Starting phenix.real_space_refine on Sat Mar 23 04:41:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8akn_15488/03_2024/8akn_15488_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8akn_15488/03_2024/8akn_15488.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8akn_15488/03_2024/8akn_15488_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8akn_15488/03_2024/8akn_15488_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8akn_15488/03_2024/8akn_15488_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8akn_15488/03_2024/8akn_15488.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8akn_15488/03_2024/8akn_15488.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8akn_15488/03_2024/8akn_15488_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8akn_15488/03_2024/8akn_15488_updated.pdb" } resolution = 2.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 4551 5.49 5 Mg 305 5.21 5 S 160 5.16 5 C 72829 2.51 5 N 26952 2.21 5 O 41714 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "0 GLU 7": "OE1" <-> "OE2" Residue "0 ARG 44": "NH1" <-> "NH2" Residue "1 ARG 3": "NH1" <-> "NH2" Residue "1 ARG 12": "NH1" <-> "NH2" Residue "1 ARG 14": "NH1" <-> "NH2" Residue "1 ARG 21": "NH1" <-> "NH2" Residue "1 ARG 33": "NH1" <-> "NH2" Residue "1 ARG 41": "NH1" <-> "NH2" Residue "2 ARG 13": "NH1" <-> "NH2" Residue "2 PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 30": "NH1" <-> "NH2" Residue "2 ARG 40": "NH1" <-> "NH2" Residue "3 ARG 24": "NH1" <-> "NH2" Residue "4 ASP 4": "OD1" <-> "OD2" Residue "4 PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 4": "NH1" <-> "NH2" Residue "A TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 15": "NH1" <-> "NH2" Residue "A ARG 18": "NH1" <-> "NH2" Residue "C GLU 44": "OE1" <-> "OE2" Residue "C GLU 52": "OE1" <-> "OE2" Residue "C GLU 78": "OE1" <-> "OE2" Residue "C ASP 123": "OD1" <-> "OD2" Residue "C PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 127": "OD1" <-> "OD2" Residue "C GLU 140": "OE1" <-> "OE2" Residue "C ASP 153": "OD1" <-> "OD2" Residue "C ASP 188": "OD1" <-> "OD2" Residue "C ASP 197": "OD1" <-> "OD2" Residue "C PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 205": "OD1" <-> "OD2" Residue "C ARG 225": "NH1" <-> "NH2" Residue "D ASP 34": "OD1" <-> "OD2" Residue "D GLU 46": "OE1" <-> "OE2" Residue "D GLU 82": "OE1" <-> "OE2" Residue "D GLU 110": "OE1" <-> "OE2" Residue "D ASP 112": "OD1" <-> "OD2" Residue "D ASP 118": "OD1" <-> "OD2" Residue "D ARG 131": "NH1" <-> "NH2" Residue "D GLU 166": "OE1" <-> "OE2" Residue "D GLU 170": "OE1" <-> "OE2" Residue "D ASP 181": "OD1" <-> "OD2" Residue "D TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 15": "OE1" <-> "OE2" Residue "E ASP 18": "OD1" <-> "OD2" Residue "E GLU 35": "OE1" <-> "OE2" Residue "E GLU 57": "OE1" <-> "OE2" Residue "E GLU 78": "OE1" <-> "OE2" Residue "E ARG 81": "NH1" <-> "NH2" Residue "E GLU 88": "OE1" <-> "OE2" Residue "E GLU 95": "OE1" <-> "OE2" Residue "E GLU 113": "OE1" <-> "OE2" Residue "E ASP 141": "OD1" <-> "OD2" Residue "E GLU 163": "OE1" <-> "OE2" Residue "E GLU 166": "OE1" <-> "OE2" Residue "E GLU 172": "OE1" <-> "OE2" Residue "E PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 187": "OE1" <-> "OE2" Residue "F GLU 10": "OE1" <-> "OE2" Residue "F ARG 45": "NH1" <-> "NH2" Residue "F PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 55": "OE1" <-> "OE2" Residue "F GLU 65": "OE1" <-> "OE2" Residue "F GLU 116": "OE1" <-> "OE2" Residue "F ASP 142": "OD1" <-> "OD2" Residue "F GLU 162": "OE1" <-> "OE2" Residue "G GLU 5": "OE1" <-> "OE2" Residue "G GLU 16": "OE1" <-> "OE2" Residue "G GLU 33": "OE1" <-> "OE2" Residue "G GLU 73": "OE1" <-> "OE2" Residue "G ASP 82": "OD1" <-> "OD2" Residue "G GLU 98": "OE1" <-> "OE2" Residue "H ASP 15": "OD1" <-> "OD2" Residue "H GLU 48": "OE1" <-> "OE2" Residue "H GLU 60": "OE1" <-> "OE2" Residue "H GLU 63": "OE1" <-> "OE2" Residue "H GLU 67": "OE1" <-> "OE2" Residue "H TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 126": "OD1" <-> "OD2" Residue "H ASP 140": "OD1" <-> "OD2" Residue "H TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 43": "OE1" <-> "OE2" Residue "I GLU 47": "OE1" <-> "OE2" Residue "I GLU 58": "OE1" <-> "OE2" Residue "I GLU 60": "OE1" <-> "OE2" Residue "J TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 36": "OE1" <-> "OE2" Residue "J TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 42": "OE1" <-> "OE2" Residue "J GLU 53": "OE1" <-> "OE2" Residue "J ASP 62": "OD1" <-> "OD2" Residue "J GLU 89": "OE1" <-> "OE2" Residue "J TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 95": "NH1" <-> "NH2" Residue "J GLU 112": "OE1" <-> "OE2" Residue "J ARG 124": "NH1" <-> "NH2" Residue "K PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 63": "OD1" <-> "OD2" Residue "K ASP 75": "OD1" <-> "OD2" Residue "K GLU 78": "OE1" <-> "OE2" Residue "K GLU 81": "OE1" <-> "OE2" Residue "L ASP 18": "OD1" <-> "OD2" Residue "L PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 72": "OD1" <-> "OD2" Residue "L GLU 76": "OE1" <-> "OE2" Residue "M ARG 14": "NH1" <-> "NH2" Residue "M GLU 25": "OE1" <-> "OE2" Residue "M ARG 56": "NH1" <-> "NH2" Residue "M GLU 70": "OE1" <-> "OE2" Residue "M ASP 109": "OD1" <-> "OD2" Residue "N ASP 11": "OD1" <-> "OD2" Residue "N ASP 58": "OD1" <-> "OD2" Residue "O ASP 18": "OD1" <-> "OD2" Residue "O TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 38": "OD1" <-> "OD2" Residue "O ASP 40": "OD1" <-> "OD2" Residue "O ARG 65": "NH1" <-> "NH2" Residue "P GLU 14": "OE1" <-> "OE2" Residue "P ASP 21": "OD1" <-> "OD2" Residue "P GLU 83": "OE1" <-> "OE2" Residue "Q ARG 28": "NH1" <-> "NH2" Residue "Q GLU 34": "OE1" <-> "OE2" Residue "Q PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 45": "OE1" <-> "OE2" Residue "Q GLU 47": "OE1" <-> "OE2" Residue "Q GLU 48": "OE1" <-> "OE2" Residue "R ASP 15": "OD1" <-> "OD2" Residue "R GLU 49": "OE1" <-> "OE2" Residue "R GLU 52": "OE1" <-> "OE2" Residue "R GLU 63": "OE1" <-> "OE2" Residue "R GLU 80": "OE1" <-> "OE2" Residue "S PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 20": "OE1" <-> "OE2" Residue "S ASP 22": "OD1" <-> "OD2" Residue "S TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 35": "OE1" <-> "OE2" Residue "T ARG 3": "NH1" <-> "NH2" Residue "T ARG 32": "NH1" <-> "NH2" Residue "T ARG 55": "NH1" <-> "NH2" Residue "T PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 64": "OD1" <-> "OD2" Residue "T GLU 65": "OE1" <-> "OE2" Residue "T ARG 81": "NH1" <-> "NH2" Residue "U TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 59": "OD1" <-> "OD2" Residue "V GLU 10": "OE1" <-> "OE2" Residue "V ASP 13": "OD1" <-> "OD2" Residue "V GLU 39": "OE1" <-> "OE2" Residue "V GLU 63": "OE1" <-> "OE2" Residue "V ARG 66": "NH1" <-> "NH2" Residue "W ARG 15": "NH1" <-> "NH2" Residue "W GLU 18": "OE1" <-> "OE2" Residue "W ASP 25": "OD1" <-> "OD2" Residue "W ASP 31": "OD1" <-> "OD2" Residue "W PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 36": "NH1" <-> "NH2" Residue "W ASP 47": "OD1" <-> "OD2" Residue "W ARG 50": "NH1" <-> "NH2" Residue "W PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 60": "OE1" <-> "OE2" Residue "W ASP 70": "OD1" <-> "OD2" Residue "W ASP 71": "OD1" <-> "OD2" Residue "W GLU 73": "OE1" <-> "OE2" Residue "W ARG 75": "NH1" <-> "NH2" Residue "W GLU 76": "OE1" <-> "OE2" Residue "W ARG 83": "NH1" <-> "NH2" Residue "W GLU 90": "OE1" <-> "OE2" Residue "W ASP 104": "OD1" <-> "OD2" Residue "W ASP 106": "OD1" <-> "OD2" Residue "W ASP 107": "OD1" <-> "OD2" Residue "W PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 114": "OE1" <-> "OE2" Residue "W ARG 116": "NH1" <-> "NH2" Residue "W PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 133": "NH1" <-> "NH2" Residue "W TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 142": "NH1" <-> "NH2" Residue "W ARG 143": "NH1" <-> "NH2" Residue "W GLU 147": "OE1" <-> "OE2" Residue "W ARG 174": "NH1" <-> "NH2" Residue "W ASP 211": "OD1" <-> "OD2" Residue "W ARG 228": "NH1" <-> "NH2" Residue "W ASP 241": "OD1" <-> "OD2" Residue "W GLU 256": "OE1" <-> "OE2" Residue "W ARG 277": "NH1" <-> "NH2" Residue "W ARG 286": "NH1" <-> "NH2" Residue "W GLU 290": "OE1" <-> "OE2" Residue "W ARG 295": "NH1" <-> "NH2" Residue "W ARG 303": "NH1" <-> "NH2" Residue "W TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 23": "OE1" <-> "OE2" Residue "c ARG 52": "NH1" <-> "NH2" Residue "c ARG 63": "NH1" <-> "NH2" Residue "c ARG 80": "NH1" <-> "NH2" Residue "c ASP 114": "OD1" <-> "OD2" Residue "c ARG 133": "NH1" <-> "NH2" Residue "c TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 167": "NH1" <-> "NH2" Residue "c ASP 168": "OD1" <-> "OD2" Residue "c TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 177": "NH1" <-> "NH2" Residue "c ARG 182": "NH1" <-> "NH2" Residue "c ARG 189": "NH1" <-> "NH2" Residue "c ARG 203": "NH1" <-> "NH2" Residue "c ARG 212": "NH1" <-> "NH2" Residue "d ARG 13": "NH1" <-> "NH2" Residue "d ARG 33": "NH1" <-> "NH2" Residue "d ASP 39": "OD1" <-> "OD2" Residue "d ARG 59": "NH1" <-> "NH2" Residue "d GLU 74": "OE1" <-> "OE2" Residue "d GLU 81": "OE1" <-> "OE2" Residue "d ARG 83": "NH1" <-> "NH2" Residue "d GLU 99": "OE1" <-> "OE2" Residue "d ASP 103": "OD1" <-> "OD2" Residue "d ARG 169": "NH1" <-> "NH2" Residue "d GLU 183": "OE1" <-> "OE2" Residue "e PHE 19": "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 ARG 102": "NH1" <-> "NH2" Residue "e ASP 116": "OD1" <-> "OD2" Residue "e GLU 122": "OE1" <-> "OE2" Residue "e PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 155": "OE1" <-> "OE2" Residue "e ARG 162": "NH1" <-> "NH2" Residue "e ARG 170": "NH1" <-> "NH2" Residue "e ASP 176": "OD1" <-> "OD2" Residue "e ASP 184": "OD1" <-> "OD2" Residue "f ASP 6": "OD1" <-> "OD2" Residue "f ASP 10": "OD1" <-> "OD2" Residue "f GLU 32": "OE1" <-> "OE2" Residue "f ARG 71": "NH1" <-> "NH2" Residue "f ARG 80": "NH1" <-> "NH2" Residue "f TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 92": "NH1" <-> "NH2" Residue "f GLU 94": "OE1" <-> "OE2" Residue "f ARG 102": "NH1" <-> "NH2" Residue "f ARG 110": "NH1" <-> "NH2" Residue "f ARG 112": "NH1" <-> "NH2" Residue "f ARG 115": "NH1" <-> "NH2" Residue "f ARG 133": "NH1" <-> "NH2" Residue "f ASP 144": "OD1" <-> "OD2" Residue "f ASP 147": "OD1" <-> "OD2" Residue "f GLU 164": "OE1" <-> "OE2" Residue "f ASP 174": "OD1" <-> "OD2" Residue "f PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ARG 3": "NH1" <-> "NH2" Residue "g ASP 39": "OD1" <-> "OD2" Residue "g GLU 42": "OE1" <-> "OE2" Residue "g PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 56": "OD1" <-> "OD2" Residue "g GLU 81": "OE1" <-> "OE2" Residue "g GLU 124": "OE1" <-> "OE2" Residue "g GLU 130": "OE1" <-> "OE2" Residue "g ASP 137": "OD1" <-> "OD2" Residue "g ASP 147": "OD1" <-> "OD2" Residue "g ARG 153": "NH1" <-> "NH2" Residue "g ARG 163": "NH1" <-> "NH2" Residue "g GLU 167": "OE1" <-> "OE2" Residue "g ARG 170": "NH1" <-> "NH2" Residue "h ASP 7": "OD1" <-> "OD2" Residue "h ARG 27": "NH1" <-> "NH2" Residue "i PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 13": "NH1" <-> "NH2" Residue "i ASP 14": "OD1" <-> "OD2" Residue "i ARG 37": "NH1" <-> "NH2" Residue "i GLU 43": "OE1" <-> "OE2" Residue "i ASP 60": "OD1" <-> "OD2" Residue "i ASP 71": "OD1" <-> "OD2" Residue "i PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 96": "NH1" <-> "NH2" Residue "i ARG 120": "NH1" <-> "NH2" Residue "j ASP 56": "OD1" <-> "OD2" Residue "j PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j GLU 110": "OE1" <-> "OE2" Residue "k GLU 10": "OE1" <-> "OE2" Residue "k ARG 21": "NH1" <-> "NH2" Residue "k ARG 33": "NH1" <-> "NH2" Residue "k ARG 41": "NH1" <-> "NH2" Residue "k ARG 47": "NH1" <-> "NH2" Residue "k ARG 60": "NH1" <-> "NH2" Residue "k PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ARG 78": "NH1" <-> "NH2" Residue "k ARG 126": "NH1" <-> "NH2" Residue "k GLU 143": "OE1" <-> "OE2" Residue "l ARG 10": "NH1" <-> "NH2" Residue "l ARG 18": "NH1" <-> "NH2" Residue "l ASP 25": "OD1" <-> "OD2" Residue "l PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ARG 40": "NH1" <-> "NH2" Residue "l ARG 44": "NH1" <-> "NH2" Residue "l ARG 50": "NH1" <-> "NH2" Residue "l ARG 55": "NH1" <-> "NH2" Residue "l GLU 90": "OE1" <-> "OE2" Residue "l ARG 114": "NH1" <-> "NH2" Residue "m ARG 12": "NH1" <-> "NH2" Residue "m ARG 17": "NH1" <-> "NH2" Residue "m ARG 22": "NH1" <-> "NH2" Residue "m ARG 46": "NH1" <-> "NH2" Residue "m ARG 63": "NH1" <-> "NH2" Residue "m ARG 64": "NH1" <-> "NH2" Residue "m ARG 69": "NH1" <-> "NH2" Residue "m ARG 71": "NH1" <-> "NH2" Residue "m GLU 82": "OE1" <-> "OE2" Residue "m ARG 96": "NH1" <-> "NH2" Residue "m ASP 117": "OD1" <-> "OD2" Residue "m ARG 118": "NH1" <-> "NH2" Residue "n ASP 2": "OD1" <-> "OD2" Residue "n ARG 10": "NH1" <-> "NH2" Residue "n ARG 16": "NH1" <-> "NH2" Residue "n ARG 25": "NH1" <-> "NH2" Residue "n TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n GLU 46": "OE1" <-> "OE2" Residue "n GLU 60": "OE1" <-> "OE2" Residue "n GLU 80": "OE1" <-> "OE2" Residue "n ARG 81": "NH1" <-> "NH2" Residue "n ASP 89": "OD1" <-> "OD2" Residue "n ARG 94": "NH1" <-> "NH2" Residue "n ARG 102": "NH1" <-> "NH2" Residue "n ARG 111": "NH1" <-> "NH2" Residue "n PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ARG 21": "NH1" <-> "NH2" Residue "o ARG 39": "NH1" <-> "NH2" Residue "o ARG 89": "NH1" <-> "NH2" Residue "o ARG 101": "NH1" <-> "NH2" Residue "o ARG 109": "NH1" <-> "NH2" Residue "p ARG 3": "NH1" <-> "NH2" Residue "p ARG 6": "NH1" <-> "NH2" Residue "p ARG 13": "NH1" <-> "NH2" Residue "p ARG 33": "NH1" <-> "NH2" Residue "p ARG 48": "NH1" <-> "NH2" Residue "p TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ASP 97": "OD1" <-> "OD2" Residue "p GLU 111": "OE1" <-> "OE2" Residue "q GLU 16": "OE1" <-> "OE2" Residue "q ARG 21": "NH1" <-> "NH2" Residue "q ASP 26": "OD1" <-> "OD2" Residue "q GLU 34": "OE1" <-> "OE2" Residue "q GLU 45": "OE1" <-> "OE2" Residue "q ARG 68": "NH1" <-> "NH2" Residue "q GLU 70": "OE1" <-> "OE2" Residue "q ARG 79": "NH1" <-> "NH2" Residue "q ARG 84": "NH1" <-> "NH2" Residue "r ASP 34": "OD1" <-> "OD2" Residue "r GLU 59": "OE1" <-> "OE2" Residue "r ASP 62": "OD1" <-> "OD2" Residue "r ARG 84": "NH1" <-> "NH2" Residue "r ARG 88": "NH1" <-> "NH2" Residue "r ARG 95": "NH1" <-> "NH2" Residue "r ASP 109": "OD1" <-> "OD2" Residue "r ARG 110": "NH1" <-> "NH2" Residue "s GLU 52": "OE1" <-> "OE2" Residue "s ARG 73": "NH1" <-> "NH2" Residue "s GLU 89": "OE1" <-> "OE2" Residue "t ARG 6": "NH1" <-> "NH2" Residue "t ARG 7": "NH1" <-> "NH2" Residue "t ASP 9": "OD1" <-> "OD2" Residue "t ARG 82": "NH1" <-> "NH2" Residue "t ARG 86": "NH1" <-> "NH2" Residue "t PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t ASP 89": "OD1" <-> "OD2" Residue "t ARG 94": "NH1" <-> "NH2" Residue "u PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u GLU 11": "OE1" <-> "OE2" Residue "u PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u GLU 41": "OE1" <-> "OE2" Residue "u ASP 43": "OD1" <-> "OD2" Residue "u PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v GLU 70": "OE1" <-> "OE2" Residue "v GLU 83": "OE1" <-> "OE2" Residue "w ARG 3": "NH1" <-> "NH2" Residue "w ARG 11": "NH1" <-> "NH2" Residue "w PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w ARG 37": "NH1" <-> "NH2" Residue "w GLU 41": "OE1" <-> "OE2" Residue "w GLU 43": "OE1" <-> "OE2" Residue "w ARG 50": "NH1" <-> "NH2" Residue "w ARG 57": "NH1" <-> "NH2" Residue "w ASP 65": "OD1" <-> "OD2" Residue "w ARG 74": "NH1" <-> "NH2" Residue "w GLU 76": "OE1" <-> "OE2" Residue "x GLU 12": "OE1" <-> "OE2" Residue "x GLU 13": "OE1" <-> "OE2" Residue "x GLU 17": "OE1" <-> "OE2" Residue "x ARG 29": "NH1" <-> "NH2" Residue "x ARG 47": "NH1" <-> "NH2" Residue "x ASP 49": "OD1" <-> "OD2" Residue "x ARG 52": "NH1" <-> "NH2" Residue "y ARG 11": "NH1" <-> "NH2" Residue "y ARG 30": "NH1" <-> "NH2" Residue "y GLU 37": "OE1" <-> "OE2" Residue "y ARG 45": "NH1" <-> "NH2" Residue "y GLU 58": "OE1" <-> "OE2" Residue "y GLU 59": "OE1" <-> "OE2" Residue "z ARG 10": "NH1" <-> "NH2" Residue "z ARG 16": "NH1" <-> "NH2" Residue "z GLU 36": "OE1" <-> "OE2" Residue "z ASP 46": "OD1" <-> "OD2" Residue "z ARG 52": "NH1" <-> "NH2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 146513 Number of models: 1 Model: "" Number of chains: 103 Chain: "0" Number of atoms: 417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 417 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 2, 'TRANS': 48} Chain: "1" 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: "2" 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: "3" 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: "4" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 480 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 2, 'TRANS': 57} Chain breaks: 1 Chain: "A" Number of atoms: 155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 155 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 6, 'TRANS': 12} Chain: "B" Number of atoms: 32608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1519, 32608 Classifications: {'RNA': 1519} Modifications used: {'rna2p': 1, 'rna2p_pur': 120, 'rna2p_pyr': 81, 'rna3p': 8, 'rna3p_pur': 744, 'rna3p_pyr': 565} Link IDs: {'rna2p': 202, 'rna3p': 1316} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 7 Chain: "C" 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: "D" 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: "E" 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: "F" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1152 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 5, 'TRANS': 150} Chain: "G" Number of atoms: 839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 839 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "H" Number of atoms: 1203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1203 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 5, 'TRANS': 147} Chain: "I" 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: "J" 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: "K" 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: "L" 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: "M" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 955 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 115} Chain: "N" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 891 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 4, 'TRANS': 110} Chain: "O" 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: "P" 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: "Q" Number of atoms: 643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 643 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 2, 'TRANS': 78} Chain: "R" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 641 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "S" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 544 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "T" Number of atoms: 668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 668 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 5, 'TRANS': 78} Chain: "U" 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: "V" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 589 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "W" Number of atoms: 2792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2792 Classifications: {'peptide': 354} Link IDs: {'PTRANS': 11, 'TRANS': 342} Chain: "X" Number of atoms: 1623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1623 Classifications: {'RNA': 76} Modifications used: {'p5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 4, 'rna3p_pur': 32, 'rna3p_pyr': 33} Link IDs: {'rna2p': 10, 'rna3p': 65} Chain: "Y" Number of atoms: 188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 188 Classifications: {'RNA': 9} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 3, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 7} Chain: "Z" Number of atoms: 1616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1616 Classifications: {'RNA': 76} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 6, 'rna3p_pur': 32, 'rna3p_pyr': 32} Link IDs: {'rna2p': 11, 'rna3p': 64} Chain: "a" Number of atoms: 59128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2753, 59128 Classifications: {'RNA': 2753} Modifications used: {'rna2p': 6, 'rna2p_pur': 267, 'rna2p_pyr': 142, 'rna3p': 16, 'rna3p_pur': 1319, 'rna3p_pyr': 1003} Link IDs: {'rna2p': 414, 'rna3p': 2338} Chain breaks: 3 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 9 Chain: "b" Number of atoms: 2549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 2549 Classifications: {'RNA': 119} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 6, 'rna3p_pur': 56, 'rna3p_pyr': 49} Link IDs: {'rna2p': 14, 'rna3p': 104} Chain: "c" Number of atoms: 2082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2082 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "d" Number of atoms: 1566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1566 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 202} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MEQ:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "e" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "f" Number of atoms: 1410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1410 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "g" Number of atoms: 1323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1323 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "h" Number of atoms: 303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 303 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 2, 'TRANS': 38} Chain: "i" 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: "j" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 946 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 5, 'TRANS': 117} Chain: "k" 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: "l" 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: "m" 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: "n" 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: "o" 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: "p" 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: "q" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'TRANS': 101} Chain: "r" 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: "s" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 738 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 1, 'TRANS': 91} Chain: "t" 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: "u" 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: "v" Number of atoms: 586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 586 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "w" 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: "x" Number of atoms: 501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 501 Classifications: {'peptide': 62} Modifications used: {'COO': 1} Link IDs: {'TRANS': 61} Chain: "y" 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: "z" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 444 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "3" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'A2G': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 89 Unusual residues: {' MG': 89} Classifications: {'undetermined': 89} Link IDs: {None: 88} Chain: "a" Number of atoms: 222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 222 Unusual residues: {' MG': 208, 'SPM': 1} Classifications: {'undetermined': 209} Link IDs: {None: 208} Chain: "b" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' MG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "c" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "d" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "0" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "1" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "2" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "3" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "B" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 189 Classifications: {'water': 189} Link IDs: {None: 188} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "W" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "X" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Y" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "a" Number of atoms: 1331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1331, 1331 Classifications: {'water': 1331} Link IDs: {None: 1330} Chain: "b" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "c" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 41 Classifications: {'water': 41} Link IDs: {None: 40} Chain: "d" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "e" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "h" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "i" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "j" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "k" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "l" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "m" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "n" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "o" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "p" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "q" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "r" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "s" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "t" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "u" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "v" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "w" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "z" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1383 SG CYS 3 11 116.629 146.873 174.413 1.00 63.87 S ATOM 1408 SG CYS 3 14 114.958 150.142 172.610 1.00 55.03 S ATOM 1511 SG CYS 3 27 118.275 149.920 174.563 1.00 55.31 S ATOM 1730 SG CYS 4 16 58.167 67.645 123.829 1.00117.15 S ATOM 1742 SG CYS 4 18 57.095 65.529 126.712 1.00128.32 S ATOM 1884 SG CYS 4 37 57.245 69.317 127.024 1.00111.13 S ATOM 1905 SG CYS 4 40 60.518 67.360 126.958 1.00108.38 S Time building chain proxies: 55.90, per 1000 atoms: 0.38 Number of scatterers: 146513 At special positions: 0 Unit cell: (264.8, 276, 221.