILE Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 43 GLU Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 93 ILE Chi-restraints excluded: chain J residue 128 ASN Chi-restraints excluded: chain J residue 142 ILE Chi-restraints excluded: chain K residue 13 ASN Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 118 LEU Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 40 SER Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 111 ILE Chi-restraints excluded: chain L residue 128 THR Chi-restraints excluded: chain M residue 41 LEU Chi-restraints excluded: chain M residue 91 TYR Chi-restraints excluded: chain M residue 96 ILE Chi-restraints excluded: chain M residue 119 LEU Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain O residue 83 LEU Chi-restraints excluded: chain O residue 90 VAL Chi-restraints excluded: chain P residue 4 ILE Chi-restraints excluded: chain P residue 14 LYS Chi-restraints excluded: chain P residue 27 GLU Chi-restraints excluded: chain P residue 76 THR Chi-restraints excluded: chain Q residue 8 VAL Chi-restraints excluded: chain Q residue 91 ASP Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain R residue 73 LYS Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 35 ILE Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 92 ARG Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain T residue 74 ILE Chi-restraints excluded: chain T residue 85 VAL Chi-restraints excluded: chain U residue 36 VAL Chi-restraints excluded: chain U residue 41 LEU Chi-restraints excluded: chain V residue 17 SER Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain V residue 92 VAL Chi-restraints excluded: chain W residue 15 ASP Chi-restraints excluded: chain W residue 38 VAL Chi-restraints excluded: chain W residue 71 VAL Chi-restraints excluded: chain X residue 71 LEU Chi-restraints excluded: chain Z residue 4 THR Chi-restraints excluded: chain Z residue 10 THR Chi-restraints excluded: chain Z residue 35 THR Chi-restraints excluded: chain 0 residue 9 THR Chi-restraints excluded: chain 0 residue 11 SER Chi-restraints excluded: chain 0 residue 12 LYS Chi-restraints excluded: chain 0 residue 23 THR Chi-restraints excluded: chain 0 residue 30 VAL Chi-restraints excluded: chain 2 residue 8 SER Chi-restraints excluded: chain 2 residue 44 VAL Chi-restraints excluded: chain 3 residue 28 ASN Chi-restraints excluded: chain 3 residue 29 LEU Chi-restraints excluded: chain 3 residue 50 VAL Chi-restraints excluded: chain 4 residue 11 CYS Chi-restraints excluded: chain 4 residue 13 ASN Chi-restraints excluded: chain 4 residue 14 CYS Chi-restraints excluded: chain 4 residue 22 VAL Chi-restraints excluded: chain 4 residue 23 ILE Chi-restraints excluded: chain 4 residue 24 ARG Chi-restraints excluded: chain 4 residue 26 ILE Chi-restraints excluded: chain 5 residue 10 GLU Chi-restraints excluded: chain 7 residue 2 THR Chi-restraints excluded: chain b residue 41 ILE Chi-restraints excluded: chain b residue 80 VAL Chi-restraints excluded: chain b residue 161 LEU Chi-restraints excluded: chain b residue 163 VAL Chi-restraints excluded: chain b residue 179 LEU Chi-restraints excluded: chain b residue 183 VAL Chi-restraints excluded: chain b residue 187 VAL Chi-restraints excluded: chain b residue 211 THR Chi-restraints excluded: chain c residue 10 ILE Chi-restraints excluded: chain c residue 31 ASP Chi-restraints excluded: chain c residue 34 ASP Chi-restraints excluded: chain c residue 76 VAL Chi-restraints excluded: chain c residue 87 LEU Chi-restraints excluded: chain c residue 97 VAL Chi-restraints excluded: chain c residue 119 SER Chi-restraints excluded: chain c residue 149 ILE Chi-restraints excluded: chain c residue 192 THR Chi-restraints excluded: chain c residue 195 VAL Chi-restraints excluded: chain d residue 30 THR Chi-restraints excluded: chain d residue 53 VAL Chi-restraints excluded: chain d residue 125 VAL Chi-restraints excluded: chain d residue 191 LEU Chi-restraints excluded: chain d residue 195 ILE Chi-restraints excluded: chain e residue 19 ASN Chi-restraints excluded: chain e residue 32 SER Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 56 VAL Chi-restraints excluded: chain e residue 65 GLU Chi-restraints excluded: chain e residue 76 LEU Chi-restraints excluded: chain e residue 105 ILE Chi-restraints excluded: chain e residue 122 ASN Chi-restraints excluded: chain e residue 134 ILE Chi-restraints excluded: chain e residue 144 LEU Chi-restraints excluded: chain e residue 153 VAL Chi-restraints excluded: chain f residue 26 THR Chi-restraints excluded: chain f residue 29 ILE Chi-restraints excluded: chain f residue 30 THR Chi-restraints excluded: chain f residue 55 HIS Chi-restraints excluded: chain g residue 6 VAL Chi-restraints excluded: chain g residue 7 ILE Chi-restraints excluded: chain g residue 22 LEU Chi-restraints excluded: chain g residue 41 SER Chi-restraints excluded: chain g residue 45 SER Chi-restraints excluded: chain g residue 49 THR Chi-restraints excluded: chain g residue 79 ARG Chi-restraints excluded: chain g residue 84 THR Chi-restraints excluded: chain g residue 94 VAL Chi-restraints excluded: chain g residue 124 LEU Chi-restraints excluded: chain h residue 40 LEU Chi-restraints excluded: chain h residue 75 ILE Chi-restraints excluded: chain h residue 112 THR Chi-restraints excluded: chain i residue 9 THR Chi-restraints excluded: chain i residue 47 VAL Chi-restraints excluded: chain i residue 48 VAL Chi-restraints excluded: chain i residue 72 ILE Chi-restraints excluded: chain i residue 116 VAL Chi-restraints excluded: chain j residue 36 VAL Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 53 ILE Chi-restraints excluded: chain j residue 74 VAL Chi-restraints excluded: chain j residue 80 THR Chi-restraints excluded: chain j residue 92 LEU Chi-restraints excluded: chain j residue 98 VAL Chi-restraints excluded: chain k residue 50 SER Chi-restraints excluded: chain k residue 58 SER Chi-restraints excluded: chain k residue 81 ASN Chi-restraints excluded: chain k residue 111 THR Chi-restraints excluded: chain k residue 116 ILE Chi-restraints excluded: chain l residue 38 TYR Chi-restraints excluded: chain l residue 55 VAL Chi-restraints excluded: chain l residue 104 CYS Chi-restraints excluded: chain m residue 9 ILE Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 64 VAL Chi-restraints excluded: chain m residue 68 ASP Chi-restraints excluded: chain m residue 69 LEU Chi-restraints excluded: chain m residue 82 ASP Chi-restraints excluded: chain m residue 89 LEU Chi-restraints excluded: chain n residue 21 PHE Chi-restraints excluded: chain n residue 79 LEU Chi-restraints excluded: chain n residue 96 LEU Chi-restraints excluded: chain o residue 3 LEU Chi-restraints excluded: chain o residue 82 ILE Chi-restraints excluded: chain p residue 3 THR Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain p residue 20 VAL Chi-restraints excluded: chain p residue 53 ASP Chi-restraints excluded: chain p residue 66 THR Chi-restraints excluded: chain q residue 7 THR Chi-restraints excluded: chain q residue 20 SER Chi-restraints excluded: chain q residue 22 VAL Chi-restraints excluded: chain q residue 29 VAL 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 40 VAL Chi-restraints excluded: chain r residue 65 LEU Chi-restraints excluded: chain s residue 27 ASP Chi-restraints excluded: chain s residue 79 THR Chi-restraints excluded: chain u residue 36 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1016 random chunks: chunk 913 optimal weight: 9.9990 chunk 694 optimal weight: 10.0000 chunk 479 optimal weight: 2.9990 chunk 102 optimal weight: 10.0000 chunk 441 optimal weight: 6.9990 chunk 620 optimal weight: 10.0000 chunk 927 optimal weight: 1.9990 chunk 982 optimal weight: 1.9990 chunk 484 optimal weight: 0.9990 chunk 879 optimal weight: 2.9990 chunk 264 optimal weight: 10.0000 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 117 GLN ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 58 ASN K 90 ASN ** K 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 66 ASN P 77 HIS ** Q 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 59 GLN ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 12 ASN X 16 ASN 2 6 GLN 2 16 HIS 4 37 GLN ** b 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 123 GLN ** e 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 16 ASN i 50 GLN ** i 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 15 GLN l 112 GLN q 50 ASN r 52 GLN r 54 GLN s 57 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 158931 Z= 0.170 Angle : 0.616 26.423 238032 Z= 0.312 Chirality : 0.040 2.051 30464 Planarity : 0.004 0.063 12558 Dihedral : 23.839 179.548 80246 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.62 % Favored : 93.26 % Rotamer: Outliers : 5.67 % Allowed : 24.81 % Favored : 69.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.11), residues: 5591 helix: 0.17 (0.12), residues: 1869 sheet: -1.08 (0.16), residues: 1006 loop : -2.09 (0.11), residues: 2716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP g 103 HIS 0.008 0.001 HIS r 74 PHE 0.030 0.002 PHE Z 53 TYR 0.020 0.002 TYR r 64 ARG 0.011 0.000 ARG J 96 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11182 Ramachandran restraints generated. 5591 Oldfield, 0 Emsley, 5591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11182 Ramachandran restraints generated. 5591 Oldfield, 0 Emsley, 5591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1619 residues out of total 4655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 264 poor density : 1355 time to evaluate : 6.203 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: C 97 LYS cc_start: 0.7513 (mmtt) cc_final: 0.6806 (tptp) REVERT: C 153 GLN cc_start: 0.8195 (OUTLIER) cc_final: 0.7094 (mm-40) REVERT: C 260 ASN cc_start: 0.7815 (t0) cc_final: 0.7535 (m-40) REVERT: C 270 ARG cc_start: 0.7572 (OUTLIER) cc_final: 0.6720 (tmm-80) REVERT: D 128 ARG cc_start: 0.8119 (mtm-85) cc_final: 0.7618 (mtp85) REVERT: D 184 ARG cc_start: 0.7358 (mtt180) cc_final: 0.7043 (mtt180) REVERT: E 1 MET cc_start: 0.6351 (ptm) cc_final: 0.3934 (mmm) REVERT: E 119 ILE cc_start: 0.8362 (mp) cc_final: 0.7938 (mm) REVERT: E 136 GLN cc_start: 0.6504 (tp-100) cc_final: 0.6198 (mm110) REVERT: E 183 PHE cc_start: 0.7385 (m-80) cc_final: 0.6747 (m-80) REVERT: F 16 LEU cc_start: 0.8328 (mm) cc_final: 0.8003 (mm) REVERT: F 77 PHE cc_start: 0.6655 (m-80) cc_final: 0.6270 (m-80) REVERT: F 96 MET cc_start: 0.8090 (ttp) cc_final: 0.7836 (tmm) REVERT: L 2 ARG cc_start: 0.7997 (OUTLIER) cc_final: 0.7748 (mmp80) REVERT: L 55 MET cc_start: 0.7844 (tpp) cc_final: 0.7354 (tpt) REVERT: M 136 MET cc_start: 0.4325 (ttp) cc_final: 0.3753 (mmt) REVERT: N 82 GLU cc_start: 0.7435 (mp0) cc_final: 0.6881 (mp0) REVERT: N 117 ASP cc_start: 0.7609 (m-30) cc_final: 0.7090 (m-30) REVERT: O 4 LYS cc_start: 0.7330 (tttm) cc_final: 0.7099 (tttm) REVERT: Q 70 ARG cc_start: 0.7718 (mmt90) cc_final: 0.7345 (mtt180) REVERT: R 18 GLN cc_start: 0.7244 (pp30) cc_final: 0.6818 (pp30) REVERT: V 20 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7799 (tp) REVERT: 5 22 MET cc_start: 0.6860 (mpp) cc_final: 0.6560 (mpp) REVERT: 7 5 MET cc_start: 0.8271 (mtm) cc_final: 0.7976 (mmm) REVERT: b 113 ARG cc_start: 0.7682 (mmm160) cc_final: 0.7309 (mmp-170) REVERT: c 121 THR cc_start: 0.7894 (m) cc_final: 0.7638 (p) REVERT: c 181 ASP cc_start: 0.7667 (t0) cc_final: 0.7450 (t70) REVERT: d 69 GLU cc_start: 0.7315 (tp30) cc_final: 0.6886 (tp30) REVERT: d 98 LEU cc_start: 0.7913 (tp) cc_final: 0.7650 (tp) REVERT: d 165 ARG cc_start: 0.5749 (mtm180) cc_final: 0.5517 (mtt180) REVERT: e 13 GLU cc_start: 0.7696 (pm20) cc_final: 0.7022 (mp0) REVERT: e 82 GLN cc_start: 0.7187 (mm110) cc_final: 0.6708 (mm-40) REVERT: e 156 LYS cc_start: 0.8586 (mtmt) cc_final: 0.8290 (mttm) REVERT: f 1 MET cc_start: 0.6374 (mmp) cc_final: 0.6034 (mmp) REVERT: f 93 LYS cc_start: 0.8258 (mmtm) cc_final: 0.7895 (tmtt) REVERT: g 22 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8147 (pp) REVERT: g 118 LEU cc_start: 0.7168 (tp) cc_final: 0.6334 (mt) REVERT: g 136 LYS cc_start: 0.8640 (tptm) cc_final: 0.7569 (mtmt) REVERT: g 142 HIS cc_start: 0.7594 (m90) cc_final: 0.7356 (m-70) REVERT: h 42 GLU cc_start: 0.8333 (tp30) cc_final: 0.8031 (tp30) REVERT: j 89 ARG cc_start: 0.7828 (mtp85) cc_final: 0.7070 (ttp80) REVERT: j 92 LEU cc_start: 0.7645 (OUTLIER) cc_final: 0.7343 (pp) REVERT: k 31 ILE cc_start: 0.9341 (mp) cc_final: 0.9097 (mt) REVERT: k 111 THR cc_start: 0.6650 (OUTLIER) cc_final: 0.6355 (t) REVERT: m 73 ILE cc_start: 0.9062 (OUTLIER) cc_final: 0.8740 (mp) REVERT: m 86 TYR cc_start: 0.7573 (t80) cc_final: 0.6883 (t80) REVERT: o 71 LYS cc_start: 0.9316 (ttpp) cc_final: 0.8965 (tttt) REVERT: o 74 ASP cc_start: 0.7351 (t70) cc_final: 0.7020 (t0) REVERT: p 34 GLU cc_start: 0.6955 (tt0) cc_final: 0.6724 (tt0) REVERT: p 76 LYS cc_start: 0.7646 (mtmt) cc_final: 0.7345 (mmmt) REVERT: q 12 VAL cc_start: 0.8375 (t) cc_final: 0.7978 (m) REVERT: q 18 GLU cc_start: 0.8284 (tm-30) cc_final: 0.7533 (tm-30) REVERT: q 19 LYS cc_start: 0.8665 (ttmm) cc_final: 0.8342 (mtpt) REVERT: q 43 LYS cc_start: 0.7032 (mtpt) cc_final: 0.6789 (mtmt) REVERT: r 48 ARG cc_start: 0.8455 (mtt180) cc_final: 0.7308 (mtt90) REVERT: r 50 LYS cc_start: 0.7778 (ptmt) cc_final: 0.7356 (ptmt) REVERT: r 57 ARG cc_start: 0.7439 (ttm170) cc_final: 0.6947 (ttm170) REVERT: t 18 ARG cc_start: 0.8147 (ttp80) cc_final: 0.7830 (ttp80) REVERT: t 25 ARG cc_start: 0.8479 (ttp-170) cc_final: 0.8226 (ttm110) REVERT: t 85 LYS cc_start: 0.7628 (tttt) cc_final: 0.7064 (mmmt) outliers start: 264 outliers final: 169 residues processed: 1489 average time/residue: 1.2787 time to fit residues: 3294.8529 Evaluate side-chains 1447 residues out of total 4655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 1270 time to evaluate : 6.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 45 ASN Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 153 GLN Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 264 ASP Chi-restraints excluded: chain C residue 270 ARG Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 32 ASN Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain E residue 94 GLN Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 110 SER Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 43 GLU Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 93 ILE Chi-restraints excluded: chain J residue 142 ILE Chi-restraints excluded: chain K residue 118 LEU Chi-restraints excluded: chain L residue 2 ARG Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 111 ILE Chi-restraints excluded: chain M residue 119 LEU Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain O residue 46 GLU Chi-restraints excluded: chain O residue 69 ASP Chi-restraints excluded: chain O residue 90 VAL Chi-restraints excluded: chain P residue 4 ILE Chi-restraints excluded: chain P residue 27 GLU Chi-restraints excluded: chain P residue 76 THR Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 66 HIS Chi-restraints excluded: chain R residue 73 LYS Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 35 ILE Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 92 ARG Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain T residue 74 ILE Chi-restraints excluded: chain U residue 36 VAL Chi-restraints excluded: chain U residue 41 LEU Chi-restraints excluded: chain V residue 20 LEU Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain V residue 89 ILE Chi-restraints excluded: chain W residue 15 ASP Chi-restraints excluded: chain W residue 71 VAL Chi-restraints excluded: chain X residue 5 CYS Chi-restraints excluded: chain X residue 25 THR Chi-restraints excluded: chain Y residue 40 SER Chi-restraints excluded: chain Y residue 53 VAL Chi-restraints excluded: chain Y residue 57 LEU Chi-restraints excluded: chain Z residue 4 THR Chi-restraints excluded: chain Z residue 10 THR Chi-restraints excluded: chain 0 residue 9 THR Chi-restraints excluded: chain 0 residue 12 LYS Chi-restraints excluded: chain 0 residue 30 VAL Chi-restraints excluded: chain 1 residue 17 THR Chi-restraints excluded: chain 2 residue 8 SER Chi-restraints excluded: chain 2 residue 44 VAL Chi-restraints excluded: chain 3 residue 28 ASN Chi-restraints excluded: chain 3 residue 33 LEU Chi-restraints excluded: chain 3 residue 50 VAL Chi-restraints excluded: chain 4 residue 11 CYS Chi-restraints excluded: chain 4 residue 14 CYS Chi-restraints excluded: chain 4 residue 24 ARG Chi-restraints excluded: chain b residue 9 MET Chi-restraints excluded: chain b residue 80 VAL Chi-restraints excluded: chain b residue 161 LEU Chi-restraints excluded: chain b residue 163 VAL Chi-restraints excluded: chain b residue 188 ASP Chi-restraints excluded: chain b residue 211 THR Chi-restraints excluded: chain c residue 87 LEU Chi-restraints excluded: chain c residue 97 VAL Chi-restraints excluded: chain c residue 119 SER Chi-restraints excluded: chain c residue 157 LEU Chi-restraints excluded: chain c residue 192 THR Chi-restraints excluded: chain d residue 28 ILE Chi-restraints excluded: chain d residue 30 THR Chi-restraints excluded: chain d residue 53 VAL Chi-restraints excluded: chain d residue 99 ASP Chi-restraints excluded: chain d residue 125 VAL Chi-restraints excluded: chain d residue 160 GLU Chi-restraints excluded: chain d residue 191 LEU Chi-restraints excluded: chain d residue 195 ILE Chi-restraints excluded: chain e residue 56 VAL Chi-restraints excluded: chain e residue 65 GLU Chi-restraints excluded: chain e residue 122 ASN Chi-restraints excluded: chain e residue 130 SER Chi-restraints excluded: chain e residue 134 ILE Chi-restraints excluded: chain e residue 141 ILE Chi-restraints excluded: chain e residue 153 VAL Chi-restraints excluded: chain f residue 30 THR Chi-restraints excluded: chain f residue 55 HIS Chi-restraints excluded: chain f residue 92 THR Chi-restraints excluded: chain g residue 6 VAL Chi-restraints excluded: chain g residue 7 ILE Chi-restraints excluded: chain g residue 22 LEU Chi-restraints excluded: chain g residue 41 SER Chi-restraints excluded: chain g residue 84 THR Chi-restraints excluded: chain h residue 61 LEU Chi-restraints excluded: chain h residue 75 ILE Chi-restraints excluded: chain h residue 112 THR Chi-restraints excluded: chain i residue 48 VAL Chi-restraints excluded: chain i residue 63 LEU Chi-restraints excluded: chain i residue 72 ILE Chi-restraints excluded: chain i residue 90 TYR Chi-restraints excluded: chain j residue 17 LEU Chi-restraints excluded: chain j residue 36 VAL Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 69 THR Chi-restraints excluded: chain j residue 74 VAL Chi-restraints excluded: chain j residue 80 THR Chi-restraints excluded: chain j residue 92 LEU Chi-restraints excluded: chain k residue 50 SER Chi-restraints excluded: chain k residue 81 ASN Chi-restraints excluded: chain k residue 111 THR Chi-restraints excluded: chain k residue 116 ILE Chi-restraints excluded: chain l residue 3 THR Chi-restraints excluded: chain l residue 25 GLU Chi-restraints excluded: chain l residue 55 VAL Chi-restraints excluded: chain l residue 80 ILE Chi-restraints excluded: chain m residue 9 ILE Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 69 LEU Chi-restraints excluded: chain m residue 73 ILE Chi-restraints excluded: chain m residue 89 LEU Chi-restraints excluded: chain n residue 21 PHE Chi-restraints excluded: chain n residue 79 LEU Chi-restraints excluded: chain n residue 96 LEU Chi-restraints excluded: chain o residue 14 GLU Chi-restraints excluded: chain o residue 66 LEU Chi-restraints excluded: chain o residue 82 ILE Chi-restraints excluded: chain p residue 3 THR Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain p residue 20 VAL Chi-restraints excluded: chain p residue 53 ASP Chi-restraints excluded: chain p residue 66 THR Chi-restraints excluded: chain q residue 7 THR Chi-restraints excluded: chain q residue 22 VAL Chi-restraints excluded: chain q residue 29 VAL Chi-restraints excluded: chain q residue 38 ILE Chi-restraints excluded: chain q residue 61 ILE 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 65 LEU Chi-restraints excluded: chain s residue 60 VAL Chi-restraints excluded: chain s residue 79 THR Chi-restraints excluded: chain u residue 36 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1016 random chunks: chunk 817 optimal weight: 7.9990 chunk 557 optimal weight: 6.9990 chunk 14 optimal weight: 20.0000 chunk 731 optimal weight: 10.0000 chunk 405 optimal weight: 8.9990 chunk 838 optimal weight: 10.0000 chunk 678 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 501 optimal weight: 7.9990 chunk 881 optimal weight: 5.9990 chunk 247 optimal weight: 10.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 128 ASN ** K 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 59 GLN ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 60 HIS S 61 ASN W 12 ASN ** W 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 20 ASN Y 31 GLN ** 4 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 177 ASN c 8 ASN c 123 GLN g 148 ASN i 31 ASN j 58 ASN k 15 GLN ** q 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 50 ASN r 52 GLN r 54 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.072 158931 Z= 0.453 Angle : 0.824 27.222 238032 Z= 0.408 Chirality : 0.048 2.007 30464 Planarity : 0.006 0.065 12558 Dihedral : 23.986 179.427 80244 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.64 % Favored : 90.22 % Rotamer: Outliers : 7.18 % Allowed : 25.35 % Favored : 67.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -1.94 (0.11), residues: 5591 helix: -0.10 (0.12), residues: 1851 sheet: -1.19 (0.16), residues: 1026 loop : -2.19 (0.11), residues: 2714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP g 103 HIS 0.009 0.002 HIS G 45 PHE 0.041 0.003 PHE Z 53 TYR 0.028 0.003 TYR g 44 ARG 0.011 0.001 ARG W 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11182 Ramachandran restraints generated. 5591 Oldfield, 0 Emsley, 5591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11182 Ramachandran restraints generated. 5591 Oldfield, 0 Emsley, 5591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1631 residues out of total 4655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 334 poor density : 1297 time to evaluate : 6.188 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: C 97 LYS cc_start: 0.7645 (mmtt) cc_final: 0.6884 (tptp) REVERT: C 153 GLN cc_start: 0.8436 (OUTLIER) cc_final: 0.7323 (mm-40) REVERT: C 270 ARG cc_start: 0.7750 (OUTLIER) cc_final: 0.6956 (tmm-80) REVERT: D 103 ASP cc_start: 0.7051 (OUTLIER) cc_final: 0.6759 (m-30) REVERT: D 184 ARG cc_start: 0.7427 (mtt180) cc_final: 0.7143 (mtt180) REVERT: E 1 MET cc_start: 0.6373 (ptm) cc_final: 0.3840 (mmm) REVERT: E 119 ILE cc_start: 0.8407 (mp) cc_final: 0.8017 (mm) REVERT: F 69 LYS cc_start: 0.8632 (mmtt) cc_final: 0.7986 (ptpt) REVERT: F 77 PHE cc_start: 0.6834 (m-80) cc_final: 0.6472 (m-80) REVERT: F 96 MET cc_start: 0.8195 (ttp) cc_final: 0.7857 (ttp) REVERT: H 80 ILE cc_start: 0.4364 (OUTLIER) cc_final: 0.3973 (tp) REVERT: J 31 GLU cc_start: 0.7689 (tp30) cc_final: 0.7344 (tp30) REVERT: J 131 ASN cc_start: 0.7690 (p0) cc_final: 0.7263 (p0) REVERT: K 32 TYR cc_start: 0.6257 (OUTLIER) cc_final: 0.5920 (p90) REVERT: K 54 LYS cc_start: 0.8332 (tttm) cc_final: 0.8095 (tttm) REVERT: M 100 LYS cc_start: 0.9017 (OUTLIER) cc_final: 0.8737 (ttmt) REVERT: M 136 MET cc_start: 0.4599 (ttp) cc_final: 0.3769 (mmt) REVERT: N 82 GLU cc_start: 0.7604 (mp0) cc_final: 0.7372 (mp0) REVERT: O 8 ILE cc_start: 0.8151 (mm) cc_final: 0.7704 (tp) REVERT: S 15 GLN cc_start: 0.8181 (tt0) cc_final: 0.7700 (tt0) REVERT: T 33 LYS cc_start: 0.7310 (OUTLIER) cc_final: 0.7074 (tptt) REVERT: 0 17 ARG cc_start: 0.8658 (mtt180) cc_final: 0.8366 (mtt180) REVERT: 1 45 GLN cc_start: 0.6539 (mp10) cc_final: 0.6307 (tp-100) REVERT: 5 22 MET cc_start: 0.6980 (mpp) cc_final: 0.6655 (mpp) REVERT: b 113 ARG cc_start: 0.7845 (mmm160) cc_final: 0.7431 (mmp-170) REVERT: c 34 ASP cc_start: 0.7639 (OUTLIER) cc_final: 0.7017 (t70) REVERT: d 69 GLU cc_start: 0.7408 (tp30) cc_final: 0.7004 (tp30) REVERT: d 165 ARG cc_start: 0.5934 (mtm180) cc_final: 0.5549 (mtt180) REVERT: e 156 LYS cc_start: 0.8618 (mtmt) cc_final: 0.8271 (mttt) REVERT: e 159 LYS cc_start: 0.7197 (mttp) cc_final: 0.6783 (mttp) REVERT: f 38 ARG cc_start: 0.7488 (mtm180) cc_final: 0.6718 (mtm180) REVERT: f 93 LYS cc_start: 0.8351 (mmtm) cc_final: 0.7943 (tmtt) REVERT: g 22 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8226 (pp) REVERT: g 118 LEU cc_start: 0.7327 (tp) cc_final: 0.6454 (mt) REVERT: g 136 LYS cc_start: 0.8685 (tptm) cc_final: 0.7602 (mtmt) REVERT: g 142 HIS cc_start: 0.7661 (m90) cc_final: 0.7267 (m-70) REVERT: h 42 GLU cc_start: 0.8425 (tp30) cc_final: 0.8208 (tp30) REVERT: i 38 TYR cc_start: 0.6865 (t80) cc_final: 0.6638 (t80) REVERT: j 92 LEU cc_start: 0.7799 (OUTLIER) cc_final: 0.7379 (pp) REVERT: k 31 ILE cc_start: 0.9385 (mp) cc_final: 0.9140 (mt) REVERT: k 111 THR cc_start: 0.6585 (OUTLIER) cc_final: 0.6315 (t) REVERT: l 43 LYS cc_start: 0.8377 (mmtm) cc_final: 0.7998 (mtpt) REVERT: m 73 ILE cc_start: 0.9095 (OUTLIER) cc_final: 0.8786 (mp) REVERT: m 83 LEU cc_start: 0.8541 (tp) cc_final: 0.8341 (tp) REVERT: m 86 TYR cc_start: 0.7657 (t80) cc_final: 0.6991 (t80) REVERT: n 43 ASN cc_start: 0.7146 (m-40) cc_final: 0.6831 (m-40) REVERT: p 76 LYS cc_start: 0.7813 (mtmt) cc_final: 0.7386 (mmmt) REVERT: q 12 VAL cc_start: 0.8567 (t) cc_final: 0.8145 (m) REVERT: q 17 MET cc_start: 0.7298 (ptt) cc_final: 0.6180 (ptp) REVERT: q 18 GLU cc_start: 0.8459 (tm-30) cc_final: 0.8056 (tp30) REVERT: q 19 LYS cc_start: 0.8702 (ttmm) cc_final: 0.8341 (mttm) REVERT: r 48 ARG cc_start: 0.8479 (mtt180) cc_final: 0.7189 (mtt90) REVERT: r 50 LYS cc_start: 0.8042 (ptmt) cc_final: 0.7613 (ptmt) REVERT: s 66 MET cc_start: 0.8480 (mpp) cc_final: 0.7885 (mpp) REVERT: t 18 ARG cc_start: 0.8367 (ttp80) cc_final: 0.8050 (ttp80) REVERT: t 25 ARG cc_start: 0.8553 (ttp-170) cc_final: 0.8199 (ttm110) REVERT: u 42 THR cc_start: 0.7732 (OUTLIER) cc_final: 0.7389 (t) outliers start: 334 outliers final: 254 residues processed: 1479 average time/residue: 1.3488 time to fit residues: 3490.4908 Evaluate side-chains 1536 residues out of total 4655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 267 poor density : 1269 time to evaluate : 6.