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 160 16.00 P 4551 15.00 Mg 305 11.99 O 41714 8.00 N 26952 7.00 C 72829 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 63.98 Conformation dependent library (CDL) restraints added in 8.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 3 101 " pdb="ZN ZN 3 101 " - pdb=" ND1 HIS 3 33 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 14 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 11 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 27 " pdb=" ZN 4 101 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 16 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 37 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 40 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 18 " Number of angles added : 9 11706 Ramachandran restraints generated. 5853 Oldfield, 0 Emsley, 5853 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10960 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: 185 helices and 73 sheets defined 39.9% alpha, 19.7% beta 1538 base pairs and 2387 stacking pairs defined. Time for finding SS restraints: 72.18 Creating SS restraints... Processing helix chain '1' and resid 8 through 16 Processing helix chain '1' and resid 17 through 25 removed outlier: 4.080A pdb=" N THR 1 24 " --> pdb=" O ALA 1 20 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N LYS 1 25 " --> pdb=" O ARG 1 21 " (cutoff:3.500A) Processing helix chain '1' and resid 26 through 38 Processing helix chain '2' and resid 7 through 14 removed outlier: 3.521A pdb=" N ARG 2 13 " --> pdb=" O GLY 2 9 " (cutoff:3.500A) Processing helix chain '2' and resid 32 through 37 removed outlier: 4.574A pdb=" N LYS 2 36 " --> pdb=" O ILE 2 32 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N ALA 2 37 " --> pdb=" O LEU 2 33 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 32 through 37' Processing helix chain '2' and resid 38 through 46 Proline residue: 2 46 - end of helix Processing helix chain '2' and resid 51 through 63 removed outlier: 4.520A pdb=" N GLY 2 56 " --> pdb=" O LYS 2 52 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N LEU 2 57 " --> pdb=" O GLY 2 53 " (cutoff:3.500A) Proline residue: 2 63 - end of helix Processing helix chain '4' and resid 41 through 46 Processing helix chain '4' and resid 55 through 64 Processing helix chain 'C' and resid 5 through 13 removed outlier: 3.926A pdb=" N MET C 9 " --> pdb=" O SER C 5 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LYS C 11 " --> pdb=" O ARG C 7 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ALA C 12 " --> pdb=" O ASP C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 32 removed outlier: 4.361A pdb=" N LYS C 28 " --> pdb=" O ASN C 24 " (cutoff:3.500A) Proline residue: C 29 - end of helix removed outlier: 5.473A pdb=" N PHE C 32 " --> pdb=" O LYS C 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 24 through 32' Processing helix chain 'C' and resid 42 through 64 Proline residue: C 48 - end of helix removed outlier: 4.260A pdb=" N LYS C 64 " --> pdb=" O ILE C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 88 Processing helix chain 'C' and resid 103 through 124 removed outlier: 4.072A pdb=" N GLN C 109 " --> pdb=" O LYS C 105 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N SER C 110 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N THR C 119 " --> pdb=" O LYS C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 130 removed outlier: 3.809A pdb=" N LEU C 129 " --> pdb=" O THR C 125 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N THR C 130 " --> pdb=" O PHE C 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 125 through 130' Processing helix chain 'C' and resid 131 through 148 removed outlier: 3.623A pdb=" N LEU C 135 " --> pdb=" O LYS C 131 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER C 147 " --> pdb=" O LYS C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 170 removed outlier: 3.670A pdb=" N GLU C 169 " --> pdb=" O ASP C 165 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N HIS C 170 " --> pdb=" O ALA C 166 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 165 through 170' Processing helix chain 'C' and resid 171 through 180 Processing helix chain 'C' and resid 206 through 227 removed outlier: 3.638A pdb=" N LEU C 212 " --> pdb=" O ARG C 208 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN C 227 " --> pdb=" O GLU C 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 12 removed outlier: 4.374A pdb=" N ARG D 11 " --> pdb=" O PRO D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 48 removed outlier: 4.306A pdb=" N ALA D 30 " --> pdb=" O THR D 26 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N ASP D 31 " --> pdb=" O LYS D 27 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL D 39 " --> pdb=" O SER D 35 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA D 48 " --> pdb=" O THR D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 78 removed outlier: 3.804A pdb=" N VAL D 76 " --> pdb=" O ARG D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 96 removed outlier: 5.451A pdb=" N GLU D 85 " --> pdb=" O GLY D 81 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS D 86 " --> pdb=" O GLU D 82 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL D 90 " --> pdb=" O LYS D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 127 Processing helix chain 'D' and resid 129 through 145 removed outlier: 3.977A pdb=" N ALA D 137 " --> pdb=" O ALA D 133 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 16 removed outlier: 4.292A pdb=" N LEU E 11 " --> pdb=" O PRO E 7 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER E 12 " --> pdb=" O LYS E 8 " (cutoff:3.500A) Processing helix chain 'E' and resid 27 through 32 removed outlier: 3.771A pdb=" N LYS E 31 " --> pdb=" O ALA E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 66 removed outlier: 3.712A pdb=" N TYR E 65 " --> pdb=" O VAL E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 83 removed outlier: 5.476A pdb=" N LYS E 83 " --> pdb=" O ALA E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 97 Processing helix chain 'E' and resid 98 through 106 Processing helix chain 'E' and resid 110 through 121 removed outlier: 3.514A pdb=" N ARG E 115 " --> pdb=" O ARG E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 152 removed outlier: 4.495A pdb=" N LYS E 151 " --> pdb=" O GLU E 147 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N GLN E 152 " --> pdb=" O LYS E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 166 removed outlier: 3.795A pdb=" N ALA E 158 " --> pdb=" O ARG E 154 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N LEU E 159 " --> pdb=" O VAL E 155 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLU E 160 " --> pdb=" O LYS E 156 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N LEU E 161 " --> pdb=" O ALA E 157 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLN E 164 " --> pdb=" O GLU E 160 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ARG E 165 " --> pdb=" O LEU E 161 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N GLU E 166 " --> pdb=" O ALA E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 192 removed outlier: 3.657A pdb=" N LEU E 191 " --> pdb=" O GLU E 187 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N SER E 192 " --> pdb=" O ARG E 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 187 through 192' Processing helix chain 'E' and resid 196 through 206 removed outlier: 4.034A pdb=" N ILE E 200 " --> pdb=" O ASN E 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 71 removed outlier: 3.622A pdb=" N ARG F 69 " --> pdb=" O GLU F 65 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N MET F 71 " --> pdb=" O ALA F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 119 removed outlier: 4.178A pdb=" N ALA F 113 " --> pdb=" O GLY F 109 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 147 removed outlier: 3.959A pdb=" N MET F 147 " --> pdb=" O GLY F 143 " (cutoff:3.500A) Processing helix chain 'F' and resid 149 through 158 Processing helix chain 'F' and resid 160 through 165 removed outlier: 3.950A pdb=" N ILE F 164 " --> pdb=" O SER F 160 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU F 165 " --> pdb=" O VAL F 161 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 160 through 165' Processing helix chain 'G' and resid 11 through 16 removed outlier: 5.393A pdb=" N GLU G 16 " --> pdb=" O PRO G 12 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 33 Processing helix chain 'G' and resid 67 through 81 removed outlier: 3.838A pdb=" N ILE G 71 " --> pdb=" O PRO G 67 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N GLU G 73 " --> pdb=" O GLU G 69 " (cutoff:3.500A) Processing helix chain 'H' and resid 20 through 31 Processing helix chain 'H' and resid 35 through 55 Processing helix chain 'H' and resid 57 through 70 removed outlier: 3.617A pdb=" N ASN H 68 " --> pdb=" O VAL H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 92 through 111 removed outlier: 3.536A pdb=" N ASN H 97 " --> pdb=" O PRO H 93 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LYS H 110 " --> pdb=" O GLU H 106 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ARG H 111 " --> pdb=" O ALA H 107 " (cutoff:3.500A) Processing helix chain 'H' and resid 115 through 130 Processing helix chain 'H' and resid 132 through 149 removed outlier: 4.598A pdb=" N GLU H 139 " --> pdb=" O VAL H 135 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ALA H 145 " --> pdb=" O VAL H 141 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ASN H 148 " --> pdb=" O MET H 144 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N LYS H 149 " --> pdb=" O ALA H 145 " (cutoff:3.500A) Processing helix chain 'I' and resid 5 through 21 Processing helix chain 'I' and resid 30 through 44 Processing helix chain 'I' and resid 112 through 120 Processing helix chain 'J' and resid 34 through 39 Processing helix chain 'J' and resid 41 through 56 Proline residue: J 51 - end of helix Processing helix chain 'J' and resid 71 through 91 Processing helix chain 'J' and resid 92 through 102 removed outlier: 4.605A pdb=" N SER J 96 " --> pdb=" O GLU J 92 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N GLU J 97 " --> pdb=" O SER J 93 " (cutoff:3.500A) Processing helix chain 'K' and resid 14 through 33 removed outlier: 4.290A pdb=" N ILE K 18 " --> pdb=" O ASP K 14 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG K 31 " --> pdb=" O GLU K 27 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N THR K 32 " --> pdb=" O THR K 28 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLY K 33 " --> pdb=" O ALA K 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 80 through 90 removed outlier: 3.799A pdb=" N ASP K 85 " --> pdb=" O GLU K 81 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N MET K 88 " --> pdb=" O VAL K 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 46 through 51 removed outlier: 4.489A pdb=" N GLY L 51 " --> pdb=" O ALA L 47 " (cutoff:3.500A) Processing helix chain 'L' and resid 54 through 59 removed outlier: 3.785A pdb=" N SER L 58 " --> pdb=" O GLY L 54 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N THR L 59 " --> pdb=" O SER L 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 54 through 59' Processing helix chain 'L' and resid 60 through 75 removed outlier: 3.657A pdb=" N LYS L 75 " --> pdb=" O ALA L 71 " (cutoff:3.500A) Processing helix chain 'L' and resid 91 through 104 removed outlier: 4.378A pdb=" N SER L 95 " --> pdb=" O PRO L 91 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N ILE L 97 " --> pdb=" O ARG L 93 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG L 98 " --> pdb=" O GLU L 94 " (cutoff:3.500A) Processing helix chain 'M' and resid 3 through 11 Proline residue: M 11 - end of helix Processing helix chain 'M' and resid 113 through 118 removed outlier: 3.647A pdb=" N TYR M 117 " --> pdb=" O ALA M 113 " (cutoff:3.500A) Processing helix chain 'N' and resid 14 through 22 removed outlier: 4.536A pdb=" N THR N 20 " --> pdb=" O VAL N 16 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N SER N 21 " --> pdb=" O ILE N 17 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ILE N 22 " --> pdb=" O ALA N 18 " (cutoff:3.500A) Processing helix chain 'N' and resid 26 through 38 Processing helix chain 'N' and resid 44 through 49 removed outlier: 5.684A pdb=" N SER N 49 " --> pdb=" O ILE N 45 " (cutoff:3.500A) Processing helix chain 'N' and resid 50 through 64 removed outlier: 4.154A pdb=" N LYS N 62 " --> pdb=" O ASP N 58 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N PHE N 63 " --> pdb=" O GLU N 59 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N VAL N 64 " --> pdb=" O VAL N 60 " (cutoff:3.500A) Processing helix chain 'N' and resid 66 through 84 removed outlier: 4.323A pdb=" N GLU N 72 " --> pdb=" O ASP N 68 " (cutoff:3.500A) Processing helix chain 'N' and resid 85 through 94 Processing helix chain 'N' and resid 106 through 111 Processing helix chain 'O' and resid 3 through 21 removed outlier: 3.614A pdb=" N GLU O 10 " --> pdb=" O MET O 6 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N PHE O 21 " --> pdb=" O ALA O 17 " (cutoff:3.500A) Processing helix chain 'O' and resid 22 through 33 removed outlier: 4.035A pdb=" N ASP O 33 " --> pdb=" O ALA O 29 " (cutoff:3.500A) Processing helix chain 'O' and resid 37 through 51 removed outlier: 3.598A pdb=" N GLN O 49 " --> pdb=" O VAL O 45 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N THR O 50 " --> pdb=" O LEU O 46 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU O 51 " --> pdb=" O LYS O 47 " (cutoff:3.500A) Processing helix chain 'O' and resid 80 through 91 Processing helix chain 'O' and resid 52 through 57 Proline residue: O 57 - end of helix Processing helix chain 'P' and resid 4 through 16 removed outlier: 3.505A pdb=" N ILE P 11 " --> pdb=" O ALA P 7 " (cutoff:3.500A) Processing helix chain 'P' and resid 24 through 44 removed outlier: 3.612A pdb=" N ASN P 37 " --> pdb=" O THR P 33 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLY P 41 " --> pdb=" O ASN P 37 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N HIS P 42 " --> pdb=" O HIS P 38 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA P 44 " --> pdb=" O GLN P 40 " (cutoff:3.500A) Processing helix chain 'P' and resid 49 through 74 removed outlier: 3.850A pdb=" N GLY P 55 " --> pdb=" O HIS P 51 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ARG P 72 " --> pdb=" O ASP P 68 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS P 73 " --> pdb=" O TYR P 69 " (cutoff:3.500A) Processing helix chain 'P' and resid 75 through 86 Processing helix chain 'Q' and resid 53 through 64 Processing helix chain 'Q' and resid 68 through 80 Processing helix chain 'S' and resid 11 through 17 Processing helix chain 'S' and resid 25 through 34 removed outlier: 4.255A pdb=" N ASN S 31 " --> pdb=" O ALA S 27 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N TYR S 32 " --> pdb=" O THR S 28 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N THR S 34 " --> pdb=" O LYS S 30 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 46 Processing helix chain 'S' and resid 48 through 66 removed outlier: 3.515A pdb=" N GLN S 54 " --> pdb=" O LYS S 50 " (cutoff:3.500A) Processing helix chain 'T' and resid 12 through 26 removed outlier: 3.501A pdb=" N GLU T 24 " --> pdb=" O GLU T 20 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SER T 25 " --> pdb=" O LYS T 21 " (cutoff:3.500A) Processing helix chain 'T' and resid 70 through 76 removed outlier: 4.403A pdb=" N PHE T 74 " --> pdb=" O LYS T 70 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ALA T 75 " --> pdb=" O LEU T 71 " (cutoff:3.500A) Proline residue: T 76 - end of helix No H-bonds generated for 'chain 'T' and resid 70 through 76' Processing helix chain 'U' and resid 4 through 41 removed outlier: 3.602A pdb=" N VAL U 35 " --> pdb=" O PHE U 31 " (cutoff:3.500A) Processing helix chain 'U' and resid 43 through 65 Proline residue: U 56 - end of helix Processing helix chain 'U' and resid 68 through 87 removed outlier: 3.568A pdb=" N ALA U 87 " --> pdb=" O ILE U 83 " (cutoff:3.500A) Processing helix chain 'V' and resid 11 through 27 Processing helix chain 'V' and resid 28 through 37 removed outlier: 4.780A pdb=" N PHE V 37 " --> pdb=" O ARG V 33 " (cutoff:3.500A) Processing helix chain 'V' and resid 40 through 68 removed outlier: 3.666A pdb=" N LYS V 59 " --> pdb=" O ARG V 55 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU V 60 " --> pdb=" O HIS V 56 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU V 63 " --> pdb=" O LYS V 59 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ASN V 64 " --> pdb=" O LEU V 60 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N ALA V 65 " --> pdb=" O ALA V 61 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ARG V 66 " --> pdb=" O ARG V 62 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N THR V 68 " --> pdb=" O ASN V 64 " (cutoff:3.500A) Processing helix chain 'W' and resid 5 through 21 removed outlier: 3.899A pdb=" N HIS W 13 " --> pdb=" O LEU W 9 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU W 17 " --> pdb=" O HIS W 13 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N GLU W 18 " --> pdb=" O GLU W 14 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N VAL W 19 " --> pdb=" O ARG W 15 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN W 20 " --> pdb=" O HIS W 16 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ALA W 21 " --> pdb=" O GLU W 17 " (cutoff:3.500A) Processing helix chain 'W' and resid 35 through 57 removed outlier: 3.854A pdb=" N ARG W 40 " --> pdb=" O ARG W 36 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N GLU W 41 " --> pdb=" O ALA W 37 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLN W 44 " --> pdb=" O ARG W 40 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU W 45 " --> pdb=" O GLU W 41 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ASP W 47 " --> pdb=" O ALA W 43 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N VAL W 48 " --> pdb=" O GLN W 44 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N CYS W 51 " --> pdb=" O ASP W 47 " (cutoff:3.500A) Processing helix chain 'W' and resid 59 through 66 removed outlier: 4.092A pdb=" N GLU W 63 " --> pdb=" O GLN W 59 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N THR W 64 " --> pdb=" O GLU W 60 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLN W 66 " --> pdb=" O ILE W 62 " (cutoff:3.500A) Processing helix chain 'W' and resid 77 through 101 removed outlier: 4.387A pdb=" N GLU W 81 " --> pdb=" O MET W 77 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU W 82 " --> pdb=" O ALA W 78 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL W 98 " --> pdb=" O GLN W 94 " (cutoff:3.500A) Processing helix chain 'W' and resid 104 through 109 removed outlier: 4.113A pdb=" N GLU W 108 " --> pdb=" O ASP W 104 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ARG W 109 " --> pdb=" O PRO W 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 104 through 109' Processing helix chain 'W' and resid 121 through 143 removed outlier: 3.711A pdb=" N ARG W 142 " --> pdb=" O TYR W 138 " (cutoff:3.500A) Processing helix chain 'W' and resid 170 through 176 removed outlier: 3.878A pdb=" N ARG W 174 " --> pdb=" O GLY W 170 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS W 176 " --> pdb=" O TYR W 172 " (cutoff:3.500A) Processing helix chain 'W' and resid 218 through 223 removed outlier: 3.750A pdb=" N LEU W 222 " --> pdb=" O ASN W 218 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N ARG W 223 " --> pdb=" O PRO W 219 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 218 through 223' Processing helix chain 'W' and resid 234 through 240 Processing helix chain 'W' and resid 262 through 299 Processing helix chain 'W' and resid 328 through 335 Processing helix chain 'W' and resid 338 through 356 removed outlier: 4.186A pdb=" N GLU W 342 " --> pdb=" O ASP W 338 " (cutoff:3.500A) Proline residue: W 343 - end of helix removed outlier: 3.517A pdb=" N ASP W 351 " --> pdb=" O GLU W 347 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA W 354 " --> pdb=" O ALA W 350 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU W 356 " --> pdb=" O GLN W 352 " (cutoff:3.500A) Processing helix chain 'c' and resid 10 through 15 removed outlier: 4.953A pdb=" N HIS c 15 " --> pdb=" O PRO c 11 " (cutoff:3.500A) Processing helix chain 'c' and resid 30 through 35 removed outlier: 3.892A pdb=" N LEU c 34 " --> pdb=" O PHE c 30 " (cutoff:3.500A) removed outlier: 5.688A 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: 3.550A 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: 3.938A pdb=" N ALA c 211 " --> pdb=" O LYS c 207 " (cutoff:3.500A) Processing helix chain 'c' and resid 221 through 226 removed outlier: 3.819A pdb=" N MET c 225 " --> pdb=" O ARG c 221 " (cutoff:3.500A) removed outlier: 5.286A 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 260 through 268 removed outlier: 4.680A pdb=" N LYS c 265 " --> pdb=" O LYS c 261 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N PHE c 266 " --> pdb=" O ARG c 262 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE c 267 " --> pdb=" O THR c 263 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N VAL c 268 " --> pdb=" O ASP c 264 " (cutoff:3.500A) Processing helix chain 'd' and resid 56 through 61 removed outlier: 5.293A pdb=" N THR d 61 " --> pdb=" O ALA d 57 " (cutoff:3.500A) Processing helix chain 'd' and resid 62 through 72 removed outlier: 3.512A pdb=" N ALA d 71 " --> pdb=" O HIS d 67 " (cutoff:3.500A) Processing helix chain 'd' and resid 98 through 103 removed outlier: 4.167A pdb=" N ALA d 102 " --> pdb=" O VAL d 98 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N ASP d 103 " --> pdb=" O GLU d 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 98 through 103' Processing helix chain 'd' and resid 120 through 125 Processing helix chain 'd' and resid 39 through 44 Processing helix chain 'e' and resid 24 through 40 removed outlier: 3.572A pdb=" N ARG e 40 " --> pdb=" O ALA e 36 " (cutoff:3.500A) Processing helix chain 'e' and resid 97 through 116 removed outlier: 3.755A pdb=" N ASP e 116 " --> pdb=" O LEU e 112 " (cutoff:3.500A) Processing helix chain 'e' and resid 130 through 142 removed outlier: 3.627A pdb=" N LEU e 134 " --> pdb=" O LYS e 130 " (cutoff:3.500A) Processing helix chain 'e' and resid 154 through 163 removed outlier: 4.486A pdb=" N ASN e 163 " --> pdb=" O LEU e 159 " (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 21 removed outlier: 5.866A pdb=" N VAL f 13 " --> pdb=" O LYS f 9 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N LYS f 14 " --> pdb=" O ASP f 10 " (cutoff:3.500A) Processing helix chain 'f' and resid 42 through 47 removed outlier: 3.644A pdb=" N ASP f 46 " --> pdb=" O GLU f 42 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LYS f 47 " --> pdb=" O ALA f 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 42 through 47' Processing helix chain 'f' and resid 48 through 62 Processing helix chain 'f' and resid 93 through 111 removed outlier: 3.724A pdb=" N ILE f 106 " --> pdb=" O ARG f 102 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA f 107 " --> pdb=" O LEU f 103 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N VAL f 108 " --> pdb=" O ILE f 104 " (cutoff:3.500A) Proline residue: f 109 - end of helix Processing helix chain 'f' and resid 162 through 174 removed outlier: 3.708A pdb=" N PHE f 173 " --> pdb=" O LEU f 169 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASP f 174 " --> pdb=" O LEU f 170 " (cutoff:3.500A) Processing helix chain 'f' and resid 134 through 139 removed outlier: 3.636A pdb=" N ILE f 137 " --> pdb=" O GLU f 134 " (cutoff:3.500A) removed outlier: 3.514A 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 Proline residue: g 8 - end of helix Processing helix chain 'g' and resid 60 through 81 Processing helix chain 'g' and resid 137 through 153 removed outlier: 3.606A pdb=" N TYR g 151 " --> pdb=" O ASP g 147 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ARG g 152 " --> pdb=" O LEU g 148 " (cutoff:3.500A) Processing helix chain 'h' and resid 22 through 28 Processing helix chain 'h' and resid 29 through 34 Processing helix chain 'i' and resid 24 through 38 removed outlier: 3.770A pdb=" N GLU i 31 " --> pdb=" O ARG i 27 " (cutoff:3.500A) Processing helix chain 'i' and resid 88 through 96 Processing helix chain 'i' and resid 97 through 110 removed outlier: 4.254A pdb=" N ILE i 101 " --> pdb=" O PRO i 97 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N MET i 108 " --> pdb=" O ALA i 104 " (cutoff:3.500A) Proline residue: i 110 - end of helix Processing helix chain 'i' and resid 112 through 123 removed outlier: 3.961A pdb=" N LYS i 121 " --> pdb=" O ALA i 117 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LEU i 122 " --> pdb=" O MET i 118 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N LYS i 123 " --> pdb=" O PHE i 119 " (cutoff:3.500A) Processing helix chain 'i' and resid 67 through 72 removed outlier: 4.296A pdb=" N LYS i 72 " --> pdb=" O ASN i 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 67 through 72' Processing helix chain 'j' and resid 112 through 119 Processing helix chain 'k' and resid 37 through 42 removed outlier: 3.984A pdb=" N ARG k 41 " --> pdb=" O GLY k 37 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N SER k 42 " --> pdb=" O GLN k 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 37 through 42' Processing helix chain 'k' and resid 56 through 62 Proline residue: k 62 - end of helix Processing helix chain 'k' and resid 68 through 75 removed outlier: 3.933A pdb=" N ALA k 72 " --> pdb=" O SER k 68 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ILE k 73 " --> pdb=" O ARG k 69 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N ALA k 75 " --> pdb=" O ALA k 71 " (cutoff:3.500A) Processing helix chain 'k' and resid 78 through 85 removed outlier: 3.775A pdb=" N LEU k 82 " --> pdb=" O ARG k 78 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ALA k 83 " --> pdb=" O LEU k 79 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LYS k 84 " --> pdb=" O SER k 80 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL k 85 " --> pdb=" O ASP k 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 78 through 85' Processing helix chain 'k' and resid 91 through 99 removed outlier: 3.661A pdb=" N LEU k 95 " --> pdb=" O ASP k 91 " (cutoff:3.500A) Processing helix chain 'k' and resid 128 through 139 Processing helix chain 'l' and resid 42 through 58 Processing helix chain 'l' and resid 109 through 125 removed outlier: 4.058A pdb=" N LYS l 123 " --> pdb=" O LEU l 119 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU l 124 " --> pdb=" O ALA l 120 " (cutoff:3.500A) Proline residue: l 125 - end of helix Processing helix chain 'm' and resid 13 through 32 Processing helix chain 'm' and resid 37 through 58 removed outlier: 3.524A pdb=" N ARG m 45 " --> pdb=" O ALA m 41 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ARG m 46 " --> pdb=" O LYS m 42 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VAL m 47 " --> pdb=" O GLU m 43 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLU m 49 " --> pdb=" O ARG m 45 " (cutoff:3.500A) Proline residue: m 50 - end of helix removed outlier: 4.506A pdb=" N THR m 57 " --> pdb=" O THR m 53 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N ASP m 58 " --> pdb=" O LEU m 54 " (cutoff:3.500A) Processing helix chain 'm' and resid 59 through 71 removed outlier: 3.855A pdb=" N THR m 70 " --> pdb=" O ALA m 66 " (cutoff:3.500A) Processing helix chain 'm' and resid 72 through 88 removed outlier: 3.861A pdb=" N LEU m 83 " --> pdb=" O LEU m 79 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N GLY m 84 " --> pdb=" O PHE m 80 " (cutoff:3.500A) Proline residue: m 85 - end of helix Processing helix chain 'n' and resid 2 through 22 removed outlier: 4.290A pdb=" N ARG n 13 " --> pdb=" O ARG n 9 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N ALA n 14 " --> pdb=" O ARG n 10 " (cutoff:3.500A) Processing helix chain 'n' and resid 55 through 63 removed outlier: 4.218A pdb=" N GLU n 60 " --> pdb=" O LYS n 56 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N GLN n 61 " --> pdb=" O ALA n 57 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU n 62 " --> pdb=" O ILE n 58 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N LYS n 63 " --> pdb=" O ALA n 59 " (cutoff:3.500A) Processing helix chain 'n' and resid 67 through 86 removed outlier: 3.815A pdb=" N LYS n 85 " --> pdb=" O ARG n 81 " (cutoff:3.500A) Processing helix chain 'n' and resid 101 through 114 Processing helix chain 'o' and resid 2 through 13 removed outlier: 4.016A pdb=" N GLN o 12 " --> pdb=" O LEU o 8 " (cutoff:3.500A) Processing helix chain 'o' and resid 97 through 104 removed outlier: 4.453A pdb=" N ARG o 101 " --> pdb=" O LEU o 97 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N GLU o 102 " --> pdb=" O TYR o 98 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ARG o 103 " --> pdb=" O TYR o 99 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N THR o 104 " --> pdb=" O LEU o 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'o' and resid 97 through 104' Processing helix chain 'p' and resid 6 through 22 removed outlier: 3.509A pdb=" N LYS p 22 " --> pdb=" O LEU p 18 " (cutoff:3.500A) Processing helix chain 'p' and resid 26 through 31 removed outlier: 3.625A pdb=" N ARG p 30 " --> pdb=" O GLY p 26 " (cutoff:3.500A) Processing helix chain 'p' and resid 32 through 37 removed outlier: 3.821A pdb=" N GLN p 37 " --> pdb=" O ARG p 33 " (cutoff:3.500A) Processing helix chain 'p' and resid 39 through 73 removed outlier: 3.911A pdb=" N ARG p 51 " --> pdb=" O TYR p 47 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LYS p 54 " --> pdb=" O ARG p 50 " (cutoff:3.500A) Processing helix chain 'p' and resid 75 through 87 Processing helix chain 'p' and resid 91 through 102 Processing helix chain 'p' and resid 103 through 118 Processing helix chain 'r' and resid 13 through 25 removed outlier: 4.076A pdb=" N VAL r 20 " --> pdb=" O LYS r 16 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LEU r 23 " --> pdb=" O LEU r 19 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ILE r 24 " --> pdb=" O VAL r 20 " (cutoff:3.500A) Processing helix chain 'r' and resid 28 through 39 Processing helix chain 'r' and resid 41 through 61 removed outlier: 3.659A pdb=" N VAL r 45 " --> pdb=" O LYS r 41 " (cutoff:3.500A) Processing helix chain 'r' and resid 65 through 70 removed outlier: 3.575A pdb=" N LEU r 69 " --> pdb=" O ASP r 65 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N LYS r 70 " --> pdb=" O ILE r 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 65 through 70' Processing helix chain 's' and resid 3 through 11 removed outlier: 4.011A pdb=" N LYS s 9 " --> pdb=" O GLU s 5 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N VAL s 10 " --> pdb=" O ARG s 6 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N LEU s 11 " --> pdb=" O LEU s 7 " (cutoff:3.500A) Processing helix chain 's' and resid 17 through 26 Processing helix chain 's' and resid 39 through 51 Processing helix chain 't' and resid 66 through 71 removed outlier: 3.883A pdb=" N VAL t 70 " --> pdb=" O GLN t 66 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N ALA t 71 " --> pdb=" O VAL t 67 " (cutoff:3.500A) No H-bonds generated for 'chain 't' and resid 66 through 71' Processing helix chain 'u' and resid 13 through 24 Processing helix chain 'u' and resid 43 through 53 removed outlier: 3.647A pdb=" N ALA u 52 " --> pdb=" O MET u 48 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N LYS u 53 " --> pdb=" O ASN u 49 " (cutoff:3.500A) Processing helix chain 'u' and resid 54 through 59 removed outlier: 4.003A pdb=" N SER u 58 " --> pdb=" O ALA u 54 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLU u 59 " --> pdb=" O GLU u 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'u' and resid 54 through 59' Processing helix chain 'w' and resid 52 through 63 Processing helix chain 'w' and resid 64 through 75 Processing helix chain 'x' and resid 2 through 10 removed outlier: 3.734A pdb=" N GLU x 8 " --> pdb=" O LYS x 4 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LYS x 9 " --> pdb=" O GLU x 5 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N SER x 10 " --> pdb=" O LEU x 6 " (cutoff:3.500A) Processing helix chain 'x' and resid 11 through 35 removed outlier: 3.634A pdb=" N THR x 16 " --> pdb=" O GLU x 12 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLU x 17 " --> pdb=" O GLU x 13 " (cutoff:3.500A) Processing helix chain 'x' and resid 39 through 62 removed outlier: 4.732A pdb=" N LEU x 43 " --> pdb=" O GLN x 39 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N LYS x 44 " --> pdb=" O SER x 40 " (cutoff:3.500A) Processing helix chain 'y' and resid 17 through 28 Processing helix chain 'y' and resid 41 through 52 Processing helix chain 'z' and resid 9 through 19 removed outlier: 4.848A pdb=" N HIS z 19 " --> pdb=" O MET z 15 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain '0' and resid 19 through 25 removed outlier: 5.933A pdb=" N HIS 0 19 " --> pdb=" O SER 0 13 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LEU 0 34 " --> pdb=" O GLU 0 51 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain '2' and resid 22 through 25 removed outlier: 5.627A pdb=" N PHE 2 22 " --> pdb=" O VAL 2 50 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain '3' and resid 1 through 5 removed outlier: 7.068A pdb=" N HIS 3 33 " --> pdb=" O CYS 3 27 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N CYS 3 27 " --> pdb=" O HIS 3 33 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N ILE 3 23 " --> pdb=" O GLN 3 37 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER 3 28 " --> pdb=" O ASN 3 13 " (cutoff:3.500A) removed outlier: 8.384A pdb=" N ASN 3 13 " --> pdb=" O SER 3 28 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain '4' and resid 20 through 25 removed outlier: 4.528A pdb=" N ASN 4 20 " --> pdb=" O CYS 4 16 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'C' and resid 15 through 18 removed outlier: 4.931A pdb=" N HIS C 15 " --> pdb=" O ILE C 41 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N HIS C 39 " --> pdb=" O GLY C 17 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'C' and resid 89 through 93 Processing sheet with id= 7, first strand: chain 'D' and resid 53 through 59 removed outlier: 3.567A pdb=" N ARG D 54 " --> pdb=" O HIS D 69 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'D' and resid 164 through 169 removed outlier: 4.863A pdb=" N GLY D 194 " --> pdb=" O THR D 191 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N THR D 191 " --> pdb=" O GLY D 194 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ASP D 181 " --> pdb=" O LYS D 204 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'E' and resid 141 through 145 removed outlier: 3.733A pdb=" N ASP E 141 " --> pdb=" O PHE E 182 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N MET E 178 " --> pdb=" O ILE E 145 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU E 179 " --> pdb=" O ASP E 174 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'F' and resid 11 through 16 removed outlier: 6.774A pdb=" N LEU F 36 " --> pdb=" O ILE F 16 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'F' and resid 84 through 88 removed outlier: 3.724A pdb=" N ALA F 99 " --> pdb=" O ASN F 122 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N ASN F 122 " --> pdb=" O ALA F 99 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'F' and resid 33 through 41 removed outlier: 6.923A pdb=" N ARG F 45 " --> pdb=" O ASP F 41 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'G' and resid 38 through 43 removed outlier: 4.244A pdb=" N ARG G 38 " --> pdb=" O ASN G 63 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N TYR G 59 " --> pdb=" O TRP G 42 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N HIS G 3 " --> pdb=" O THR G 92 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ARG G 86 " --> pdb=" O MET G 9 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'G' and resid 44 through 47 removed outlier: 6.740A pdb=" N HIS G 55 " --> pdb=" O LEU G 47 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'H' and resid 72 through 77 removed outlier: 6.439A pdb=" N THR H 72 " --> pdb=" O VAL H 91 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'I' and resid 23 through 29 removed outlier: 5.864A pdb=" N ALA I 23 " --> pdb=" O LEU I 63 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASP I 48 " --> pdb=" O THR I 62 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'I' and resid 74 through 77 removed outlier: 6.746A pdb=" N VAL I 103 " --> pdb=" O ILE I 126 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'J' and resid 5 through 11 removed outlier: 4.529A pdb=" N LYS J 27 " --> pdb=" O LEU J 61 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU J 63 " --> pdb=" O LYS J 27 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'K' and resid 39 through 42 removed outlier: 4.455A pdb=" N LEU K 71 " --> pdb=" O LEU K 42 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'K' and resid 44 through 52 Processing sheet with id= 21, first strand: chain 'L' and resid 29 through 36 removed outlier: 3.598A pdb=" N ASN L 29 " --> pdb=" O SER L 26 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'M' and resid 29 through 32 removed outlier: 5.019A pdb=" N LEU M 81 " --> pdb=" O VAL M 98 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'M' and resid 36 through 41 removed outlier: 3.730A pdb=" N ARG M 36 " --> pdb=" O ARG M 54 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N LYS M 51 " --> pdb=" O ILE M 67 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N PHE M 61 " --> pdb=" O LEU M 57 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'Q' and resid 4 through 10 removed outlier: 3.830A pdb=" N GLY Q 37 " --> pdb=" O VAL Q 19 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N GLY Q 49 " --> pdb=" O ASN Q 40 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'R' and resid 7 through 11 removed outlier: 6.973A pdb=" N GLU R 60 " --> pdb=" O VAL R 76 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'R' and resid 19 through 30 No H-bonds generated for sheet with id= 26 Processing sheet with id= 27, first strand: chain 'T' and resid 30 through 34 removed outlier: 4.750A pdb=" N LEU T 47 " --> pdb=" O VAL T 62 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'W' and resid 144 through 149 removed outlier: 6.964A pdb=" N ILE W 163 " --> pdb=" O MET W 149 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N LYS W 160 " --> pdb=" O ALA W 117 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N ASN W 110 " --> pdb=" O GLU W 208 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG W 308 " --> pdb=" O GLY W 181 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N VAL W 187 " --> pdb=" O PHE W 312 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'W' and resid 224 through 228 Processing sheet with id= 30, first strand: chain 'W' and resid 150 through 153 Processing sheet with id= 31, first strand: chain 'c' and resid 2 through 6 removed outlier: 5.729A pdb=" N VAL c 16 " --> pdb=" O CYS c 6 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'c' and resid 73 through 78 removed outlier: 4.990A pdb=" N ILE c 74 " --> pdb=" O SER c 118 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N SER c 118 " --> pdb=" O ILE c 74 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ASP c 114 " --> pdb=" O VAL c 78 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N GLY c 127 " --> pdb=" O GLN c 115 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N GLN c 117 " --> pdb=" O GLY c 127 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'c' and resid 80 through 83 removed outlier: 5.324A pdb=" N ASN c 90 " --> pdb=" O ALA c 106 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'c' and resid 138 through 142 removed outlier: 4.187A pdb=" N SER c 139 " --> pdb=" O ILE c 164 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N THR c 173 " --> pdb=" O VAL c 165 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU c 180 " --> pdb=" O LEU c 176 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'd' and resid 3 through 6 removed outlier: 4.099A pdb=" N GLU d 168 " --> pdb=" O SER d 113 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'd' and resid 10 through 16 removed outlier: 3.646A pdb=" N GLY d 10 " --> pdb=" O VAL d 26 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL d 20 " --> pdb=" O THR d 16 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'd' and resid 79 through 84 removed outlier: 5.623A pdb=" N ARG d 46 " --> pdb=" O LEU d 84 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N GLN d 49 " --> pdb=" O THR d 35 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N GLN d 94 " --> pdb=" O VAL d 34 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'd' and resid 105 through 108 removed outlier: 6.346A pdb=" N LYS d 105 " --> pdb=" O VAL d 177 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'e' and resid 1 through 6 removed outlier: 3.691A pdb=" N MET e 1 " --> pdb=" O VAL e 14 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU e 5 " --> pdb=" O SER e 10 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER e 10 " --> pdb=" O LEU e 5 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'e' and resid 117 through 120 removed outlier: 5.692A pdb=" N ARG e 117 " --> pdb=" O ASP e 184 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'f' and resid 65 through 69 removed outlier: 4.864A pdb=" N ILE f 85 " --> pdb=" O VAL f 40 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS f 33 " --> pdb=" O THR f 157 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N GLY f 39 " --> pdb=" O GLY f 151 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N GLY f 151 " --> pdb=" O GLY f 39 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N THR f 158 " --> pdb=" O GLY f 126 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N GLY f 126 " --> pdb=" O THR f 158 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'g' and resid 16 through 19 removed outlier: 3.554A pdb=" N LYS g 18 " --> pdb=" O THR g 25 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'g' and resid 41 through 45 Processing sheet with id= 44, first strand: chain 'g' and resid 82 through 89 removed outlier: 5.757A pdb=" N THR g 129 " --> pdb=" O LEU g 89 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'g' and resid 94 through 99 removed outlier: 6.349A pdb=" N ASN g 101 " --> pdb=" O LEU g 117 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'h' and resid 17 through 21 removed outlier: 4.605A pdb=" N ASP h 17 " --> pdb=" O LEU h 5 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N GLN h 2 " --> pdb=" O ALA h 39 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N LYS h 35 " --> pdb=" O LEU h 6 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'i' and resid 52 through 57 removed outlier: 4.861A pdb=" N ASP i 19 " --> pdb=" O LEU i 140 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'i' and resid 74 through 78 removed outlier: 7.603A pdb=" N GLY i 83 " --> pdb=" O THR i 78 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'j' and resid 6 through 9 removed outlier: 4.334A pdb=" N THR j 6 " --> pdb=" O CYS j 21 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'j' and resid 39 through 42 Processing sheet with id= 51, first strand: chain 'j' and resid 63 through 66 removed outlier: 4.198A pdb=" N LYS j 66 " --> pdb=" O GLY j 81 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N GLY j 81 " --> pdb=" O LYS j 66 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'j' and resid 68 through 71 removed outlier: 3.749A pdb=" N SER j 75 " --> pdb=" O ARG j 71 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'l' and resid 62 through 65 removed outlier: 3.516A pdb=" N TYR l 103 " --> pdb=" O LEU l 33 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N LEU l 33 " --> pdb=" O LEU l 102 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LYS l 100 " --> pdb=" O ALA l 35 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'l' and resid 30 through 36 removed outlier: 7.782A pdb=" N SER l 30 " --> pdb=" O LYS l 133 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LYS l 127 " --> pdb=" O VAL l 36 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'm' and resid 33 through 36 removed outlier: 4.993A pdb=" N ARG m 103 " --> pdb=" O ASN m 107 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N GLY m 101 " --> pdb=" O PRO m 109 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ALA m 111 " --> pdb=" O LYS m 99 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LYS m 99 " --> pdb=" O ALA m 111 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ILE m 113 " --> pdb=" O ILE m 97 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ILE m 97 " --> pdb=" O ILE m 113 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N LEU m 115 " --> pdb=" O THR m 95 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N THR m 95 " --> pdb=" O LEU m 115 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'n' and resid 49 through 53 removed outlier: 6.551A pdb=" N ILE n 35 " --> pdb=" O THR n 53 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'o' and resid 49 through 53 removed outlier: 3.565A pdb=" N ALA o 49 " --> pdb=" O THR o 60 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N ARG o 53 " --> pdb=" O HIS o 56 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N THR o 60 " --> pdb=" O ILE o 48 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N THR o 25 " --> pdb=" O LYS o 87 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'o' and resid 58 through 64 Processing sheet with id= 59, first strand: chain 'q' and resid 11 through 15 Processing sheet with id= 60, first strand: chain 'q' and resid 18 through 21 removed outlier: 4.288A pdb=" N GLN q 18 " --> pdb=" O ILE q 98 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ASP q 95 " --> pdb=" O VAL q 64 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LYS q 60 " --> pdb=" O THR q 99 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'q' and resid 57 through 60 Processing sheet with id= 62, first strand: chain 'q' and resid 65 through 68 Processing sheet with id= 63, first strand: chain 'q' and resid 71 through 78 removed outlier: 4.197A pdb=" N TYR q 83 " --> pdb=" O ARG q 78 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'r' and resid 2 through 8 Processing sheet with id= 65, first strand: chain 's' and resid 12 through 15 removed outlier: 5.149A pdb=" N VAL s 31 " --> pdb=" O HIS s 15 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS s 81 " --> pdb=" O VAL s 34 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N LYS s 66 " --> pdb=" O ARG s 77 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N ASP s 79 " --> pdb=" O LYS s 64 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N LYS s 64 " --> pdb=" O ASP s 79 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LYS s 81 " --> pdb=" O VAL s 62 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N VAL s 62 " --> pdb=" O LYS s 81 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ALA s 83 " --> pdb=" O THR s 60 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N THR s 60 " --> pdb=" O ALA s 83 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL s 85 " --> pdb=" O VAL s 58 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N VAL s 58 " --> pdb=" O VAL s 85 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 't' and resid 82 through 87 removed outlier: 4.316A pdb=" N ARG t 82 " --> pdb=" O LYS t 97 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N ARG t 94 " --> pdb=" O ILE t 103 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLU t 101 " --> pdb=" O PHE t 96 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'u' and resid 69 through 72 removed outlier: 6.701A pdb=" N ALA u 39 " --> pdb=" O ARG u 9 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE u 89 " --> pdb=" O PRO u 27 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'v' and resid 51 through 54 removed outlier: 3.902A pdb=" N THR v 58 " --> pdb=" O GLY v 54 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'v' and resid 65 through 71 Processing sheet with id= 70, first strand: chain 'w' and resid 12 through 19 removed outlier: 4.478A pdb=" N ASN w 23 " --> pdb=" O SER w 19 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'w' and resid 35 through 41 removed outlier: 3.758A pdb=" N ARG w 45 " --> pdb=" O VAL w 40 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'y' and resid 33 through 39 removed outlier: 4.457A pdb=" N HIS y 34 " --> pdb=" O GLN y 9 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N MET y 54 " --> pdb=" O THR y 10 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'z' and resid 29 through 32 removed outlier: 4.375A pdb=" N GLU z 36 " --> pdb=" O ASP z 31 " (cutoff:3.500A) 2010 hydrogen bonds defined for protein. 5934 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3833 hydrogen bonds 5966 hydrogen bond angles 0 basepair planarities 1538 basepair parallelities 2387 stacking parallelities Total time for adding SS restraints: 346.59 Time building geometry restraints manager: 68.