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 153 GLN Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 264 ASP Chi-restraints excluded: chain C residue 270 ARG Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 32 ASN Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 94 GLN Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 191 ASP Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 177 PHE Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 24 ILE Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 110 SER Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 125 CYS Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 80 ILE Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 43 GLU Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 93 ILE Chi-restraints excluded: chain J residue 101 ILE Chi-restraints excluded: chain J residue 128 ASN Chi-restraints excluded: chain J residue 142 ILE Chi-restraints excluded: chain K residue 13 ASN Chi-restraints excluded: chain K residue 32 TYR Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 90 ASN Chi-restraints excluded: chain K residue 118 LEU Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 82 LEU Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 111 ILE Chi-restraints excluded: chain L residue 128 THR Chi-restraints excluded: chain M residue 41 LEU Chi-restraints excluded: chain M residue 91 TYR Chi-restraints excluded: chain M residue 96 ILE Chi-restraints excluded: chain M residue 100 LYS Chi-restraints excluded: chain M residue 115 GLU Chi-restraints excluded: chain M residue 119 LEU Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain O residue 5 SER Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 46 GLU Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain O residue 69 ASP Chi-restraints excluded: chain O residue 83 LEU Chi-restraints excluded: chain O residue 90 VAL Chi-restraints excluded: chain P residue 4 ILE Chi-restraints excluded: chain P residue 27 GLU Chi-restraints excluded: chain P residue 48 ILE Chi-restraints excluded: chain P residue 76 THR Chi-restraints excluded: chain P residue 85 SER Chi-restraints excluded: chain Q residue 8 VAL Chi-restraints excluded: chain Q residue 39 VAL Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 66 HIS Chi-restraints excluded: chain R residue 73 LYS Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 33 LEU Chi-restraints excluded: chain S residue 35 ILE Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 85 ILE Chi-restraints excluded: chain S residue 101 SER Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain T residue 33 LYS Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain T residue 53 VAL Chi-restraints excluded: chain T residue 74 ILE Chi-restraints excluded: chain T residue 85 VAL Chi-restraints excluded: chain U residue 36 VAL Chi-restraints excluded: chain U residue 41 LEU Chi-restraints excluded: chain V residue 43 ASP Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain V residue 89 ILE Chi-restraints excluded: chain W residue 15 ASP Chi-restraints excluded: chain W residue 21 LEU Chi-restraints excluded: chain W residue 71 VAL Chi-restraints excluded: chain X residue 5 CYS Chi-restraints excluded: chain X residue 43 GLU Chi-restraints excluded: chain X residue 71 LEU Chi-restraints excluded: chain Y residue 8 GLU Chi-restraints excluded: chain Y residue 40 SER Chi-restraints excluded: chain Y residue 50 VAL Chi-restraints excluded: chain Z residue 4 THR Chi-restraints excluded: chain Z residue 5 ILE Chi-restraints excluded: chain Z residue 10 THR Chi-restraints excluded: chain Z residue 35 THR Chi-restraints excluded: chain 0 residue 9 THR Chi-restraints excluded: chain 0 residue 11 SER Chi-restraints excluded: chain 0 residue 23 THR Chi-restraints excluded: chain 0 residue 30 VAL Chi-restraints excluded: chain 2 residue 8 SER Chi-restraints excluded: chain 2 residue 15 SER Chi-restraints excluded: chain 2 residue 44 VAL Chi-restraints excluded: chain 3 residue 28 ASN Chi-restraints excluded: chain 3 residue 50 VAL Chi-restraints excluded: chain 4 residue 11 CYS Chi-restraints excluded: chain 4 residue 13 ASN Chi-restraints excluded: chain 4 residue 14 CYS Chi-restraints excluded: chain 4 residue 22 VAL Chi-restraints excluded: chain 4 residue 24 ARG Chi-restraints excluded: chain 5 residue 10 GLU Chi-restraints excluded: chain 5 residue 12 ILE Chi-restraints excluded: chain b residue 41 ILE Chi-restraints excluded: chain b residue 161 LEU Chi-restraints excluded: chain b residue 163 VAL Chi-restraints excluded: chain b residue 179 LEU Chi-restraints excluded: chain b residue 183 VAL Chi-restraints excluded: chain b residue 188 ASP Chi-restraints excluded: chain b residue 211 THR Chi-restraints excluded: chain b residue 221 VAL Chi-restraints excluded: chain c residue 10 ILE Chi-restraints excluded: chain c residue 34 ASP Chi-restraints excluded: chain c residue 76 VAL Chi-restraints excluded: chain c residue 87 LEU Chi-restraints excluded: chain c residue 97 VAL Chi-restraints excluded: chain c residue 119 SER Chi-restraints excluded: chain c residue 121 THR Chi-restraints excluded: chain c residue 149 ILE Chi-restraints excluded: chain c residue 157 LEU Chi-restraints excluded: chain c residue 183 ASP Chi-restraints excluded: chain c residue 192 THR Chi-restraints excluded: chain d residue 30 THR Chi-restraints excluded: chain d residue 53 VAL Chi-restraints excluded: chain d residue 125 VAL Chi-restraints excluded: chain d residue 191 LEU Chi-restraints excluded: chain d residue 195 ILE Chi-restraints excluded: chain e residue 19 ASN Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 36 LEU Chi-restraints excluded: chain e residue 56 VAL Chi-restraints excluded: chain e residue 65 GLU Chi-restraints excluded: chain e residue 105 ILE Chi-restraints excluded: chain e residue 122 ASN Chi-restraints excluded: chain e residue 134 ILE Chi-restraints excluded: chain e residue 144 LEU Chi-restraints excluded: chain e residue 153 VAL Chi-restraints excluded: chain f residue 23 GLU Chi-restraints excluded: chain f residue 29 ILE Chi-restraints excluded: chain f residue 30 THR Chi-restraints excluded: chain f residue 55 HIS Chi-restraints excluded: chain g residue 6 VAL Chi-restraints excluded: chain g residue 7 ILE Chi-restraints excluded: chain g residue 22 LEU Chi-restraints excluded: chain g residue 41 SER Chi-restraints excluded: chain g residue 45 SER Chi-restraints excluded: chain g residue 49 THR Chi-restraints excluded: chain g residue 72 THR Chi-restraints excluded: chain g residue 94 VAL Chi-restraints excluded: chain g residue 124 LEU Chi-restraints excluded: chain h residue 51 VAL Chi-restraints excluded: chain h residue 75 ILE Chi-restraints excluded: chain h residue 112 THR Chi-restraints excluded: chain i residue 48 VAL Chi-restraints excluded: chain i residue 63 LEU Chi-restraints excluded: chain i residue 72 ILE Chi-restraints excluded: chain i residue 90 TYR Chi-restraints excluded: chain i residue 116 VAL Chi-restraints excluded: chain j residue 36 VAL Chi-restraints excluded: chain j residue 42 LEU Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 69 THR Chi-restraints excluded: chain j residue 74 VAL Chi-restraints excluded: chain j residue 80 THR Chi-restraints excluded: chain j residue 92 LEU Chi-restraints excluded: chain k residue 50 SER Chi-restraints excluded: chain k residue 58 SER Chi-restraints excluded: chain k residue 74 VAL Chi-restraints excluded: chain k residue 81 ASN Chi-restraints excluded: chain k residue 111 THR Chi-restraints excluded: chain k residue 116 ILE Chi-restraints excluded: chain l residue 3 THR Chi-restraints excluded: chain l residue 25 GLU Chi-restraints excluded: chain l residue 38 TYR Chi-restraints excluded: chain l residue 55 VAL Chi-restraints excluded: chain l residue 64 THR Chi-restraints excluded: chain m residue 9 ILE Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 65 VAL Chi-restraints excluded: chain m residue 69 LEU Chi-restraints excluded: chain m residue 73 ILE Chi-restraints excluded: chain m residue 82 ASP Chi-restraints excluded: chain m residue 89 LEU Chi-restraints excluded: chain n residue 21 PHE Chi-restraints excluded: chain n residue 34 VAL Chi-restraints excluded: chain n residue 58 SER Chi-restraints excluded: chain n residue 79 LEU Chi-restraints excluded: chain n residue 96 LEU Chi-restraints excluded: chain o residue 3 LEU Chi-restraints excluded: chain o residue 10 LYS Chi-restraints excluded: chain o residue 82 ILE Chi-restraints excluded: chain p residue 3 THR Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain p residue 20 VAL Chi-restraints excluded: chain p residue 52 LEU Chi-restraints excluded: chain p residue 53 ASP Chi-restraints excluded: chain p residue 66 THR Chi-restraints excluded: chain q residue 7 THR Chi-restraints excluded: chain q residue 22 VAL Chi-restraints excluded: chain q residue 29 VAL Chi-restraints excluded: chain q residue 38 ILE Chi-restraints excluded: chain q residue 61 ILE 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 40 VAL Chi-restraints excluded: chain r residue 65 LEU Chi-restraints excluded: chain r residue 71 THR Chi-restraints excluded: chain s residue 27 ASP Chi-restraints excluded: chain s residue 47 LEU Chi-restraints excluded: chain s residue 60 VAL Chi-restraints excluded: chain t residue 27 MET Chi-restraints excluded: chain u residue 36 GLU Chi-restraints excluded: chain u residue 42 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1016 random chunks: chunk 330 optimal weight: 7.9990 chunk 884 optimal weight: 8.9990 chunk 194 optimal weight: 8.9990 chunk 576 optimal weight: 1.9990 chunk 242 optimal weight: 8.9990 chunk 983 optimal weight: 0.9980 chunk 816 optimal weight: 2.9990 chunk 455 optimal weight: 10.0000 chunk 81 optimal weight: 4.9990 chunk 325 optimal weight: 0.7980 chunk 516 optimal weight: 1.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 117 GLN ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 128 ASN ** K 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 66 ASN ** Q 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 59 GLN ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 24 ASN V 49 ASN W 46 HIS X 16 ASN ** 4 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 123 GLN d 54 GLN d 74 ASN ** e 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 16 ASN ** i 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 96 HIS ** q 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 50 ASN r 52 GLN r 54 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 158931 Z= 0.157 Angle : 0.620 26.584 238032 Z= 0.314 Chirality : 0.040 2.048 30464 Planarity : 0.004 0.062 12558 Dihedral : 23.824 179.665 80244 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.90 % Favored : 92.99 % Rotamer: Outliers : 5.48 % Allowed : 27.82 % Favored : 66.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.11), residues: 5591 helix: 0.34 (0.12), residues: 1871 sheet: -1.01 (0.16), residues: 1002 loop : -2.03 (0.11), residues: 2718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP g 103 HIS 0.008 0.001 HIS r 74 PHE 0.037 0.002 PHE Z 53 TYR 0.032 0.002 TYR V 57 ARG 0.009 0.000 ARG W 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11182 Ramachandran restraints generated. 5591 Oldfield, 0 Emsley, 5591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11182 Ramachandran restraints generated. 5591 Oldfield, 0 Emsley, 5591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1588 residues out of total 4655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 255 poor density : 1333 time to evaluate : 6.216 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: C 97 LYS cc_start: 0.7550 (mmtt) cc_final: 0.6826 (tptp) REVERT: C 153 GLN cc_start: 0.8144 (OUTLIER) cc_final: 0.7091 (mm-40) REVERT: C 260 ASN cc_start: 0.7876 (OUTLIER) cc_final: 0.7529 (m-40) REVERT: C 270 ARG cc_start: 0.7692 (OUTLIER) cc_final: 0.6940 (tmm-80) REVERT: D 103 ASP cc_start: 0.6891 (OUTLIER) cc_final: 0.6672 (m-30) REVERT: D 184 ARG cc_start: 0.7446 (mtt180) cc_final: 0.7226 (mtt180) REVERT: E 1 MET cc_start: 0.6368 (ptm) cc_final: 0.3853 (mmm) REVERT: E 119 ILE cc_start: 0.8279 (mp) cc_final: 0.7919 (mm) REVERT: E 136 GLN cc_start: 0.6476 (tp-100) cc_final: 0.6151 (mm-40) REVERT: F 16 LEU cc_start: 0.8403 (mm) cc_final: 0.7951 (mm) REVERT: F 57 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.7821 (mp) REVERT: F 77 PHE cc_start: 0.6723 (m-80) cc_final: 0.6382 (m-80) REVERT: F 96 MET cc_start: 0.8065 (ttp) cc_final: 0.7765 (ttp) REVERT: G 55 ARG cc_start: 0.6769 (ttm170) cc_final: 0.5953 (ttm170) REVERT: L 1 MET cc_start: 0.6930 (OUTLIER) cc_final: 0.5698 (mmm) REVERT: M 130 PHE cc_start: 0.8135 (t80) cc_final: 0.7812 (t80) REVERT: M 136 MET cc_start: 0.4452 (ttp) cc_final: 0.3592 (mmt) REVERT: N 117 ASP cc_start: 0.7579 (m-30) cc_final: 0.7146 (m-30) REVERT: O 4 LYS cc_start: 0.7234 (tttm) cc_final: 0.6988 (tttm) REVERT: O 97 PHE cc_start: 0.8190 (m-80) cc_final: 0.7878 (m-80) REVERT: O 104 GLN cc_start: 0.8485 (tp40) cc_final: 0.8099 (tp40) REVERT: R 18 GLN cc_start: 0.7349 (pp30) cc_final: 0.6944 (pp30) REVERT: S 61 ASN cc_start: 0.7258 (m110) cc_final: 0.6769 (p0) REVERT: U 88 GLU cc_start: 0.6801 (OUTLIER) cc_final: 0.6593 (tm-30) REVERT: V 25 LYS cc_start: 0.8012 (OUTLIER) cc_final: 0.7748 (ptpt) REVERT: V 73 LYS cc_start: 0.7803 (mmtt) cc_final: 0.7322 (mtmt) REVERT: W 11 ARG cc_start: 0.6972 (ptt-90) cc_final: 0.6754 (ptp90) REVERT: Z 56 LYS cc_start: 0.8446 (tttt) cc_final: 0.8177 (pttp) REVERT: 0 17 ARG cc_start: 0.8531 (mtt180) cc_final: 0.8288 (mtt180) REVERT: 1 45 GLN cc_start: 0.6328 (mp10) cc_final: 0.6108 (tp-100) REVERT: 5 22 MET cc_start: 0.6884 (mpp) cc_final: 0.6565 (mpp) REVERT: b 50 PHE cc_start: 0.7697 (OUTLIER) cc_final: 0.7203 (m-80) REVERT: b 113 ARG cc_start: 0.7754 (mmm160) cc_final: 0.7366 (mmp-170) REVERT: c 121 THR cc_start: 0.7714 (OUTLIER) cc_final: 0.7513 (p) REVERT: c 125 GLU cc_start: 0.7023 (mt-10) cc_final: 0.6737 (mt-10) REVERT: c 206 GLU cc_start: 0.7354 (tt0) cc_final: 0.6880 (tt0) REVERT: d 69 GLU cc_start: 0.7290 (tp30) cc_final: 0.6863 (tp30) REVERT: d 74 ASN cc_start: 0.7834 (m-40) cc_final: 0.7069 (p0) REVERT: d 98 LEU cc_start: 0.7846 (tp) cc_final: 0.7608 (tp) REVERT: e 13 GLU cc_start: 0.7725 (pm20) cc_final: 0.7091 (mp0) REVERT: e 156 LYS cc_start: 0.8574 (mtmt) cc_final: 0.8297 (mttt) REVERT: f 38 ARG cc_start: 0.7302 (mtm180) cc_final: 0.6774 (mtm180) REVERT: f 93 LYS cc_start: 0.8338 (mmtm) cc_final: 0.7938 (tmtt) REVERT: g 22 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.8090 (pp) REVERT: g 118 LEU cc_start: 0.7211 (tp) cc_final: 0.6482 (mt) REVERT: g 136 LYS cc_start: 0.8690 (tptm) cc_final: 0.7567 (mtmt) REVERT: g 142 HIS cc_start: 0.7681 (m90) cc_final: 0.7173 (m-70) REVERT: h 42 GLU cc_start: 0.8245 (tp30) cc_final: 0.7898 (tp30) REVERT: j 59 LYS cc_start: 0.8871 (OUTLIER) cc_final: 0.8591 (tptt) REVERT: j 89 ARG cc_start: 0.7743 (mtp85) cc_final: 0.6811 (ttp80) REVERT: j 92 LEU cc_start: 0.7525 (OUTLIER) cc_final: 0.7189 (pp) REVERT: k 31 ILE cc_start: 0.9336 (mp) cc_final: 0.9097 (mt) REVERT: k 111 THR cc_start: 0.6669 (OUTLIER) cc_final: 0.6379 (t) REVERT: l 43 LYS cc_start: 0.8165 (mmtm) cc_final: 0.7823 (mtpt) REVERT: l 70 GLU cc_start: 0.7166 (mt-10) cc_final: 0.6830 (mt-10) REVERT: m 69 LEU cc_start: 0.8817 (tp) cc_final: 0.8536 (tp) REVERT: m 73 ILE cc_start: 0.9039 (OUTLIER) cc_final: 0.8725 (mp) REVERT: m 86 TYR cc_start: 0.7573 (t80) cc_final: 0.6936 (t80) REVERT: o 63 ARG cc_start: 0.8476 (OUTLIER) cc_final: 0.8252 (ttp-170) REVERT: o 71 LYS cc_start: 0.8948 (tttm) cc_final: 0.8711 (tttt) REVERT: p 76 LYS cc_start: 0.7637 (mtmt) cc_final: 0.7324 (mmmt) REVERT: q 12 VAL cc_start: 0.8422 (t) cc_final: 0.8029 (m) REVERT: q 17 MET cc_start: 0.6923 (ptt) cc_final: 0.6199 (ptp) REVERT: q 18 GLU cc_start: 0.8314 (tm-30) cc_final: 0.8039 (tp30) REVERT: q 19 LYS cc_start: 0.8688 (ttmm) cc_final: 0.8309 (tttp) REVERT: r 48 ARG cc_start: 0.8388 (mtt180) cc_final: 0.7169 (mtt90) REVERT: r 50 LYS cc_start: 0.7782 (ptmt) cc_final: 0.7323 (ptmt) REVERT: r 57 ARG cc_start: 0.7400 (ttm170) cc_final: 0.7052 (ttm170) REVERT: s 66 MET cc_start: 0.8287 (mpp) cc_final: 0.7795 (mpp) REVERT: t 18 ARG cc_start: 0.8057 (ttp80) cc_final: 0.7849 (ttp80) REVERT: t 25 ARG cc_start: 0.8453 (ttp-170) cc_final: 0.8226 (ttm110) REVERT: t 85 LYS cc_start: 0.7611 (tttt) cc_final: 0.7163 (mmmt) REVERT: u 42 THR cc_start: 0.7519 (OUTLIER) cc_final: 0.7163 (t) outliers start: 255 outliers final: 191 residues processed: 1468 average time/residue: 1.2792 time to fit residues: 3255.1337 Evaluate side-chains 1485 residues out of total 4655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 208 poor density : 1277 time to evaluate : 5.