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 17278 1.33 - 1.45: 68697 1.45 - 1.58: 61451 1.58 - 1.70: 9101 1.70 - 1.83: 285 Bond restraints: 156812 Sorted by residual: bond pdb=" C4 5MU a 747 " pdb=" C5 5MU a 747 " ideal model delta sigma weight residual 1.802 1.444 0.358 2.00e-02 2.50e+03 3.20e+02 bond pdb=" C4 5MU a1939 " pdb=" C5 5MU a1939 " ideal model delta sigma weight residual 1.802 1.445 0.357 2.00e-02 2.50e+03 3.19e+02 bond pdb=" N1 5MU a1939 " pdb=" C6 5MU a1939 " ideal model delta sigma weight residual 1.635 1.381 0.254 2.00e-02 2.50e+03 1.61e+02 bond pdb=" N1 5MU a 747 " pdb=" C6 5MU a 747 " ideal model delta sigma weight residual 1.635 1.387 0.248 2.00e-02 2.50e+03 1.54e+02 bond pdb=" N6 6MZ a1618 " pdb=" C9 6MZ a1618 " ideal model delta sigma weight residual 1.464 1.681 -0.217 2.00e-02 2.50e+03 1.17e+02 ... (remaining 156807 not shown) Histogram of bond angle deviations from ideal: 78.17 - 89.47: 2 89.47 - 100.76: 6000 100.76 - 112.06: 95666 112.06 - 123.36: 99423 123.36 - 134.65: 33135 Bond angle restraints: 234226 Sorted by residual: angle pdb=" O3' C a1617 " pdb=" P 6MZ a1618 " pdb=" O2P 6MZ a1618 " ideal model delta sigma weight residual 108.00 78.17 29.83 3.00e+00 1.11e-01 9.89e+01 angle pdb=" O3' C a1617 " pdb=" P 6MZ a1618 " pdb=" O1P 6MZ a1618 " ideal model delta sigma weight residual 108.00 80.50 27.50 3.00e+00 1.11e-01 8.40e+01 angle pdb=" O3' G a 329 " pdb=" P A a 330 " pdb=" O5' A a 330 " ideal model delta sigma weight residual 104.00 90.74 13.26 1.50e+00 4.44e-01 7.81e+01 angle pdb=" O3' U a 827 " pdb=" C3' U a 827 " pdb=" C2' U a 827 " ideal model delta sigma weight residual 113.70 102.76 10.94 1.50e+00 4.44e-01 5.32e+01 angle pdb=" O3' G B 976 " pdb=" P A B 977 " pdb=" O5' A B 977 " ideal model delta sigma weight residual 104.00 93.10 10.90 1.50e+00 4.44e-01 5.28e+01 ... (remaining 234221 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.36: 89093 35.36 - 70.73: 9977 70.73 - 106.09: 1244 106.09 - 141.46: 16 141.46 - 176.82: 16 Dihedral angle restraints: 100346 sinusoidal: 83359 harmonic: 16987 Sorted by residual: dihedral pdb=" O4' U B 365 " pdb=" C1' U B 365 " pdb=" N1 U B 365 " pdb=" C2 U B 365 " ideal model delta sinusoidal sigma weight residual 200.00 53.79 146.21 1 1.50e+01 4.44e-03 7.81e+01 dihedral pdb=" O4' U X 20 " pdb=" C1' U X 20 " pdb=" N1 U X 20 " pdb=" C2 U X 20 " ideal model delta sinusoidal sigma weight residual 200.00 55.57 144.43 1 1.50e+01 4.44e-03 7.74e+01 dihedral pdb=" O4' U a1779 " pdb=" C1' U a1779 " pdb=" N1 U a1779 " pdb=" C2 U a1779 " ideal model delta sinusoidal sigma weight residual 200.00 57.84 142.16 1 1.50e+01 4.44e-03 7.64e+01 ... (remaining 100343 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.130: 20280 0.130 - 0.259: 6397 0.259 - 0.389: 642 0.389 - 0.519: 2335 0.519 - 0.649: 115 Chirality restraints: 29769 Sorted by residual: chirality pdb=" P C a1170 " pdb=" OP1 C a1170 " pdb=" OP2 C a1170 " pdb=" O5' C a1170 " both_signs ideal model delta sigma weight residual True 2.41 -3.06 -0.65 2.00e-01 2.50e+01 1.05e+01 chirality pdb=" P C a2824 " pdb=" OP1 C a2824 " pdb=" OP2 C a2824 " pdb=" O5' C a2824 " both_signs ideal model delta sigma weight residual True 2.41 -3.05 -0.64 2.00e-01 2.50e+01 1.01e+01 chirality pdb=" P G a1107 " pdb=" OP1 G a1107 " pdb=" OP2 G a1107 " pdb=" O5' G a1107 " both_signs ideal model delta sigma weight residual True 2.41 -3.04 -0.63 2.00e-01 2.50e+01 9.91e+00 ... (remaining 29766 not shown) Planarity restraints: 12793 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 2MG B1207 " -0.096 2.00e-02 2.50e+03 6.25e-01 8.79e+03 pdb=" C4' 2MG B1207 " -0.446 2.00e-02 2.50e+03 pdb=" O4' 2MG B1207 " -0.693 2.00e-02 2.50e+03 pdb=" C3' 2MG B1207 " 0.629 2.00e-02 2.50e+03 pdb=" O3' 2MG B1207 " 0.673 2.00e-02 2.50e+03 pdb=" C2' 2MG B1207 " 0.147 2.00e-02 2.50e+03 pdb=" O2' 2MG B1207 " -0.992 2.00e-02 2.50e+03 pdb=" C1' 2MG B1207 " -0.190 2.00e-02 2.50e+03 pdb=" N9 2MG B1207 " 0.967 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG a2445 " -0.070 2.00e-02 2.50e+03 6.12e-01 8.43e+03 pdb=" C4' 2MG a2445 " -0.427 2.00e-02 2.50e+03 pdb=" O4' 2MG a2445 " -0.680 2.00e-02 2.50e+03 pdb=" C3' 2MG a2445 " 0.657 2.00e-02 2.50e+03 pdb=" O3' 2MG a2445 " 0.657 2.00e-02 2.50e+03 pdb=" C2' 2MG a2445 " 0.149 2.00e-02 2.50e+03 pdb=" O2' 2MG a2445 " -0.980 2.00e-02 2.50e+03 pdb=" C1' 2MG a2445 " -0.216 2.00e-02 2.50e+03 pdb=" N9 2MG a2445 " 0.911 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 5MC B1407 " -0.093 2.00e-02 2.50e+03 5.98e-01 8.04e+03 pdb=" C4' 5MC B1407 " -0.438 2.00e-02 2.50e+03 pdb=" O4' 5MC B1407 " -0.610 2.00e-02 2.50e+03 pdb=" C3' 5MC B1407 " 0.626 2.00e-02 2.50e+03 pdb=" O3' 5MC B1407 " 0.636 2.00e-02 2.50e+03 pdb=" C2' 5MC B1407 " 0.161 2.00e-02 2.50e+03 pdb=" O2' 5MC B1407 " -0.968 2.00e-02 2.50e+03 pdb=" C1' 5MC B1407 " -0.226 2.00e-02 2.50e+03 pdb=" N1 5MC B1407 " 0.913 2.00e-02 2.50e+03 ... (remaining 12790 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.20: 630 2.20 - 2.88: 45320 2.88 - 3.55: 231531 3.55 - 4.23: 486149 4.23 - 4.90: 634780 Nonbonded interactions: 1398410 Sorted by model distance: nonbonded pdb=" C5 G B 324 " pdb="MG MG B1649 " model vdw 1.528 2.390 nonbonded pdb=" C4 G B 324 " pdb="MG MG B1649 " model vdw 1.570 2.390 nonbonded pdb=" C5 G B 774 " pdb="MG MG B1665 " model vdw 1.742 2.390 nonbonded pdb=" C6 G B 774 " pdb="MG MG B1665 " model vdw 1.767 2.390 nonbonded pdb="MG MG a6017 " pdb=" O HOH a6947 " model vdw 1.817 2.170 ... (remaining 1398405 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 13.020 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: 44.690 Check model and map are aligned: 1.550 Set scattering table: 0.970 Process input model: 664.100 Find NCS groups from input model: 2.830 Set up NCS constraints: 0.330 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:14.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 741.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 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 : 0.013 0.358 156812 Z= 0.796 Angle : 1.774 29.832 234226 Z= 1.061 Chirality : 0.169 0.649 29769 Planarity : 0.021 0.625 12793 Dihedral : 22.667 176.821 89386 Min Nonbonded Distance : 1.528 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.89 % Allowed : 5.93 % Favored : 93.18 % Rotamer: Outliers : 2.19 % Allowed : 4.89 % Favored : 92.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.31 (0.09), residues: 5853 helix: -2.85 (0.08), residues: 1995 sheet: -1.66 (0.14), residues: 1077 loop : -1.77 (0.10), residues: 2781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.004 TRP D 201 HIS 0.015 0.002 HIS u 44 PHE 0.033 0.004 PHE u 26 TYR 0.044 0.004 TYR p 32 ARG 0.018 0.002 ARG 0 6 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11706 Ramachandran restraints generated. 5853 Oldfield, 0 Emsley, 5853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11706 Ramachandran restraints generated. 5853 Oldfield, 0 Emsley, 5853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1319 residues out of total 4889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 1212 time to evaluate : 6.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 44 ARG cc_start: 0.7116 (mtp180) cc_final: 0.6654 (ttp80) REVERT: 0 50 LYS cc_start: 0.6458 (mtmt) cc_final: 0.6240 (mttt) REVERT: 1 25 LYS cc_start: 0.7658 (pptt) cc_final: 0.6443 (ptmt) REVERT: 2 15 LYS cc_start: 0.7631 (mptt) cc_final: 0.6838 (mmmm) REVERT: 2 52 LYS cc_start: 0.6301 (tttm) cc_final: 0.5750 (tppt) REVERT: 3 8 LYS cc_start: 0.7524 (mttt) cc_final: 0.6848 (mtpt) REVERT: 3 15 LYS cc_start: 0.7502 (mttt) cc_final: 0.6777 (mttt) REVERT: 4 1 MET cc_start: 0.7013 (mtm) cc_final: 0.6799 (mtt) REVERT: 4 34 LEU cc_start: 0.5316 (OUTLIER) cc_final: 0.4478 (pp) REVERT: C 32 PHE cc_start: 0.4758 (OUTLIER) cc_final: 0.4484 (t80) REVERT: C 35 ARG cc_start: 0.4969 (mtm110) cc_final: 0.4443 (ptp90) REVERT: C 37 LYS cc_start: 0.4586 (mttp) cc_final: 0.3946 (mmtm) REVERT: C 43 LEU cc_start: 0.5754 (mt) cc_final: 0.5247 (mt) REVERT: C 49 MET cc_start: 0.4911 (mtp) cc_final: 0.4547 (mtt) REVERT: C 66 LYS cc_start: 0.6088 (mtmt) cc_final: 0.5768 (mttp) REVERT: C 69 PHE cc_start: 0.7088 (m-80) cc_final: 0.6846 (m-80) REVERT: C 100 MET cc_start: 0.6420 (mtp) cc_final: 0.6075 (mtt) REVERT: C 105 LYS cc_start: 0.6455 (OUTLIER) cc_final: 0.6144 (pttt) REVERT: C 112 LYS cc_start: 0.5431 (tttm) cc_final: 0.4986 (tppt) REVERT: C 154 MET cc_start: 0.6445 (ttp) cc_final: 0.6204 (ttm) REVERT: C 170 HIS cc_start: 0.6858 (p-80) cc_final: 0.6561 (p90) REVERT: C 178 ASN cc_start: 0.6331 (t0) cc_final: 0.6012 (m-40) REVERT: C 197 ASP cc_start: 0.5586 (t0) cc_final: 0.5306 (m-30) REVERT: C 208 ARG cc_start: 0.4065 (ttp-110) cc_final: 0.3192 (mmp80) REVERT: C 220 THR cc_start: 0.6326 (t) cc_final: 0.6079 (m) REVERT: C 222 ARG cc_start: 0.4154 (OUTLIER) cc_final: 0.3845 (mtm-85) REVERT: D 27 LYS cc_start: 0.4842 (pmtt) cc_final: 0.4196 (pttp) REVERT: D 28 GLU cc_start: 0.5681 (mt-10) cc_final: 0.5101 (mp0) REVERT: D 38 LYS cc_start: 0.6482 (mttt) cc_final: 0.6119 (mttm) REVERT: D 46 GLU cc_start: 0.5387 (OUTLIER) cc_final: 0.5066 (mm-30) REVERT: D 54 ARG cc_start: 0.6147 (ttt180) cc_final: 0.5893 (ttt-90) REVERT: D 59 ARG cc_start: 0.6886 (mtt-85) cc_final: 0.6436 (mtp85) REVERT: D 65 ARG cc_start: 0.6164 (ttp80) cc_final: 0.5405 (ttm-80) REVERT: D 72 ARG cc_start: 0.4741 (mmm-85) cc_final: 0.3782 (mmm160) REVERT: D 89 LYS cc_start: 0.4309 (mttt) cc_final: 0.4012 (mmtp) REVERT: D 108 LYS cc_start: 0.6253 (mttt) cc_final: 0.5821 (mttm) REVERT: D 110 GLU cc_start: 0.5699 (mp0) cc_final: 0.4899 (pm20) REVERT: D 122 SER cc_start: 0.6643 (m) cc_final: 0.6304 (p) REVERT: D 129 MET cc_start: 0.5632 (mmm) cc_final: 0.4531 (tmm) REVERT: D 131 ARG cc_start: 0.6509 (mtm-85) cc_final: 0.6100 (ttm170) REVERT: D 132 ARG cc_start: 0.5549 (tpp80) cc_final: 0.4860 (tpt170) REVERT: D 165 THR cc_start: 0.7300 (m) cc_final: 0.6966 (t) REVERT: D 166 GLU cc_start: 0.7208 (mm-30) cc_final: 0.6881 (mm-30) REVERT: D 169 ARG cc_start: 0.6508 (ttm-80) cc_final: 0.5331 (ttp80) REVERT: D 170 GLU cc_start: 0.6780 (tt0) cc_final: 0.6396 (mt-10) REVERT: D 179 ARG cc_start: 0.7096 (ptt180) cc_final: 0.6884 (ptt180) REVERT: D 185 ASN cc_start: 0.8613 (t0) cc_final: 0.8167 (t160) REVERT: D 188 GLU cc_start: 0.6595 (mt-10) cc_final: 0.6238 (mt-10) REVERT: E 20 PHE cc_start: 0.6174 (m-80) cc_final: 0.5790 (m-80) REVERT: E 44 ARG cc_start: 0.4570 (ttm110) cc_final: 0.3892 (tmm-80) REVERT: E 51 TYR cc_start: 0.7288 (t80) cc_final: 0.6968 (t80) REVERT: E 73 ARG cc_start: 0.6459 (ttp80) cc_final: 0.5298 (ttm-80) REVERT: E 78 GLU cc_start: 0.6204 (tt0) cc_final: 0.5952 (tp30) REVERT: E 83 LYS cc_start: 0.6146 (mmtp) cc_final: 0.5845 (mttt) REVERT: E 113 GLU cc_start: 0.6801 (tp30) cc_final: 0.6535 (tt0) REVERT: E 124 MET cc_start: 0.6739 (mtm) cc_final: 0.6078 (mtt) REVERT: E 128 ARG cc_start: 0.5367 (mtt-85) cc_final: 0.4838 (mmm160) REVERT: E 146 ARG cc_start: 0.5043 (ttp-170) cc_final: 0.4732 (ptm160) REVERT: E 148 LYS cc_start: 0.5160 (ttpp) cc_final: 0.4755 (ttpp) REVERT: E 171 LEU cc_start: 0.6000 (tp) cc_final: 0.5609 (tp) REVERT: E 197 GLU cc_start: 0.6597 (pm20) cc_final: 0.6261 (pm20) REVERT: E 198 HIS cc_start: 0.6490 (p90) cc_final: 0.5991 (p-80) REVERT: F 13 GLU cc_start: 0.6318 (mt-10) cc_final: 0.5395 (pt0) REVERT: F 14 LYS cc_start: 0.6771 (ttmt) cc_final: 0.6225 (mtpp) REVERT: F 23 LYS cc_start: 0.7728 (ptmm) cc_final: 0.7308 (ptmt) REVERT: F 26 LYS cc_start: 0.6905 (tmtm) cc_final: 0.6584 (ttmm) REVERT: F 45 ARG cc_start: 0.6477 (mtp-110) cc_final: 0.6152 (mtp85) REVERT: F 61 GLN cc_start: 0.6231 (tm-30) cc_final: 0.5850 (tm130) REVERT: F 62 LYS cc_start: 0.7421 (mttt) cc_final: 0.7221 (mttt) REVERT: F 65 GLU cc_start: 0.6431 (mt-10) cc_final: 0.5961 (mm-30) REVERT: F 72 ILE cc_start: 0.6791 (pt) cc_final: 0.6567 (pp) REVERT: F 93 ARG cc_start: 0.7308 (mtm110) cc_final: 0.6971 (mpp-170) REVERT: F 95 PHE cc_start: 0.8321 (t80) cc_final: 0.8111 (t80) REVERT: F 111 MET cc_start: 0.7891 (mtp) cc_final: 0.7631 (mtp) REVERT: F 156 LYS cc_start: 0.6615 (ptpp) cc_final: 0.6206 (pttt) REVERT: F 159 LYS cc_start: 0.6881 (mmtt) cc_final: 0.6655 (mptt) REVERT: G 15 SER cc_start: 0.5950 (t) cc_final: 0.5737 (m) REVERT: G 37 HIS cc_start: 0.6324 (OUTLIER) cc_final: 0.5925 (p-80) REVERT: G 62 MET cc_start: 0.6713 (ptp) cc_final: 0.6345 (ptm) REVERT: G 87 SER cc_start: 0.7568 (p) cc_final: 0.7264 (p) REVERT: G 91 ARG cc_start: 0.7261 (OUTLIER) cc_final: 0.6926 (ttt180) REVERT: G 92 THR cc_start: 0.6452 (m) cc_final: 0.6115 (p) REVERT: H 26 PHE cc_start: 0.7518 (t80) cc_final: 0.7253 (t80) REVERT: H 33 ASP cc_start: 0.7022 (m-30) cc_final: 0.6796 (m-30) REVERT: H 41 SER cc_start: 0.5927 (p) cc_final: 0.5666 (m) REVERT: H 58 GLU cc_start: 0.4741 (mp0) cc_final: 0.4502 (mp0) REVERT: H 70 ARG cc_start: 0.5352 (mtm-85) cc_final: 0.4927 (mtt180) REVERT: H 72 THR cc_start: 0.6410 (m) cc_final: 0.6161 (p) REVERT: H 76 LYS cc_start: 0.4962 (mttt) cc_final: 0.4536 (mmtt) REVERT: H 97 ASN cc_start: 0.7026 (m-40) cc_final: 0.6685 (m-40) REVERT: H 106 GLU cc_start: 0.5683 (mt-10) cc_final: 0.5321 (tt0) REVERT: H 119 ARG cc_start: 0.6643 (mtm180) cc_final: 0.6282 (mtt180) REVERT: H 138 ARG cc_start: 0.5196 (tmm160) cc_final: 0.4976 (tmm160) REVERT: H 139 GLU cc_start: 0.6327 (mt-10) cc_final: 0.6084 (mt-10) REVERT: H 146 GLU cc_start: 0.4874 (tm-30) cc_final: 0.4629 (mm-30) REVERT: H 149 LYS cc_start: 0.6018 (tppt) cc_final: 0.5671 (ttpp) REVERT: I 41 LYS cc_start: 0.7093 (tttt) cc_final: 0.6691 (tptp) REVERT: I 43 GLU cc_start: 0.7153 (mm-30) cc_final: 0.6696 (mm-30) REVERT: I 50 LYS cc_start: 0.6139 (ptmt) cc_final: 0.5919 (pttt) REVERT: I 62 THR cc_start: 0.7848 (m) cc_final: 0.7645 (m) REVERT: I 69 LYS cc_start: 0.6114 (mtpp) cc_final: 0.5744 (mtmm) REVERT: I 76 GLN cc_start: 0.6724 (mt0) cc_final: 0.6421 (tt0) REVERT: I 88 ARG cc_start: 0.6562 (mtm-85) cc_final: 0.6255 (mtm180) REVERT: I 96 MET cc_start: 0.7420 (mtp) cc_final: 0.7081 (ttt) REVERT: I 114 ARG cc_start: 0.6385 (ttm110) cc_final: 0.5885 (ttm-80) REVERT: J 27 LYS cc_start: 0.5129 (OUTLIER) cc_final: 0.4733 (ptpt) REVERT: J 49 ARG cc_start: 0.4792 (mtm-85) cc_final: 0.4583 (mtm-85) REVERT: J 85 ARG cc_start: 0.6516 (OUTLIER) cc_final: 0.6111 (mtt180) REVERT: J 110 GLN cc_start: 0.7511 (mm110) cc_final: 0.7217 (mm-40) REVERT: J 119 ARG cc_start: 0.6484 (ptm-80) cc_final: 0.6008 (ptp-110) REVERT: K 11 LYS cc_start: 0.6930 (mttt) cc_final: 0.6501 (mmmt) REVERT: K 27 GLU cc_start: 0.3856 (OUTLIER) cc_final: 0.3483 (pt0) REVERT: K 60 ASP cc_start: 0.7794 (m-30) cc_final: 0.7590 (m-30) REVERT: K 88 MET cc_start: 0.3987 (mmt) cc_final: 0.3373 (mtm) REVERT: L 27 PHE cc_start: 0.6979 (m-80) cc_final: 0.6763 (m-10) REVERT: L 34 ILE cc_start: 0.7605 (mt) cc_final: 0.7290 (mm) REVERT: L 40 ASN cc_start: 0.7178 (m-40) cc_final: 0.6829 (m110) REVERT: L 56 ARG cc_start: 0.7182 (mtm-85) cc_final: 0.6714 (mtt-85) REVERT: L 77 TYR cc_start: 0.6425 (m-80) cc_final: 0.5977 (m-80) REVERT: L 83 GLU cc_start: 0.6512 (mt-10) cc_final: 0.6230 (mt-10) REVERT: L 106 ARG cc_start: 0.4949 (ttt180) cc_final: 0.4255 (tpt170) REVERT: L 126 LYS cc_start: 0.7402 (tttt) cc_final: 0.7144 (tttm) REVERT: M 10 LYS cc_start: 0.6393 (tttt) cc_final: 0.6169 (ttpt) REVERT: M 36 ARG cc_start: 0.6879 (ttp80) cc_final: 0.6581 (ttp-170) REVERT: M 40 THR cc_start: 0.8064 (t) cc_final: 0.7616 (p) REVERT: M 43 LYS cc_start: 0.7351 (ptpt) cc_final: 0.7071 (pttt) REVERT: M 49 LEU cc_start: 0.7599 (mt) cc_final: 0.7391 (mm) REVERT: M 54 ARG cc_start: 0.7165 (ttm-80) cc_final: 0.6962 (ttt90) REVERT: M 64 THR cc_start: 0.8329 (m) cc_final: 0.7793 (p) REVERT: M 75 GLN cc_start: 0.6595 (mp10) cc_final: 0.6305 (pm20) REVERT: M 88 LYS cc_start: 0.7174 (tmtt) cc_final: 0.6841 (tttp) REVERT: M 94 ARG cc_start: 0.7525 (ptp-170) cc_final: 0.7254 (mtm180) REVERT: M 111 LYS cc_start: 0.7377 (mmmt) cc_final: 0.7078 (mmtt) REVERT: N 4 ILE cc_start: 0.6331 (mt) cc_final: 0.5767 (mp) REVERT: N 9 ILE cc_start: 0.5528 (pt) cc_final: 0.5297 (pp) REVERT: N 11 ASP cc_start: 0.5349 (OUTLIER) cc_final: 0.5000 (p0) REVERT: N 78 LYS cc_start: 0.5592 (tttm) cc_final: 0.5135 (tptp) REVERT: N 81 MET cc_start: 0.7441 (mtm) cc_final: 0.6689 (mtm) REVERT: N 92 ARG cc_start: 0.6865 (mtt180) cc_final: 0.6533 (mtm-85) REVERT: N 93 ARG cc_start: 0.6155 (mmt-90) cc_final: 0.5335 (mmp80) REVERT: N 95 LEU cc_start: 0.7264 (mt) cc_final: 0.6918 (mt) REVERT: O 12 LYS cc_start: 0.6514 (tttt) cc_final: 0.6288 (tttt) REVERT: O 20 TYR cc_start: 0.7007 (m-80) cc_final: 0.6771 (m-80) REVERT: O 33 ASP cc_start: 0.3535 (OUTLIER) cc_final: 0.3191 (t0) REVERT: O 47 LYS cc_start: 0.5667 (tmtt) cc_final: 0.5058 (tttt) REVERT: O 53 ARG cc_start: 0.6054 (mtt180) cc_final: 0.5824 (mtt180) REVERT: P 38 HIS cc_start: 0.6999 (t70) cc_final: 0.6789 (t-90) REVERT: P 47 LYS cc_start: 0.7401 (mptp) cc_final: 0.6992 (mmmt) REVERT: P 77 ARG cc_start: 0.6754 (mtp180) cc_final: 0.6540 (mtm180) REVERT: Q 1 MET cc_start: 0.6798 (pmm) cc_final: 0.6237 (pmm) REVERT: Q 14 ARG cc_start: 0.6923 (mtp-110) cc_final: 0.6596 (mtp85) REVERT: Q 76 LYS cc_start: 0.5187 (OUTLIER) cc_final: 0.4479 (mmtm) REVERT: R 9 GLN cc_start: 0.6872 (tt0) cc_final: 0.6666 (tt0) REVERT: R 45 HIS cc_start: 0.7453 (m90) cc_final: 0.7179 (m90) REVERT: R 69 LYS cc_start: 0.6836 (ptmm) cc_final: 0.6598 (tttt) REVERT: S 16 GLU cc_start: 0.4265 (OUTLIER) cc_final: 0.4012 (tm-30) REVERT: S 38 LYS cc_start: 0.7221 (mtpt) cc_final: 0.6998 (mtpt) REVERT: S 48 ARG cc_start: 0.6381 (mtm110) cc_final: 0.6159 (mtp-110) REVERT: S 54 GLN cc_start: 0.7175 (mt0) cc_final: 0.6932 (mt0) REVERT: S 61 ARG cc_start: 0.7439 (mtt180) cc_final: 0.7103 (mtt90) REVERT: T 44 MET cc_start: 0.6093 (mtt) cc_final: 0.5461 (mtt) REVERT: U 15 GLU cc_start: 0.7110 (tp30) cc_final: 0.6564 (tp30) REVERT: U 24 ARG cc_start: 0.6830 (mmm160) cc_final: 0.6231 (mpt90) REVERT: U 27 MET cc_start: 0.6786 (ttm) cc_final: 0.6453 (ttp) REVERT: U 33 LYS cc_start: 0.6520 (mttm) cc_final: 0.5476 (ttpp) REVERT: U 54 MET cc_start: 0.6354 (tmm) cc_final: 0.6114 (tmm) REVERT: U 55 GLN cc_start: 0.7113 (tt0) cc_final: 0.6712 (tt0) REVERT: U 60 ARG cc_start: 0.6651 (ttp-110) cc_final: 0.6364 (ttm170) REVERT: U 64 LYS cc_start: 0.6639 (mmtm) cc_final: 0.6407 (mmtm) REVERT: V 21 ARG cc_start: 0.4426 (ttt90) cc_final: 0.3590 (tpm-80) REVERT: V 33 ARG cc_start: 0.5385 (mtt90) cc_final: 0.4882 (mmm160) REVERT: V 36 GLU cc_start: 0.6794 (tt0) cc_final: 0.6155 (mm-30) REVERT: V 39 GLU cc_start: 0.6499 (mt-10) cc_final: 0.5716 (pm20) REVERT: V 47 ARG cc_start: 0.5930 (ptt90) cc_final: 0.5535 (ptt-90) REVERT: V 49 LYS cc_start: 0.6656 (tptp) cc_final: 0.6244 (tptp) REVERT: W 143 ARG cc_start: 0.5777 (OUTLIER) cc_final: 0.5453 (mmt-90) REVERT: W 155 GLU cc_start: 0.5591 (mm-30) cc_final: 0.5081 (mt-10) REVERT: W 160 LYS cc_start: 0.6880 (mmtt) cc_final: 0.6142 (mtpp) REVERT: W 165 LYS cc_start: 0.6528 (tttt) cc_final: 0.6098 (ttmm) REVERT: W 193 GLN cc_start: 0.7047 (mm-40) cc_final: 0.6563 (mt0) REVERT: W 208 GLU cc_start: 0.5928 (tt0) cc_final: 0.5068 (mp0) REVERT: W 223 ARG cc_start: 0.7507 (ttp-170) cc_final: 0.6995 (ttp-170) REVERT: W 255 VAL cc_start: 0.8184 (OUTLIER) cc_final: 0.7962 (t) REVERT: W 269 LYS cc_start: 0.7643 (tptp) cc_final: 0.7320 (tptt) REVERT: W 282 GLU cc_start: 0.5523 (pt0) cc_final: 0.5167 (mm-30) REVERT: W 286 ARG cc_start: 0.5568 (mtt-85) cc_final: 0.4944 (mtm180) REVERT: W 287 GLN cc_start: 0.5737 (mt0) cc_final: 0.4899 (tm-30) REVERT: W 294 ARG cc_start: 0.6910 (ttp-110) cc_final: 0.6703 (ttm110) REVERT: W 328 ARG cc_start: 0.6725 (mtp85) cc_final: 0.6172 (mtp180) REVERT: W 330 ASP cc_start: 0.5359 (m-30) cc_final: 0.5067 (p0) REVERT: W 334 GLU cc_start: 0.5320 (mt-10) cc_final: 0.4982 (mm-30) REVERT: c 5 LYS cc_start: 0.7202 (tttp) cc_final: 0.6380 (tptp) REVERT: c 18 LYS cc_start: 0.7751 (ptpt) cc_final: 0.7401 (mtmm) REVERT: c 66 ASP cc_start: 0.8156 (t70) cc_final: 0.7844 (t0) REVERT: c 111 LYS cc_start: 0.6543 (ptpp) cc_final: 0.5693 (mttm) REVERT: c 181 MET cc_start: 0.8180 (tpp) cc_final: 0.7650 (mmm) REVERT: c 203 ARG cc_start: 0.7599 (ptt90) cc_final: 0.7249 (ptp-110) REVERT: c 259 SER cc_start: 0.7632 (p) cc_final: 0.7399 (t) REVERT: c 269 ARG cc_start: 0.7381 (ttp-170) cc_final: 0.6894 (ttp80) REVERT: d 7 LYS cc_start: 0.7944 (ttmt) cc_final: 0.7281 (ttpp) REVERT: d 70 LYS cc_start: 0.6986 (tttt) cc_final: 0.6704 (tttt) REVERT: d 89 GLU cc_start: 0.6698 (tp30) cc_final: 0.5887 (pt0) REVERT: d 91 THR cc_start: 0.7358 (p) cc_final: 0.6909 (m) REVERT: d 99 GLU cc_start: 0.6449 (mm-30) cc_final: 0.5939 (mp0) REVERT: d 105 LYS cc_start: 0.7726 (mmtp) cc_final: 0.7088 (mmtm) REVERT: d 161 MET cc_start: 0.8734 (mtt) cc_final: 0.8268 (mtp) REVERT: d 199 SER cc_start: 0.7901 (m) cc_final: 0.7693 (t) REVERT: d 204 LYS cc_start: 0.8248 (mttt) cc_final: 0.7867 (mmtp) REVERT: e 22 ASP cc_start: 0.6570 (p0) cc_final: 0.6096 (t70) REVERT: e 132 LYS cc_start: 0.7033 (tttm) cc_final: 0.6588 (ttmt) REVERT: e 144 GLU cc_start: 0.5974 (mt-10) cc_final: 0.5743 (pt0) REVERT: e 198 GLU cc_start: 0.6178 (tt0) cc_final: 0.5520 (mm-30) REVERT: e 199 MET cc_start: 0.6020 (ttp) cc_final: 0.5548 (ttp) REVERT: f 11 GLU cc_start: 0.5821 (mm-30) cc_final: 0.5148 (mp0) REVERT: f 30 ARG cc_start: 0.6084 (mpp80) cc_final: 0.5499 (mtm-85) REVERT: f 33 LYS cc_start: 0.8138 (pttt) cc_final: 0.7921 (pttt) REVERT: f 50 LEU cc_start: 0.5222 (tm) cc_final: 0.4664 (tp) REVERT: f 60 ILE cc_start: 0.7437 (mt) cc_final: 0.6903 (mp) REVERT: f 64 LYS cc_start: 0.7001 (tmtp) cc_final: 0.6773 (tttp) REVERT: f 78 LYS cc_start: 0.6262 (mptp) cc_final: 0.5617 (mmmt) REVERT: f 112 ARG cc_start: 0.5273 (ttp-110) cc_final: 0.5048 (mtp180) REVERT: f 129 SER cc_start: 0.7256 (m) cc_final: 0.6937 (t) REVERT: f 130 MET cc_start: 0.7064 (ptm) cc_final: 0.6815 (ptm) REVERT: f 136 ILE cc_start: 0.5665 (mm) cc_final: 0.5346 (pp) REVERT: f 140 GLU cc_start: 0.5511 (mp0) cc_final: 0.5170 (mp0) REVERT: g 6 LYS cc_start: 0.4450 (mmtt) cc_final: 0.4227 (mmmm) REVERT: g 9 VAL cc_start: 0.4632 (m) cc_final: 0.4394 (p) REVERT: g 15 VAL cc_start: 0.4729 (OUTLIER) cc_final: 0.4445 (t) REVERT: g 86 LYS cc_start: 0.6842 (OUTLIER) cc_final: 0.5769 (pttt) REVERT: g 115 HIS cc_start: 0.6924 (t-90) cc_final: 0.6647 (t70) REVERT: g 127 THR cc_start: 0.5855 (m) cc_final: 0.5462 (p) REVERT: g 152 ARG cc_start: 0.7341 (tpp-160) cc_final: 0.6937 (mmt-90) REVERT: g 158 LYS cc_start: 0.6671 (mtmt) cc_final: 0.6286 (mtpt) REVERT: h 21 VAL cc_start: 0.5891 (p) cc_final: 0.5453 (t) REVERT: i 1 MET cc_start: 0.5141 (ptm) cc_final: 0.4234 (tpp) REVERT: i 2 LYS cc_start: 0.6964 (mttt) cc_final: 0.6660 (mtpt) REVERT: i 34 ARG cc_start: 0.7777 (ttt-90) cc_final: 0.7259 (mtp85) REVERT: i 61 LYS cc_start: 0.6966 (mttt) cc_final: 0.6379 (mmtm) REVERT: i 85 LYS cc_start: 0.7795 (mmtt) cc_final: 0.7561 (mmtt) REVERT: i 91 GLU cc_start: 0.7538 (mt-10) cc_final: 0.7196 (mt-10) REVERT: i 95 ARG cc_start: 0.6281 (ttt180) cc_final: 0.5765 (mpt-90) REVERT: i 96 ARG cc_start: 0.6751 (ptt-90) cc_final: 0.6461 (ptt-90) REVERT: i 128 ASN cc_start: 0.7540 (t0) cc_final: 0.7167 (t0) REVERT: i 129 GLU cc_start: 0.7006 (mm-30) cc_final: 0.6691 (mm-30) REVERT: j 17 ARG cc_start: 0.7225 (mmt90) cc_final: 0.6737 (mmm160) REVERT: j 29 HIS cc_start: 0.7239 (m-70) cc_final: 0.6756 (m90) REVERT: j 45 GLU cc_start: 0.7383 (mt-10) cc_final: 0.7123 (mt-10) REVERT: j 51 LYS cc_start: 0.7150 (mtpp) cc_final: 0.6787 (mtmt) REVERT: j 53 LYS cc_start: 0.6788 (mmtt) cc_final: 0.6007 (ttpp) REVERT: j 54 LYS cc_start: 0.7355 (tttt) cc_final: 0.7143 (tttm) REVERT: j 66 LYS cc_start: 0.8201 (mtpt) cc_final: 0.7836 (mtpm) REVERT: j 88 ASN cc_start: 0.6102 (m-40) cc_final: 0.5450 (t0) REVERT: j 93 GLN cc_start: 0.6944 (OUTLIER) cc_final: 0.6650 (mm-40) REVERT: j 105 ARG cc_start: 0.6270 (tpp-160) cc_final: 0.5826 (mmt-90) REVERT: j 114 LYS cc_start: 0.6163 (mppt) cc_final: 0.5739 (mmpt) REVERT: k 78 ARG cc_start: 0.6856 (mtt90) cc_final: 0.5691 (mtp-110) REVERT: k 120 VAL cc_start: 0.7777 (t) cc_final: 0.7561 (p) REVERT: l 6 ARG cc_start: 0.6951 (mtt180) cc_final: 0.6442 (mtp85) REVERT: l 12 MET cc_start: 0.8381 (ttm) cc_final: 0.8107 (ttm) REVERT: l 22 GLN cc_start: 0.7477 (mm-40) cc_final: 0.5947 (mt0) REVERT: l 55 ARG cc_start: 0.6726 (ttm110) cc_final: 0.6319 (ttm110) REVERT: l 75 GLU cc_start: 0.7458 (mt-10) cc_final: 0.7237 (mt-10) REVERT: l 105 MET cc_start: 0.8135 (ttm) cc_final: 0.7880 (ttm) REVERT: l 133 LYS cc_start: 0.6355 (ttmt) cc_final: 0.5680 (ttmt) REVERT: l 134 THR cc_start: 0.6045 (p) cc_final: 0.5720 (p) REVERT: l 136 MET cc_start: 0.4885 (mtp) cc_final: 0.4647 (mtp) REVERT: m 18 GLN cc_start: 0.8073 (tt0) cc_final: 0.7749 (tt0) REVERT: m 72 ASP cc_start: 0.7517 (t0) cc_final: 0.7220 (t0) REVERT: m 98 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7799 (mp) REVERT: n 13 ARG cc_start: 0.6412 (tpp-160) cc_final: 0.5834 (tpt90) REVERT: n 16 ARG cc_start: 0.7175 (mmt-90) cc_final: 0.6757 (mmp80) REVERT: n 20 GLU cc_start: 0.6403 (pt0) cc_final: 0.5695 (tm-30) REVERT: n 46 GLU cc_start: 0.6335 (mm-30) cc_final: 0.5738 (tm-30) REVERT: n 76 LYS cc_start: 0.6607 (tttp) cc_final: 0.6316 (ttpt) REVERT: n 85 LYS cc_start: 0.6505 (mtpm) cc_final: 0.6104 (mttp) REVERT: n 98 GLN cc_start: 0.7510 (mm-40) cc_final: 0.7200 (mm-40) REVERT: n 108 ASP cc_start: 0.7454 (m-30) cc_final: 0.7149 (m-30) REVERT: o 7 GLN cc_start: 0.6841 (tp40) cc_final: 0.6524 (tt0) REVERT: o 10 GLN cc_start: 0.7039 (mm-40) cc_final: 0.6291 (mm-40) REVERT: o 11 GLU cc_start: 0.7334 (pt0) cc_final: 0.6989 (pt0) REVERT: o 29 LYS cc_start: 0.7671 (mmtt) cc_final: 0.7256 (mptm) REVERT: o 38 LYS cc_start: 0.6672 (tttt) cc_final: 0.6393 (tttp) REVERT: o 63 LYS cc_start: 0.7659 (ptmm) cc_final: 0.7122 (pttt) REVERT: o 68 GLU cc_start: 0.6065 (mm-30) cc_final: 0.4961 (tp30) REVERT: o 82 ASP cc_start: 0.7757 (t70) cc_final: 0.7537 (t0) REVERT: o 83 SER cc_start: 0.7719 (t) cc_final: 0.7486 (p) REVERT: o 89 ARG cc_start: 0.7258 (mtm180) cc_final: 0.6229 (mmt180) REVERT: p 11 ARG cc_start: 0.6948 (tpm170) cc_final: 0.6098 (ttp-110) REVERT: p 16 LYS cc_start: 0.7952 (ttpt) cc_final: 0.7580 (tttt) REVERT: p 71 GLN cc_start: 0.7209 (mm-40) cc_final: 0.6977 (tp40) REVERT: p 78 LYS cc_start: 0.7944 (mmmt) cc_final: 0.7580 (mttm) REVERT: p 85 LYS cc_start: 0.7440 (mttt) cc_final: 0.7092 (mtmm) REVERT: p 89 GLU cc_start: 0.7192 (mt-10) cc_final: 0.6955 (mt-10) REVERT: p 112 LYS cc_start: 0.7357 (OUTLIER) cc_final: 0.7110 (ttmt) REVERT: q 1 MET cc_start: 0.6451 (ttm) cc_final: 0.6196 (ttm) REVERT: q 73 LYS cc_start: 0.7966 (mmtp) cc_final: 0.7435 (mmpt) REVERT: r 28 LYS cc_start: 0.7282 (mtpt) cc_final: 0.6359 (mttm) REVERT: r 30 SER cc_start: 0.7348 (p) cc_final: 0.6967 (m) REVERT: r 34 ASP cc_start: 0.6948 (m-30) cc_final: 0.6683 (m-30) REVERT: r 52 GLU cc_start: 0.7254 (mt-10) cc_final: 0.7045 (mt-10) REVERT: r 62 ASP cc_start: 0.6853 (OUTLIER) cc_final: 0.6615 (m-30) REVERT: r 73 LYS cc_start: 0.7852 (mttm) cc_final: 0.7547 (mttt) REVERT: r 86 MET cc_start: 0.8179 (tpp) cc_final: 0.6963 (ttm) REVERT: s 1 MET cc_start: 0.4442 (ttt) cc_final: 0.3999 (mtp) REVERT: s 9 LYS cc_start: 0.7098 (mmtt) cc_final: 0.6520 (mtpt) REVERT: s 12 ARG cc_start: 0.7743 (mmm160) cc_final: 0.7434 (mmm-85) REVERT: s 14 PRO cc_start: 0.7771 (Cg_endo) cc_final: 0.7550 (Cg_exo) REVERT: s 18 GLU cc_start: 0.7084 (mt-10) cc_final: 0.6235 (mp0) REVERT: s 24 MET cc_start: 0.6243 (tpt) cc_final: 0.5911 (tpt) REVERT: s 33 LYS cc_start: 0.7433 (tttt) cc_final: 0.6583 (mttp) REVERT: s 50 LEU cc_start: 0.7289 (mt) cc_final: 0.7039 (mp) REVERT: s 89 GLU cc_start: 0.5145 (OUTLIER) cc_final: 0.4830 (mm-30) REVERT: s 93 LEU cc_start: 0.2257 (OUTLIER) cc_final: 0.1975 (tp) REVERT: t 7 ARG cc_start: 0.6199 (ttt180) cc_final: 0.5590 (ttm110) REVERT: t 24 LYS cc_start: 0.7023 (ttpt) cc_final: 0.6700 (tttt) REVERT: t 43 LYS cc_start: 0.7155 (mtmm) cc_final: 0.6710 (mttp) REVERT: t 46 GLN cc_start: 0.6738 (tp40) cc_final: 0.4941 (pt0) REVERT: t 61 LYS cc_start: 0.6579 (ptmm) cc_final: 0.6264 (pttt) REVERT: u 2 PHE cc_start: 0.6900 (m-80) cc_final: 0.6253 (m-80) REVERT: u 12 GLN cc_start: 0.7398 (pt0) cc_final: 0.6919 (pp30) REVERT: u 24 ASN cc_start: 0.6476 (t0) cc_final: 0.6193 (t0) REVERT: u 42 LEU cc_start: 0.8290 (mt) cc_final: 0.8065 (mt) REVERT: u 73 LYS cc_start: 0.7175 (mttt) cc_final: 0.6644 (mtpm) REVERT: u 79 ARG cc_start: 0.8053 (mtt-85) cc_final: 0.7819 (mtt-85) REVERT: v 25 ARG cc_start: 0.7985 (mmt90) cc_final: 0.7242 (mpt180) REVERT: v 66 LYS cc_start: 0.8034 (mtmt) cc_final: 0.6520 (tmtt) REVERT: v 72 LYS cc_start: 0.7480 (mtmm) cc_final: 0.7216 (mtpp) REVERT: v 75 LYS cc_start: 0.7271 (mttt) cc_final: 0.6766 (mttp) REVERT: v 83 GLU cc_start: 0.6596 (mm-30) cc_final: 0.5991 (mt-10) REVERT: w 2 SER cc_start: 0.7720 (p) cc_final: 0.7451 (m) REVERT: w 40 VAL cc_start: 0.6925 (OUTLIER) cc_final: 0.6704 (m) REVERT: w 54 LYS cc_start: 0.7491 (tmmt) cc_final: 0.6871 (tttp) REVERT: w 65 ASP cc_start: 0.7008 (m-30) cc_final: 0.6628 (m-30) REVERT: w 70 GLU cc_start: 0.5938 (mt-10) cc_final: 0.5405 (mt-10) REVERT: x 23 ARG cc_start: 0.6748 (ttm110) cc_final: 0.6240 (mtt90) REVERT: x 24 GLU cc_start: 0.6642 (tt0) cc_final: 0.6321 (tt0) REVERT: x 44 LYS cc_start: 0.6746 (ttmt) cc_final: 0.6424 (ttmm) REVERT: x 56 LEU cc_start: 0.7408 (OUTLIER) cc_final: 0.7093 (mm) REVERT: y 21 LYS cc_start: 0.7797 (mttt) cc_final: 0.7551 (mtpp) REVERT: y 41 THR cc_start: 0.6586 (m) cc_final: 0.5962 (p) REVERT: y 56 LYS cc_start: 0.7423 (pttt) cc_final: 0.7110 (pttp) REVERT: z 12 LYS cc_start: 0.7846 (tppt) cc_final: 0.7391 (mmtp) outliers start: 107 outliers final: 16 residues processed: 1288 average time/residue: 2.4457 time to fit residues: 4367.7923 Evaluate side-chains 1002 residues out of total 4889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 960 time to evaluate : 6.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 34 LEU Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 105 LYS Chi-restraints excluded: chain C residue 222 ARG Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 105 GLU Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain G residue 37 HIS Chi-restraints excluded: chain G residue 91 ARG Chi-restraints excluded: chain J residue 27 LYS Chi-restraints excluded: chain J residue 85 ARG Chi-restraints excluded: chain K residue 27 GLU Chi-restraints excluded: chain L residue 129 VAL Chi-restraints excluded: chain M residue 34 CYS Chi-restraints excluded: chain N residue 11 ASP Chi-restraints excluded: chain N residue 68 ASP Chi-restraints excluded: chain O residue 33 ASP Chi-restraints excluded: chain Q residue 76 LYS Chi-restraints excluded: chain R residue 67 LEU Chi-restraints excluded: chain S residue 16 GLU Chi-restraints excluded: chain V residue 3 VAL Chi-restraints excluded: chain W residue 143 ARG Chi-restraints excluded: chain W residue 254 VAL Chi-restraints excluded: chain W residue 255 VAL Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain g residue 15 VAL Chi-restraints excluded: chain g residue 36 THR Chi-restraints excluded: chain g residue 86 LYS Chi-restraints excluded: chain g residue 141 ILE Chi-restraints excluded: chain j residue 93 GLN Chi-restraints excluded: chain l residue 80 VAL Chi-restraints excluded: chain m residue 51 LEU Chi-restraints excluded: chain m residue 98 LEU Chi-restraints excluded: chain p residue 112 LYS Chi-restraints excluded: chain r residue 62 ASP Chi-restraints excluded: chain r residue 66 ILE Chi-restraints excluded: chain s residue 89 GLU Chi-restraints excluded: chain s residue 93 LEU Chi-restraints excluded: chain u residue 62 THR Chi-restraints excluded: chain w residue 40 VAL Chi-restraints excluded: chain x residue 56 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1023 random chunks: chunk 863 optimal weight: 1.9990 chunk 775 optimal weight: 0.6980 chunk 430 optimal weight: 0.9990 chunk 264 optimal weight: 6.9990 chunk 523 optimal weight: 0.7980 chunk 414 optimal weight: 1.9990 chunk 801 optimal weight: 6.9990 chunk 310 optimal weight: 2.9990 chunk 487 optimal weight: 7.9990 chunk 596 optimal weight: 7.9990 chunk 928 optimal weight: 3.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 29 GLN 4 41 HIS C 51 ASN C 177 ASN E 36 GLN E 89 ASN F 19 ASN F 97 GLN F 132 ASN G 3 HIS H 68 ASN H 122 ASN J 110 GLN K 15 HIS P 37 ASN Q 26 ASN R 9 GLN S 31 ASN T 14 HIS T 52 HIS T 83 HIS U 3 ASN U 75 HIS U 78 ASN W 248 HIS W 288 GLN W 307 ASN W 314 GLN W 346 GLN c 153 GLN e 165 HIS e 195 GLN i 136 GLN k 104 GLN n 100 HIS q 18 GLN q 86 GLN s 48 GLN t 40 ASN t 74 ASN x 58 ASN z 6 ASN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 156812 Z= 0.178 Angle : 0.663 16.294 234226 Z= 0.360 Chirality : 0.037 0.372 29769 Planarity : 0.006 0.136 12793 Dihedral : 23.235 179.381 77697 Min Nonbonded Distance : 1.738 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.46 % Favored : 97.37 % Rotamer: Outliers : 2.56 % Allowed : 10.05 % Favored : 87.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.10), residues: 5853 helix: 0.27 (0.11), residues: 2033 sheet: -0.93 (0.14), residues: 1138 loop : -0.64 (0.11), residues: 2682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP c 248 HIS 0.006 0.001 HIS z 19 PHE 0.017 0.002 PHE V 12 TYR 0.020 0.002 TYR M 117 ARG 0.005 0.001 ARG k 2 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11706 Ramachandran restraints generated. 5853 Oldfield, 0 Emsley, 5853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11706 Ramachandran restraints generated. 5853 Oldfield, 0 Emsley, 5853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1188 residues out of total 4889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 1063 time to evaluate : 6.218 Fit side-chains revert: symmetry clash REVERT: 0 33 LYS cc_start: 0.6165 (tptt) cc_final: 0.5839 (mmtp) REVERT: 0 44 ARG cc_start: 0.7180 (mtp180) cc_final: 0.6807 (mtm110) REVERT: 2 15 LYS cc_start: 0.7375 (mptt) cc_final: 0.6660 (mmmm) REVERT: 2 52 LYS cc_start: 0.6103 (tttm) cc_final: 0.5813 (ttpp) REVERT: 3 8 LYS cc_start: 0.7563 (mttt) cc_final: 0.6835 (mtmt) REVERT: 3 15 LYS cc_start: 0.7482 (mttt) cc_final: 0.6760 (mttt) REVERT: C 32 PHE cc_start: 0.4926 (OUTLIER) cc_final: 0.4672 (t80) REVERT: C 45 LYS cc_start: 0.4906 (mmmt) cc_final: 0.3886 (tppt) REVERT: C 49 MET cc_start: 0.4548 (mtp) cc_final: 0.4129 (mtt) REVERT: C 66 LYS cc_start: 0.6123 (mtmt) cc_final: 0.5790 (mttp) REVERT: C 105 LYS cc_start: 0.6698 (OUTLIER) cc_final: 0.6371 (pttt) REVERT: C 112 LYS cc_start: 0.5124 (tttm) cc_final: 0.4819 (tppt) REVERT: C 143 LYS cc_start: 0.4465 (tmmt) cc_final: 0.4007 (tttt) REVERT: C 151 ILE cc_start: 0.6014 (mt) cc_final: 0.5760 (pt) REVERT: C 152 LYS cc_start: 0.5949 (ptmm) cc_final: 0.5700 (ptpt) REVERT: C 154 MET cc_start: 0.6465 (ttp) cc_final: 0.6237 (ttm) REVERT: C 168 HIS cc_start: 0.6514 (t-90) cc_final: 0.6180 (t-90) REVERT: C 170 HIS cc_start: 0.6705 (p-80) cc_final: 0.6367 (p90) REVERT: C 178 ASN cc_start: 0.6168 (t0) cc_final: 0.5846 (m-40) REVERT: C 197 ASP cc_start: 0.5421 (t0) cc_final: 0.5131 (m-30) REVERT: C 222 ARG cc_start: 0.4096 (OUTLIER) cc_final: 0.3838 (mtm-85) REVERT: C 225 ARG cc_start: 0.2682 (mtp85) cc_final: 0.1959 (ttp80) REVERT: D 27 LYS cc_start: 0.4915 (pmtt) cc_final: 0.4228 (pttp) REVERT: D 28 GLU cc_start: 0.5553 (mt-10) cc_final: 0.5100 (mp0) REVERT: D 46 GLU cc_start: 0.5048 (OUTLIER) cc_final: 0.4417 (mm-30) REVERT: D 59 ARG cc_start: 0.6863 (mtt-85) cc_final: 0.6525 (mtp85) REVERT: D 72 ARG cc_start: 0.4712 (mmm-85) cc_final: 0.3772 (mmm160) REVERT: D 85 GLU cc_start: 0.5636 (tp30) cc_final: 0.5366 (tp30) REVERT: D 88 ARG cc_start: 0.4418 (ttp80) cc_final: 0.4151 (ttp-110) REVERT: D 108 LYS cc_start: 0.6209 (mttt) cc_final: 0.5765 (mptp) REVERT: D 110 GLU cc_start: 0.5784 (mp0) cc_final: 0.5123 (mp0) REVERT: D 122 SER cc_start: 0.6531 (m) cc_final: 0.6234 (p) REVERT: D 129 MET cc_start: 0.5961 (mmm) cc_final: 0.5566 (mtm) REVERT: D 132 ARG cc_start: 0.5266 (tpp80) cc_final: 0.4894 (ttt-90) REVERT: D 144 LEU cc_start: 0.6466 (OUTLIER) cc_final: 0.6086 (mp) REVERT: D 165 THR cc_start: 0.7308 (m) cc_final: 0.7095 (t) REVERT: D 166 GLU cc_start: 0.7161 (mm-30) cc_final: 0.6834 (mm-30) REVERT: D 169 ARG cc_start: 0.6597 (ttm-80) cc_final: 0.5349 (ttp80) REVERT: D 170 GLU cc_start: 0.6898 (tt0) cc_final: 0.6427 (mt-10) REVERT: D 185 ASN cc_start: 0.8403 (t0) cc_final: 0.8074 (t160) REVERT: E 20 PHE cc_start: 0.6141 (m-80) cc_final: 0.5819 (m-80) REVERT: E 33 LYS cc_start: 0.6503 (mtpm) cc_final: 0.6206 (mtmm) REVERT: E 44 ARG cc_start: 0.4554 (ttm110) cc_final: 0.3835 (tmm-80) REVERT: E 51 TYR cc_start: 0.7470 (t80) cc_final: 0.7232 (t80) REVERT: E 73 ARG cc_start: 0.6283 (ttp80) cc_final: 0.5106 (ttm-80) REVERT: E 78 GLU cc_start: 0.6564 (tt0) cc_final: 0.6040 (tp30) REVERT: E 113 GLU cc_start: 0.7046 (tp30) cc_final: 0.6786 (tt0) REVERT: E 119 SER cc_start: 0.6594 (t) cc_final: 0.6194 (p) REVERT: E 124 MET cc_start: 0.6613 (mtm) cc_final: 0.6163 (mtt) REVERT: E 126 ASN cc_start: 0.7196 (m-40) cc_final: 0.6977 (m-40) REVERT: E 128 ARG cc_start: 0.5375 (mtt-85) cc_final: 0.4873 (mmm160) REVERT: E 148 LYS cc_start: 0.5152 (ttpp) cc_final: 0.4818 (ttpp) REVERT: E 171 LEU cc_start: 0.6214 (tp) cc_final: 0.5819 (tp) REVERT: F 13 GLU cc_start: 0.6490 (mt-10) cc_final: 0.5428 (pt0) REVERT: F 14 LYS cc_start: 0.6722 (ttmt) cc_final: 0.6199 (mmtp) REVERT: F 26 LYS cc_start: 0.6862 (tmtm) cc_final: 0.6536 (ttmt) REVERT: F 45 ARG cc_start: 0.6374 (mtp-110) cc_final: 0.6110 (mtp85) REVERT: F 61 GLN cc_start: 0.6154 (tm-30) cc_final: 0.5479 (tm130) REVERT: F 65 GLU cc_start: 0.6200 (mt-10) cc_final: 0.5488 (mm-30) REVERT: F 80 THR cc_start: 0.7489 (t) cc_final: 0.7029 (m) REVERT: F 111 MET cc_start: 0.7919 (mtp) cc_final: 0.7701 (mtp) REVERT: F 116 GLU cc_start: 0.6578 (tt0) cc_final: 0.5945 (tm-30) REVERT: F 156 LYS cc_start: 0.6573 (ptpp) cc_final: 0.6208 (pttt) REVERT: F 159 LYS cc_start: 0.6858 (mmtt) cc_final: 0.6571 (mptp) REVERT: G 15 SER cc_start: 0.5836 (t) cc_final: 0.5406 (m) REVERT: G 37 HIS cc_start: 0.5898 (OUTLIER) cc_final: 0.4416 (p-80) REVERT: G 56 LYS cc_start: 0.6801 (mtpt) cc_final: 0.6126 (mttp) REVERT: G 62 MET cc_start: 0.6591 (ptp) cc_final: 0.6376 (ptm) REVERT: G 79 ARG cc_start: 0.5413 (ttm-80) cc_final: 0.4139 (ttp-110) REVERT: G 87 SER cc_start: 0.7534 (p) cc_final: 0.7245 (p) REVERT: G 91 ARG cc_start: 0.7044 (OUTLIER) cc_final: 0.6703 (ttt180) REVERT: H 26 PHE cc_start: 0.7474 (t80) cc_final: 0.7262 (t80) REVERT: H 33 ASP cc_start: 0.6721 (m-30) cc_final: 0.6512 (m-30) REVERT: H 41 SER cc_start: 0.5975 (p) cc_final: 0.5653 (m) REVERT: H 60 GLU cc_start: 0.5625 (mt-10) cc_final: 0.5067 (mp0) REVERT: H 78 ARG cc_start: 0.2889 (ptm-80) cc_final: 0.2668 (tpt90) REVERT: H 92 ARG cc_start: 0.4596 (mpp-170) cc_final: 0.4348 (mpt180) REVERT: H 119 ARG cc_start: 0.6533 (mtm180) cc_final: 0.6178 (mtt180) REVERT: H 139 GLU cc_start: 0.6370 (mt-10) cc_final: 0.6026 (mt-10) REVERT: H 146 GLU cc_start: 0.4871 (tm-30) cc_final: 0.4626 (tp30) REVERT: H 149 LYS cc_start: 0.5812 (tppt) cc_final: 0.5602 (tppp) REVERT: I 3 MET cc_start: 0.7188 (tpp) cc_final: 0.6977 (tpt) REVERT: I 31 LYS cc_start: 0.6367 (mtmm) cc_final: 0.6147 (mtmt) REVERT: I 41 LYS cc_start: 0.7337 (tttt) cc_final: 0.6814 (tptp) REVERT: I 43 GLU cc_start: 0.7367 (mm-30) cc_final: 0.6906 (mm-30) REVERT: I 69 LYS cc_start: 0.6215 (mtpp) cc_final: 0.5620 (tptm) REVERT: I 76 GLN cc_start: 0.6587 (mt0) cc_final: 0.6262 (tt0) REVERT: I 88 ARG cc_start: 0.6810 (mtm-85) cc_final: 0.6305 (mtm180) REVERT: I 91 GLU cc_start: 0.5855 (mt-10) cc_final: 0.5267 (pt0) REVERT: I 96 MET cc_start: 0.7499 (mtp) cc_final: 0.7120 (ttt) REVERT: I 111 MET cc_start: 0.8180 (ptp) cc_final: 0.7849 (ptp) REVERT: I 114 ARG cc_start: 0.6351 (ttm110) cc_final: 0.5763 (ptm160) REVERT: J 27 LYS cc_start: 0.5281 (OUTLIER) cc_final: 0.4955 (ptpt) REVERT: J 42 GLU cc_start: 0.5633 (mm-30) cc_final: 0.5361 (mm-30) REVERT: J 85 ARG cc_start: 0.6251 (OUTLIER) cc_final: 0.5901 (mtt180) REVERT: J 104 VAL cc_start: 0.7078 (t) cc_final: 0.6807 (t) REVERT: J 119 ARG cc_start: 0.6489 (ptm-80) cc_final: 0.5999 (ptp-110) REVERT: K 11 LYS cc_start: 0.6975 (mttt) cc_final: 0.6433 (mmmt) REVERT: K 16 ARG cc_start: 0.5188 (mtm-85) cc_final: 0.4987 (mtt90) REVERT: K 88 MET cc_start: 0.3822 (mmt) cc_final: 0.3249 (mtm) REVERT: L 27 PHE cc_start: 0.7049 (m-80) cc_final: 0.6735 (m-10) REVERT: L 34 ILE cc_start: 0.7547 (mt) cc_final: 0.7286 (mm) REVERT: L 40 ASN cc_start: 0.7120 (m-40) cc_final: 0.6866 (m110) REVERT: L 106 ARG cc_start: 0.5016 (ttt180) cc_final: 0.4356 (tpt90) REVERT: M 10 LYS cc_start: 0.6190 (tttt) cc_final: 0.5605 (tttm) REVERT: M 36 ARG cc_start: 0.7122 (ttp80) cc_final: 0.6665 (ttt-90) REVERT: M 40 THR cc_start: 0.8035 (t) cc_final: 0.7619 (p) REVERT: M 43 LYS cc_start: 0.7346 (ptpt) cc_final: 0.6901 (pttt) REVERT: M 44 LYS cc_start: 0.7139 (ptmt) cc_final: 0.6892 (tmmm) REVERT: M 49 LEU cc_start: 0.7508 (mt) cc_final: 0.7256 (mm) REVERT: M 54 ARG cc_start: 0.7091 (ttm-80) cc_final: 0.6758 (ttt90) REVERT: M 64 THR cc_start: 0.8297 (m) cc_final: 0.7783 (p) REVERT: M 94 ARG cc_start: 0.7396 (ptp-170) cc_final: 0.7190 (mtm180) REVERT: M 111 LYS cc_start: 0.7407 (mmmt) cc_final: 0.7030 (mmtt) REVERT: M 112 GLN cc_start: 0.7912 (mt0) cc_final: 0.7673 (mt0) REVERT: N 78 LYS cc_start: 0.5789 (tttm) cc_final: 0.5292 (tptp) REVERT: N 81 MET cc_start: 0.7236 (mtm) cc_final: 0.6535 (mtm) REVERT: N 92 ARG cc_start: 0.6813 (mtt180) cc_final: 0.6578 (mtm-85) REVERT: N 93 ARG cc_start: 0.6048 (mmt-90) cc_final: 0.5224 (mmp80) REVERT: N 110 LYS cc_start: 0.7309 (OUTLIER) cc_final: 0.6976 (mttm) REVERT: O 16 LEU cc_start: 0.6495 (mt) cc_final: 0.6171 (mt) REVERT: O 23 LYS cc_start: 0.5469 (tppp) cc_final: 0.5228 (tppp) REVERT: P 47 LYS cc_start: 0.7583 (mptp) cc_final: 0.7333 (mptp) REVERT: P 61 SER cc_start: 0.7349 (m) cc_final: 0.7000 (p) REVERT: Q 1 MET cc_start: 0.6658 (pmm) cc_final: 0.6181 (pmm) REVERT: Q 14 ARG cc_start: 0.6986 (mtp-110) cc_final: 0.6609 (mtp85) REVERT: Q 68 SER cc_start: 0.7433 (t) cc_final: 0.7018 (p) REVERT: Q 76 LYS cc_start: 0.5108 (OUTLIER) cc_final: 0.4381 (mmtm) REVERT: R 9 GLN cc_start: 0.6801 (tt0) cc_final: 0.6521 (tt0) REVERT: R 45 HIS cc_start: 0.7387 (m90) cc_final: 0.7097 (m170) REVERT: S 16 GLU cc_start: 0.4098 (OUTLIER) cc_final: 0.3840 (mm-30) REVERT: S 48 ARG cc_start: 0.6428 (mtm110) cc_final: 0.6217 (mtp-110) REVERT: S 54 GLN cc_start: 0.7092 (mt0) cc_final: 0.6858 (mt0) REVERT: T 16 LEU cc_start: 0.5070 (tp) cc_final: 0.4848 (tt) REVERT: T 44 MET cc_start: 0.6020 (mtt) cc_final: 0.5482 (mtt) REVERT: U 24 ARG cc_start: 0.6714 (mmm160) cc_final: 0.6070 (mmm160) REVERT: U 54 MET cc_start: 0.6219 (tmm) cc_final: 0.6007 (tmm) REVERT: U 55 GLN cc_start: 0.7119 (tt0) cc_final: 0.6759 (tt0) REVERT: U 60 ARG cc_start: 0.6578 (ttp-110) cc_final: 0.6337 (ttm110) REVERT: U 61 GLN cc_start: 0.6814 (mm-40) cc_final: 0.6460 (mm110) REVERT: V 22 SER cc_start: 0.5312 (t) cc_final: 0.4734 (p) REVERT: V 33 ARG cc_start: 0.5535 (mtt90) cc_final: 0.5020 (mmm160) REVERT: V 36 GLU cc_start: 0.6947 (tt0) cc_final: 0.6627 (mt-10) REVERT: V 39 GLU cc_start: 0.6552 (mt-10) cc_final: 0.5644 (mm-30) REVERT: V 47 ARG cc_start: 0.5795 (ptt90) cc_final: 0.5434 (ptt-90) REVERT: V 49 LYS cc_start: 0.6250 (tptp) cc_final: 0.5829 (tptp) REVERT: W 96 LEU cc_start: 0.3021 (OUTLIER) cc_final: 0.2715 (mp) REVERT: W 109 ARG cc_start: 0.6260 (ptm-80) cc_final: 0.5833 (ptt180) REVERT: W 142 ARG cc_start: 0.5702 (mtp85) cc_final: 0.5316 (mtt-85) REVERT: W 143 ARG cc_start: 0.5681 (OUTLIER) cc_final: 0.5004 (mpp-170) REVERT: W 160 LYS cc_start: 0.7075 (mmtt) cc_final: 0.6269 (mtpp) REVERT: W 165 LYS cc_start: 0.6333 (tttt) cc_final: 0.6120 (ttmt) REVERT: W 169 ASP cc_start: 0.4268 (t0) cc_final: 0.4006 (m-30) REVERT: W 208 GLU cc_start: 0.5707 (tt0) cc_final: 0.5397 (tt0) REVERT: W 223 ARG cc_start: 0.7460 (ttp-170) cc_final: 0.6888 (ttp-170) REVERT: W 269 LYS cc_start: 0.7570 (tptp) cc_final: 0.7248 (tptm) REVERT: W 282 GLU cc_start: 0.5283 (pt0) cc_final: 0.5045 (mm-30) REVERT: W 287 GLN cc_start: 0.5539 (mt0) cc_final: 0.4915 (tm-30) REVERT: W 318 THR cc_start: 0.7866 (OUTLIER) cc_final: 0.7631 (m) REVERT: W 328 ARG cc_start: 0.6772 (mtp85) cc_final: 0.5780 (mtp180) REVERT: W 330 ASP cc_start: 0.5305 (m-30) cc_final: 0.4944 (p0) REVERT: W 331 GLU cc_start: 0.6238 (mm-30) cc_final: 0.5093 (pp20) REVERT: W 334 GLU cc_start: 0.4941 (mt-10) cc_final: 0.4675 (mm-30) REVERT: c 5 LYS cc_start: 0.7249 (tttp) cc_final: 0.6360 (tptp) REVERT: c 18 LYS cc_start: 0.7675 (ptpt) cc_final: 0.7453 (mtmt) REVERT: c 66 ASP cc_start: 0.8062 (t0) cc_final: 0.7734 (t0) REVERT: c 111 LYS cc_start: 0.6509 (ptpp) cc_final: 0.5625 (mttm) REVERT: c 117 GLN cc_start: 0.7626 (tp40) cc_final: 0.7390 (tt0) REVERT: c 181 MET cc_start: 0.8163 (tpp) cc_final: 0.7666 (mmm) REVERT: c 199 GLU cc_start: 0.7471 (mt-10) cc_final: 0.6545 (pm20) REVERT: c 203 ARG cc_start: 0.7701 (ptt90) cc_final: 0.7342 (ptp-110) REVERT: c 264 ASP cc_start: 0.7752 (m-30) cc_final: 0.7433 (m-30) REVERT: c 269 ARG cc_start: 0.7302 (ttp-170) cc_final: 0.6859 (ttp80) REVERT: d 1 MET cc_start: 0.3856 (OUTLIER) cc_final: 0.2767 (mtp) REVERT: d 7 LYS cc_start: 0.7802 (ttmt) cc_final: 0.7113 (ttpp) REVERT: d 70 LYS cc_start: 0.6910 (tttt) cc_final: 0.6606 (tttt) REVERT: d 89 GLU cc_start: 0.6994 (tp30) cc_final: 0.6106 (pt0) REVERT: d 91 THR cc_start: 0.7351 (p) cc_final: 0.6824 (m) REVERT: d 99 GLU cc_start: 0.6435 (mm-30) cc_final: 0.5855 (mp0) REVERT: d 161 MET cc_start: 0.8619 (mtt) cc_final: 0.8161 (mtp) REVERT: d 204 LYS cc_start: 0.8202 (mttt) cc_final: 0.7821 (mttp) REVERT: e 18 THR cc_start: 0.7327 (m) cc_final: 0.7038 (m) REVERT: e 22 ASP cc_start: 0.6596 (p0) cc_final: 0.6038 (m-30) REVERT: e 132 LYS cc_start: 0.6930 (tttm) cc_final: 0.6693 (ttpt) REVERT: e 137 LYS cc_start: 0.6829 (tttt) cc_final: 0.6587 (tttm) REVERT: e 144 GLU cc_start: 0.6069 (mt-10) cc_final: 0.5786 (pt0) REVERT: e 153 LEU cc_start: 0.4373 (OUTLIER) cc_final: 0.4164 (tm) REVERT: e 191 ASP cc_start: 0.6100 (t0) cc_final: 0.5559 (p0) REVERT: e 198 GLU cc_start: 0.6197 (tt0) cc_final: 0.5583 (mm-30) REVERT: e 199 MET cc_start: 0.5804 (ttp) cc_final: 0.5357 (ttp) REVERT: f 11 GLU cc_start: 0.5388 (mm-30) cc_final: 0.5011 (mp0) REVERT: f 30 ARG cc_start: 0.6048 (mpp80) cc_final: 0.5568 (mtm-85) REVERT: f 50 LEU cc_start: 0.5076 (tm) cc_final: 0.4595 (tp) REVERT: f 60 ILE cc_start: 0.7202 (mt) cc_final: 0.6920 (mt) REVERT: f 88 LYS cc_start: 0.7570 (OUTLIER) cc_final: 0.6980 (ptpt) REVERT: f 101 GLU cc_start: 0.6139 (tt0) cc_final: 0.5799 (tt0) REVERT: f 129 SER cc_start: 0.7406 (m) cc_final: 0.7014 (t) REVERT: g 6 LYS cc_start: 0.4450 (mmtt) cc_final: 0.4244 (mmmm) REVERT: g 9 VAL cc_start: 0.4660 (m) cc_final: 0.4196 (p) REVERT: g 74 SER cc_start: 0.6837 (m) cc_final: 0.6564 (t) REVERT: g 95 ARG cc_start: 0.6295 (mtm110) cc_final: 0.5661 (mtm-85) REVERT: g 124 GLU cc_start: 0.5729 (mp0) cc_final: 0.5239 (pt0) REVERT: g 127 THR cc_start: 0.6197 (OUTLIER) cc_final: 0.5770 (p) REVERT: h 3 VAL cc_start: 0.6240 (m) cc_final: 0.5997 (t) REVERT: h 21 VAL cc_start: 0.5437 (OUTLIER) cc_final: 0.5097 (t) REVERT: i 1 MET cc_start: 0.5155 (ptm) cc_final: 0.4145 (tpt) REVERT: i 2 LYS cc_start: 0.7021 (mttt) cc_final: 0.6571 (mttt) REVERT: i 34 ARG cc_start: 0.7608 (ttt-90) cc_final: 0.7148 (mtp85) REVERT: i 61 LYS cc_start: 0.7101 (mttt) cc_final: 0.6623 (mmtm) REVERT: i 85 LYS cc_start: 0.7792 (mmtt) cc_final: 0.7580 (mmtt) REVERT: i 91 GLU cc_start: 0.7478 (mt-10) cc_final: 0.7239 (mt-10) REVERT: i 95 ARG cc_start: 0.6072 (ttt180) cc_final: 0.5358 (mpt-90) REVERT: i 96 ARG cc_start: 0.6691 (ptt-90) cc_final: 0.5080 (mmt180) REVERT: i 118 MET cc_start: 0.8388 (mtt) cc_final: 0.8124 (mtt) REVERT: i 128 ASN cc_start: 0.7617 (t0) cc_final: 0.7272 (t0) REVERT: i 129 GLU cc_start: 0.7079 (mm-30) cc_final: 0.6822 (mm-30) REVERT: i 136 GLN cc_start: 0.7468 (mt0) cc_final: 0.7236 (mt0) REVERT: j 1 MET cc_start: 0.8359 (OUTLIER) cc_final: 0.8116 (ttp) REVERT: j 17 ARG cc_start: 0.7212 (mmt90) cc_final: 0.6714 (mmm160) REVERT: j 29 HIS cc_start: 0.7049 (m-70) cc_final: 0.6602 (m90) REVERT: j 45 GLU cc_start: 0.7399 (mt-10) cc_final: 0.7141 (mt-10) REVERT: j 51 LYS cc_start: 0.7314 (mtpp) cc_final: 0.6799 (mtmt) REVERT: j 98 ARG cc_start: 0.6862 (mmt-90) cc_final: 0.6345 (mmm160) REVERT: j 105 ARG cc_start: 0.6207 (tpp-160) cc_final: 0.5910 (mmt-90) REVERT: j 113 MET cc_start: 0.5822 (mmt) cc_final: 0.5445 (mmp) REVERT: j 114 LYS cc_start: 0.5970 (mppt) cc_final: 0.5525 (mmpt) REVERT: k 106 GLU cc_start: 0.7712 (mt-10) cc_final: 0.7008 (mm-30) REVERT: l 6 ARG cc_start: 0.6799 (mtt180) cc_final: 0.6285 (mtm110) REVERT: l 22 GLN cc_start: 0.7529 (mm-40) cc_final: 0.6116 (mt0) REVERT: l 55 ARG cc_start: 0.6670 (ttm110) cc_final: 0.6131 (ttm110) REVERT: l 127 LYS cc_start: 0.7721 (OUTLIER) cc_final: 0.7505 (mttp) REVERT: l 129 THR cc_start: 0.7952 (p) cc_final: 0.7653 (t) REVERT: l 132 THR cc_start: 0.7217 (m) cc_final: 0.6863 (p) REVERT: l 136 MET cc_start: 0.4996 (mtp) cc_final: 0.4749 (mtp) REVERT: m 18 GLN cc_start: 0.8065 (tt0) cc_final: 0.7745 (tt0) REVERT: m 72 ASP cc_start: 0.7609 (t0) cc_final: 0.7223 (t70) REVERT: n 13 ARG cc_start: 0.6497 (tpp-160) cc_final: 0.5505 (ttp80) REVERT: n 16 ARG cc_start: 0.7160 (mmt-90) cc_final: 0.6798 (mmp80) REVERT: n 19 GLN cc_start: 0.7249 (tt0) cc_final: 0.6364 (tt0) REVERT: n 20 GLU cc_start: 0.6065 (pt0) cc_final: 0.5375 (tm-30) REVERT: n 55 GLU cc_start: 0.6465 (mt-10) cc_final: 0.6261 (mt-10) REVERT: n 76 LYS cc_start: 0.6578 (tttp) cc_final: 0.6260 (ttpt) REVERT: n 81 ARG cc_start: 0.7258 (OUTLIER) cc_final: 0.5985 (mtm-85) REVERT: n 85 LYS cc_start: 0.6296 (mtpm) cc_final: 0.6027 (mttp) REVERT: n 98 GLN cc_start: 0.7541 (mm-40) cc_final: 0.7269 (tp40) REVERT: o 6 LYS cc_start: 0.6281 (ttpp) cc_final: 0.5927 (ttpp) REVERT: o 7 GLN cc_start: 0.6595 (tp40) cc_final: 0.6279 (tt0) REVERT: o 10 GLN cc_start: 0.6851 (mm-40) cc_final: 0.6198 (mt0) REVERT: o 63 LYS cc_start: 0.7698 (ptmm) cc_final: 0.7201 (pttt) REVERT: o 68 GLU cc_start: 0.5975 (mm-30) cc_final: 0.5771 (mp0) REVERT: o 89 ARG cc_start: 0.7161 (mtm180) cc_final: 0.6133 (mmt180) REVERT: p 11 ARG cc_start: 0.6894 (tpm170) cc_final: 0.6184 (ttp-110) REVERT: p 15 LYS cc_start: 0.7746 (mtpt) cc_final: 0.7296 (ttmm) REVERT: p 16 LYS cc_start: 0.7720 (ttpt) cc_final: 0.7460 (ttmt) REVERT: p 78 LYS cc_start: 0.8150 (mmmt) cc_final: 0.7830 (mttm) REVERT: p 85 LYS cc_start: 0.7281 (mttt) cc_final: 0.7010 (mmtm) REVERT: p 112 LYS cc_start: 0.7036 (OUTLIER) cc_final: 0.6665 (tppp) REVERT: q 48 LYS cc_start: 0.7545 (mttm) cc_final: 0.6948 (mttt) REVERT: q 60 LYS cc_start: 0.7119 (mtmt) cc_final: 0.6786 (mtmp) REVERT: q 73 LYS cc_start: 0.7899 (mmtp) cc_final: 0.7360 (mmpt) REVERT: r 28 LYS cc_start: 0.7199 (mtpt) cc_final: 0.6168 (mmtm) REVERT: r 52 GLU cc_start: 0.7395 (mt-10) cc_final: 0.7185 (mt-10) REVERT: r 73 LYS cc_start: 0.7825 (mttm) cc_final: 0.7406 (mtpm) REVERT: r 86 MET cc_start: 0.8065 (tpp) cc_final: 0.7192 (ttp) REVERT: s 3 ARG cc_start: 0.4957 (mtt-85) cc_final: 0.4728 (mtm-85) REVERT: s 5 GLU cc_start: 0.6456 (mt-10) cc_final: 0.5738 (pp20) REVERT: s 9 LYS cc_start: 0.6975 (mmtt) cc_final: 0.6513 (mtpt) REVERT: s 12 ARG cc_start: 0.7700 (mmm160) cc_final: 0.7488 (mmm160) REVERT: s 18 GLU cc_start: 0.7127 (mt-10) cc_final: 0.5958 (mp0) REVERT: s 24 MET cc_start: 0.6223 (tpt) cc_final: 0.5891 (tpt) REVERT: s 33 LYS cc_start: 0.7312 (tttt) cc_final: 0.6475 (mttp) REVERT: s 50 LEU cc_start: 0.7201 (mt) cc_final: 0.6943 (mp) REVERT: s 93 LEU cc_start: 0.2313 (OUTLIER) cc_final: 0.2065 (tp) REVERT: t 7 ARG cc_start: 0.6160 (ttt180) cc_final: 0.5427 (ttm110) REVERT: t 10 GLU cc_start: 0.6872 (OUTLIER) cc_final: 0.5632 (pm20) REVERT: t 24 LYS cc_start: 0.6948 (ttpt) cc_final: 0.6642 (ttmm) REVERT: t 43 LYS cc_start: 0.7129 (mtmm) cc_final: 0.6766 (mttp) REVERT: t 61 LYS cc_start: 0.6363 (ptmm) cc_final: 0.6107 (pttt) REVERT: t 72 ILE cc_start: 0.7556 (tp) cc_final: 0.7307 (tt) REVERT: t 86 ARG cc_start: 0.7569 (mtm-85) cc_final: 0.7139 (mtm180) REVERT: u 2 PHE cc_start: 0.7140 (m-80) cc_final: 0.6590 (m-80) REVERT: u 12 GLN cc_start: 0.7321 (pt0) cc_final: 0.6939 (pt0) REVERT: u 42 LEU cc_start: 0.8160 (mt) cc_final: 0.7956 (mt) REVERT: u 43 ASP cc_start: 0.7230 (t0) cc_final: 0.6815 (t0) REVERT: u 58 SER cc_start: 0.7598 (OUTLIER) cc_final: 0.7354 (p) REVERT: u 65 VAL cc_start: 0.5801 (OUTLIER) cc_final: 0.5541 (t) REVERT: u 73 LYS cc_start: 0.7052 (mttt) cc_final: 0.6635 (mtpm) REVERT: u 77 VAL cc_start: 0.8202 (p) cc_final: 0.7917 (t) REVERT: u 79 ARG cc_start: 0.8023 (mtt-85) cc_final: 0.7773 (mtt-85) REVERT: v 25 ARG cc_start: 0.8048 (mmt90) cc_final: 0.7409 (mpt180) REVERT: v 70 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7390 (mp0) REVERT: v 72 LYS cc_start: 0.7621 (mtmm) cc_final: 0.7417 (mtpp) REVERT: v 83 GLU cc_start: 0.6612 (mm-30) cc_final: 0.6018 (mt-10) REVERT: w 2 SER cc_start: 0.7719 (p) cc_final: 0.7340 (m) REVERT: w 45 ARG cc_start: 0.6032 (OUTLIER) cc_final: 0.5743 (ttt-90) REVERT: w 54 LYS cc_start: 0.7412 (tmmt) cc_final: 0.6929 (tttp) REVERT: w 65 ASP cc_start: 0.7032 (m-30) cc_final: 0.6655 (m-30) REVERT: x 24 GLU cc_start: 0.6739 (tt0) cc_final: 0.6440 (tt0) REVERT: x 44 LYS cc_start: 0.7084 (ttmt) cc_final: 0.6830 (ttmm) REVERT: x 56 LEU cc_start: 0.7384 (OUTLIER) cc_final: 0.7159 (mm) REVERT: y 21 LYS cc_start: 0.7630 (mttt) cc_final: 0.7336 (mttm) REVERT: y 41 THR cc_start: 0.6834 (m) cc_final: 0.6275 (p) REVERT: y 56 LYS cc_start: 0.7312 (pttt) cc_final: 0.7054 (pttp) REVERT: y 57 VAL cc_start: 0.7033 (OUTLIER) cc_final: 0.6662 (p) REVERT: z 12 LYS cc_start: 0.7575 (tppt) cc_final: 0.7240 (mmtp) REVERT: z 32 LYS cc_start: 0.6900 (ptpt) cc_final: 0.6651 (ptmm) outliers start: 125 outliers final: 38 residues processed: 1134 average time/residue: 2.4922 time to fit residues: 3900.6204 Evaluate side-chains 1054 residues out of total 4889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 984 time to evaluate : 6.