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 4 VAL Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 153 GLN Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 260 ASN Chi-restraints excluded: chain C residue 264 ASP Chi-restraints excluded: chain C residue 270 ARG Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 32 ASN Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain E residue 73 ILE Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 191 ASP Chi-restraints excluded: chain E residue 195 GLN Chi-restraints excluded: chain F residue 24 SER Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 177 PHE Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 110 SER Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 43 GLU Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 129 GLU Chi-restraints excluded: chain J residue 142 ILE Chi-restraints excluded: chain K residue 118 LEU Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 76 GLU Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 111 ILE Chi-restraints excluded: chain L residue 126 ARG Chi-restraints excluded: chain L residue 128 THR Chi-restraints excluded: chain M residue 96 ILE Chi-restraints excluded: chain M residue 119 LEU Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 46 GLU Chi-restraints excluded: chain O residue 83 LEU Chi-restraints excluded: chain O residue 90 VAL Chi-restraints excluded: chain P residue 4 ILE Chi-restraints excluded: chain P residue 27 GLU Chi-restraints excluded: chain P residue 76 THR Chi-restraints excluded: chain Q residue 8 VAL Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 66 HIS Chi-restraints excluded: chain R residue 73 LYS Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 35 ILE Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain T residue 74 ILE Chi-restraints excluded: chain T residue 85 VAL Chi-restraints excluded: chain U residue 36 VAL Chi-restraints excluded: chain U residue 41 LEU Chi-restraints excluded: chain U residue 88 GLU Chi-restraints excluded: chain V residue 25 LYS Chi-restraints excluded: chain V residue 43 ASP Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain V residue 89 ILE Chi-restraints excluded: chain W residue 15 ASP Chi-restraints excluded: chain W residue 21 LEU Chi-restraints excluded: chain W residue 71 VAL Chi-restraints excluded: chain X residue 71 LEU Chi-restraints excluded: chain Y residue 8 GLU Chi-restraints excluded: chain Y residue 57 LEU Chi-restraints excluded: chain Z residue 4 THR Chi-restraints excluded: chain Z residue 10 THR Chi-restraints excluded: chain 0 residue 9 THR Chi-restraints excluded: chain 0 residue 12 LYS Chi-restraints excluded: chain 0 residue 30 VAL Chi-restraints excluded: chain 1 residue 17 THR Chi-restraints excluded: chain 2 residue 8 SER Chi-restraints excluded: chain 2 residue 44 VAL Chi-restraints excluded: chain 3 residue 28 ASN Chi-restraints excluded: chain 4 residue 10 LEU Chi-restraints excluded: chain 4 residue 11 CYS Chi-restraints excluded: chain 4 residue 14 CYS Chi-restraints excluded: chain 4 residue 22 VAL Chi-restraints excluded: chain 5 residue 10 GLU Chi-restraints excluded: chain b residue 50 PHE Chi-restraints excluded: chain b residue 80 VAL Chi-restraints excluded: chain b residue 153 ASP Chi-restraints excluded: chain b residue 161 LEU Chi-restraints excluded: chain b residue 163 VAL Chi-restraints excluded: chain b residue 183 VAL Chi-restraints excluded: chain b residue 187 VAL Chi-restraints excluded: chain b residue 188 ASP Chi-restraints excluded: chain b residue 211 THR Chi-restraints excluded: chain b residue 221 VAL Chi-restraints excluded: chain c residue 10 ILE Chi-restraints excluded: chain c residue 77 ILE Chi-restraints excluded: chain c residue 87 LEU Chi-restraints excluded: chain c residue 97 VAL Chi-restraints excluded: chain c residue 121 THR Chi-restraints excluded: chain c residue 157 LEU Chi-restraints excluded: chain c residue 183 ASP Chi-restraints excluded: chain c residue 192 THR Chi-restraints excluded: chain d residue 20 PHE Chi-restraints excluded: chain d residue 30 THR Chi-restraints excluded: chain d residue 53 VAL Chi-restraints excluded: chain d residue 67 VAL Chi-restraints excluded: chain d residue 99 ASP Chi-restraints excluded: chain d residue 102 VAL Chi-restraints excluded: chain d residue 125 VAL Chi-restraints excluded: chain d residue 191 LEU Chi-restraints excluded: chain d residue 195 ILE Chi-restraints excluded: chain d residue 200 ILE Chi-restraints excluded: chain e residue 56 VAL Chi-restraints excluded: chain e residue 65 GLU Chi-restraints excluded: chain e residue 105 ILE Chi-restraints excluded: chain e residue 122 ASN Chi-restraints excluded: chain e residue 134 ILE Chi-restraints excluded: chain e residue 141 ILE Chi-restraints excluded: chain e residue 144 LEU Chi-restraints excluded: chain f residue 23 GLU Chi-restraints excluded: chain f residue 29 ILE Chi-restraints excluded: chain f residue 30 THR Chi-restraints excluded: chain f residue 55 HIS Chi-restraints excluded: chain f residue 92 THR Chi-restraints excluded: chain g residue 6 VAL Chi-restraints excluded: chain g residue 7 ILE Chi-restraints excluded: chain g residue 22 LEU Chi-restraints excluded: chain g residue 41 SER Chi-restraints excluded: chain g residue 45 SER Chi-restraints excluded: chain g residue 49 THR Chi-restraints excluded: chain g residue 84 THR Chi-restraints excluded: chain g residue 126 ASP Chi-restraints excluded: chain h residue 75 ILE Chi-restraints excluded: chain h residue 112 THR Chi-restraints excluded: chain i residue 48 VAL Chi-restraints excluded: chain i residue 63 LEU Chi-restraints excluded: chain i residue 72 ILE Chi-restraints excluded: chain i residue 90 TYR Chi-restraints excluded: chain j residue 36 VAL Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 59 LYS Chi-restraints excluded: chain j residue 69 THR Chi-restraints excluded: chain j residue 74 VAL Chi-restraints excluded: chain j residue 80 THR Chi-restraints excluded: chain j residue 92 LEU Chi-restraints excluded: chain k residue 50 SER Chi-restraints excluded: chain k residue 81 ASN Chi-restraints excluded: chain k residue 82 LEU Chi-restraints excluded: chain k residue 111 THR Chi-restraints excluded: chain k residue 116 ILE Chi-restraints excluded: chain l residue 3 THR Chi-restraints excluded: chain l residue 25 GLU Chi-restraints excluded: chain l residue 55 VAL Chi-restraints excluded: chain l residue 64 THR Chi-restraints excluded: chain l residue 80 ILE Chi-restraints excluded: chain m residue 9 ILE Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 65 VAL Chi-restraints excluded: chain m residue 73 ILE Chi-restraints excluded: chain m residue 89 LEU Chi-restraints excluded: chain n residue 21 PHE Chi-restraints excluded: chain n residue 34 VAL Chi-restraints excluded: chain n residue 79 LEU Chi-restraints excluded: chain n residue 96 LEU Chi-restraints excluded: chain o residue 10 LYS Chi-restraints excluded: chain o residue 63 ARG Chi-restraints excluded: chain o residue 66 LEU Chi-restraints excluded: chain o residue 82 ILE Chi-restraints excluded: chain p residue 3 THR Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain p residue 53 ASP Chi-restraints excluded: chain q residue 7 THR Chi-restraints excluded: chain q residue 22 VAL Chi-restraints excluded: chain q residue 29 VAL Chi-restraints excluded: chain q residue 38 ILE Chi-restraints excluded: chain q residue 61 ILE 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 s residue 60 VAL Chi-restraints excluded: chain u residue 36 GLU Chi-restraints excluded: chain u residue 42 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1016 random chunks: chunk 947 optimal weight: 4.9990 chunk 110 optimal weight: 20.0000 chunk 560 optimal weight: 7.9990 chunk 717 optimal weight: 10.0000 chunk 556 optimal weight: 1.9990 chunk 827 optimal weight: 6.9990 chunk 548 optimal weight: 9.9990 chunk 979 optimal weight: 0.0870 chunk 612 optimal weight: 7.9990 chunk 597 optimal weight: 0.5980 chunk 452 optimal weight: 1.9990 overall best weight: 1.9364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 128 ASN ** K 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 66 ASN ** Q 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 49 ASN Y 20 ASN ** 2 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 177 ASN d 54 GLN ** e 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 16 ASN ** i 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 50 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 158931 Z= 0.159 Angle : 0.600 26.366 238032 Z= 0.301 Chirality : 0.039 2.062 30464 Planarity : 0.004 0.065 12558 Dihedral : 23.747 179.714 80244 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.85 % Favored : 92.06 % Rotamer: Outliers : 5.56 % Allowed : 28.23 % Favored : 66.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.11), residues: 5591 helix: 0.57 (0.12), residues: 1874 sheet: -0.93 (0.16), residues: 1005 loop : -1.94 (0.11), residues: 2712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP g 103 HIS 0.009 0.001 HIS r 74 PHE 0.038 0.002 PHE Z 53 TYR 0.039 0.002 TYR V 57 ARG 0.009 0.000 ARG W 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11182 Ramachandran restraints generated. 5591 Oldfield, 0 Emsley, 5591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11182 Ramachandran restraints generated. 5591 Oldfield, 0 Emsley, 5591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1577 residues out of total 4655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 259 poor density : 1318 time to evaluate : 6.221 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: C 97 LYS cc_start: 0.7605 (mmtt) cc_final: 0.7101 (tptt) REVERT: C 153 GLN cc_start: 0.8108 (OUTLIER) cc_final: 0.7000 (mm-40) REVERT: C 213 TRP cc_start: 0.8367 (p90) cc_final: 0.8099 (p90) REVERT: C 260 ASN cc_start: 0.7818 (OUTLIER) cc_final: 0.7602 (m-40) REVERT: C 270 ARG cc_start: 0.7667 (OUTLIER) cc_final: 0.6909 (tmm-80) REVERT: E 1 MET cc_start: 0.6387 (ptm) cc_final: 0.3921 (mmm) REVERT: E 41 GLN cc_start: 0.8444 (tt0) cc_final: 0.8176 (tt0) REVERT: E 119 ILE cc_start: 0.8236 (mp) cc_final: 0.7885 (mm) REVERT: E 136 GLN cc_start: 0.6450 (tp-100) cc_final: 0.6157 (mm-40) REVERT: F 69 LYS cc_start: 0.8529 (mmtt) cc_final: 0.7938 (ptpt) REVERT: F 77 PHE cc_start: 0.6747 (m-80) cc_final: 0.6356 (m-80) REVERT: F 96 MET cc_start: 0.7952 (ttp) cc_final: 0.7647 (ttp) REVERT: G 55 ARG cc_start: 0.6647 (ttm170) cc_final: 0.5831 (ttm170) REVERT: G 83 PHE cc_start: 0.6971 (m-10) cc_final: 0.6754 (m-80) REVERT: L 1 MET cc_start: 0.6989 (OUTLIER) cc_final: 0.5718 (mmm) REVERT: L 95 LEU cc_start: 0.8529 (tp) cc_final: 0.8174 (mt) REVERT: M 130 PHE cc_start: 0.8041 (t80) cc_final: 0.7701 (t80) REVERT: M 136 MET cc_start: 0.4370 (ttp) cc_final: 0.3466 (mmt) REVERT: N 82 GLU cc_start: 0.7543 (mp0) cc_final: 0.6961 (mp0) REVERT: R 1 MET cc_start: 0.6359 (tmm) cc_final: 0.6047 (tmm) REVERT: R 16 GLU cc_start: 0.7867 (mp0) cc_final: 0.7470 (mp0) REVERT: R 18 GLN cc_start: 0.7323 (pp30) cc_final: 0.7018 (pp30) REVERT: R 41 ILE cc_start: 0.8711 (mp) cc_final: 0.8482 (tp) REVERT: U 88 GLU cc_start: 0.6922 (OUTLIER) cc_final: 0.6718 (tm-30) REVERT: V 73 LYS cc_start: 0.7773 (mmtt) cc_final: 0.7349 (mtmt) REVERT: X 38 PHE cc_start: 0.8467 (m-80) cc_final: 0.8005 (m-80) REVERT: X 40 VAL cc_start: 0.7983 (t) cc_final: 0.7465 (m) REVERT: 0 17 ARG cc_start: 0.8532 (mtt180) cc_final: 0.8290 (mtt180) REVERT: 1 45 GLN cc_start: 0.6375 (mp10) cc_final: 0.6111 (tp-100) REVERT: 5 22 MET cc_start: 0.6890 (mpp) cc_final: 0.6618 (mpp) REVERT: b 30 PHE cc_start: 0.7800 (m-80) cc_final: 0.7590 (m-10) REVERT: b 113 ARG cc_start: 0.7743 (mmm160) cc_final: 0.7345 (mmp-170) REVERT: c 121 THR cc_start: 0.7840 (OUTLIER) cc_final: 0.7618 (p) REVERT: c 206 GLU cc_start: 0.7347 (tt0) cc_final: 0.6887 (tt0) REVERT: d 69 GLU cc_start: 0.7192 (tp30) cc_final: 0.6765 (tp30) REVERT: d 98 LEU cc_start: 0.7810 (tp) cc_final: 0.7542 (tp) REVERT: e 13 GLU cc_start: 0.7547 (pm20) cc_final: 0.7203 (mp0) REVERT: e 156 LYS cc_start: 0.8620 (mtmt) cc_final: 0.8296 (mttm) REVERT: f 38 ARG cc_start: 0.7246 (mtm180) cc_final: 0.6719 (mtm180) REVERT: f 39 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7931 (mt) REVERT: f 75 GLU cc_start: 0.8371 (mm-30) cc_final: 0.8170 (tp30) REVERT: f 93 LYS cc_start: 0.8221 (mmtm) cc_final: 0.7857 (tmtt) REVERT: g 118 LEU cc_start: 0.7205 (tp) cc_final: 0.6470 (mt) REVERT: g 136 LYS cc_start: 0.8704 (tptm) cc_final: 0.7613 (mtmt) REVERT: h 42 GLU cc_start: 0.8228 (tp30) cc_final: 0.7915 (tp30) REVERT: h 84 ARG cc_start: 0.8544 (mmm-85) cc_final: 0.8181 (mmm160) REVERT: i 68 LYS cc_start: 0.8052 (mmmt) cc_final: 0.7836 (mmtt) REVERT: j 59 LYS cc_start: 0.8877 (OUTLIER) cc_final: 0.8622 (tptt) REVERT: j 89 ARG cc_start: 0.7860 (mtp85) cc_final: 0.6998 (ttp80) REVERT: j 92 LEU cc_start: 0.7488 (OUTLIER) cc_final: 0.7204 (pp) REVERT: k 31 ILE cc_start: 0.9309 (mp) cc_final: 0.9096 (mt) REVERT: k 70 CYS cc_start: 0.8096 (OUTLIER) cc_final: 0.7583 (t) REVERT: k 87 LYS cc_start: 0.7447 (ttpt) cc_final: 0.7246 (ttpt) REVERT: k 111 THR cc_start: 0.6714 (OUTLIER) cc_final: 0.6456 (t) REVERT: l 70 GLU cc_start: 0.7311 (mt-10) cc_final: 0.6942 (mt-10) REVERT: l 112 GLN cc_start: 0.8718 (pm20) cc_final: 0.8368 (pm20) REVERT: m 69 LEU cc_start: 0.8811 (tp) cc_final: 0.8525 (tp) REVERT: m 73 ILE cc_start: 0.9051 (OUTLIER) cc_final: 0.8738 (mp) REVERT: m 86 TYR cc_start: 0.7605 (t80) cc_final: 0.6971 (t80) REVERT: p 76 LYS cc_start: 0.7603 (mtmt) cc_final: 0.7315 (mmmt) REVERT: q 12 VAL cc_start: 0.8387 (t) cc_final: 0.8000 (m) REVERT: q 19 LYS cc_start: 0.8497 (ttmm) cc_final: 0.8118 (tttp) REVERT: r 48 ARG cc_start: 0.8347 (mtt180) cc_final: 0.7178 (mtt90) REVERT: r 50 LYS cc_start: 0.7770 (ptmt) cc_final: 0.7329 (ptmt) REVERT: r 57 ARG cc_start: 0.7387 (ttm170) cc_final: 0.7025 (ttm170) REVERT: t 25 ARG cc_start: 0.8449 (ttp-170) cc_final: 0.8134 (ttp-110) REVERT: t 85 LYS cc_start: 0.7579 (tttt) cc_final: 0.7142 (mmmt) REVERT: u 42 THR cc_start: 0.7597 (OUTLIER) cc_final: 0.7235 (t) outliers start: 259 outliers final: 196 residues processed: 1460 average time/residue: 1.3866 time to fit residues: 3539.7688 Evaluate side-chains 1480 residues out of total 4655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 209 poor density : 1271 time to evaluate : 6.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 4 VAL Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 153 GLN Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 260 ASN Chi-restraints excluded: chain C residue 264 ASP Chi-restraints excluded: chain C residue 270 ARG Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 32 ASN Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain E residue 73 ILE Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 191 ASP Chi-restraints excluded: chain E residue 195 GLN Chi-restraints excluded: chain F residue 24 SER Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 110 SER Chi-restraints excluded: chain G residue 141 ILE Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 43 GLU Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 93 ILE Chi-restraints excluded: chain J residue 128 ASN Chi-restraints excluded: chain J residue 142 ILE Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 118 LEU Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 111 ILE Chi-restraints excluded: chain L residue 126 ARG Chi-restraints excluded: chain L residue 128 THR Chi-restraints excluded: chain M residue 96 ILE Chi-restraints excluded: chain M residue 119 LEU Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain O residue 69 ASP Chi-restraints excluded: chain O residue 83 LEU Chi-restraints excluded: chain O residue 90 VAL Chi-restraints excluded: chain P residue 4 ILE Chi-restraints excluded: chain P residue 26 VAL Chi-restraints excluded: chain P residue 76 THR Chi-restraints excluded: chain Q residue 8 VAL Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 66 HIS Chi-restraints excluded: chain R residue 73 LYS Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 35 ILE Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain T residue 15 HIS Chi-restraints excluded: chain T residue 74 ILE Chi-restraints excluded: chain T residue 85 VAL Chi-restraints excluded: chain U residue 36 VAL Chi-restraints excluded: chain U residue 41 LEU Chi-restraints excluded: chain U residue 88 GLU Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain V residue 89 ILE Chi-restraints excluded: chain W residue 15 ASP Chi-restraints excluded: chain W residue 21 LEU Chi-restraints excluded: chain W residue 71 VAL Chi-restraints excluded: chain X residue 43 GLU Chi-restraints excluded: chain X residue 71 LEU Chi-restraints excluded: chain Y residue 8 GLU Chi-restraints excluded: chain Z residue 4 THR Chi-restraints excluded: chain Z residue 10 THR Chi-restraints excluded: chain 0 residue 9 THR Chi-restraints excluded: chain 0 residue 12 LYS Chi-restraints excluded: chain 0 residue 30 VAL Chi-restraints excluded: chain 1 residue 17 THR Chi-restraints excluded: chain 2 residue 44 VAL Chi-restraints excluded: chain 3 residue 28 ASN Chi-restraints excluded: chain 3 residue 50 VAL Chi-restraints excluded: chain 4 residue 11 CYS Chi-restraints excluded: chain 4 residue 14 CYS Chi-restraints excluded: chain 4 residue 22 VAL Chi-restraints excluded: chain 5 residue 10 GLU Chi-restraints excluded: chain b residue 41 ILE Chi-restraints excluded: chain b residue 80 VAL Chi-restraints excluded: chain b residue 153 ASP Chi-restraints excluded: chain b residue 161 LEU Chi-restraints excluded: chain b residue 163 VAL Chi-restraints excluded: chain b residue 183 VAL Chi-restraints excluded: chain b residue 187 VAL Chi-restraints excluded: chain b residue 188 ASP Chi-restraints excluded: chain b residue 211 THR Chi-restraints excluded: chain b residue 221 VAL Chi-restraints excluded: chain c residue 10 ILE Chi-restraints excluded: chain c residue 76 VAL Chi-restraints excluded: chain c residue 97 VAL Chi-restraints excluded: chain c residue 121 THR Chi-restraints excluded: chain c residue 157 LEU Chi-restraints excluded: chain c residue 183 ASP Chi-restraints excluded: chain c residue 192 THR Chi-restraints excluded: chain c residue 195 VAL Chi-restraints excluded: chain d residue 5 LEU Chi-restraints excluded: chain d residue 30 THR Chi-restraints excluded: chain d residue 53 VAL Chi-restraints excluded: chain d residue 67 VAL Chi-restraints excluded: chain d residue 102 VAL Chi-restraints excluded: chain d residue 138 SER Chi-restraints excluded: chain d residue 169 THR Chi-restraints excluded: chain d residue 191 LEU Chi-restraints excluded: chain d residue 195 ILE Chi-restraints excluded: chain d residue 200 ILE Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 36 LEU Chi-restraints excluded: chain e residue 56 VAL Chi-restraints excluded: chain e residue 65 GLU Chi-restraints excluded: chain e residue 122 ASN Chi-restraints excluded: chain e residue 134 ILE Chi-restraints excluded: chain e residue 141 ILE Chi-restraints excluded: chain e residue 144 LEU Chi-restraints excluded: chain f residue 23 GLU Chi-restraints excluded: chain f residue 30 THR Chi-restraints excluded: chain f residue 33 GLU Chi-restraints excluded: chain f residue 39 LEU Chi-restraints excluded: chain f residue 55 HIS Chi-restraints excluded: chain f residue 78 PHE Chi-restraints excluded: chain f residue 92 THR Chi-restraints excluded: chain g residue 6 VAL Chi-restraints excluded: chain g residue 7 ILE Chi-restraints excluded: chain g residue 41 SER Chi-restraints excluded: chain g residue 84 THR Chi-restraints excluded: chain g residue 126 ASP Chi-restraints excluded: chain h residue 63 LEU Chi-restraints excluded: chain h residue 75 ILE Chi-restraints excluded: chain h residue 112 THR Chi-restraints excluded: chain i residue 48 VAL Chi-restraints excluded: chain i residue 63 LEU Chi-restraints excluded: chain i residue 72 ILE Chi-restraints excluded: chain i residue 90 TYR Chi-restraints excluded: chain j residue 36 VAL Chi-restraints excluded: chain j residue 42 LEU Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 59 LYS Chi-restraints excluded: chain j residue 69 THR Chi-restraints excluded: chain j residue 80 THR Chi-restraints excluded: chain j residue 92 LEU Chi-restraints excluded: chain k residue 58 SER Chi-restraints excluded: chain k residue 70 CYS Chi-restraints excluded: chain k residue 81 ASN Chi-restraints excluded: chain k residue 82 LEU Chi-restraints excluded: chain k residue 111 THR Chi-restraints excluded: chain k residue 116 ILE Chi-restraints excluded: chain l residue 3 THR Chi-restraints excluded: chain l residue 25 GLU Chi-restraints excluded: chain l residue 52 VAL Chi-restraints excluded: chain l residue 55 VAL Chi-restraints excluded: chain l residue 64 THR Chi-restraints excluded: chain l residue 80 ILE Chi-restraints excluded: chain m residue 9 ILE Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 65 VAL Chi-restraints excluded: chain m residue 73 ILE Chi-restraints excluded: chain m residue 89 LEU Chi-restraints excluded: chain n residue 21 PHE Chi-restraints excluded: chain n residue 34 VAL Chi-restraints excluded: chain n residue 79 LEU Chi-restraints excluded: chain n residue 96 LEU Chi-restraints excluded: chain o residue 3 LEU Chi-restraints excluded: chain o residue 10 LYS Chi-restraints excluded: chain o residue 82 ILE Chi-restraints excluded: chain p residue 3 THR Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain p residue 53 ASP Chi-restraints excluded: chain q residue 7 THR Chi-restraints excluded: chain q residue 22 VAL Chi-restraints excluded: chain q residue 29 VAL Chi-restraints excluded: chain q residue 38 ILE Chi-restraints excluded: chain q residue 61 ILE 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 s residue 60 VAL Chi-restraints excluded: chain u residue 36 GLU Chi-restraints excluded: chain u residue 42 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1016 random chunks: chunk 605 optimal weight: 8.9990 chunk 391 optimal weight: 3.9990 chunk 584 optimal weight: 9.9990 chunk 294 optimal weight: 10.0000 chunk 192 optimal weight: 10.0000 chunk 189 optimal weight: 10.0000 chunk 622 optimal weight: 20.0000 chunk 667 optimal weight: 20.0000 chunk 484 optimal weight: 8.9990 chunk 91 optimal weight: 10.0000 chunk 769 optimal weight: 20.0000 overall best weight: 8.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 10 GLN P 66 ASN ** Q 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 59 GLN ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 43 ASN ** 2 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 54 GLN ** f 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 15 GLN ** k 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 96 HIS ** o 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 50 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.090 158931 Z= 0.495 Angle : 0.875 27.569 238032 Z= 0.432 Chirality : 0.050 2.005 30464 Planarity : 0.006 0.076 12558 Dihedral : 24.009 179.658 80243 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 15.98 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.28 % Favored : 89.59 % Rotamer: Outliers : 6.57 % Allowed : 28.08 % Favored : 65.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -1.86 (0.11), residues: 5591 helix: -0.03 (0.12), residues: 1852 sheet: -1.11 (0.16), residues: 1039 loop : -2.17 (0.11), residues: 2700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP g 103 HIS 0.013 0.002 HIS J 130 PHE 0.047 0.003 PHE Z 53 TYR 0.041 0.003 TYR S 38 ARG 0.013 0.001 ARG W 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11182 Ramachandran restraints generated. 5591 Oldfield, 0 Emsley, 5591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11182 Ramachandran restraints generated. 