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 28 ARG Chi-restraints excluded: chain 1 residue 41 ARG Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 105 LYS Chi-restraints excluded: chain C residue 222 ARG Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain G residue 37 HIS Chi-restraints excluded: chain G residue 91 ARG Chi-restraints excluded: chain H residue 75 VAL Chi-restraints excluded: chain I residue 90 ASP Chi-restraints excluded: chain J residue 27 LYS Chi-restraints excluded: chain J residue 85 ARG Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 129 VAL Chi-restraints excluded: chain M residue 34 CYS Chi-restraints excluded: chain M residue 86 ARG Chi-restraints excluded: chain N residue 27 LYS Chi-restraints excluded: chain N residue 68 ASP Chi-restraints excluded: chain N residue 110 LYS Chi-restraints excluded: chain O residue 5 SER Chi-restraints excluded: chain P residue 83 GLU Chi-restraints excluded: chain Q residue 76 LYS Chi-restraints excluded: chain R residue 42 THR Chi-restraints excluded: chain R residue 67 LEU Chi-restraints excluded: chain S residue 16 GLU Chi-restraints excluded: chain V residue 3 VAL Chi-restraints excluded: chain W residue 96 LEU Chi-restraints excluded: chain W residue 143 ARG Chi-restraints excluded: chain W residue 192 SER Chi-restraints excluded: chain W residue 254 VAL Chi-restraints excluded: chain W residue 318 THR Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 92 VAL Chi-restraints excluded: chain e residue 153 LEU Chi-restraints excluded: chain f residue 88 LYS Chi-restraints excluded: chain g residue 15 VAL Chi-restraints excluded: chain g residue 23 VAL Chi-restraints excluded: chain g residue 36 THR Chi-restraints excluded: chain g residue 44 LYS Chi-restraints excluded: chain g residue 87 LEU Chi-restraints excluded: chain g residue 127 THR Chi-restraints excluded: chain g residue 155 GLU Chi-restraints excluded: chain g residue 168 VAL Chi-restraints excluded: chain h residue 21 VAL Chi-restraints excluded: chain j residue 1 MET Chi-restraints excluded: chain l residue 30 SER Chi-restraints excluded: chain l residue 127 LYS Chi-restraints excluded: chain n residue 81 ARG Chi-restraints excluded: chain o residue 85 SER Chi-restraints excluded: chain p residue 112 LYS Chi-restraints excluded: chain q residue 33 VAL Chi-restraints excluded: chain r residue 66 ILE Chi-restraints excluded: chain s residue 93 LEU Chi-restraints excluded: chain t residue 10 GLU Chi-restraints excluded: chain u residue 58 SER Chi-restraints excluded: chain u residue 62 THR Chi-restraints excluded: chain u residue 65 VAL Chi-restraints excluded: chain v residue 30 SER Chi-restraints excluded: chain v residue 70 GLU Chi-restraints excluded: chain v residue 78 LYS Chi-restraints excluded: chain w residue 45 ARG Chi-restraints excluded: chain x residue 40 SER Chi-restraints excluded: chain x residue 56 LEU Chi-restraints excluded: chain y residue 57 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1023 random chunks: chunk 516 optimal weight: 8.9990 chunk 288 optimal weight: 4.9990 chunk 773 optimal weight: 10.0000 chunk 632 optimal weight: 7.9990 chunk 256 optimal weight: 0.7980 chunk 930 optimal weight: 5.9990 chunk 1005 optimal weight: 7.9990 chunk 828 optimal weight: 10.0000 chunk 922 optimal weight: 0.0770 chunk 317 optimal weight: 7.9990 chunk 746 optimal weight: 5.9990 overall best weight: 3.5744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 29 GLN C 18 HIS C 51 ASN C 177 ASN E 198 HIS F 19 ASN ** F 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 97 GLN ** G 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 68 ASN H 97 ASN J 31 ASN J 110 GLN K 56 HIS L 15 GLN L 22 HIS P 37 ASN P 46 HIS U 68 HIS W 248 HIS W 349 GLN g 64 GLN k 104 GLN q 18 GLN x 27 ASN x 58 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 156812 Z= 0.321 Angle : 0.789 16.444 234226 Z= 0.413 Chirality : 0.043 0.398 29769 Planarity : 0.008 0.154 12793 Dihedral : 23.296 176.943 77664 Min Nonbonded Distance : 1.664 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.68 % Favored : 97.16 % Rotamer: Outliers : 3.13 % Allowed : 11.74 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.11), residues: 5853 helix: 0.77 (0.11), residues: 2045 sheet: -0.56 (0.14), residues: 1170 loop : -0.35 (0.12), residues: 2638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 201 HIS 0.011 0.002 HIS w 34 PHE 0.021 0.003 PHE m 21 TYR 0.025 0.003 TYR r 38 ARG 0.009 0.001 ARG F 93 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11706 Ramachandran restraints generated. 5853 Oldfield, 0 Emsley, 5853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11706 Ramachandran restraints generated. 5853 Oldfield, 0 Emsley, 5853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1146 residues out of total 4889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 993 time to evaluate : 6.379 Fit side-chains revert: symmetry clash REVERT: 0 33 LYS cc_start: 0.6391 (tptt) cc_final: 0.6096 (mmtp) REVERT: 0 44 ARG cc_start: 0.7180 (mtp180) cc_final: 0.6819 (mtm110) REVERT: 2 15 LYS cc_start: 0.7401 (mptt) cc_final: 0.6695 (mmmm) REVERT: 2 52 LYS cc_start: 0.5956 (tttm) cc_final: 0.5499 (tppt) REVERT: 3 8 LYS cc_start: 0.7572 (mttt) cc_final: 0.6829 (mtmt) REVERT: 3 15 LYS cc_start: 0.7533 (mttt) cc_final: 0.6737 (mttt) REVERT: C 49 MET cc_start: 0.4618 (mtp) cc_final: 0.4321 (mtt) REVERT: C 100 MET cc_start: 0.6490 (mtt) cc_final: 0.6243 (ttp) REVERT: C 105 LYS cc_start: 0.6884 (OUTLIER) cc_final: 0.6457 (ptpt) REVERT: C 112 LYS cc_start: 0.5228 (tttm) cc_final: 0.4869 (tppt) REVERT: C 143 LYS cc_start: 0.4437 (tmmt) cc_final: 0.4056 (tttt) REVERT: C 153 ASP cc_start: 0.5100 (m-30) cc_final: 0.4814 (p0) REVERT: C 170 HIS cc_start: 0.6755 (p-80) cc_final: 0.6374 (p90) REVERT: C 178 ASN cc_start: 0.6211 (t0) cc_final: 0.5987 (m-40) REVERT: D 27 LYS cc_start: 0.4960 (pmtt) cc_final: 0.4361 (pttp) REVERT: D 28 GLU cc_start: 0.6028 (mt-10) cc_final: 0.5475 (mp0) REVERT: D 46 GLU cc_start: 0.5162 (OUTLIER) cc_final: 0.4451 (mm-30) REVERT: D 72 ARG cc_start: 0.4496 (mmm-85) cc_final: 0.4159 (mtm180) REVERT: D 108 LYS cc_start: 0.6190 (mttt) cc_final: 0.5967 (mttm) REVERT: D 122 SER cc_start: 0.6531 (m) cc_final: 0.6213 (p) REVERT: D 129 MET cc_start: 0.6056 (mmm) cc_final: 0.5574 (mtt) REVERT: D 131 ARG cc_start: 0.6336 (ttm170) cc_final: 0.6003 (ttm110) REVERT: D 169 ARG cc_start: 0.6551 (ttm-80) cc_final: 0.5331 (ttp80) REVERT: D 170 GLU cc_start: 0.6758 (tt0) cc_final: 0.6394 (mt-10) REVERT: E 20 PHE cc_start: 0.6168 (m-80) cc_final: 0.5956 (m-80) REVERT: E 29 ASP cc_start: 0.5289 (OUTLIER) cc_final: 0.4745 (p0) REVERT: E 44 ARG cc_start: 0.4637 (ttm110) cc_final: 0.3719 (tmm-80) REVERT: E 73 ARG cc_start: 0.6441 (ttp80) cc_final: 0.5258 (ttm-80) REVERT: E 78 GLU cc_start: 0.6736 (tt0) cc_final: 0.6391 (tp30) REVERT: E 113 GLU cc_start: 0.7038 (tp30) cc_final: 0.6690 (tt0) REVERT: E 119 SER cc_start: 0.6616 (t) cc_final: 0.6250 (p) REVERT: E 124 MET cc_start: 0.6670 (mtm) cc_final: 0.6240 (mtt) REVERT: E 126 ASN cc_start: 0.7017 (m-40) cc_final: 0.6658 (m-40) REVERT: E 128 ARG cc_start: 0.5408 (mtt-85) cc_final: 0.4891 (mmm-85) REVERT: E 141 ASP cc_start: 0.5987 (m-30) cc_final: 0.5738 (m-30) REVERT: E 148 LYS cc_start: 0.5124 (ttpp) cc_final: 0.4761 (ttpp) REVERT: E 171 LEU cc_start: 0.6105 (OUTLIER) cc_final: 0.5754 (tp) REVERT: F 26 LYS cc_start: 0.6822 (tmtm) cc_final: 0.6476 (ttmt) REVERT: F 45 ARG cc_start: 0.6375 (mtp-110) cc_final: 0.5695 (mmm160) REVERT: F 61 GLN cc_start: 0.6275 (tm-30) cc_final: 0.5532 (tm130) REVERT: F 65 GLU cc_start: 0.6387 (mt-10) cc_final: 0.5755 (mm-30) REVERT: F 70 ASN cc_start: 0.5397 (m110) cc_final: 0.5186 (m110) REVERT: F 74 VAL cc_start: 0.6721 (t) cc_final: 0.6428 (p) REVERT: F 116 GLU cc_start: 0.6839 (tt0) cc_final: 0.6196 (tt0) REVERT: F 156 LYS cc_start: 0.6675 (ptpp) cc_final: 0.6268 (pttt) REVERT: F 159 LYS cc_start: 0.6807 (mmtt) cc_final: 0.6518 (mptp) REVERT: G 2 ARG cc_start: 0.6126 (mtp85) cc_final: 0.5882 (mtt180) REVERT: G 5 GLU cc_start: 0.7247 (tt0) cc_final: 0.7031 (tt0) REVERT: G 15 SER cc_start: 0.5845 (t) cc_final: 0.5448 (m) REVERT: G 37 HIS cc_start: 0.5929 (OUTLIER) cc_final: 0.4540 (p-80) REVERT: G 56 LYS cc_start: 0.6670 (mtpt) cc_final: 0.5994 (mttp) REVERT: G 62 MET cc_start: 0.6656 (ptp) cc_final: 0.6434 (ptm) REVERT: G 87 SER cc_start: 0.7459 (p) cc_final: 0.7236 (m) REVERT: H 41 SER cc_start: 0.6104 (p) cc_final: 0.5740 (m) REVERT: H 92 ARG cc_start: 0.4532 (mpp-170) cc_final: 0.4285 (mpt180) REVERT: H 96 ARG cc_start: 0.6036 (mtt90) cc_final: 0.5607 (mtt180) REVERT: H 111 ARG cc_start: 0.5113 (mtp85) cc_final: 0.4862 (mtt-85) REVERT: H 119 ARG cc_start: 0.6567 (mtm180) cc_final: 0.6194 (mtt180) REVERT: H 129 GLU cc_start: 0.4163 (mm-30) cc_final: 0.3870 (mm-30) REVERT: H 137 LYS cc_start: 0.4981 (ptmm) cc_final: 0.4592 (tptt) REVERT: H 139 GLU cc_start: 0.6466 (mt-10) cc_final: 0.5514 (mm-30) REVERT: I 42 GLU cc_start: 0.6377 (pt0) cc_final: 0.6055 (mt-10) REVERT: I 43 GLU cc_start: 0.7658 (mm-30) cc_final: 0.7187 (mm-30) REVERT: I 50 LYS cc_start: 0.6248 (ttpt) cc_final: 0.5219 (pttt) REVERT: I 69 LYS cc_start: 0.6184 (mtpp) cc_final: 0.5595 (tptm) REVERT: I 76 GLN cc_start: 0.6775 (mt0) cc_final: 0.6342 (tt0) REVERT: I 89 LYS cc_start: 0.6246 (ptmt) cc_final: 0.5742 (tmtt) REVERT: I 96 MET cc_start: 0.7485 (mtp) cc_final: 0.7108 (ttt) REVERT: I 111 MET cc_start: 0.8175 (ptp) cc_final: 0.7882 (ptp) REVERT: I 114 ARG cc_start: 0.6472 (ttm110) cc_final: 0.5976 (ttm-80) REVERT: J 27 LYS cc_start: 0.5352 (OUTLIER) cc_final: 0.5144 (pttt) REVERT: J 42 GLU cc_start: 0.5570 (mm-30) cc_final: 0.5341 (mm-30) REVERT: J 49 ARG cc_start: 0.5039 (mtm-85) cc_final: 0.4202 (ptp90) REVERT: J 85 ARG cc_start: 0.6276 (OUTLIER) cc_final: 0.5816 (mtt180) REVERT: J 88 MET cc_start: 0.5722 (OUTLIER) cc_final: 0.4913 (mtt) REVERT: J 91 ASP cc_start: 0.5228 (t70) cc_final: 0.4993 (t0) REVERT: J 104 VAL cc_start: 0.7099 (t) cc_final: 0.6795 (t) REVERT: J 119 ARG cc_start: 0.6814 (ptm-80) cc_final: 0.6168 (ptp-110) REVERT: K 11 LYS cc_start: 0.6950 (mttt) cc_final: 0.6497 (mmtt) REVERT: K 88 MET cc_start: 0.3650 (mmt) cc_final: 0.3048 (mtm) REVERT: L 34 ILE cc_start: 0.7517 (mt) cc_final: 0.7309 (mm) REVERT: L 40 ASN cc_start: 0.7368 (m-40) cc_final: 0.7154 (m110) REVERT: L 105 PHE cc_start: 0.6676 (m-80) cc_final: 0.6384 (m-80) REVERT: L 106 ARG cc_start: 0.4750 (ttt180) cc_final: 0.4180 (tpt90) REVERT: M 10 LYS cc_start: 0.6126 (tttt) cc_final: 0.5554 (tttm) REVERT: M 40 THR cc_start: 0.7975 (t) cc_final: 0.7496 (p) REVERT: M 43 LYS cc_start: 0.7334 (ptpt) cc_final: 0.6938 (pttt) REVERT: M 49 LEU cc_start: 0.7462 (mt) cc_final: 0.7107 (mm) REVERT: M 54 ARG cc_start: 0.7091 (ttm-80) cc_final: 0.6858 (ttt90) REVERT: M 64 THR cc_start: 0.8246 (m) cc_final: 0.7761 (p) REVERT: M 75 GLN cc_start: 0.7067 (pm20) cc_final: 0.6644 (pm20) REVERT: M 88 LYS cc_start: 0.7162 (OUTLIER) cc_final: 0.6222 (tttt) REVERT: M 111 LYS cc_start: 0.7422 (mmmt) cc_final: 0.7205 (mmtm) REVERT: M 121 ARG cc_start: 0.6659 (ttt-90) cc_final: 0.6445 (ttt-90) REVERT: N 13 LYS cc_start: 0.5998 (OUTLIER) cc_final: 0.5678 (mtmt) REVERT: N 68 ASP cc_start: 0.5478 (OUTLIER) cc_final: 0.5025 (t70) REVERT: N 78 LYS cc_start: 0.5863 (tttm) cc_final: 0.5469 (tptp) REVERT: N 81 MET cc_start: 0.7249 (mtm) cc_final: 0.6462 (mtm) REVERT: N 92 ARG cc_start: 0.6766 (mtt180) cc_final: 0.6510 (mtm-85) REVERT: N 93 ARG cc_start: 0.6050 (mmt-90) cc_final: 0.5188 (mmp80) REVERT: N 110 LYS cc_start: 0.7376 (OUTLIER) cc_final: 0.6752 (mttm) REVERT: N 113 ARG cc_start: 0.5189 (OUTLIER) cc_final: 0.4526 (mmm-85) REVERT: N 114 LYS cc_start: 0.4705 (mttp) cc_final: 0.4347 (mptp) REVERT: P 61 SER cc_start: 0.7370 (m) cc_final: 0.7068 (p) REVERT: Q 1 MET cc_start: 0.6783 (pmm) cc_final: 0.6173 (pmm) REVERT: R 11 ARG cc_start: 0.7039 (ttm110) cc_final: 0.6107 (mmt-90) REVERT: R 45 HIS cc_start: 0.7281 (m90) cc_final: 0.7026 (m170) REVERT: S 16 GLU cc_start: 0.3971 (OUTLIER) cc_final: 0.3627 (tm-30) REVERT: S 54 GLN cc_start: 0.7032 (mt0) cc_final: 0.6814 (mt0) REVERT: T 16 LEU cc_start: 0.5054 (tp) cc_final: 0.4845 (tt) REVERT: T 44 MET cc_start: 0.6083 (mtt) cc_final: 0.5650 (mtt) REVERT: U 24 ARG cc_start: 0.6866 (mmm160) cc_final: 0.6341 (mmm160) REVERT: U 54 MET cc_start: 0.6032 (tmm) cc_final: 0.5727 (tmm) REVERT: U 55 GLN cc_start: 0.7093 (tt0) cc_final: 0.6814 (tt0) REVERT: U 60 ARG cc_start: 0.6561 (ttp-110) cc_final: 0.6238 (ttm170) REVERT: V 21 ARG cc_start: 0.4716 (ttt90) cc_final: 0.4324 (mmp80) REVERT: V 33 ARG cc_start: 0.5606 (mtt90) cc_final: 0.5051 (mmm160) REVERT: V 36 GLU cc_start: 0.6918 (OUTLIER) cc_final: 0.6577 (mt-10) REVERT: V 39 GLU cc_start: 0.6592 (mt-10) cc_final: 0.5708 (pm20) REVERT: V 47 ARG cc_start: 0.5929 (ptt90) cc_final: 0.5535 (ptt-90) REVERT: V 49 LYS cc_start: 0.6377 (tptp) cc_final: 0.5956 (tptp) REVERT: W 109 ARG cc_start: 0.6133 (ptm160) cc_final: 0.5893 (ptt180) REVERT: W 142 ARG cc_start: 0.5622 (mtp85) cc_final: 0.5392 (mtt-85) REVERT: W 143 ARG cc_start: 0.5756 (OUTLIER) cc_final: 0.5205 (mpp-170) REVERT: W 169 ASP cc_start: 0.4559 (t0) cc_final: 0.4188 (m-30) REVERT: W 269 LYS cc_start: 0.7661 (tptp) cc_final: 0.7417 (tptt) REVERT: W 285 LYS cc_start: 0.5955 (tttp) cc_final: 0.5591 (ttpt) REVERT: W 287 GLN cc_start: 0.5411 (mt0) cc_final: 0.4881 (tm-30) REVERT: W 318 THR cc_start: 0.7852 (OUTLIER) cc_final: 0.7589 (m) REVERT: W 328 ARG cc_start: 0.6514 (mtp85) cc_final: 0.5586 (mtp180) REVERT: W 330 ASP cc_start: 0.5289 (m-30) cc_final: 0.4870 (p0) REVERT: W 331 GLU cc_start: 0.6229 (mm-30) cc_final: 0.5110 (pp20) REVERT: W 334 GLU cc_start: 0.5264 (mt-10) cc_final: 0.4965 (mm-30) REVERT: c 5 LYS cc_start: 0.7119 (tttp) cc_final: 0.6430 (tptp) REVERT: c 66 ASP cc_start: 0.7957 (t0) cc_final: 0.7608 (t0) REVERT: c 97 LYS cc_start: 0.7387 (mtpp) cc_final: 0.6457 (mmpt) REVERT: c 111 LYS cc_start: 0.6601 (ptpp) cc_final: 0.5656 (mttm) REVERT: c 117 GLN cc_start: 0.7618 (tp40) cc_final: 0.7057 (tt0) REVERT: c 181 MET cc_start: 0.8167 (tpp) cc_final: 0.7725 (mmm) REVERT: c 199 GLU cc_start: 0.7470 (mt-10) cc_final: 0.6569 (pm20) REVERT: c 203 ARG cc_start: 0.7718 (ptt90) cc_final: 0.7309 (ptp-110) REVERT: c 269 ARG cc_start: 0.7360 (ttp-170) cc_final: 0.6920 (ttp80) REVERT: d 1 MET cc_start: 0.3873 (OUTLIER) cc_final: 0.2797 (mtp) REVERT: d 7 LYS cc_start: 0.7990 (ttmt) cc_final: 0.7275 (ttpp) REVERT: d 17 GLU cc_start: 0.6460 (pm20) cc_final: 0.6000 (mt-10) REVERT: d 70 LYS cc_start: 0.6977 (tttt) cc_final: 0.6615 (tttt) REVERT: d 204 LYS cc_start: 0.8199 (mttt) cc_final: 0.7934 (mttp) REVERT: e 22 ASP cc_start: 0.6600 (p0) cc_final: 0.6115 (m-30) REVERT: e 132 LYS cc_start: 0.6946 (tttm) cc_final: 0.6722 (ttpt) REVERT: e 199 MET cc_start: 0.5533 (ttp) cc_final: 0.5332 (ttp) REVERT: f 30 ARG cc_start: 0.6018 (mpp80) cc_final: 0.5543 (mtm-85) REVERT: f 60 ILE cc_start: 0.7283 (mt) cc_final: 0.6731 (mp) REVERT: f 125 ARG cc_start: 0.4955 (tpp-160) cc_final: 0.4667 (mtp180) REVERT: f 129 SER cc_start: 0.7411 (m) cc_final: 0.7043 (t) REVERT: g 9 VAL cc_start: 0.4275 (m) cc_final: 0.3738 (p) REVERT: g 74 SER cc_start: 0.6791 (m) cc_final: 0.6538 (t) REVERT: g 95 ARG cc_start: 0.6166 (mtm110) cc_final: 0.5311 (ptm160) REVERT: i 34 ARG cc_start: 0.7616 (ttt-90) cc_final: 0.7194 (mtp85) REVERT: i 61 LYS cc_start: 0.7080 (mttt) cc_final: 0.6561 (mmtm) REVERT: i 91 GLU cc_start: 0.7565 (mt-10) cc_final: 0.7306 (mt-10) REVERT: i 95 ARG cc_start: 0.5879 (ttt180) cc_final: 0.5245 (mpt-90) REVERT: i 96 ARG cc_start: 0.6560 (ptt-90) cc_final: 0.4808 (mmm-85) REVERT: i 118 MET cc_start: 0.8379 (mtt) cc_final: 0.8116 (mtt) REVERT: i 128 ASN cc_start: 0.7893 (t0) cc_final: 0.7648 (t0) REVERT: j 1 MET cc_start: 0.8243 (OUTLIER) cc_final: 0.8022 (ttp) REVERT: j 17 ARG cc_start: 0.7180 (mmt90) cc_final: 0.6665 (mmm160) REVERT: j 29 HIS cc_start: 0.7119 (m-70) cc_final: 0.6696 (m90) REVERT: j 45 GLU cc_start: 0.7289 (mt-10) cc_final: 0.7000 (mt-10) REVERT: j 51 LYS cc_start: 0.7350 (mtpp) cc_final: 0.7011 (mttt) REVERT: j 89 ASN cc_start: 0.6253 (m-40) cc_final: 0.5757 (t0) REVERT: j 98 ARG cc_start: 0.7050 (mmt-90) cc_final: 0.6441 (mtp180) REVERT: j 114 LYS cc_start: 0.5949 (mppt) cc_final: 0.5495 (mmpt) REVERT: k 106 GLU cc_start: 0.7801 (mt-10) cc_final: 0.7062 (mm-30) REVERT: k 141 LYS cc_start: 0.6075 (tmtm) cc_final: 0.5585 (mtmt) REVERT: l 6 ARG cc_start: 0.6779 (mtt180) cc_final: 0.6345 (mtm110) REVERT: l 55 ARG cc_start: 0.6851 (ttm110) cc_final: 0.6357 (ttm110) REVERT: l 110 GLU cc_start: 0.7219 (OUTLIER) cc_final: 0.6751 (tm-30) REVERT: l 136 MET cc_start: 0.5474 (mtp) cc_final: 0.5231 (ttp) REVERT: m 18 GLN cc_start: 0.8079 (tt0) cc_final: 0.7779 (tt0) REVERT: m 72 ASP cc_start: 0.7653 (t0) cc_final: 0.7240 (t70) REVERT: n 13 ARG cc_start: 0.6548 (tpp-160) cc_final: 0.5981 (tpt90) REVERT: n 19 GLN cc_start: 0.7270 (tt0) cc_final: 0.6478 (tt0) REVERT: n 20 GLU cc_start: 0.6036 (pt0) cc_final: 0.5370 (tm-30) REVERT: n 76 LYS cc_start: 0.6681 (tttp) cc_final: 0.6353 (ttpt) REVERT: n 81 ARG cc_start: 0.7263 (OUTLIER) cc_final: 0.5790 (mtm-85) REVERT: n 98 GLN cc_start: 0.7561 (mm-40) cc_final: 0.7287 (mm-40) REVERT: n 104 GLN cc_start: 0.7764 (tt0) cc_final: 0.7425 (tt0) REVERT: o 6 LYS cc_start: 0.6141 (ttpp) cc_final: 0.5802 (tmmt) REVERT: o 7 GLN cc_start: 0.6532 (tp40) cc_final: 0.6195 (tt0) REVERT: o 10 GLN cc_start: 0.6856 (mm-40) cc_final: 0.6152 (mt0) REVERT: o 11 GLU cc_start: 0.7383 (pt0) cc_final: 0.6824 (pt0) REVERT: o 63 LYS cc_start: 0.7618 (ptmm) cc_final: 0.7182 (pttt) REVERT: o 89 ARG cc_start: 0.7146 (mtm180) cc_final: 0.6060 (mmt180) REVERT: o 112 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7641 (mt-10) REVERT: p 11 ARG cc_start: 0.6869 (tpm170) cc_final: 0.6235 (ttp-110) REVERT: p 15 LYS cc_start: 0.7753 (mtpt) cc_final: 0.7328 (ttmm) REVERT: p 16 LYS cc_start: 0.7715 (ttpt) cc_final: 0.7424 (tttt) REVERT: p 78 LYS cc_start: 0.8213 (mmmt) cc_final: 0.7944 (mttm) REVERT: p 85 LYS cc_start: 0.7208 (mttt) cc_final: 0.6955 (mmtm) REVERT: p 112 LYS cc_start: 0.6963 (OUTLIER) cc_final: 0.6501 (tppp) REVERT: q 60 LYS cc_start: 0.7168 (mtmt) cc_final: 0.6604 (mttm) REVERT: q 73 LYS cc_start: 0.7865 (mmtp) cc_final: 0.7304 (mmpt) REVERT: r 28 LYS cc_start: 0.7182 (mtpt) cc_final: 0.6153 (mmtm) REVERT: r 68 ASP cc_start: 0.6933 (m-30) cc_final: 0.6367 (m-30) REVERT: r 73 LYS cc_start: 0.7713 (mttm) cc_final: 0.7357 (mtpm) REVERT: r 86 MET cc_start: 0.8036 (tpp) cc_final: 0.7259 (ttp) REVERT: s 3 ARG cc_start: 0.5012 (mtt-85) cc_final: 0.4622 (mtm-85) REVERT: s 5 GLU cc_start: 0.6518 (mt-10) cc_final: 0.5738 (pp20) REVERT: s 9 LYS cc_start: 0.6857 (mmtt) cc_final: 0.6452 (mtpt) REVERT: s 18 GLU cc_start: 0.7101 (mt-10) cc_final: 0.6016 (mp0) REVERT: s 26 LYS cc_start: 0.6249 (ttmt) cc_final: 0.5553 (tppp) REVERT: s 33 LYS cc_start: 0.7333 (tttt) cc_final: 0.6484 (mttp) REVERT: s 50 LEU cc_start: 0.7245 (mt) cc_final: 0.7010 (mp) REVERT: s 69 ARG cc_start: 0.6512 (mtt-85) cc_final: 0.5948 (mtm110) REVERT: t 7 ARG cc_start: 0.6266 (ttt180) cc_final: 0.5521 (ttm110) REVERT: t 10 GLU cc_start: 0.7051 (OUTLIER) cc_final: 0.5765 (pm20) REVERT: t 24 LYS cc_start: 0.7055 (ttpt) cc_final: 0.6722 (tttm) REVERT: t 43 LYS cc_start: 0.7131 (mtmm) cc_final: 0.6829 (mttp) REVERT: t 72 ILE cc_start: 0.7430 (tp) cc_final: 0.7173 (tt) REVERT: u 10 LYS cc_start: 0.6237 (mttp) cc_final: 0.5569 (mmmt) REVERT: u 43 ASP cc_start: 0.7320 (t0) cc_final: 0.6859 (t0) REVERT: u 73 LYS cc_start: 0.7226 (mttt) cc_final: 0.7018 (mttm) REVERT: u 79 ARG cc_start: 0.8066 (mtt-85) cc_final: 0.7829 (mtt-85) REVERT: v 25 ARG cc_start: 0.8180 (mmt90) cc_final: 0.7595 (mpt180) REVERT: v 70 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7352 (mp0) REVERT: v 78 LYS cc_start: 0.8084 (OUTLIER) cc_final: 0.7791 (mtmm) REVERT: v 83 GLU cc_start: 0.6649 (mm-30) cc_final: 0.5987 (mt-10) REVERT: w 54 LYS cc_start: 0.7534 (OUTLIER) cc_final: 0.6958 (tttp) REVERT: w 65 ASP cc_start: 0.7160 (m-30) cc_final: 0.6728 (m-30) REVERT: x 24 GLU cc_start: 0.6751 (tt0) cc_final: 0.6500 (tt0) REVERT: x 44 LYS cc_start: 0.7083 (ttmt) cc_final: 0.6812 (ttmm) REVERT: x 56 LEU cc_start: 0.7453 (mt) cc_final: 0.7129 (mm) REVERT: y 56 LYS cc_start: 0.7330 (pttt) cc_final: 0.7079 (pttp) REVERT: y 57 VAL cc_start: 0.7029 (OUTLIER) cc_final: 0.6625 (p) REVERT: z 37 LYS cc_start: 0.7723 (mttt) cc_final: 0.7224 (mtpm) outliers start: 153 outliers final: 54 residues processed: 1077 average time/residue: 2.4827 time to fit residues: 3703.3061 Evaluate side-chains 1024 residues out of total 4889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 942 time to evaluate : 6.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 28 ARG Chi-restraints excluded: chain 1 residue 41 ARG Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 105 LYS Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 167 LYS Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain G residue 37 HIS Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain I residue 90 ASP Chi-restraints excluded: chain J residue 27 LYS Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 73 SER Chi-restraints excluded: chain J residue 85 ARG Chi-restraints excluded: chain J residue 88 MET Chi-restraints excluded: chain K residue 7 ARG Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 129 VAL Chi-restraints excluded: chain M residue 34 CYS Chi-restraints excluded: chain M residue 86 ARG Chi-restraints excluded: chain M residue 88 LYS Chi-restraints excluded: chain M residue 109 ASP Chi-restraints excluded: chain N residue 13 LYS Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 27 LYS Chi-restraints excluded: chain N residue 68 ASP Chi-restraints excluded: chain N residue 110 LYS Chi-restraints excluded: chain N residue 113 ARG Chi-restraints excluded: chain O residue 33 ASP Chi-restraints excluded: chain O residue 83 LYS Chi-restraints excluded: chain R residue 29 VAL Chi-restraints excluded: chain R residue 42 THR Chi-restraints excluded: chain R residue 67 LEU Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain S residue 16 GLU Chi-restraints excluded: chain U residue 23 SER Chi-restraints excluded: chain U residue 69 LYS Chi-restraints excluded: chain V residue 3 VAL Chi-restraints excluded: chain V residue 36 GLU Chi-restraints excluded: chain W residue 143 ARG Chi-restraints excluded: chain W residue 318 THR Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain g residue 15 VAL Chi-restraints excluded: chain g residue 36 THR Chi-restraints excluded: chain g residue 44 LYS Chi-restraints excluded: chain g residue 87 LEU Chi-restraints excluded: chain g residue 155 GLU Chi-restraints excluded: chain h residue 21 VAL Chi-restraints excluded: chain i residue 138 GLN Chi-restraints excluded: chain j residue 1 MET Chi-restraints excluded: chain j residue 76 VAL Chi-restraints excluded: chain k residue 94 THR Chi-restraints excluded: chain k residue 103 ILE Chi-restraints excluded: chain l residue 30 SER Chi-restraints excluded: chain l residue 110 GLU Chi-restraints excluded: chain m residue 89 SER Chi-restraints excluded: chain n residue 81 ARG Chi-restraints excluded: chain o residue 85 SER Chi-restraints excluded: chain o residue 104 THR Chi-restraints excluded: chain o residue 112 GLU Chi-restraints excluded: chain p residue 112 LYS Chi-restraints excluded: chain q residue 33 VAL Chi-restraints excluded: chain q residue 99 THR Chi-restraints excluded: chain r residue 66 ILE Chi-restraints excluded: chain t residue 10 GLU Chi-restraints excluded: chain u residue 58 SER Chi-restraints excluded: chain v residue 30 SER Chi-restraints excluded: chain v residue 70 GLU Chi-restraints excluded: chain v residue 78 LYS Chi-restraints excluded: chain w residue 54 LYS Chi-restraints excluded: chain x residue 40 SER Chi-restraints excluded: chain y residue 57 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1023 random chunks: chunk 919 optimal weight: 2.9990 chunk 699 optimal weight: 6.9990 chunk 483 optimal weight: 20.0000 chunk 103 optimal weight: 8.9990 chunk 444 optimal weight: 10.0000 chunk 624 optimal weight: 9.9990 chunk 934 optimal weight: 4.9990 chunk 988 optimal weight: 4.9990 chunk 487 optimal weight: 9.9990 chunk 885 optimal weight: 7.9990 chunk 266 optimal weight: 2.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 29 GLN 4 61 ASN C 18 HIS C 177 ASN E 198 HIS F 19 ASN F 77 ASN ** F 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 68 ASN H 97 ASN H 153 HIS J 110 GLN ** L 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 37 ASN P 46 HIS T 57 HIS U 68 HIS W 16 HIS W 248 HIS g 64 GLN h 2 GLN h 11 ASN i 131 ASN k 104 GLN n 98 GLN q 18 GLN s 48 GLN t 53 ASN u 12 GLN x 27 ASN x 58 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.098 156812 Z= 0.392 Angle : 0.867 17.891 234226 Z= 0.446 Chirality : 0.046 0.394 29769 Planarity : 0.008 0.157 12793 Dihedral : 23.378 177.363 77644 Min Nonbonded Distance : 1.739 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.75 % Favored : 97.10 % Rotamer: Outliers : 4.11 % Allowed : 12.73 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.10), residues: 5853 helix: 0.53 (0.11), residues: 2051 sheet: -0.44 (0.14), residues: 1178 loop : -0.35 (0.12), residues: 2624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP D 201 HIS 0.014 0.002 HIS P 46 PHE 0.024 0.003 PHE m 21 TYR 0.028 0.003 TYR r 38 ARG 0.009 0.001 ARG c 43 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11706 Ramachandran restraints generated. 5853 Oldfield, 0 Emsley, 5853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11706 Ramachandran restraints generated. 5853 Oldfield, 0 Emsley, 5853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1162 residues out of total 4889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 201 poor density : 961 time to evaluate : 6.359 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 33 LYS cc_start: 0.6481 (tptt) cc_final: 0.6154 (mmtp) REVERT: 2 15 LYS cc_start: 0.7435 (mptt) cc_final: 0.6703 (mmmm) REVERT: 2 52 LYS cc_start: 0.5990 (tttm) cc_final: 0.5558 (tppt) REVERT: 3 8 LYS cc_start: 0.7521 (mttt) cc_final: 0.6882 (mtmt) REVERT: 3 12 ARG cc_start: 0.6554 (ptt180) cc_final: 0.5673 (pmt170) REVERT: 3 15 LYS cc_start: 0.7545 (mttt) cc_final: 0.6749 (mttt) REVERT: C 49 MET cc_start: 0.4614 (mtp) cc_final: 0.4348 (mtt) REVERT: C 100 MET cc_start: 0.6526 (mtt) cc_final: 0.6299 (ttp) REVERT: C 105 LYS cc_start: 0.6741 (OUTLIER) cc_final: 0.6334 (ptpt) REVERT: C 143 LYS cc_start: 0.4435 (tmmt) cc_final: 0.3975 (tttt) REVERT: C 178 ASN cc_start: 0.6308 (t0) cc_final: 0.6033 (m-40) REVERT: D 27 LYS cc_start: 0.4895 (pmtt) cc_final: 0.4391 (ttpp) REVERT: D 28 GLU cc_start: 0.6002 (mt-10) cc_final: 0.5515 (mp0) REVERT: D 49 LYS cc_start: 0.5110 (OUTLIER) cc_final: 0.4715 (mmtt) REVERT: D 72 ARG cc_start: 0.4690 (mmm-85) cc_final: 0.4402 (mtm180) REVERT: D 75 ILE cc_start: 0.5046 (OUTLIER) cc_final: 0.4840 (pt) REVERT: D 122 SER cc_start: 0.6568 (m) cc_final: 0.6228 (p) REVERT: D 129 MET cc_start: 0.5868 (mmm) cc_final: 0.5387 (mtm) REVERT: D 169 ARG cc_start: 0.6706 (ttm-80) cc_final: 0.5436 (ttp80) REVERT: D 170 GLU cc_start: 0.6828 (tt0) cc_final: 0.6612 (mt-10) REVERT: D 195 VAL cc_start: 0.7377 (OUTLIER) cc_final: 0.6973 (m) REVERT: E 15 GLU cc_start: 0.6782 (mp0) cc_final: 0.6517 (mm-30) REVERT: E 20 PHE cc_start: 0.6406 (m-80) cc_final: 0.6095 (m-80) REVERT: E 29 ASP cc_start: 0.5480 (OUTLIER) cc_final: 0.4972 (p0) REVERT: E 44 ARG cc_start: 0.4585 (ttm110) cc_final: 0.4122 (ttt-90) REVERT: E 73 ARG cc_start: 0.6434 (ttp80) cc_final: 0.5507 (ttm-80) REVERT: E 78 GLU cc_start: 0.6601 (tt0) cc_final: 0.6269 (tp30) REVERT: E 113 GLU cc_start: 0.7095 (tp30) cc_final: 0.6728 (tt0) REVERT: E 119 SER cc_start: 0.6699 (t) cc_final: 0.6329 (p) REVERT: E 124 MET cc_start: 0.6656 (mtm) cc_final: 0.6272 (mtt) REVERT: E 126 ASN cc_start: 0.6843 (m-40) cc_final: 0.6487 (m-40) REVERT: E 128 ARG cc_start: 0.5329 (mtt-85) cc_final: 0.4890 (mmm-85) REVERT: E 141 ASP cc_start: 0.6076 (m-30) cc_final: 0.5850 (m-30) REVERT: E 144 SER cc_start: 0.6737 (p) cc_final: 0.6493 (t) REVERT: E 148 LYS cc_start: 0.5148 (ttpp) cc_final: 0.4876 (ttpp) REVERT: E 151 LYS cc_start: 0.4317 (pptt) cc_final: 0.4006 (mttm) REVERT: F 12 GLN cc_start: 0.6075 (mp10) cc_final: 0.5345 (tt0) REVERT: F 26 LYS cc_start: 0.6782 (tmtm) cc_final: 0.6463 (ttmt) REVERT: F 45 ARG cc_start: 0.6423 (mtp-110) cc_final: 0.5800 (mmm160) REVERT: F 55 GLU cc_start: 0.6452 (mt-10) cc_final: 0.6155 (mt-10) REVERT: F 61 GLN cc_start: 0.6256 (tm-30) cc_final: 0.5511 (tm130) REVERT: F 65 GLU cc_start: 0.6290 (mt-10) cc_final: 0.5789 (mm-30) REVERT: F 70 ASN cc_start: 0.5470 (m110) cc_final: 0.5266 (m110) REVERT: F 116 GLU cc_start: 0.6897 (tt0) cc_final: 0.6460 (tt0) REVERT: F 156 LYS cc_start: 0.6681 (ptpp) cc_final: 0.6283 (pttt) REVERT: F 159 LYS cc_start: 0.6862 (mmtt) cc_final: 0.6573 (mptp) REVERT: G 2 ARG cc_start: 0.6154 (mtp85) cc_final: 0.5879 (mtt180) REVERT: G 15 SER cc_start: 0.6009 (t) cc_final: 0.5546 (m) REVERT: G 37 HIS cc_start: 0.6094 (OUTLIER) cc_final: 0.4709 (p-80) REVERT: G 46 GLN cc_start: 0.5993 (tp40) cc_final: 0.5726 (tp-100) REVERT: G 56 LYS cc_start: 0.6739 (mtpt) cc_final: 0.5975 (mttp) REVERT: G 62 MET cc_start: 0.6654 (ptp) cc_final: 0.6369 (ptm) REVERT: G 87 SER cc_start: 0.7538 (p) cc_final: 0.7298 (m) REVERT: G 92 THR cc_start: 0.6069 (OUTLIER) cc_final: 0.5683 (p) REVERT: G 98 GLU cc_start: 0.3638 (OUTLIER) cc_final: 0.3124 (tp30) REVERT: H 41 SER cc_start: 0.6130 (p) cc_final: 0.5706 (m) REVERT: H 53 ARG cc_start: 0.5764 (mtm-85) cc_final: 0.5541 (ttm170) REVERT: H 79 ARG cc_start: 0.3417 (ttt180) cc_final: 0.3157 (mtt90) REVERT: H 92 ARG cc_start: 0.4740 (mpp-170) cc_final: 0.4366 (mpt180) REVERT: H 96 ARG cc_start: 0.5994 (mtt90) cc_final: 0.5773 (mtt180) REVERT: H 106 GLU cc_start: 0.6613 (OUTLIER) cc_final: 0.6333 (tt0) REVERT: H 119 ARG cc_start: 0.6453 (mtm180) cc_final: 0.6111 (mtt180) REVERT: H 129 GLU cc_start: 0.4358 (mm-30) cc_final: 0.3969 (mm-30) REVERT: H 137 LYS cc_start: 0.5012 (ptmm) cc_final: 0.4550 (tptt) REVERT: H 139 GLU cc_start: 0.6510 (mt-10) cc_final: 0.5420 (mm-30) REVERT: I 26 THR cc_start: 0.7546 (m) cc_final: 0.7086 (p) REVERT: I 42 GLU cc_start: 0.6383 (pt0) cc_final: 0.6107 (mt-10) REVERT: I 43 GLU cc_start: 0.7702 (mm-30) cc_final: 0.7277 (mm-30) REVERT: I 48 ASP cc_start: 0.6593 (t70) cc_final: 0.6390 (t70) REVERT: I 50 LYS cc_start: 0.6200 (ttpt) cc_final: 0.5865 (ttpt) REVERT: I 69 LYS cc_start: 0.6239 (mtpp) cc_final: 0.5571 (tptm) REVERT: I 76 GLN cc_start: 0.6842 (mt0) cc_final: 0.6336 (tt0) REVERT: I 88 ARG cc_start: 0.6784 (mtm180) cc_final: 0.6223 (mtt180) REVERT: I 89 LYS cc_start: 0.6377 (ptmt) cc_final: 0.5878 (ttpp) REVERT: I 96 MET cc_start: 0.7474 (ttp) cc_final: 0.7002 (ttt) REVERT: I 111 MET cc_start: 0.8117 (ptp) cc_final: 0.7810 (ptp) REVERT: I 114 ARG cc_start: 0.6433 (ttm110) cc_final: 0.5891 (ttp80) REVERT: J 27 LYS cc_start: 0.5424 (OUTLIER) cc_final: 0.5210 (pttt) REVERT: J 49 ARG cc_start: 0.5178 (mtm-85) cc_final: 0.4418 (ptp90) REVERT: J 85 ARG cc_start: 0.6255 (OUTLIER) cc_final: 0.5806 (mtt180) REVERT: J 88 MET cc_start: 0.5734 (OUTLIER) cc_final: 0.5060 (mtt) REVERT: J 91 ASP cc_start: 0.5054 (t70) cc_final: 0.4815 (t0) REVERT: J 104 VAL cc_start: 0.7072 (t) cc_final: 0.6793 (t) REVERT: J 119 ARG cc_start: 0.6877 (ptm-80) cc_final: 0.6231 (ptp-110) REVERT: K 7 ARG cc_start: 0.5204 (OUTLIER) cc_final: 0.4052 (mtm180) REVERT: K 11 LYS cc_start: 0.6944 (mttt) cc_final: 0.6474 (mmtt) REVERT: K 88 MET cc_start: 0.3407 (mmt) cc_final: 0.2914 (mtp) REVERT: L 40 ASN cc_start: 0.7464 (m-40) cc_final: 0.7229 (m110) REVERT: L 83 GLU cc_start: 0.6576 (mt-10) cc_final: 0.6230 (mt-10) REVERT: L 105 PHE cc_start: 0.6534 (m-80) cc_final: 0.6070 (m-80) REVERT: L 106 ARG cc_start: 0.4707 (ttt180) cc_final: 0.4195 (tpt90) REVERT: M 10 LYS cc_start: 0.6252 (tttt) cc_final: 0.5683 (tttm) REVERT: M 34 CYS cc_start: 0.7314 (OUTLIER) cc_final: 0.6958 (m) REVERT: M 40 THR cc_start: 0.7965 (t) cc_final: 0.7398 (p) REVERT: M 43 LYS cc_start: 0.7409 (ptpt) cc_final: 0.6927 (pttt) REVERT: M 49 LEU cc_start: 0.7490 (mt) cc_final: 0.7099 (mm) REVERT: M 64 THR cc_start: 0.8221 (m) cc_final: 0.7775 (p) REVERT: M 75 GLN cc_start: 0.7093 (pm20) cc_final: 0.6829 (pm20) REVERT: M 76 GLU cc_start: 0.6142 (tt0) cc_final: 0.5577 (tt0) REVERT: M 111 LYS cc_start: 0.7324 (mmmt) cc_final: 0.7095 (mmtm) REVERT: N 13 LYS cc_start: 0.5951 (OUTLIER) cc_final: 0.5643 (mtmt) REVERT: N 68 ASP cc_start: 0.5285 (OUTLIER) cc_final: 0.4632 (t0) REVERT: N 78 LYS cc_start: 0.5712 (tttm) cc_final: 0.4961 (ptpt) REVERT: N 81 MET cc_start: 0.7293 (mtm) cc_final: 0.6407 (mtm) REVERT: N 92 ARG cc_start: 0.6792 (mtt180) cc_final: 0.6539 (mtm-85) REVERT: N 93 ARG cc_start: 0.5952 (mmt-90) cc_final: 0.5117 (mmp80) REVERT: N 110 LYS cc_start: 0.7355 (OUTLIER) cc_final: 0.6734 (mttm) REVERT: N 113 ARG cc_start: 0.5172 (OUTLIER) cc_final: 0.4536 (mmm-85) REVERT: O 39 GLU cc_start: 0.5024 (tm-30) cc_final: 0.4547 (tp30) REVERT: O 41 ARG cc_start: 0.4507 (mtt180) cc_final: 0.4296 (ttm-80) REVERT: P 61 SER cc_start: 0.7373 (m) cc_final: 0.7075 (p) REVERT: Q 1 MET cc_start: 0.6761 (pmm) cc_final: 0.6126 (pmm) REVERT: R 6 ARG cc_start: 0.5074 (OUTLIER) cc_final: 0.4346 (ttp-170) REVERT: R 11 ARG cc_start: 0.6807 (ttm110) cc_final: 0.6100 (mmt-90) REVERT: R 40 ARG cc_start: 0.6571 (OUTLIER) cc_final: 0.6026 (mtp180) REVERT: R 45 HIS cc_start: 0.7394 (m90) cc_final: 0.7088 (m170) REVERT: S 16 GLU cc_start: 0.4113 (OUTLIER) cc_final: 0.3776 (tm-30) REVERT: T 44 MET cc_start: 0.6026 (mtt) cc_final: 0.5591 (mtt) REVERT: U 24 ARG cc_start: 0.6932 (mmm160) cc_final: 0.6533 (mmm160) REVERT: U 55 GLN cc_start: 0.7038 (tt0) cc_final: 0.6553 (tt0) REVERT: U 60 ARG cc_start: 0.6551 (ttp-110) cc_final: 0.6231 (ttm170) REVERT: V 21 ARG cc_start: 0.4757 (ttt90) cc_final: 0.4160 (mmm160) REVERT: V 33 ARG cc_start: 0.5483 (mtt90) cc_final: 0.4983 (mmm160) REVERT: V 36 GLU cc_start: 0.6884 (OUTLIER) cc_final: 0.6538 (mt-10) REVERT: V 47 ARG cc_start: 0.5896 (ptt90) cc_final: 0.5505 (ptt-90) REVERT: V 49 LYS cc_start: 0.6439 (tptp) cc_final: 0.6110 (tptp) REVERT: V 63 GLU cc_start: 0.2326 (OUTLIER) cc_final: 0.2093 (mm-30) REVERT: W 13 HIS cc_start: 0.2256 (OUTLIER) cc_final: 0.1921 (m90) REVERT: W 143 ARG cc_start: 0.5664 (OUTLIER) cc_final: 0.5037 (mpp-170) REVERT: W 146 VAL cc_start: 0.6440 (m) cc_final: 0.6183 (t) REVERT: W 169 ASP cc_start: 0.4565 (t0) cc_final: 0.4237 (m-30) REVERT: W 269 LYS cc_start: 0.7725 (tptp) cc_final: 0.7435 (tptt) REVERT: W 287 GLN cc_start: 0.5371 (mt0) cc_final: 0.4871 (tm-30) REVERT: W 317 VAL cc_start: 0.7814 (OUTLIER) cc_final: 0.7532 (p) REVERT: W 318 THR cc_start: 0.7856 (OUTLIER) cc_final: 0.7650 (m) REVERT: W 328 ARG cc_start: 0.6718 (mtp85) cc_final: 0.6319 (mtp180) REVERT: W 330 ASP cc_start: 0.5207 (m-30) cc_final: 0.4722 (p0) REVERT: W 334 GLU cc_start: 0.5161 (mt-10) cc_final: 0.4921 (mm-30) REVERT: c 5 LYS cc_start: 0.7149 (tttp) cc_final: 0.6572 (tptp) REVERT: c 66 ASP cc_start: 0.8055 (t0) cc_final: 0.7785 (t0) REVERT: c 97 LYS cc_start: 0.7315 (mtpp) cc_final: 0.6543 (mmpt) REVERT: c 181 MET cc_start: 0.8156 (tpp) cc_final: 0.7674 (mmm) REVERT: c 199 GLU cc_start: 0.7462 (mt-10) cc_final: 0.6552 (pm20) REVERT: c 203 ARG cc_start: 0.7666 (ptt90) cc_final: 0.7265 (ptp-110) REVERT: c 269 ARG cc_start: 0.7368 (ttp-170) cc_final: 0.6920 (ttp80) REVERT: d 1 MET cc_start: 0.3835 (OUTLIER) cc_final: 0.2849 (mtt) REVERT: d 7 LYS cc_start: 0.8049 (ttmt) cc_final: 0.7330 (ttpp) REVERT: d 17 GLU cc_start: 0.6300 (pm20) cc_final: 0.6003 (mt-10) REVERT: d 18 ASP cc_start: 0.5684 (OUTLIER) cc_final: 0.5417 (t70) REVERT: d 70 LYS cc_start: 0.6993 (tttt) cc_final: 0.6632 (tttt) REVERT: d 128 ARG cc_start: 0.7982 (OUTLIER) cc_final: 0.7330 (mtp180) REVERT: e 22 ASP cc_start: 0.6684 (p0) cc_final: 0.6151 (m-30) REVERT: e 132 LYS cc_start: 0.6992 (tttm) cc_final: 0.6732 (ttpt) REVERT: e 199 MET cc_start: 0.5433 (ttp) cc_final: 0.5186 (ttp) REVERT: f 30 ARG cc_start: 0.6181 (mpp80) cc_final: 0.5631 (mtm-85) REVERT: f 60 ILE cc_start: 0.7282 (mt) cc_final: 0.6902 (mm) REVERT: f 88 LYS cc_start: 0.7552 (OUTLIER) cc_final: 0.7240 (ptpt) REVERT: f 125 ARG cc_start: 0.5188 (tpp-160) cc_final: 0.4928 (mmt90) REVERT: f 129 SER cc_start: 0.7418 (m) cc_final: 0.7066 (t) REVERT: f 178 ARG cc_start: 0.4951 (ptt-90) cc_final: 0.4353 (ptp-170) REVERT: g 9 VAL cc_start: 0.4088 (m) cc_final: 0.3655 (p) REVERT: g 51 THR cc_start: 0.5563 (m) cc_final: 0.5105 (p) REVERT: g 74 SER cc_start: 0.6828 (m) cc_final: 0.6566 (t) REVERT: g 95 ARG cc_start: 0.5977 (mtm110) cc_final: 0.5351 (mtm-85) REVERT: i 34 ARG cc_start: 0.7629 (ttt-90) cc_final: 0.7146 (mtp85) REVERT: i 61 LYS cc_start: 0.7109 (mttt) cc_final: 0.6666 (mmtm) REVERT: i 91 GLU cc_start: 0.7470 (mt-10) cc_final: 0.7252 (mt-10) REVERT: i 95 ARG cc_start: 0.5971 (ttt180) cc_final: 0.5392 (mpt-90) REVERT: i 96 ARG cc_start: 0.6672 (ptt-90) cc_final: 0.4831 (mmm-85) REVERT: i 118 MET cc_start: 0.8384 (mtt) cc_final: 0.8128 (mtt) REVERT: i 128 ASN cc_start: 0.7769 (t0) cc_final: 0.7548 (t0) REVERT: j 1 MET cc_start: 0.8256 (OUTLIER) cc_final: 0.8004 (ttp) REVERT: j 17 ARG cc_start: 0.7223 (mmt90) cc_final: 0.6719 (mmm160) REVERT: j 29 HIS cc_start: 0.7218 (m-70) cc_final: 0.6811 (m90) REVERT: j 45 GLU cc_start: 0.7293 (mt-10) cc_final: 0.7022 (mt-10) REVERT: j 51 LYS cc_start: 0.7415 (mtpp) cc_final: 0.7037 (mttt) REVERT: j 53 LYS cc_start: 0.6955 (mptm) cc_final: 0.6163 (tttm) REVERT: j 89 ASN cc_start: 0.6379 (m-40) cc_final: 0.5911 (t0) REVERT: j 98 ARG cc_start: 0.6975 (mmt-90) cc_final: 0.6479 (mtm180) REVERT: j 105 ARG cc_start: 0.5890 (OUTLIER) cc_final: 0.5403 (mtt-85) REVERT: j 114 LYS cc_start: 0.6224 (mppt) cc_final: 0.5745 (mmpt) REVERT: k 106 GLU cc_start: 0.7838 (mt-10) cc_final: 0.7033 (mm-30) REVERT: k 141 LYS cc_start: 0.6409 (tmtm) cc_final: 0.5727 (mtmt) REVERT: l 6 ARG cc_start: 0.6799 (mtt180) cc_final: 0.6395 (mtm110) REVERT: l 47 GLU cc_start: 0.7595 (tp30) cc_final: 0.7352 (tp30) REVERT: l 110 GLU cc_start: 0.7184 (OUTLIER) cc_final: 0.6749 (tm-30) REVERT: m 18 GLN cc_start: 0.8084 (tt0) cc_final: 0.7775 (tt0) REVERT: m 72 ASP cc_start: 0.7655 (t0) cc_final: 0.7257 (t70) REVERT: n 13 ARG cc_start: 0.6609 (tpp-160) cc_final: 0.6090 (tpt90) REVERT: n 19 GLN cc_start: 0.7333 (tt0) cc_final: 0.6479 (tt0) REVERT: n 20 GLU cc_start: 0.5999 (pt0) cc_final: 0.5730 (mt-10) REVERT: n 56 LYS cc_start: 0.5757 (mptt) cc_final: 0.5118 (mtpm) REVERT: n 81 ARG cc_start: 0.7221 (OUTLIER) cc_final: 0.5705 (mtm-85) REVERT: n 98 GLN cc_start: 0.7498 (mm110) cc_final: 0.7245 (mm-40) REVERT: n 104 GLN cc_start: 0.7747 (tt0) cc_final: 0.7409 (tt0) REVERT: o 6 LYS cc_start: 0.6115 (ttpp) cc_final: 0.5641 (tmmt) REVERT: o 7 GLN cc_start: 0.6581 (tp40) cc_final: 0.6222 (tt0) REVERT: o 10 GLN cc_start: 0.6912 (mm-40) cc_final: 0.6183 (mt0) REVERT: o 11 GLU cc_start: 0.7362 (pt0) cc_final: 0.6830 (pt0) REVERT: o 63 LYS cc_start: 0.7623 (ptmm) cc_final: 0.7199 (pttt) REVERT: o 68 GLU cc_start: 0.6017 (mm-30) cc_final: 0.5707 (mp0) REVERT: o 89 ARG cc_start: 0.7109 (mtm180) cc_final: 0.6002 (mmt180) REVERT: p 9 ILE cc_start: 0.7792 (OUTLIER) cc_final: 0.7561 (mp) REVERT: p 11 ARG cc_start: 0.6948 (tpm170) cc_final: 0.6315 (ttp-110) REVERT: p 85 LYS cc_start: 0.7159 (mttt) cc_final: 0.6887 (mmtm) REVERT: p 104 VAL cc_start: 0.6440 (t) cc_final: 0.6188 (m) REVERT: p 112 LYS cc_start: 0.6904 (OUTLIER) cc_final: 0.6572 (tppp) REVERT: q 60 LYS cc_start: 0.7209 (mtmt) cc_final: 0.6630 (mttm) REVERT: q 73 LYS cc_start: 0.7901 (mmtp) cc_final: 0.7324 (mmpt) REVERT: r 28 LYS cc_start: 0.7122 (mtpt) cc_final: 0.6107 (mmtm) REVERT: r 66 ILE cc_start: 0.6976 (OUTLIER) cc_final: 0.6350 (pt) REVERT: r 68 ASP cc_start: 0.6930 (m-30) cc_final: 0.6540 (m-30) REVERT: r 73 LYS cc_start: 0.7675 (mttm) cc_final: 0.7332 (mtpm) REVERT: r 86 MET cc_start: 0.8070 (tpp) cc_final: 0.7318 (ttp) REVERT: s 5 GLU cc_start: 0.6639 (mt-10) cc_final: 0.5722 (pp20) REVERT: s 9 LYS cc_start: 0.6820 (mmtt) cc_final: 0.6410 (mtpt) REVERT: s 18 GLU cc_start: 0.7099 (mt-10) cc_final: 0.6012 (mp0) REVERT: s 25 GLU cc_start: 0.6570 (pt0) cc_final: 0.6309 (pt0) REVERT: s 33 LYS cc_start: 0.7365 (tttt) cc_final: 0.6549 (mttp) REVERT: s 50 LEU cc_start: 0.7311 (mt) cc_final: 0.7066 (mp) REVERT: s 51 PHE cc_start: 0.7038 (m-10) cc_final: 0.6682 (m-10) REVERT: s 69 ARG cc_start: 0.6631 (mtt-85) cc_final: 0.5932 (mtm-85) REVERT: t 7 ARG cc_start: 0.6256 (ttt180) cc_final: 0.5467 (ttm110) REVERT: t 10 GLU cc_start: 0.7086 (OUTLIER) cc_final: 0.5705 (pm20) REVERT: t 37 GLU cc_start: 0.6361 (pp20) cc_final: 0.5996 (tm-30) REVERT: t 43 LYS cc_start: 0.7152 (mtmm) cc_final: 0.6888 (mttp) REVERT: t 72 ILE cc_start: 0.7401 (tp) cc_final: 0.7083 (tt) REVERT: t 86 ARG cc_start: 0.7590 (mtm-85) cc_final: 0.6997 (mtm180) REVERT: u 10 LYS cc_start: 0.6315 (mttp) cc_final: 0.5608 (mmmt) REVERT: u 43 ASP cc_start: 0.7404 (t0) cc_final: 0.6873 (t0) REVERT: u 46 LYS cc_start: 0.7007 (mmtp) cc_final: 0.6535 (mttm) REVERT: v 78 LYS cc_start: 0.8109 (OUTLIER) cc_final: 0.7761 (mtmm) REVERT: v 83 GLU cc_start: 0.6682 (mm-30) cc_final: 0.6155 (mt-10) REVERT: w 45 ARG cc_start: 0.6013 (OUTLIER) cc_final: 0.5806 (ptt-90) REVERT: w 54 LYS cc_start: 0.7553 (OUTLIER) cc_final: 0.6985 (tttp) REVERT: x 4 LYS cc_start: 0.5375 (OUTLIER) cc_final: 0.5008 (mmmt) REVERT: x 24 GLU cc_start: 0.6841 (tt0) cc_final: 0.6640 (tt0) REVERT: x 44 LYS cc_start: 0.7043 (ttmt) cc_final: 0.6816 (ttmm) REVERT: y 56 LYS cc_start: 0.7398 (pttt) cc_final: 0.7106 (pttp) outliers start: 201 outliers final: 82 residues processed: 1084 average time/residue: 2.4792 time to fit residues: 3732.0286 Evaluate side-chains 1041 residues out of total 4889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 916 time to evaluate : 6.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 28 ARG Chi-restraints excluded: chain 0 residue 37 LYS Chi-restraints excluded: chain 1 residue 41 ARG Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 105 LYS Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 116 ASP Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain D residue 49 LYS Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 167 LYS Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain G residue 37 HIS Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain G residue 98 GLU Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 106 GLU Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain I residue 90 ASP Chi-restraints excluded: chain J residue 27 LYS Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 67 VAL Chi-restraints excluded: chain J residue 73 SER Chi-restraints excluded: chain J residue 85 ARG Chi-restraints excluded: chain J residue 88 MET Chi-restraints excluded: chain K residue 7 ARG Chi-restraints excluded: chain K residue 71 LEU Chi-restraints excluded: chain K residue 75 ASP Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 129 VAL Chi-restraints excluded: chain M residue 3 THR Chi-restraints excluded: chain M residue 34 CYS Chi-restraints excluded: chain M residue 86 ARG Chi-restraints excluded: chain N residue 11 ASP Chi-restraints excluded: chain N residue 13 LYS Chi-restraints excluded: chain N residue 16 VAL Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 27 LYS Chi-restraints excluded: chain N residue 68 ASP Chi-restraints excluded: chain N residue 95 LEU Chi-restraints excluded: chain N residue 110 LYS Chi-restraints excluded: chain N residue 113 ARG Chi-restraints excluded: chain O residue 5 SER Chi-restraints excluded: chain O residue 33 ASP Chi-restraints excluded: chain O residue 83 LYS Chi-restraints excluded: chain P residue 83 GLU Chi-restraints excluded: chain R residue 6 ARG Chi-restraints excluded: chain R residue 29 VAL Chi-restraints excluded: chain R residue 39 LYS Chi-restraints excluded: chain R residue 40 ARG Chi-restraints excluded: chain R residue 42 THR Chi-restraints excluded: chain R residue 67 LEU Chi-restraints excluded: chain R residue 72 SER Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain S residue 16 GLU Chi-restraints excluded: chain U residue 23 SER Chi-restraints excluded: chain U residue 69 LYS Chi-restraints excluded: chain V residue 3 VAL Chi-restraints excluded: chain V residue 36 GLU Chi-restraints excluded: chain V residue 63 GLU Chi-restraints excluded: chain W residue 13 HIS Chi-restraints excluded: chain W residue 143 ARG Chi-restraints excluded: chain W residue 317 VAL Chi-restraints excluded: chain W residue 318 THR Chi-restraints excluded: chain W residue 325 THR Chi-restraints excluded: chain W residue 356 LEU Chi-restraints excluded: chain c residue 129 THR Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 18 ASP Chi-restraints excluded: chain d residue 91 THR Chi-restraints excluded: chain d residue 128 ARG Chi-restraints excluded: chain e residue 12 LEU Chi-restraints excluded: chain e residue 144 GLU Chi-restraints excluded: chain f residue 88 LYS Chi-restraints excluded: chain g residue 15 VAL Chi-restraints excluded: chain g residue 36 THR Chi-restraints excluded: chain g residue 44 LYS Chi-restraints excluded: chain g residue 87 LEU Chi-restraints excluded: chain g residue 106 SER Chi-restraints excluded: chain g residue 141 ILE Chi-restraints excluded: chain g residue 155 GLU Chi-restraints excluded: chain g residue 171 THR Chi-restraints excluded: chain h residue 21 VAL Chi-restraints excluded: chain i residue 106 LYS Chi-restraints excluded: chain i residue 138 GLN Chi-restraints excluded: chain j residue 1 MET Chi-restraints excluded: chain j residue 76 VAL Chi-restraints excluded: chain j residue 105 ARG Chi-restraints excluded: chain k residue 103 ILE Chi-restraints excluded: chain l residue 30 SER Chi-restraints excluded: chain l residue 80 VAL Chi-restraints excluded: chain l residue 110 GLU Chi-restraints excluded: chain m residue 15 SER Chi-restraints excluded: chain m residue 89 SER Chi-restraints excluded: chain n residue 81 ARG Chi-restraints excluded: chain o residue 85 SER Chi-restraints excluded: chain o residue 104 THR Chi-restraints excluded: chain p residue 9 ILE Chi-restraints excluded: chain p residue 112 LYS Chi-restraints excluded: chain q residue 33 VAL Chi-restraints excluded: chain q residue 64 VAL Chi-restraints excluded: chain q residue 99 THR Chi-restraints excluded: chain r residue 66 ILE Chi-restraints excluded: chain t residue 10 GLU Chi-restraints excluded: chain u residue 58 SER Chi-restraints excluded: chain u residue 61 LEU Chi-restraints excluded: chain u residue 62 THR Chi-restraints excluded: chain u residue 65 VAL Chi-restraints excluded: chain v residue 30 SER Chi-restraints excluded: chain v residue 78 LYS Chi-restraints excluded: chain w residue 45 ARG Chi-restraints excluded: chain w residue 54 LYS Chi-restraints excluded: chain x residue 4 LYS Chi-restraints excluded: chain x residue 40 SER Chi-restraints excluded: chain y residue 41 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1023 random chunks: chunk 823 optimal weight: 0.1980 chunk 561 optimal weight: 10.0000 chunk 14 optimal weight: 7.9990 chunk 736 optimal weight: 9.9990 chunk 407 optimal weight: 10.0000 chunk 843 optimal weight: 5.9990 chunk 683 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 chunk 504 optimal weight: 7.9990 chunk 887 optimal weight: 0.9980 chunk 249 optimal weight: 0.6980 overall best weight: 2.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 29 GLN C 18 HIS E 198 HIS F 19 ASN F 77 ASN ** F 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 3 HIS H 97 ASN H 130 ASN J 110 GLN ** L 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 14 HIS P 37 ASN P 46 HIS U 68 HIS W 248 HIS c 153 GLN g 64 GLN i 136 GLN k 104 GLN n 104 GLN ** q 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 48 GLN u 12 GLN x 58 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 156812 Z= 0.259 Angle : 0.717 15.609 234226 Z= 0.382 Chirality : 0.040 0.378 29769 Planarity : 0.007 0.146 12793 Dihedral : 23.276 177.171 77641 Min Nonbonded Distance : 1.780 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.44 % Favored : 97.42 % Rotamer: Outliers : 3.70 % Allowed : 13.93 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.11), residues: 5853 helix: 0.90 (0.11), residues: 2055 sheet: -0.32 (0.14), residues: 1176 loop : -0.21 (0.12), residues: 2622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 201 HIS 0.010 0.001 HIS w 34 PHE 0.020 0.002 PHE m 21 TYR 0.024 0.002 TYR r 38 ARG 0.006 0.001 ARG k 2 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11706 Ramachandran restraints generated. 5853 Oldfield, 0 Emsley, 5853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11706 Ramachandran restraints generated. 5853 Oldfield, 0 Emsley, 5853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1114 residues out of total 4889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 933 time to evaluate : 6.