5591 Oldfield, 0 Emsley, 5591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1586 residues out of total 4655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 306 poor density : 1280 time to evaluate : 5.556 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: C 97 LYS cc_start: 0.7617 (mmtt) cc_final: 0.6857 (tptp) REVERT: C 153 GLN cc_start: 0.8438 (OUTLIER) cc_final: 0.7452 (mt0) REVERT: C 260 ASN cc_start: 0.7793 (OUTLIER) cc_final: 0.7556 (m-40) REVERT: C 270 ARG cc_start: 0.7854 (OUTLIER) cc_final: 0.7080 (tmm-80) REVERT: D 1 MET cc_start: 0.6969 (ptt) cc_final: 0.6703 (ptt) REVERT: E 1 MET cc_start: 0.6518 (ptm) cc_final: 0.4359 (mmm) REVERT: E 46 GLN cc_start: 0.8266 (mp10) cc_final: 0.7762 (mp10) REVERT: E 119 ILE cc_start: 0.8329 (mp) cc_final: 0.8015 (mm) REVERT: F 69 LYS cc_start: 0.8679 (mmtt) cc_final: 0.8034 (ptpt) REVERT: F 77 PHE cc_start: 0.6914 (m-80) cc_final: 0.6570 (m-80) REVERT: F 96 MET cc_start: 0.8185 (ttp) cc_final: 0.7812 (ttp) REVERT: G 83 PHE cc_start: 0.7033 (m-10) cc_final: 0.6816 (m-80) REVERT: H 48 GLU cc_start: 0.1269 (OUTLIER) cc_final: 0.0236 (pp20) REVERT: H 80 ILE cc_start: 0.4419 (OUTLIER) cc_final: 0.4069 (tp) REVERT: K 29 HIS cc_start: 0.8492 (t-90) cc_final: 0.8290 (t-90) REVERT: K 32 TYR cc_start: 0.6390 (OUTLIER) cc_final: 0.6006 (p90) REVERT: M 136 MET cc_start: 0.4742 (ttp) cc_final: 0.3809 (mmt) REVERT: O 8 ILE cc_start: 0.8244 (mm) cc_final: 0.7832 (tp) REVERT: O 58 ILE cc_start: 0.7770 (mm) cc_final: 0.7300 (mp) REVERT: P 27 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7179 (mm-30) REVERT: R 18 GLN cc_start: 0.7875 (pp30) cc_final: 0.7423 (pp30) REVERT: R 41 ILE cc_start: 0.8696 (mp) cc_final: 0.8488 (tp) REVERT: S 15 GLN cc_start: 0.8206 (tt0) cc_final: 0.7758 (tt0) REVERT: U 88 GLU cc_start: 0.7297 (OUTLIER) cc_final: 0.7096 (tm-30) REVERT: V 55 GLU cc_start: 0.7325 (OUTLIER) cc_final: 0.7100 (mt-10) REVERT: X 68 LEU cc_start: 0.9072 (mt) cc_final: 0.8795 (mt) REVERT: Y 48 ARG cc_start: 0.8830 (mmt-90) cc_final: 0.8438 (mmt90) REVERT: 0 12 LYS cc_start: 0.8544 (mmtt) cc_final: 0.8230 (mtpt) REVERT: 5 22 MET cc_start: 0.7002 (mpp) cc_final: 0.6659 (mpp) REVERT: b 50 PHE cc_start: 0.7659 (OUTLIER) cc_final: 0.7103 (m-80) REVERT: b 113 ARG cc_start: 0.7757 (mmm160) cc_final: 0.7354 (mmp-170) REVERT: b 200 ILE cc_start: 0.7608 (mp) cc_final: 0.7370 (mp) REVERT: d 69 GLU cc_start: 0.7374 (tp30) cc_final: 0.6987 (tp30) REVERT: e 156 LYS cc_start: 0.8609 (mtmt) cc_final: 0.8266 (mttt) REVERT: f 38 ARG cc_start: 0.7360 (mtm180) cc_final: 0.6939 (mtm180) REVERT: f 39 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7670 (mt) REVERT: f 75 GLU cc_start: 0.8487 (mm-30) cc_final: 0.8286 (mm-30) REVERT: f 93 LYS cc_start: 0.8274 (mmtm) cc_final: 0.7914 (tmtt) REVERT: g 136 LYS cc_start: 0.8703 (tptm) cc_final: 0.7653 (mtmt) REVERT: h 42 GLU cc_start: 0.8316 (tp30) cc_final: 0.8103 (tp30) REVERT: h 111 MET cc_start: 0.8028 (ppp) cc_final: 0.7763 (ppp) REVERT: i 113 ARG cc_start: 0.8204 (ptm-80) cc_final: 0.7868 (ptm-80) REVERT: i 124 ARG cc_start: 0.7859 (mtp-110) cc_final: 0.7620 (mtp180) REVERT: j 59 LYS cc_start: 0.8785 (OUTLIER) cc_final: 0.8506 (tptt) REVERT: j 89 ARG cc_start: 0.7430 (mtp85) cc_final: 0.6724 (ttp80) REVERT: j 92 LEU cc_start: 0.7680 (OUTLIER) cc_final: 0.7252 (pp) REVERT: k 31 ILE cc_start: 0.9376 (mp) cc_final: 0.9162 (mt) REVERT: k 70 CYS cc_start: 0.8339 (OUTLIER) cc_final: 0.7798 (t) REVERT: k 87 LYS cc_start: 0.7543 (ttpt) cc_final: 0.7241 (ttpt) REVERT: l 67 ILE cc_start: 0.8713 (mp) cc_final: 0.8412 (mp) REVERT: m 73 ILE cc_start: 0.9090 (OUTLIER) cc_final: 0.8718 (mp) REVERT: n 92 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7183 (mp0) REVERT: o 63 ARG cc_start: 0.8522 (OUTLIER) cc_final: 0.8306 (ttt180) REVERT: p 76 LYS cc_start: 0.7758 (mtmt) cc_final: 0.7315 (mmmt) REVERT: r 48 ARG cc_start: 0.8484 (mtt180) cc_final: 0.7247 (mtt90) REVERT: r 50 LYS cc_start: 0.8281 (ptmt) cc_final: 0.7796 (ptmt) REVERT: t 25 ARG cc_start: 0.8583 (ttp-170) cc_final: 0.8275 (ttm110) REVERT: u 42 THR cc_start: 0.7648 (OUTLIER) cc_final: 0.7321 (t) REVERT: u 69 ARG cc_start: 0.2666 (OUTLIER) cc_final: 0.2301 (ttm170) outliers start: 306 outliers final: 234 residues processed: 1463 average time/residue: 1.3064 time to fit residues: 3337.4998 Evaluate side-chains 1502 residues out of total 4655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 253 poor density : 1249 time to evaluate : 6.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 4 VAL Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 153 GLN Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 229 ASP 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 260 ASN Chi-restraints excluded: chain C residue 264 ASP Chi-restraints excluded: chain C residue 270 ARG Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 32 ASN Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 191 ASP Chi-restraints excluded: chain F residue 24 SER Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain F residue 177 PHE Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 110 SER Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 141 ILE Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 48 GLU Chi-restraints excluded: chain H residue 80 ILE Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 43 GLU Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 93 ILE Chi-restraints excluded: chain K residue 13 ASN Chi-restraints excluded: chain K residue 32 TYR Chi-restraints excluded: chain K residue 59 LYS Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 86 LEU Chi-restraints excluded: chain K residue 90 ASN Chi-restraints excluded: chain K residue 118 LEU Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 111 ILE Chi-restraints excluded: chain L residue 126 ARG Chi-restraints excluded: chain L residue 128 THR Chi-restraints excluded: chain M residue 41 LEU Chi-restraints excluded: chain M residue 91 TYR Chi-restraints excluded: chain M residue 96 ILE Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain O residue 69 ASP Chi-restraints excluded: chain O residue 83 LEU Chi-restraints excluded: chain O residue 90 VAL Chi-restraints excluded: chain P residue 4 ILE Chi-restraints excluded: chain P residue 26 VAL Chi-restraints excluded: chain P residue 27 GLU Chi-restraints excluded: chain P residue 76 THR Chi-restraints excluded: chain Q residue 8 VAL Chi-restraints excluded: chain Q residue 97 ASP Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 66 HIS Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 73 LYS Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 35 ILE Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 101 SER Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain T residue 74 ILE Chi-restraints excluded: chain T residue 85 VAL Chi-restraints excluded: chain U residue 36 VAL Chi-restraints excluded: chain U residue 41 LEU Chi-restraints excluded: chain U residue 88 GLU Chi-restraints excluded: chain V residue 55 GLU Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain V residue 89 ILE Chi-restraints excluded: chain W residue 21 LEU Chi-restraints excluded: chain W residue 71 VAL Chi-restraints excluded: chain X residue 5 CYS Chi-restraints excluded: chain X residue 43 GLU Chi-restraints excluded: chain X residue 65 ASP Chi-restraints excluded: chain X residue 71 LEU Chi-restraints excluded: chain Y residue 8 GLU Chi-restraints excluded: chain Z residue 4 THR Chi-restraints excluded: chain Z residue 10 THR Chi-restraints excluded: chain Z residue 35 THR Chi-restraints excluded: chain 0 residue 9 THR Chi-restraints excluded: chain 0 residue 30 VAL Chi-restraints excluded: chain 2 residue 8 SER Chi-restraints excluded: chain 2 residue 44 VAL Chi-restraints excluded: chain 3 residue 28 ASN Chi-restraints excluded: chain 3 residue 50 VAL Chi-restraints excluded: chain 4 residue 11 CYS Chi-restraints excluded: chain 4 residue 14 CYS Chi-restraints excluded: chain 4 residue 22 VAL Chi-restraints excluded: chain 4 residue 24 ARG Chi-restraints excluded: chain 5 residue 10 GLU Chi-restraints excluded: chain 7 residue 4 SER Chi-restraints excluded: chain b residue 41 ILE Chi-restraints excluded: chain b residue 50 PHE Chi-restraints excluded: chain b residue 153 ASP Chi-restraints excluded: chain b residue 161 LEU Chi-restraints excluded: chain b residue 179 LEU Chi-restraints excluded: chain b residue 183 VAL Chi-restraints excluded: chain b residue 187 VAL Chi-restraints excluded: chain b residue 188 ASP Chi-restraints excluded: chain b residue 211 THR Chi-restraints excluded: chain b residue 221 VAL Chi-restraints excluded: chain c residue 10 ILE Chi-restraints excluded: chain c residue 76 VAL Chi-restraints excluded: chain c residue 87 LEU Chi-restraints excluded: chain c residue 97 VAL Chi-restraints excluded: chain c residue 119 SER Chi-restraints excluded: chain c residue 157 LEU Chi-restraints excluded: chain c residue 183 ASP Chi-restraints excluded: chain c residue 192 THR Chi-restraints excluded: chain c residue 195 VAL Chi-restraints excluded: chain d residue 20 PHE Chi-restraints excluded: chain d residue 30 THR Chi-restraints excluded: chain d residue 53 VAL Chi-restraints excluded: chain d residue 67 VAL Chi-restraints excluded: chain d residue 102 VAL Chi-restraints excluded: chain d residue 125 VAL Chi-restraints excluded: chain d residue 138 SER Chi-restraints excluded: chain d residue 169 THR Chi-restraints excluded: chain d residue 191 LEU Chi-restraints excluded: chain d residue 195 ILE Chi-restraints excluded: chain d residue 200 ILE Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 56 VAL Chi-restraints excluded: chain e residue 65 GLU Chi-restraints excluded: chain e residue 105 ILE Chi-restraints excluded: chain e residue 122 ASN Chi-restraints excluded: chain e residue 134 ILE Chi-restraints excluded: chain e residue 141 ILE Chi-restraints excluded: chain e residue 144 LEU Chi-restraints excluded: chain e residue 164 ILE Chi-restraints excluded: chain f residue 23 GLU Chi-restraints excluded: chain f residue 29 ILE Chi-restraints excluded: chain f residue 30 THR Chi-restraints excluded: chain f residue 33 GLU Chi-restraints excluded: chain f residue 39 LEU Chi-restraints excluded: chain f residue 55 HIS Chi-restraints excluded: chain f residue 92 THR Chi-restraints excluded: chain g residue 6 VAL Chi-restraints excluded: chain g residue 7 ILE Chi-restraints excluded: chain g residue 41 SER Chi-restraints excluded: chain g residue 45 SER Chi-restraints excluded: chain g residue 49 THR Chi-restraints excluded: chain g residue 66 LEU Chi-restraints excluded: chain g residue 84 THR Chi-restraints excluded: chain g residue 126 ASP Chi-restraints excluded: chain h residue 40 LEU Chi-restraints excluded: chain h residue 75 ILE Chi-restraints excluded: chain h residue 112 THR Chi-restraints excluded: chain i residue 48 VAL Chi-restraints excluded: chain i residue 58 VAL Chi-restraints excluded: chain i residue 63 LEU Chi-restraints excluded: chain i residue 72 ILE Chi-restraints excluded: chain i residue 116 VAL Chi-restraints excluded: chain j residue 36 VAL Chi-restraints excluded: chain j residue 42 LEU Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 59 LYS Chi-restraints excluded: chain j residue 69 THR Chi-restraints excluded: chain j residue 74 VAL Chi-restraints excluded: chain j residue 80 THR Chi-restraints excluded: chain j residue 92 LEU Chi-restraints excluded: chain k residue 50 SER Chi-restraints excluded: chain k residue 58 SER Chi-restraints excluded: chain k residue 70 CYS Chi-restraints excluded: chain k residue 81 ASN Chi-restraints excluded: chain k residue 82 LEU Chi-restraints excluded: chain k residue 111 THR Chi-restraints excluded: chain k residue 116 ILE Chi-restraints excluded: chain l residue 3 THR Chi-restraints excluded: chain l residue 25 GLU Chi-restraints excluded: chain l residue 55 VAL Chi-restraints excluded: chain l residue 64 THR Chi-restraints excluded: chain l residue 80 ILE Chi-restraints excluded: chain m residue 9 ILE Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 56 LEU Chi-restraints excluded: chain m residue 65 VAL Chi-restraints excluded: chain m residue 73 ILE Chi-restraints excluded: chain m residue 89 LEU Chi-restraints excluded: chain n residue 21 PHE Chi-restraints excluded: chain n residue 34 VAL Chi-restraints excluded: chain n residue 92 GLU Chi-restraints excluded: chain n residue 96 LEU Chi-restraints excluded: chain o residue 3 LEU Chi-restraints excluded: chain o residue 63 ARG Chi-restraints excluded: chain o residue 82 ILE Chi-restraints excluded: chain p residue 3 THR Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain p residue 53 ASP Chi-restraints excluded: chain p residue 66 THR Chi-restraints excluded: chain q residue 7 THR Chi-restraints excluded: chain q residue 20 SER Chi-restraints excluded: chain q residue 22 VAL Chi-restraints excluded: chain q residue 29 VAL Chi-restraints excluded: chain q residue 38 ILE Chi-restraints excluded: chain q residue 61 ILE 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 s residue 27 ASP Chi-restraints excluded: chain s residue 60 VAL Chi-restraints excluded: chain s residue 79 THR Chi-restraints excluded: chain t residue 27 MET Chi-restraints excluded: chain u residue 36 GLU Chi-restraints excluded: chain u residue 42 THR Chi-restraints excluded: chain u residue 69 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1016 random chunks: chunk 890 optimal weight: 6.9990 chunk 938 optimal weight: 3.9990 chunk 855 optimal weight: 9.9990 chunk 912 optimal weight: 20.0000 chunk 937 optimal weight: 0.6980 chunk 549 optimal weight: 7.9990 chunk 397 optimal weight: 7.9990 chunk 716 optimal weight: 6.9990 chunk 280 optimal weight: 9.9990 chunk 824 optimal weight: 9.9990 chunk 863 optimal weight: 7.9990 overall best weight: 5.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 59 GLN ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 54 GLN ** h 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 15 GLN ** q 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 50 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 158931 Z= 0.330 Angle : 0.745 27.217 238032 Z= 0.373 Chirality : 0.045 2.024 30464 Planarity : 0.005 0.075 12558 Dihedral : 23.918 179.198 80243 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.39 % Favored : 90.48 % Rotamer: Outliers : 5.91 % Allowed : 29.11 % Favored : 64.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -1.81 (0.11), residues: 5591 helix: 0.06 (0.12), residues: 1853 sheet: -1.14 (0.16), residues: 1022 loop : -2.15 (0.11), residues: 2716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP g 103 HIS 0.010 0.001 HIS q 47 PHE 0.048 0.002 PHE Z 53 TYR 0.030 0.002 TYR V 57 ARG 0.012 0.001 ARG t 18 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11182 Ramachandran restraints generated. 5591 Oldfield, 0 Emsley, 5591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11182 Ramachandran restraints generated. 5591 Oldfield, 0 Emsley, 5591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1530 residues out of total 4655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 275 poor density : 1255 time to evaluate : 6.216 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: C 97 LYS cc_start: 0.7629 (mmtt) cc_final: 0.6849 (tptp) REVERT: C 153 GLN cc_start: 0.8348 (OUTLIER) cc_final: 0.7297 (mm-40) REVERT: C 260 ASN cc_start: 0.7765 (OUTLIER) cc_final: 0.7492 (m-40) REVERT: C 270 ARG cc_start: 0.7758 (OUTLIER) cc_final: 0.7077 (tmm-80) REVERT: D 1 MET cc_start: 0.7012 (ptt) cc_final: 0.6454 (ptt) REVERT: D 99 GLU cc_start: 0.6217 (OUTLIER) cc_final: 0.5967 (mt-10) REVERT: E 1 MET cc_start: 0.6590 (ptm) cc_final: 0.4369 (mmm) REVERT: E 119 ILE cc_start: 0.8319 (mp) cc_final: 0.7983 (mm) REVERT: F 77 PHE cc_start: 0.6751 (m-80) cc_final: 0.6412 (m-80) REVERT: F 96 MET cc_start: 0.8024 (ttp) cc_final: 0.7725 (ttp) REVERT: H 48 GLU cc_start: 0.1643 (OUTLIER) cc_final: 0.0646 (pp20) REVERT: J 121 LYS cc_start: 0.8617 (OUTLIER) cc_final: 0.8401 (mtmm) REVERT: K 32 TYR cc_start: 0.6327 (OUTLIER) cc_final: 0.5971 (p90) REVERT: M 136 MET cc_start: 0.4634 (ttp) cc_final: 0.3882 (mmt) REVERT: O 104 GLN cc_start: 0.8469 (tp40) cc_final: 0.8119 (tp40) REVERT: R 41 ILE cc_start: 0.8667 (mp) cc_final: 0.8447 (tp) REVERT: W 15 ASP cc_start: 0.6726 (OUTLIER) cc_final: 0.6444 (m-30) REVERT: Y 48 ARG cc_start: 0.8806 (mmt-90) cc_final: 0.8402 (mmt90) REVERT: 1 45 GLN cc_start: 0.6344 (mp10) cc_final: 0.6044 (tp-100) REVERT: 5 22 MET cc_start: 0.6913 (mpp) cc_final: 0.6557 (mpp) REVERT: b 113 ARG cc_start: 0.7799 (mmm160) cc_final: 0.7391 (mmp-170) REVERT: d 69 GLU cc_start: 0.7341 (tp30) cc_final: 0.6905 (tp30) REVERT: e 13 GLU cc_start: 0.7733 (pm20) cc_final: 0.6924 (mp0) REVERT: e 156 LYS cc_start: 0.8632 (mtmt) cc_final: 0.8278 (mttt) REVERT: f 38 ARG cc_start: 0.7279 (mtm180) cc_final: 0.6668 (mtm180) REVERT: f 39 LEU cc_start: 0.7998 (OUTLIER) cc_final: 0.7720 (mt) REVERT: f 93 LYS cc_start: 0.8265 (mmtm) cc_final: 0.7906 (tmtt) REVERT: g 136 LYS cc_start: 0.8752 (tptm) cc_final: 0.7662 (mtmt) REVERT: h 42 GLU cc_start: 0.8285 (tp30) cc_final: 0.8071 (tp30) REVERT: j 89 ARG cc_start: 0.7464 (mtp85) cc_final: 0.6707 (ttp80) REVERT: j 92 LEU cc_start: 0.7642 (OUTLIER) cc_final: 0.7235 (pp) REVERT: k 31 ILE cc_start: 0.9343 (mp) cc_final: 0.9120 (mt) REVERT: k 70 CYS cc_start: 0.8294 (OUTLIER) cc_final: 0.7734 (t) REVERT: l 70 GLU cc_start: 0.7335 (mt-10) cc_final: 0.7115 (mt-10) REVERT: m 73 ILE cc_start: 0.9088 (OUTLIER) cc_final: 0.8763 (mp) REVERT: n 89 MET cc_start: 0.8678 (mmp) cc_final: 0.8345 (mmm) REVERT: n 92 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7286 (mp0) REVERT: o 63 ARG cc_start: 0.8448 (OUTLIER) cc_final: 0.8210 (ttp-170) REVERT: o 89 ARG cc_start: 0.7705 (tpt170) cc_final: 0.6058 (tpp80) REVERT: p 76 LYS cc_start: 0.7781 (mtmt) cc_final: 0.7360 (mmmt) REVERT: q 12 VAL cc_start: 0.8628 (t) cc_final: 0.8290 (m) REVERT: r 48 ARG cc_start: 0.8474 (mtt180) cc_final: 0.7230 (mtt90) REVERT: r 50 LYS cc_start: 0.8198 (ptmt) cc_final: 0.7728 (ptmt) REVERT: t 25 ARG cc_start: 0.8528 (ttp-170) cc_final: 0.8218 (ttm110) REVERT: u 42 THR cc_start: 0.7709 (OUTLIER) cc_final: 0.7374 (t) outliers start: 275 outliers final: 235 residues processed: 1418 average time/residue: 1.2624 time to fit residues: 3099.8078 Evaluate side-chains 1490 residues out of total 4655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 250 poor density : 1240 time to evaluate : 5.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 4 VAL Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 45 ASN Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 153 GLN Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 225 MET Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 239 ASN Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 260 ASN Chi-restraints excluded: chain C residue 264 ASP Chi-restraints excluded: chain C residue 270 ARG Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 32 ASN Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 191 ASP Chi-restraints excluded: chain F residue 24 SER Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain F residue 177 PHE Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 110 SER Chi-restraints excluded: chain G residue 141 ILE Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 48 GLU Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 43 GLU Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 93 ILE Chi-restraints excluded: chain J residue 121 LYS Chi-restraints excluded: chain K residue 13 ASN Chi-restraints excluded: chain K residue 32 TYR Chi-restraints excluded: chain K residue 59 LYS Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 80 ASP Chi-restraints excluded: chain K residue 90 ASN Chi-restraints excluded: chain K residue 118 LEU Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 111 ILE Chi-restraints excluded: chain L residue 126 ARG Chi-restraints excluded: chain L residue 128 THR Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 41 LEU Chi-restraints excluded: chain M residue 91 TYR Chi-restraints excluded: chain M residue 96 ILE Chi-restraints excluded: chain M residue 115 GLU Chi-restraints excluded: chain M residue 119 LEU Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain O residue 83 LEU Chi-restraints excluded: chain O residue 90 VAL Chi-restraints excluded: chain P residue 4 ILE Chi-restraints excluded: chain P residue 26 VAL Chi-restraints excluded: chain P residue 76 THR Chi-restraints excluded: chain P residue 85 SER Chi-restraints excluded: chain Q residue 8 VAL Chi-restraints excluded: chain Q residue 39 VAL Chi-restraints excluded: chain Q residue 97 ASP Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 66 HIS Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 73 LYS Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 35 ILE Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 101 SER Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain T residue 2 ILE Chi-restraints excluded: chain T residue 15 HIS Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain T residue 74 ILE Chi-restraints excluded: chain U residue 36 VAL Chi-restraints excluded: chain U residue 41 LEU Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain V residue 89 ILE Chi-restraints excluded: chain W residue 15 ASP Chi-restraints excluded: chain W residue 21 LEU Chi-restraints excluded: chain W residue 71 VAL Chi-restraints excluded: chain X residue 5 CYS Chi-restraints excluded: chain X residue 43 GLU Chi-restraints excluded: chain X residue 65 ASP Chi-restraints excluded: chain X residue 71 LEU Chi-restraints excluded: chain Y residue 8 GLU Chi-restraints excluded: chain Y residue 40 SER Chi-restraints excluded: chain Z residue 4 THR Chi-restraints excluded: chain Z residue 10 THR Chi-restraints excluded: chain 0 residue 9 THR Chi-restraints excluded: chain 0 residue 30 VAL Chi-restraints excluded: chain 2 residue 44 VAL Chi-restraints excluded: chain 3 residue 28 ASN Chi-restraints excluded: chain 3 residue 50 VAL Chi-restraints excluded: chain 4 residue 11 CYS Chi-restraints excluded: chain 4 residue 14 CYS Chi-restraints excluded: chain 4 residue 22 VAL Chi-restraints excluded: chain 4 residue 24 ARG Chi-restraints excluded: chain 5 residue 10 GLU Chi-restraints excluded: chain 5 residue 12 ILE Chi-restraints excluded: chain 7 residue 2 THR Chi-restraints excluded: chain b residue 41 ILE Chi-restraints excluded: chain b residue 153 ASP Chi-restraints excluded: chain b residue 161 LEU Chi-restraints excluded: chain b residue 163 VAL Chi-restraints excluded: chain b residue 179 LEU Chi-restraints excluded: chain b residue 183 VAL Chi-restraints excluded: chain b residue 187 VAL Chi-restraints excluded: chain b residue 211 THR Chi-restraints excluded: chain b residue 221 VAL Chi-restraints excluded: chain c residue 10 ILE Chi-restraints excluded: chain c residue 76 VAL Chi-restraints excluded: chain c residue 97 VAL Chi-restraints excluded: chain c residue 119 SER Chi-restraints excluded: chain c residue 120 ILE Chi-restraints excluded: chain c residue 157 LEU Chi-restraints excluded: chain c residue 183 ASP Chi-restraints excluded: chain c residue 192 THR Chi-restraints excluded: chain c residue 195 VAL Chi-restraints excluded: chain d residue 20 PHE Chi-restraints excluded: chain d residue 28 ILE Chi-restraints excluded: chain d residue 30 THR Chi-restraints excluded: chain d residue 53 VAL Chi-restraints excluded: chain d residue 67 VAL Chi-restraints excluded: chain d residue 102 VAL Chi-restraints excluded: chain d residue 125 VAL Chi-restraints excluded: chain d residue 138 SER Chi-restraints excluded: chain d residue 169 THR Chi-restraints excluded: chain d residue 191 LEU Chi-restraints excluded: chain d residue 195 ILE Chi-restraints excluded: chain d residue 200 ILE Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 56 VAL Chi-restraints excluded: chain e residue 65 GLU Chi-restraints excluded: chain e residue 105 ILE Chi-restraints excluded: chain e residue 122 ASN Chi-restraints excluded: chain e residue 134 ILE Chi-restraints excluded: chain e residue 144 LEU Chi-restraints excluded: chain f residue 23 GLU Chi-restraints excluded: chain f residue 29 ILE Chi-restraints excluded: chain f residue 30 THR Chi-restraints excluded: chain f residue 33 GLU Chi-restraints excluded: chain f residue 39 LEU Chi-restraints excluded: chain f residue 55 HIS Chi-restraints excluded: chain f residue 92 THR Chi-restraints excluded: chain g residue 6 VAL Chi-restraints excluded: chain g residue 7 ILE Chi-restraints excluded: chain g residue 41 SER Chi-restraints excluded: chain g residue 45 SER Chi-restraints excluded: chain g residue 49 THR Chi-restraints excluded: chain g residue 84 THR Chi-restraints excluded: chain g residue 87 VAL Chi-restraints excluded: chain g residue 126 ASP Chi-restraints excluded: chain h residue 40 LEU Chi-restraints excluded: chain h residue 75 ILE Chi-restraints excluded: chain h residue 112 THR Chi-restraints excluded: chain i residue 48 VAL Chi-restraints excluded: chain i residue 63 LEU Chi-restraints excluded: chain i residue 72 ILE Chi-restraints excluded: chain i residue 116 VAL Chi-restraints excluded: chain j residue 36 VAL Chi-restraints excluded: chain j residue 42 LEU Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 59 LYS Chi-restraints excluded: chain j residue 69 THR Chi-restraints excluded: chain j residue 80 THR Chi-restraints excluded: chain j residue 92 LEU Chi-restraints excluded: chain k residue 50 SER Chi-restraints excluded: chain k residue 58 SER Chi-restraints excluded: chain k residue 70 CYS Chi-restraints excluded: chain k residue 81 ASN Chi-restraints excluded: chain k residue 116 ILE Chi-restraints excluded: chain l residue 3 THR Chi-restraints excluded: chain l residue 25 GLU Chi-restraints excluded: chain l residue 55 VAL Chi-restraints excluded: chain l residue 64 THR Chi-restraints excluded: chain l residue 80 ILE Chi-restraints excluded: chain m residue 9 ILE Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 56 LEU Chi-restraints excluded: chain m residue 65 VAL Chi-restraints excluded: chain m residue 73 ILE Chi-restraints excluded: chain m residue 89 LEU Chi-restraints excluded: chain n residue 21 PHE Chi-restraints excluded: chain n residue 34 VAL Chi-restraints excluded: chain n residue 92 GLU Chi-restraints excluded: chain n residue 96 LEU Chi-restraints excluded: chain o residue 3 LEU Chi-restraints excluded: chain o residue 63 ARG Chi-restraints excluded: chain o residue 82 ILE Chi-restraints excluded: chain p residue 3 THR Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain p residue 53 ASP Chi-restraints excluded: chain p residue 66 THR Chi-restraints excluded: chain q residue 7 THR Chi-restraints excluded: chain q residue 20 SER Chi-restraints excluded: chain q residue 22 VAL Chi-restraints excluded: chain q residue 29 VAL Chi-restraints excluded: chain q residue 38 ILE Chi-restraints excluded: chain q residue 61 ILE 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 s residue 27 ASP Chi-restraints excluded: chain s residue 33 THR Chi-restraints excluded: chain s residue 60 VAL Chi-restraints excluded: chain s residue 63 THR Chi-restraints excluded: chain s residue 79 THR Chi-restraints excluded: chain u residue 36 GLU Chi-restraints excluded: chain u residue 42 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1016 random chunks: chunk 909 optimal weight: 9.9990 chunk 599 optimal weight: 0.9990 chunk 964 optimal weight: 5.9990 chunk 588 optimal weight: 4.9990 chunk 457 optimal weight: 1.9990 chunk 670 optimal weight: 20.0000 chunk 1012 optimal weight: 10.0000 chunk 931 optimal weight: 5.9990 chunk 806 optimal weight: 2.9990 chunk 83 optimal weight: 10.0000 chunk 622 optimal weight: 20.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 53 HIS ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 GLN ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 66 ASN ** Q 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 25 GLN ** 2 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 54 GLN h 16 ASN ** h 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 15 GLN ** q 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 50 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 158931 Z= 0.228 Angle : 0.664 26.720 238032 Z= 0.333 Chirality : 0.041 2.044 30464 Planarity : 0.005 0.070 12558 Dihedral : 23.803 179.708 80243 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.71 % Favored : 91.18 % Rotamer: Outliers : 5.13 % Allowed : 30.08 % Favored : 64.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.11), residues: 5591 helix: 0.28 (0.12), residues: 1863 sheet: -1.05 (0.16), residues: 1008 loop : -2.05 (0.11), residues: 2720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP g 103 HIS 0.019 0.001 HIS W 46 PHE 0.044 0.002 PHE Z 53 TYR 0.025 0.002 TYR V 57 ARG 0.013 0.001 ARG t 18 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11182 Ramachandran restraints generated. 5591 Oldfield, 0 Emsley, 5591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11182 Ramachandran restraints generated. 5591 Oldfield, 0 Emsley, 5591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1505 residues out of total 4655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 239 poor density : 1266 time to evaluate : 6.161 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: C 97 LYS cc_start: 0.7603 (mmtt) cc_final: 0.6852 (tptp) REVERT: C 153 GLN cc_start: 0.8155 (OUTLIER) cc_final: 0.7124 (mm-40) REVERT: C 260 ASN cc_start: 0.7883 (OUTLIER) cc_final: 0.7549 (m-40) REVERT: C 270 ARG cc_start: 0.7774 (OUTLIER) cc_final: 0.7127 (tmm-80) REVERT: D 99 GLU cc_start: 0.6110 (OUTLIER) cc_final: 0.5890 (mt-10) REVERT: E 1 MET cc_start: 0.6514 (ptm) cc_final: 0.4383 (mmm) REVERT: E 119 ILE cc_start: 0.8324 (mp) cc_final: 0.7984 (mm) REVERT: F 77 PHE cc_start: 0.6740 (m-80) cc_final: 0.6394 (m-80) REVERT: H 48 GLU cc_start: 0.1365 (OUTLIER) cc_final: 0.0506 (pp20) REVERT: J 31 GLU cc_start: 0.7292 (tp30) cc_final: 0.6733 (tt0) REVERT: J 121 LYS cc_start: 0.8509 (OUTLIER) cc_final: 0.8253 (mtmt) REVERT: K 32 TYR cc_start: 0.6407 (OUTLIER) cc_final: 0.6108 (p90) REVERT: M 130 PHE cc_start: 0.8081 (t80) cc_final: 0.7792 (t80) REVERT: M 136 MET cc_start: 0.4672 (ttp) cc_final: 0.3913 (mmt) REVERT: N 82 GLU cc_start: 0.7693 (mp0) cc_final: 0.7139 (mp0) REVERT: N 117 ASP cc_start: 0.7402 (m-30) cc_final: 0.7109 (m-30) REVERT: O 97 PHE cc_start: 0.8260 (m-80) cc_final: 0.7920 (m-80) REVERT: R 21 ARG cc_start: 0.7836 (ttt-90) cc_final: 0.7591 (tmm-80) REVERT: R 60 LYS cc_start: 0.8129 (mmtm) cc_final: 0.6307 (tttp) REVERT: S 48 LYS cc_start: 0.8429 (tttp) cc_final: 0.8118 (ttpt) REVERT: T 1 MET cc_start: 0.4864 (tpt) cc_final: 0.2999 (ptm) REVERT: X 71 LEU cc_start: 0.7958 (OUTLIER) cc_final: 0.7368 (mm) REVERT: Y 48 ARG cc_start: 0.8780 (mmt-90) cc_final: 0.8331 (mmt90) REVERT: 1 45 GLN cc_start: 0.6237 (mp10) cc_final: 0.5711 (tp-100) REVERT: 5 22 MET cc_start: 0.6968 (mpp) cc_final: 0.6615 (mpp) REVERT: b 50 PHE cc_start: 0.7848 (OUTLIER) cc_final: 0.7387 (m-80) REVERT: b 113 ARG cc_start: 0.7795 (mmm160) cc_final: 0.7339 (mmp-170) REVERT: d 69 GLU cc_start: 0.7235 (tp30) cc_final: 0.6800 (tp30) REVERT: e 13 GLU cc_start: 0.7647 (pm20) cc_final: 0.7039 (mp0) REVERT: e 156 LYS cc_start: 0.8619 (mtmt) cc_final: 0.8302 (mttm) REVERT: f 38 ARG cc_start: 0.7213 (mtm180) cc_final: 0.6652 (mtm180) REVERT: f 39 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7795 (mt) REVERT: f 93 LYS cc_start: 0.8240 (mmtm) cc_final: 0.7896 (tmtt) REVERT: g 22 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7669 (tt) REVERT: g 136 LYS cc_start: 0.8739 (tptm) cc_final: 0.7633 (mtmt) REVERT: h 42 GLU cc_start: 0.8257 (tp30) cc_final: 0.8040 (tp30) REVERT: j 89 ARG cc_start: 0.7502 (mtp85) cc_final: 0.6760 (ttp80) REVERT: j 92 LEU cc_start: 0.7669 (OUTLIER) cc_final: 0.7315 (pp) REVERT: k 31 ILE cc_start: 0.9323 (mp) cc_final: 0.9102 (mt) REVERT: k 70 CYS cc_start: 0.8241 (OUTLIER) cc_final: 0.7687 (t) REVERT: k 111 THR cc_start: 0.6770 (OUTLIER) cc_final: 0.6537 (t) REVERT: k 116 ILE cc_start: 0.7694 (OUTLIER) cc_final: 0.7314 (tp) REVERT: m 31 LYS cc_start: 0.8946 (tppt) cc_final: 0.8700 (mmmt) REVERT: m 73 ILE cc_start: 0.9061 (OUTLIER) cc_final: 0.8733 (mp) REVERT: n 39 GLU cc_start: 0.7316 (tp30) cc_final: 0.7011 (tm-30) REVERT: n 92 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7264 (mp0) REVERT: p 76 LYS cc_start: 0.7672 (mtmt) cc_final: 0.7333 (mmmt) REVERT: q 12 VAL cc_start: 0.8561 (t) cc_final: 0.8222 (m) REVERT: q 19 LYS cc_start: 0.8485 (mmtt) cc_final: 0.8084 (mmtt) REVERT: r 48 ARG cc_start: 0.8418 (mtt180) cc_final: 0.7085 (mtt90) REVERT: r 50 LYS cc_start: 0.8027 (ptmt) cc_final: 0.7597 (ptmt) REVERT: r 57 ARG cc_start: 0.7676 (ttm170) cc_final: 0.7329 (ttm170) REVERT: s 63 THR cc_start: 0.8445 (OUTLIER) cc_final: 0.8131 (p) REVERT: t 25 ARG cc_start: 0.8469 (ttp-170) cc_final: 0.8092 (ttm110) REVERT: t 85 LYS cc_start: 0.7641 (tttt) cc_final: 0.7135 (mmmt) REVERT: u 42 THR cc_start: 0.7632 (OUTLIER) cc_final: 0.7272 (t) outliers start: 239 outliers final: 194 residues processed: 1401 average time/residue: 1.2872 time to fit residues: 3121.3667 Evaluate side-chains 1457 residues out of total 4655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 213 poor density : 1244 time to evaluate : 6.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 4 VAL Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 153 GLN Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 260 ASN Chi-restraints excluded: chain C residue 264 ASP Chi-restraints excluded: chain C residue 270 ARG Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 32 ASN Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 191 ASP Chi-restraints excluded: chain F residue 24 SER Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain F residue 177 PHE Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 110 SER Chi-restraints excluded: chain G residue 141 ILE Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 48 GLU Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 43 GLU Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 93 ILE Chi-restraints excluded: chain J residue 121 LYS Chi-restraints excluded: chain K residue 13 ASN Chi-restraints excluded: chain K residue 32 TYR Chi-restraints excluded: chain K residue 59 LYS Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 118 LEU Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 82 LEU Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 111 ILE Chi-restraints excluded: chain L residue 128 THR Chi-restraints excluded: chain M residue 41 LEU Chi-restraints excluded: chain M residue 91 TYR Chi-restraints excluded: chain M residue 96 ILE Chi-restraints excluded: chain M residue 119 LEU Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain O residue 69 ASP Chi-restraints excluded: chain O residue 90 VAL Chi-restraints excluded: chain P residue 4 ILE Chi-restraints excluded: chain P residue 26 VAL Chi-restraints excluded: chain P residue 76 THR Chi-restraints excluded: chain Q residue 8 VAL Chi-restraints excluded: chain Q residue 39 VAL Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 66 HIS Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 73 LYS Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 35 ILE Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain T residue 74 ILE Chi-restraints excluded: chain U residue 36 VAL Chi-restraints excluded: chain U residue 41 LEU Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain V residue 89 ILE Chi-restraints excluded: chain W residue 21 LEU Chi-restraints excluded: chain W residue 71 VAL Chi-restraints excluded: chain X residue 5 CYS Chi-restraints excluded: chain X residue 65 ASP Chi-restraints excluded: chain X residue 71 LEU Chi-restraints excluded: chain Y residue 40 SER Chi-restraints excluded: chain Y residue 57 LEU Chi-restraints excluded: chain Z residue 4 THR Chi-restraints excluded: chain Z residue 10 THR Chi-restraints excluded: chain Z residue 35 THR Chi-restraints excluded: chain 0 residue 9 THR Chi-restraints excluded: chain 0 residue 30 VAL Chi-restraints excluded: chain 2 residue 44 VAL Chi-restraints excluded: chain 3 residue 28 ASN Chi-restraints excluded: chain 3 residue 50 VAL Chi-restraints excluded: chain 4 residue 11 CYS Chi-restraints excluded: chain 4 residue 14 CYS Chi-restraints excluded: chain 4 residue 22 VAL Chi-restraints excluded: chain 4 residue 24 ARG Chi-restraints excluded: chain 5 residue 10 GLU Chi-restraints excluded: chain b residue 50 PHE Chi-restraints excluded: chain b residue 161 LEU Chi-restraints excluded: chain b residue 163 VAL Chi-restraints excluded: chain b residue 183 VAL Chi-restraints excluded: chain b residue 187 VAL Chi-restraints excluded: chain b residue 188 ASP Chi-restraints excluded: chain b residue 211 THR Chi-restraints excluded: chain b residue 221 VAL Chi-restraints excluded: chain c residue 10 ILE Chi-restraints excluded: chain c residue 87 LEU Chi-restraints excluded: chain c residue 97 VAL Chi-restraints excluded: chain c residue 119 SER Chi-restraints excluded: chain c residue 157 LEU Chi-restraints excluded: chain c residue 183 ASP Chi-restraints excluded: chain c residue 192 THR Chi-restraints excluded: chain c residue 195 VAL Chi-restraints excluded: chain d residue 30 THR Chi-restraints excluded: chain d residue 53 VAL Chi-restraints excluded: chain d residue 67 VAL Chi-restraints excluded: chain d residue 138 SER Chi-restraints excluded: chain d residue 169 THR Chi-restraints excluded: chain d residue 191 LEU Chi-restraints excluded: chain d residue 195 ILE Chi-restraints excluded: chain d residue 200 ILE Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 56 VAL Chi-restraints excluded: chain e residue 65 GLU Chi-restraints excluded: chain e residue 105 ILE Chi-restraints excluded: chain e residue 122 ASN Chi-restraints excluded: chain e residue 134 ILE Chi-restraints excluded: chain e residue 144 LEU Chi-restraints excluded: chain e residue 164 ILE Chi-restraints excluded: chain f residue 23 GLU Chi-restraints excluded: chain f residue 29 ILE Chi-restraints excluded: chain f residue 30 THR Chi-restraints excluded: chain f residue 33 GLU Chi-restraints excluded: chain f residue 39 LEU Chi-restraints excluded: chain f residue 55 HIS Chi-restraints excluded: chain f residue 92 THR Chi-restraints excluded: chain g residue 6 VAL Chi-restraints excluded: chain g residue 7 ILE Chi-restraints excluded: chain g residue 22 LEU Chi-restraints excluded: chain g residue 41 SER Chi-restraints excluded: chain g residue 49 THR Chi-restraints excluded: chain g residue 84 THR Chi-restraints excluded: chain g residue 126 ASP Chi-restraints excluded: chain h residue 40 LEU Chi-restraints excluded: chain h residue 75 ILE Chi-restraints excluded: chain h residue 112 THR Chi-restraints excluded: chain i residue 48 VAL Chi-restraints excluded: chain i residue 63 LEU Chi-restraints excluded: chain i residue 72 ILE Chi-restraints excluded: chain j residue 36 VAL Chi-restraints excluded: chain j residue 42 LEU Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 69 THR Chi-restraints excluded: chain j residue 80 THR Chi-restraints excluded: chain j residue 92 LEU Chi-restraints excluded: chain k residue 58 SER Chi-restraints excluded: chain k residue 70 CYS Chi-restraints excluded: chain k residue 81 ASN Chi-restraints excluded: chain k residue 111 THR Chi-restraints excluded: chain k residue 116 ILE Chi-restraints excluded: chain l residue 3 THR Chi-restraints excluded: chain l residue 25 GLU Chi-restraints excluded: chain l residue 55 VAL Chi-restraints excluded: chain l residue 64 THR Chi-restraints excluded: chain l residue 80 ILE Chi-restraints excluded: chain m residue 9 ILE Chi-restraints excluded: chain m residue 56 LEU Chi-restraints excluded: chain m residue 65 VAL Chi-restraints excluded: chain m residue 73 ILE Chi-restraints excluded: chain m residue 89 LEU Chi-restraints excluded: chain n residue 21 PHE Chi-restraints excluded: chain n residue 34 VAL Chi-restraints excluded: chain n residue 92 GLU Chi-restraints excluded: chain n residue 96 LEU Chi-restraints excluded: chain o residue 3 LEU Chi-restraints excluded: chain o residue 82 ILE Chi-restraints excluded: chain p residue 3 THR Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain p residue 53 ASP Chi-restraints excluded: chain p residue 66 THR Chi-restraints excluded: chain q residue 7 THR Chi-restraints excluded: chain q residue 22 VAL Chi-restraints excluded: chain q residue 29 VAL Chi-restraints excluded: chain q residue 38 ILE Chi-restraints excluded: chain q residue 61 ILE 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 s residue 27 ASP Chi-restraints excluded: chain s residue 60 VAL Chi-restraints excluded: chain s residue 63 THR Chi-restraints excluded: chain s residue 79 THR Chi-restraints excluded: chain u residue 36 GLU Chi-restraints excluded: chain u residue 42 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1016 random chunks: chunk 494 optimal weight: 3.9990 chunk 640 optimal weight: 20.0000 chunk 858 optimal weight: 3.9990 chunk 246 optimal weight: 10.0000 chunk 743 optimal weight: 10.0000 chunk 119 optimal weight: 10.0000 chunk 223 optimal weight: 10.0000 chunk 807 optimal weight: 4.9990 chunk 337 optimal weight: 4.9990 chunk 828 optimal weight: 0.0370 chunk 102 optimal weight: 10.0000 overall best weight: 3.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 20 HIS ** 2 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 15 GLN q 47 HIS q 50 ASN ** t 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.127589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.105043 restraints weight = 338508.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.106978 restraints weight = 125212.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.108088 restraints weight = 72783.367| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 158931 Z= 0.238 Angle : 0.667 26.572 238032 Z= 0.335 Chirality : 0.041 2.044 30464 Planarity : 0.005 0.073 12558 Dihedral : 23.799 179.306 80243 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.87 % Favored : 91.02 % Rotamer: Outliers : 5.18 % Allowed : 30.35 % Favored : 64.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.11), residues: 5591 helix: 0.33 (0.12), residues: 1873 sheet: -1.02 (0.16), residues: 1007 loop : -2.05 (0.11), residues: 2711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP g 103 HIS 0.010 0.001 HIS r 74 PHE 0.045 0.002 PHE Z 53 TYR 0.028 0.002 TYR o 78 ARG 0.013 0.001 ARG t 18 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 43047.68 seconds wall clock time: 750 minutes 28.91 seconds (45028.91 seconds total)