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 33 LYS cc_start: 0.6482 (tptt) cc_final: 0.6171 (mmtp) REVERT: 1 41 ARG cc_start: 0.7222 (OUTLIER) cc_final: 0.6025 (ppt170) REVERT: 2 15 LYS cc_start: 0.7408 (mptt) cc_final: 0.6694 (mmmm) REVERT: 2 52 LYS cc_start: 0.5832 (tttm) cc_final: 0.5450 (tppt) REVERT: 3 8 LYS cc_start: 0.7582 (mttt) cc_final: 0.6877 (mtmt) REVERT: 3 12 ARG cc_start: 0.6551 (ptt180) cc_final: 0.5674 (pmt170) REVERT: 3 15 LYS cc_start: 0.7568 (mttt) cc_final: 0.6767 (mptt) REVERT: C 49 MET cc_start: 0.4632 (mtp) cc_final: 0.4317 (mtt) REVERT: C 100 MET cc_start: 0.6620 (mtt) cc_final: 0.6373 (ttp) REVERT: C 105 LYS cc_start: 0.6871 (OUTLIER) cc_final: 0.6459 (ptpt) REVERT: C 178 ASN cc_start: 0.6255 (t0) cc_final: 0.5993 (m-40) REVERT: D 27 LYS cc_start: 0.4946 (pmtt) cc_final: 0.4703 (tmtp) REVERT: D 28 GLU cc_start: 0.6030 (mt-10) cc_final: 0.5316 (pm20) REVERT: D 46 GLU cc_start: 0.5469 (tp30) cc_final: 0.4706 (mm-30) REVERT: D 49 LYS cc_start: 0.5111 (OUTLIER) cc_final: 0.4726 (mmtt) REVERT: D 72 ARG cc_start: 0.4654 (mmm-85) cc_final: 0.4451 (mtm180) REVERT: D 88 ARG cc_start: 0.5092 (OUTLIER) cc_final: 0.4679 (ttt-90) REVERT: D 122 SER cc_start: 0.6480 (m) cc_final: 0.6179 (p) REVERT: D 129 MET cc_start: 0.5990 (mmm) cc_final: 0.5502 (mtm) REVERT: D 132 ARG cc_start: 0.5840 (OUTLIER) cc_final: 0.5063 (tmm-80) REVERT: E 20 PHE cc_start: 0.6477 (m-80) cc_final: 0.6106 (m-80) REVERT: E 29 ASP cc_start: 0.5441 (OUTLIER) cc_final: 0.5012 (p0) REVERT: E 44 ARG cc_start: 0.4640 (ttm110) cc_final: 0.4216 (ttt-90) REVERT: E 73 ARG cc_start: 0.6452 (ttp80) cc_final: 0.5521 (ttm-80) REVERT: E 78 GLU cc_start: 0.6641 (tt0) cc_final: 0.6289 (tp30) REVERT: E 113 GLU cc_start: 0.7078 (tp30) cc_final: 0.6731 (tt0) REVERT: E 119 SER cc_start: 0.6619 (t) cc_final: 0.6298 (p) REVERT: E 124 MET cc_start: 0.6686 (mtm) cc_final: 0.6281 (mtt) REVERT: E 126 ASN cc_start: 0.6788 (m-40) cc_final: 0.6448 (m-40) REVERT: E 128 ARG cc_start: 0.5283 (mtt-85) cc_final: 0.4805 (mmm-85) REVERT: E 148 LYS cc_start: 0.5187 (ttpp) cc_final: 0.4861 (tttp) REVERT: E 151 LYS cc_start: 0.4355 (pptt) cc_final: 0.3969 (mttm) REVERT: F 12 GLN cc_start: 0.5999 (mp10) cc_final: 0.5301 (tt0) REVERT: F 26 LYS cc_start: 0.6876 (tmtm) cc_final: 0.6613 (ttmm) REVERT: F 45 ARG cc_start: 0.6352 (mtp-110) cc_final: 0.5833 (mmm160) REVERT: F 55 GLU cc_start: 0.6368 (mt-10) cc_final: 0.6143 (mt-10) REVERT: F 61 GLN cc_start: 0.6192 (tm-30) cc_final: 0.5734 (tm130) REVERT: F 65 GLU cc_start: 0.6153 (mt-10) cc_final: 0.5849 (mm-30) REVERT: F 70 ASN cc_start: 0.5444 (m110) cc_final: 0.5241 (m110) REVERT: F 116 GLU cc_start: 0.6995 (tt0) cc_final: 0.6520 (tt0) REVERT: F 156 LYS cc_start: 0.6706 (ptpp) cc_final: 0.6296 (pttt) REVERT: G 2 ARG cc_start: 0.6104 (OUTLIER) cc_final: 0.5815 (mtt180) REVERT: G 15 SER cc_start: 0.5923 (t) cc_final: 0.5439 (m) REVERT: G 37 HIS cc_start: 0.6058 (OUTLIER) cc_final: 0.4766 (p-80) REVERT: G 46 GLN cc_start: 0.6014 (tp40) cc_final: 0.5787 (tp-100) REVERT: G 56 LYS cc_start: 0.6700 (mtpt) cc_final: 0.5992 (mttp) REVERT: G 62 MET cc_start: 0.6681 (ptp) cc_final: 0.6429 (ptm) REVERT: G 98 GLU cc_start: 0.3643 (OUTLIER) cc_final: 0.3164 (tp30) REVERT: H 41 SER cc_start: 0.6107 (p) cc_final: 0.5730 (m) REVERT: H 53 ARG cc_start: 0.5629 (mtm-85) cc_final: 0.5423 (ttm170) REVERT: H 79 ARG cc_start: 0.3423 (ttt180) cc_final: 0.3158 (mtt90) REVERT: H 92 ARG cc_start: 0.4769 (mpp-170) cc_final: 0.4376 (mpt180) REVERT: H 96 ARG cc_start: 0.6029 (mtt90) cc_final: 0.5821 (mtt180) REVERT: H 106 GLU cc_start: 0.6592 (OUTLIER) cc_final: 0.6326 (tt0) REVERT: H 119 ARG cc_start: 0.6542 (mtm180) cc_final: 0.6232 (mtt180) REVERT: H 129 GLU cc_start: 0.4207 (mm-30) cc_final: 0.3855 (mm-30) REVERT: H 137 LYS cc_start: 0.4892 (ptmm) cc_final: 0.4463 (tptt) REVERT: H 139 GLU cc_start: 0.6413 (mt-10) cc_final: 0.5330 (mm-30) REVERT: H 149 LYS cc_start: 0.6220 (OUTLIER) cc_final: 0.5744 (tppt) REVERT: I 26 THR cc_start: 0.7515 (m) cc_final: 0.7047 (p) REVERT: I 43 GLU cc_start: 0.7779 (mm-30) cc_final: 0.7438 (mm-30) REVERT: I 50 LYS cc_start: 0.6155 (ttpt) cc_final: 0.5757 (ttpt) REVERT: I 69 LYS cc_start: 0.6248 (mtpp) cc_final: 0.5601 (tptm) REVERT: I 76 GLN cc_start: 0.6919 (mt0) cc_final: 0.6434 (tt0) REVERT: I 89 LYS cc_start: 0.6344 (ptmt) cc_final: 0.5890 (ttpp) REVERT: I 96 MET cc_start: 0.7495 (ttp) cc_final: 0.7111 (ttt) REVERT: I 111 MET cc_start: 0.8144 (ptp) cc_final: 0.7857 (ptp) REVERT: I 114 ARG cc_start: 0.6445 (ttm110) cc_final: 0.5960 (ttp80) REVERT: J 27 LYS cc_start: 0.5350 (OUTLIER) cc_final: 0.5128 (pttt) REVERT: J 49 ARG cc_start: 0.5163 (mtm-85) cc_final: 0.4363 (ptp90) REVERT: J 85 ARG cc_start: 0.6216 (OUTLIER) cc_final: 0.5808 (mtt180) REVERT: J 88 MET cc_start: 0.5629 (OUTLIER) cc_final: 0.4938 (mtt) REVERT: J 91 ASP cc_start: 0.4983 (t70) cc_final: 0.4705 (t0) REVERT: J 104 VAL cc_start: 0.7100 (t) cc_final: 0.6808 (t) REVERT: J 119 ARG cc_start: 0.6745 (ptm-80) cc_final: 0.6125 (ptp-110) REVERT: K 7 ARG cc_start: 0.5054 (OUTLIER) cc_final: 0.3982 (mtm180) REVERT: K 11 LYS cc_start: 0.6996 (mttt) cc_final: 0.6514 (mmtt) REVERT: K 88 MET cc_start: 0.3465 (mmt) cc_final: 0.2971 (mtp) REVERT: L 40 ASN cc_start: 0.7448 (m-40) cc_final: 0.7193 (m110) REVERT: L 83 GLU cc_start: 0.6574 (mt-10) cc_final: 0.6370 (mt-10) REVERT: L 98 ARG cc_start: 0.5888 (mtt-85) cc_final: 0.5504 (mtm-85) REVERT: L 105 PHE cc_start: 0.6634 (m-80) cc_final: 0.6130 (m-80) REVERT: L 106 ARG cc_start: 0.4713 (ttt180) cc_final: 0.4188 (tpt90) REVERT: M 10 LYS cc_start: 0.6280 (tttt) cc_final: 0.5746 (tttm) REVERT: M 40 THR cc_start: 0.7973 (t) cc_final: 0.7389 (p) REVERT: M 43 LYS cc_start: 0.7396 (ptpt) cc_final: 0.7004 (pttt) REVERT: M 49 LEU cc_start: 0.7489 (mt) cc_final: 0.7121 (mm) REVERT: M 64 THR cc_start: 0.8239 (m) cc_final: 0.7782 (p) REVERT: M 75 GLN cc_start: 0.7201 (OUTLIER) cc_final: 0.6883 (pm20) REVERT: M 76 GLU cc_start: 0.6142 (tt0) cc_final: 0.5564 (tt0) REVERT: M 88 LYS cc_start: 0.7050 (OUTLIER) cc_final: 0.6050 (tttt) REVERT: M 111 LYS cc_start: 0.7317 (mmmt) cc_final: 0.7090 (mmtm) REVERT: M 121 ARG cc_start: 0.6591 (ttt-90) cc_final: 0.6129 (ttt180) REVERT: N 13 LYS cc_start: 0.5955 (OUTLIER) cc_final: 0.5646 (mtmt) REVERT: N 68 ASP cc_start: 0.5374 (OUTLIER) cc_final: 0.4804 (t70) REVERT: N 78 LYS cc_start: 0.5758 (tttm) cc_final: 0.5025 (ptpt) REVERT: N 81 MET cc_start: 0.7240 (mtm) cc_final: 0.6364 (mtm) REVERT: N 93 ARG cc_start: 0.5932 (mmt-90) cc_final: 0.5079 (mmp80) REVERT: N 110 LYS cc_start: 0.7256 (OUTLIER) cc_final: 0.6685 (mttm) REVERT: O 39 GLU cc_start: 0.4963 (tm-30) cc_final: 0.4510 (tp30) REVERT: P 61 SER cc_start: 0.7368 (m) cc_final: 0.7070 (p) REVERT: Q 1 MET cc_start: 0.6792 (pmm) cc_final: 0.6250 (pmm) REVERT: R 11 ARG cc_start: 0.6745 (ttm110) cc_final: 0.6070 (mmt-90) REVERT: R 40 ARG cc_start: 0.6522 (OUTLIER) cc_final: 0.5919 (mtp180) REVERT: R 45 HIS cc_start: 0.7471 (m90) cc_final: 0.7217 (m170) REVERT: S 16 GLU cc_start: 0.4092 (OUTLIER) cc_final: 0.3697 (tm-30) REVERT: T 44 MET cc_start: 0.6117 (mtt) cc_final: 0.5709 (mtt) REVERT: U 24 ARG cc_start: 0.7036 (mmm160) cc_final: 0.6624 (mmm160) REVERT: U 55 GLN cc_start: 0.7107 (tt0) cc_final: 0.6803 (tt0) REVERT: V 21 ARG cc_start: 0.4815 (ttt90) cc_final: 0.4295 (mmm160) REVERT: V 33 ARG cc_start: 0.5601 (mtt90) cc_final: 0.5055 (mmm160) REVERT: V 36 GLU cc_start: 0.6906 (OUTLIER) cc_final: 0.6518 (mt-10) REVERT: V 39 GLU cc_start: 0.6528 (mt-10) cc_final: 0.5611 (pm20) REVERT: V 47 ARG cc_start: 0.5855 (ptt90) cc_final: 0.5507 (ptt-90) REVERT: V 49 LYS cc_start: 0.6446 (tptp) cc_final: 0.6123 (tptp) REVERT: W 143 ARG cc_start: 0.5704 (OUTLIER) cc_final: 0.5048 (mpp-170) REVERT: W 146 VAL cc_start: 0.6416 (m) cc_final: 0.6161 (t) REVERT: W 149 MET cc_start: 0.6925 (mmm) cc_final: 0.6625 (mmp) REVERT: W 169 ASP cc_start: 0.4638 (t0) cc_final: 0.4231 (m-30) REVERT: W 269 LYS cc_start: 0.7701 (tptp) cc_final: 0.7435 (tptt) REVERT: W 285 LYS cc_start: 0.6088 (tttp) cc_final: 0.5675 (ttpt) REVERT: W 287 GLN cc_start: 0.5402 (mt0) cc_final: 0.4895 (tm-30) REVERT: W 317 VAL cc_start: 0.7758 (OUTLIER) cc_final: 0.7515 (p) REVERT: W 318 THR cc_start: 0.7834 (OUTLIER) cc_final: 0.7625 (m) REVERT: W 330 ASP cc_start: 0.5308 (m-30) cc_final: 0.4833 (p0) REVERT: W 336 LYS cc_start: 0.6576 (mttt) cc_final: 0.6126 (mmmt) REVERT: c 5 LYS cc_start: 0.7106 (tttp) cc_final: 0.6346 (tptp) REVERT: c 66 ASP cc_start: 0.7952 (t0) cc_final: 0.7703 (t0) REVERT: c 97 LYS cc_start: 0.7385 (mtpp) cc_final: 0.6616 (mmpt) REVERT: c 181 MET cc_start: 0.8170 (tpp) cc_final: 0.7642 (mmm) REVERT: c 182 ARG cc_start: 0.8396 (OUTLIER) cc_final: 0.8036 (ttt90) REVERT: c 199 GLU cc_start: 0.7508 (mt-10) cc_final: 0.6565 (pm20) REVERT: c 203 ARG cc_start: 0.7659 (ptt90) cc_final: 0.7278 (ptp-110) REVERT: c 269 ARG cc_start: 0.7371 (ttp-170) cc_final: 0.6941 (ttp80) REVERT: d 1 MET cc_start: 0.3751 (OUTLIER) cc_final: 0.2771 (mtt) REVERT: d 7 LYS cc_start: 0.8040 (ttmt) cc_final: 0.7318 (ttpp) REVERT: d 18 ASP cc_start: 0.5750 (OUTLIER) cc_final: 0.5522 (t70) REVERT: d 70 LYS cc_start: 0.7018 (tttt) cc_final: 0.6649 (tttt) REVERT: d 105 LYS cc_start: 0.7742 (mmtt) cc_final: 0.7295 (mmtm) REVERT: e 22 ASP cc_start: 0.6688 (p0) cc_final: 0.6166 (m-30) REVERT: e 132 LYS cc_start: 0.6916 (tttm) cc_final: 0.6703 (ttpt) REVERT: f 30 ARG cc_start: 0.6113 (mpp80) cc_final: 0.5563 (mtm-85) REVERT: f 56 ASP cc_start: 0.5821 (m-30) cc_final: 0.5587 (m-30) REVERT: f 60 ILE cc_start: 0.7289 (mt) cc_final: 0.6926 (mm) REVERT: f 88 LYS cc_start: 0.7559 (OUTLIER) cc_final: 0.7271 (ptpt) REVERT: f 125 ARG cc_start: 0.5190 (tpp-160) cc_final: 0.4902 (mtp180) REVERT: f 129 SER cc_start: 0.7430 (m) cc_final: 0.7065 (t) REVERT: f 178 ARG cc_start: 0.5077 (ptt-90) cc_final: 0.4408 (ptp-170) REVERT: g 9 VAL cc_start: 0.4001 (m) cc_final: 0.3624 (p) REVERT: g 51 THR cc_start: 0.5421 (m) cc_final: 0.4958 (p) REVERT: g 74 SER cc_start: 0.6788 (m) cc_final: 0.6522 (t) REVERT: g 95 ARG cc_start: 0.5954 (mtm110) cc_final: 0.5426 (mtm-85) REVERT: h 21 VAL cc_start: 0.5579 (OUTLIER) cc_final: 0.5313 (t) REVERT: i 34 ARG cc_start: 0.7616 (ttt-90) cc_final: 0.7144 (mtp85) REVERT: i 61 LYS cc_start: 0.7193 (mttt) cc_final: 0.6764 (mmtm) REVERT: i 91 GLU cc_start: 0.7480 (mt-10) cc_final: 0.7269 (mt-10) REVERT: i 95 ARG cc_start: 0.5944 (ttt180) cc_final: 0.5376 (mpt-90) REVERT: i 96 ARG cc_start: 0.6584 (ptt-90) cc_final: 0.4802 (mmm-85) REVERT: i 118 MET cc_start: 0.8364 (mtt) cc_final: 0.8142 (mtt) REVERT: i 128 ASN cc_start: 0.7736 (t0) cc_final: 0.7418 (t0) REVERT: j 17 ARG cc_start: 0.7171 (mmt90) cc_final: 0.6672 (mmm160) REVERT: j 29 HIS cc_start: 0.7181 (m-70) cc_final: 0.6786 (m90) REVERT: j 45 GLU cc_start: 0.7270 (mt-10) cc_final: 0.6998 (mt-10) REVERT: j 51 LYS cc_start: 0.7431 (mtpp) cc_final: 0.7051 (mttt) REVERT: j 53 LYS cc_start: 0.6958 (mptm) cc_final: 0.6166 (tttm) REVERT: j 88 ASN cc_start: 0.6896 (OUTLIER) cc_final: 0.6183 (t0) REVERT: j 89 ASN cc_start: 0.6414 (m-40) cc_final: 0.5902 (t0) REVERT: j 98 ARG cc_start: 0.7013 (mmt-90) cc_final: 0.6495 (mtm180) REVERT: j 105 ARG cc_start: 0.5959 (OUTLIER) cc_final: 0.5453 (mtt-85) REVERT: j 114 LYS cc_start: 0.6109 (mppt) cc_final: 0.5651 (mmpt) REVERT: k 141 LYS cc_start: 0.6360 (tmtm) cc_final: 0.5671 (mtmt) REVERT: l 1 MET cc_start: 0.6011 (OUTLIER) cc_final: 0.5567 (ttp) REVERT: l 6 ARG cc_start: 0.6770 (mtt180) cc_final: 0.6379 (mtm110) REVERT: l 110 GLU cc_start: 0.7271 (OUTLIER) cc_final: 0.6833 (tt0) REVERT: l 133 LYS cc_start: 0.6391 (ttpt) cc_final: 0.5859 (ttmt) REVERT: l 136 MET cc_start: 0.5613 (ttp) cc_final: 0.5331 (ttp) REVERT: m 18 GLN cc_start: 0.8101 (tt0) cc_final: 0.7785 (tt0) REVERT: m 72 ASP cc_start: 0.7610 (t0) cc_final: 0.7203 (t70) REVERT: n 13 ARG cc_start: 0.6570 (tpp-160) cc_final: 0.5673 (ttp80) REVERT: n 19 GLN cc_start: 0.7368 (tt0) cc_final: 0.6505 (tt0) REVERT: n 20 GLU cc_start: 0.5951 (pt0) cc_final: 0.5659 (mt-10) REVERT: n 56 LYS cc_start: 0.5710 (mptt) cc_final: 0.5053 (mtpm) REVERT: n 81 ARG cc_start: 0.7165 (OUTLIER) cc_final: 0.5695 (mtm-85) REVERT: n 104 GLN cc_start: 0.7750 (tt0) cc_final: 0.7411 (tt0) REVERT: o 6 LYS cc_start: 0.6146 (ttpp) cc_final: 0.5699 (tmmt) REVERT: o 7 GLN cc_start: 0.6552 (tp40) cc_final: 0.6308 (tp40) REVERT: o 10 GLN cc_start: 0.6929 (mm-40) cc_final: 0.6204 (mt0) REVERT: o 11 GLU cc_start: 0.7329 (pt0) cc_final: 0.6815 (pt0) REVERT: o 63 LYS cc_start: 0.7618 (ptmm) cc_final: 0.7193 (pttt) REVERT: o 68 GLU cc_start: 0.5999 (mm-30) cc_final: 0.5712 (mp0) REVERT: o 89 ARG cc_start: 0.7101 (mtm180) cc_final: 0.5992 (mmt180) REVERT: o 112 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7586 (mt-10) REVERT: p 9 ILE cc_start: 0.7789 (OUTLIER) cc_final: 0.7567 (mp) REVERT: p 11 ARG cc_start: 0.6991 (tpm170) cc_final: 0.6311 (ttp-110) REVERT: p 85 LYS cc_start: 0.7191 (mttt) cc_final: 0.6898 (mmtm) REVERT: p 112 LYS cc_start: 0.6945 (OUTLIER) cc_final: 0.6553 (tppp) REVERT: q 60 LYS cc_start: 0.7217 (mtmt) cc_final: 0.6681 (mttm) REVERT: q 73 LYS cc_start: 0.7881 (mmtp) cc_final: 0.7300 (mmpt) REVERT: r 28 LYS cc_start: 0.7110 (mtpt) cc_final: 0.6088 (mmtm) REVERT: r 68 ASP cc_start: 0.6814 (m-30) cc_final: 0.6543 (m-30) REVERT: r 73 LYS cc_start: 0.7601 (mttm) cc_final: 0.7301 (mtpm) REVERT: r 86 MET cc_start: 0.8053 (tpp) cc_final: 0.7288 (ttp) REVERT: s 5 GLU cc_start: 0.6600 (mt-10) cc_final: 0.5662 (pp20) REVERT: s 9 LYS cc_start: 0.6856 (mmtt) cc_final: 0.6463 (mtpt) REVERT: s 18 GLU cc_start: 0.7020 (mt-10) cc_final: 0.5948 (mp0) REVERT: s 25 GLU cc_start: 0.6582 (pt0) cc_final: 0.6344 (pt0) REVERT: s 33 LYS cc_start: 0.7396 (tttt) cc_final: 0.6586 (mttp) REVERT: s 50 LEU cc_start: 0.7406 (mt) cc_final: 0.7167 (mp) REVERT: s 51 PHE cc_start: 0.7065 (m-10) cc_final: 0.6721 (m-10) REVERT: s 69 ARG cc_start: 0.6649 (mtt-85) cc_final: 0.6077 (mtm110) REVERT: t 7 ARG cc_start: 0.6005 (ttt180) cc_final: 0.5246 (ttm110) REVERT: t 10 GLU cc_start: 0.7030 (OUTLIER) cc_final: 0.5744 (pm20) REVERT: t 37 GLU cc_start: 0.6403 (pp20) cc_final: 0.5953 (tm-30) REVERT: t 43 LYS cc_start: 0.7156 (mtmm) cc_final: 0.6932 (mttp) REVERT: t 72 ILE cc_start: 0.7355 (tp) cc_final: 0.7047 (tt) REVERT: t 86 ARG cc_start: 0.7559 (mtm-85) cc_final: 0.7026 (mtm180) REVERT: u 43 ASP cc_start: 0.7382 (t0) cc_final: 0.6814 (t0) REVERT: u 46 LYS cc_start: 0.6967 (mmtp) cc_final: 0.6500 (mttm) REVERT: v 70 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.7407 (mp0) REVERT: v 78 LYS cc_start: 0.8040 (mtmp) cc_final: 0.7707 (mtmm) REVERT: v 83 GLU cc_start: 0.6709 (mm-30) cc_final: 0.6170 (mt-10) REVERT: w 54 LYS cc_start: 0.7534 (OUTLIER) cc_final: 0.6980 (tttp) REVERT: x 24 GLU cc_start: 0.6843 (tt0) cc_final: 0.6610 (tt0) REVERT: x 44 LYS cc_start: 0.7052 (ttmt) cc_final: 0.6841 (ttmm) REVERT: y 56 LYS cc_start: 0.7364 (pttt) cc_final: 0.7074 (pttp) REVERT: z 32 LYS cc_start: 0.6934 (OUTLIER) cc_final: 0.6610 (ptmm) outliers start: 181 outliers final: 88 residues processed: 1032 average time/residue: 2.5013 time to fit residues: 3573.8269 Evaluate side-chains 1040 residues out of total 4889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 909 time to evaluate : 6.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 28 ARG Chi-restraints excluded: chain 0 residue 37 LYS Chi-restraints excluded: chain 1 residue 41 ARG Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain C residue 105 LYS Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain D residue 49 LYS Chi-restraints excluded: chain D residue 88 ARG Chi-restraints excluded: chain D residue 132 ARG Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 207 ILE Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain F residue 14 LYS Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain G residue 2 ARG Chi-restraints excluded: chain G residue 37 HIS Chi-restraints excluded: chain G residue 98 GLU Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 73 VAL Chi-restraints excluded: chain H residue 75 VAL Chi-restraints excluded: chain H residue 106 GLU Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 149 LYS Chi-restraints excluded: chain I residue 90 ASP Chi-restraints excluded: chain J residue 27 LYS Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 73 SER Chi-restraints excluded: chain J residue 85 ARG Chi-restraints excluded: chain J residue 88 MET Chi-restraints excluded: chain J residue 107 ASP Chi-restraints excluded: chain K residue 7 ARG Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 129 VAL Chi-restraints excluded: chain M residue 75 GLN Chi-restraints excluded: chain M residue 86 ARG Chi-restraints excluded: chain M residue 88 LYS Chi-restraints excluded: chain N residue 11 ASP Chi-restraints excluded: chain N residue 13 LYS Chi-restraints excluded: chain N residue 16 VAL Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 27 LYS Chi-restraints excluded: chain N residue 68 ASP Chi-restraints excluded: chain N residue 110 LYS Chi-restraints excluded: chain O residue 5 SER Chi-restraints excluded: chain O residue 23 LYS Chi-restraints excluded: chain O residue 33 ASP Chi-restraints excluded: chain O residue 83 LYS Chi-restraints excluded: chain P residue 83 GLU Chi-restraints excluded: chain R residue 29 VAL Chi-restraints excluded: chain R residue 39 LYS Chi-restraints excluded: chain R residue 40 ARG Chi-restraints excluded: chain R residue 42 THR Chi-restraints excluded: chain R residue 67 LEU Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain S residue 16 GLU Chi-restraints excluded: chain T residue 7 LYS Chi-restraints excluded: chain T residue 11 ILE Chi-restraints excluded: chain T residue 70 LYS Chi-restraints excluded: chain U residue 23 SER Chi-restraints excluded: chain U residue 69 LYS Chi-restraints excluded: chain V residue 3 VAL Chi-restraints excluded: chain V residue 36 GLU Chi-restraints excluded: chain W residue 90 GLU Chi-restraints excluded: chain W residue 109 ARG Chi-restraints excluded: chain W residue 143 ARG Chi-restraints excluded: chain W residue 317 VAL Chi-restraints excluded: chain W residue 318 THR Chi-restraints excluded: chain W residue 325 THR Chi-restraints excluded: chain W residue 356 LEU Chi-restraints excluded: chain c residue 111 LYS Chi-restraints excluded: chain c residue 115 GLN Chi-restraints excluded: chain c residue 129 THR Chi-restraints excluded: chain c residue 182 ARG Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 18 ASP Chi-restraints excluded: chain d residue 91 THR Chi-restraints excluded: chain e residue 12 LEU Chi-restraints excluded: chain e residue 126 VAL Chi-restraints excluded: chain f residue 88 LYS Chi-restraints excluded: chain g residue 15 VAL Chi-restraints excluded: chain g residue 36 THR Chi-restraints excluded: chain g residue 47 ASP Chi-restraints excluded: chain g residue 87 LEU Chi-restraints excluded: chain g residue 106 SER Chi-restraints excluded: chain g residue 122 THR Chi-restraints excluded: chain g residue 155 GLU Chi-restraints excluded: chain g residue 171 THR Chi-restraints excluded: chain h residue 21 VAL Chi-restraints excluded: chain i residue 106 LYS Chi-restraints excluded: chain i residue 138 GLN Chi-restraints excluded: chain j residue 76 VAL Chi-restraints excluded: chain j residue 88 ASN Chi-restraints excluded: chain j residue 105 ARG Chi-restraints excluded: chain k residue 94 THR Chi-restraints excluded: chain k residue 103 ILE Chi-restraints excluded: chain l residue 1 MET Chi-restraints excluded: chain l residue 63 ILE Chi-restraints excluded: chain l residue 110 GLU Chi-restraints excluded: chain m residue 15 SER Chi-restraints excluded: chain m residue 89 SER Chi-restraints excluded: chain n residue 81 ARG Chi-restraints excluded: chain o residue 34 GLU Chi-restraints excluded: chain o residue 85 SER Chi-restraints excluded: chain o residue 104 THR Chi-restraints excluded: chain o residue 112 GLU Chi-restraints excluded: chain p residue 9 ILE Chi-restraints excluded: chain p residue 22 LYS Chi-restraints excluded: chain p residue 112 LYS Chi-restraints excluded: chain q residue 33 VAL Chi-restraints excluded: chain r residue 66 ILE Chi-restraints excluded: chain r residue 70 LYS Chi-restraints excluded: chain t residue 10 GLU Chi-restraints excluded: chain u residue 53 LYS Chi-restraints excluded: chain u residue 58 SER Chi-restraints excluded: chain u residue 61 LEU Chi-restraints excluded: chain u residue 62 THR Chi-restraints excluded: chain u residue 65 VAL Chi-restraints excluded: chain v residue 30 SER Chi-restraints excluded: chain v residue 70 GLU Chi-restraints excluded: chain w residue 54 LYS Chi-restraints excluded: chain x residue 40 SER Chi-restraints excluded: chain y residue 19 LYS Chi-restraints excluded: chain y residue 41 THR Chi-restraints excluded: chain z residue 32 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1023 random chunks: chunk 332 optimal weight: 9.9990 chunk 890 optimal weight: 10.0000 chunk 195 optimal weight: 8.9990 chunk 580 optimal weight: 7.9990 chunk 244 optimal weight: 8.9990 chunk 989 optimal weight: 6.9990 chunk 821 optimal weight: 8.9990 chunk 458 optimal weight: 7.9990 chunk 82 optimal weight: 8.9990 chunk 327 optimal weight: 1.9990 chunk 519 optimal weight: 7.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 29 GLN C 18 HIS E 198 HIS F 19 ASN F 77 ASN ** F 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 3 HIS H 97 ASN J 110 GLN L 118 HIS ** L 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 37 ASN P 46 HIS S 54 GLN U 68 HIS W 59 GLN W 97 GLN ** W 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 64 GLN i 136 GLN k 104 GLN u 12 GLN x 27 ASN x 58 ASN z 42 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.107 156812 Z= 0.537 Angle : 1.024 20.534 234226 Z= 0.512 Chirality : 0.053 0.406 29769 Planarity : 0.009 0.164 12793 Dihedral : 23.474 177.443 77640 Min Nonbonded Distance : 1.700 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.18 % Favored : 96.69 % Rotamer: Outliers : 4.42 % Allowed : 14.08 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.10), residues: 5853 helix: 0.18 (0.11), residues: 2051 sheet: -0.43 (0.14), residues: 1161 loop : -0.47 (0.11), residues: 2641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.004 TRP d 80 HIS 0.016 0.003 HIS P 46 PHE 0.028 0.004 PHE d 118 TYR 0.031 0.004 TYR r 38 ARG 0.012 0.002 ARG F 93 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11706 Ramachandran restraints generated. 5853 Oldfield, 0 Emsley, 5853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11706 Ramachandran restraints generated. 5853 Oldfield, 0 Emsley, 5853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1133 residues out of total 4889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 216 poor density : 917 time to evaluate : 6.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 33 LYS cc_start: 0.6482 (tptt) cc_final: 0.6150 (mmtp) REVERT: 2 52 LYS cc_start: 0.6012 (tttm) cc_final: 0.5595 (tppt) REVERT: 3 8 LYS cc_start: 0.7557 (mttt) cc_final: 0.6840 (mtmt) REVERT: 3 12 ARG cc_start: 0.6526 (ptt180) cc_final: 0.5633 (pmt170) REVERT: 3 15 LYS cc_start: 0.7647 (mttt) cc_final: 0.6834 (mttt) REVERT: C 16 PHE cc_start: 0.5747 (m-80) cc_final: 0.5486 (m-80) REVERT: C 49 MET cc_start: 0.4584 (mtp) cc_final: 0.4311 (mtt) REVERT: C 100 MET cc_start: 0.6544 (mtt) cc_final: 0.6276 (ttp) REVERT: C 105 LYS cc_start: 0.6842 (OUTLIER) cc_final: 0.6446 (ptpt) REVERT: C 178 ASN cc_start: 0.6401 (t0) cc_final: 0.6087 (m-40) REVERT: D 27 LYS cc_start: 0.4786 (pmtt) cc_final: 0.4365 (ttpp) REVERT: D 28 GLU cc_start: 0.6021 (mt-10) cc_final: 0.5506 (mp0) REVERT: D 46 GLU cc_start: 0.5399 (tp30) cc_final: 0.4861 (mm-30) REVERT: D 72 ARG cc_start: 0.4612 (mmm-85) cc_final: 0.4397 (mtm180) REVERT: D 88 ARG cc_start: 0.5110 (OUTLIER) cc_final: 0.4642 (ttp80) REVERT: D 122 SER cc_start: 0.6613 (m) cc_final: 0.6258 (p) REVERT: D 129 MET cc_start: 0.5908 (mmm) cc_final: 0.5214 (mtm) REVERT: D 132 ARG cc_start: 0.5777 (OUTLIER) cc_final: 0.5487 (ptm-80) REVERT: D 170 GLU cc_start: 0.7143 (mt-10) cc_final: 0.6937 (mt-10) REVERT: E 29 ASP cc_start: 0.5384 (OUTLIER) cc_final: 0.4928 (p0) REVERT: E 44 ARG cc_start: 0.4546 (ttm110) cc_final: 0.3818 (mmt180) REVERT: E 73 ARG cc_start: 0.6419 (ttp80) cc_final: 0.5468 (ttm-80) REVERT: E 78 GLU cc_start: 0.6608 (tt0) cc_final: 0.6272 (tp30) REVERT: E 113 GLU cc_start: 0.7025 (tp30) cc_final: 0.6654 (tt0) REVERT: E 119 SER cc_start: 0.6744 (t) cc_final: 0.6364 (p) REVERT: E 124 MET cc_start: 0.6804 (mtm) cc_final: 0.6462 (mtt) REVERT: E 128 ARG cc_start: 0.5228 (mtt-85) cc_final: 0.4762 (mmm-85) REVERT: E 144 SER cc_start: 0.6849 (p) cc_final: 0.6614 (t) REVERT: E 148 LYS cc_start: 0.5211 (ttpp) cc_final: 0.4174 (tptp) REVERT: E 151 LYS cc_start: 0.4334 (pptt) cc_final: 0.4048 (mttm) REVERT: E 160 GLU cc_start: 0.4154 (pt0) cc_final: 0.3678 (tt0) REVERT: E 171 LEU cc_start: 0.5878 (OUTLIER) cc_final: 0.5631 (mt) REVERT: F 26 LYS cc_start: 0.6869 (tmtm) cc_final: 0.6560 (ttmt) REVERT: F 45 ARG cc_start: 0.6461 (mtp-110) cc_final: 0.5813 (mmm160) REVERT: F 55 GLU cc_start: 0.6446 (mt-10) cc_final: 0.6209 (mt-10) REVERT: F 61 GLN cc_start: 0.6227 (tm-30) cc_final: 0.5736 (tm130) REVERT: F 65 GLU cc_start: 0.6168 (mt-10) cc_final: 0.5900 (mm-30) REVERT: F 116 GLU cc_start: 0.7010 (tt0) cc_final: 0.6534 (tt0) REVERT: F 156 LYS cc_start: 0.6712 (ptpp) cc_final: 0.6305 (pttt) REVERT: G 15 SER cc_start: 0.5930 (t) cc_final: 0.5411 (m) REVERT: G 46 GLN cc_start: 0.5957 (tp40) cc_final: 0.5751 (tp-100) REVERT: G 56 LYS cc_start: 0.6717 (mtpt) cc_final: 0.6000 (mttp) REVERT: G 62 MET cc_start: 0.6770 (ptp) cc_final: 0.6307 (ptt) REVERT: G 92 THR cc_start: 0.6015 (OUTLIER) cc_final: 0.5614 (p) REVERT: G 98 GLU cc_start: 0.3595 (OUTLIER) cc_final: 0.3152 (tp30) REVERT: H 41 SER cc_start: 0.6232 (p) cc_final: 0.5750 (m) REVERT: H 79 ARG cc_start: 0.3618 (ttt180) cc_final: 0.3317 (mtt90) REVERT: H 92 ARG cc_start: 0.4781 (mpp-170) cc_final: 0.4423 (mpt180) REVERT: H 96 ARG cc_start: 0.5903 (mtt90) cc_final: 0.5681 (mtt180) REVERT: H 106 GLU cc_start: 0.6615 (OUTLIER) cc_final: 0.6327 (tt0) REVERT: H 119 ARG cc_start: 0.6407 (mtm180) cc_final: 0.6110 (mtt180) REVERT: H 129 GLU cc_start: 0.4578 (mm-30) cc_final: 0.4044 (mp0) REVERT: H 137 LYS cc_start: 0.5011 (ptmm) cc_final: 0.4628 (tptt) REVERT: H 139 GLU cc_start: 0.6491 (mt-10) cc_final: 0.5387 (mm-30) REVERT: H 149 LYS cc_start: 0.6231 (OUTLIER) cc_final: 0.5871 (ttpp) REVERT: I 26 THR cc_start: 0.7574 (m) cc_final: 0.7135 (p) REVERT: I 43 GLU cc_start: 0.7751 (mm-30) cc_final: 0.7376 (mm-30) REVERT: I 48 ASP cc_start: 0.6670 (t70) cc_final: 0.6315 (t70) REVERT: I 50 LYS cc_start: 0.6159 (ttpt) cc_final: 0.5778 (ttpt) REVERT: I 69 LYS cc_start: 0.6209 (mtpp) cc_final: 0.5564 (tptm) REVERT: I 76 GLN cc_start: 0.7008 (OUTLIER) cc_final: 0.6422 (tt0) REVERT: I 89 LYS cc_start: 0.6201 (ptmt) cc_final: 0.5675 (ttpp) REVERT: I 96 MET cc_start: 0.7461 (ttp) cc_final: 0.7113 (ttt) REVERT: I 111 MET cc_start: 0.8134 (ptp) cc_final: 0.7819 (ptp) REVERT: I 114 ARG cc_start: 0.6497 (ttm110) cc_final: 0.5922 (ttp-110) REVERT: J 27 LYS cc_start: 0.5347 (OUTLIER) cc_final: 0.5112 (pttt) REVERT: J 88 MET cc_start: 0.5717 (OUTLIER) cc_final: 0.5142 (mtt) REVERT: J 91 ASP cc_start: 0.4957 (t70) cc_final: 0.4726 (t0) REVERT: J 104 VAL cc_start: 0.7122 (t) cc_final: 0.6875 (t) REVERT: K 7 ARG cc_start: 0.5257 (OUTLIER) cc_final: 0.3931 (mtm180) REVERT: K 11 LYS cc_start: 0.7017 (mttt) cc_final: 0.6547 (mmmt) REVERT: K 75 ASP cc_start: 0.4783 (OUTLIER) cc_final: 0.4247 (p0) REVERT: K 88 MET cc_start: 0.3672 (mmt) cc_final: 0.3466 (mmt) REVERT: L 83 GLU cc_start: 0.6552 (mt-10) cc_final: 0.6135 (mt-10) REVERT: L 98 ARG cc_start: 0.5879 (mtt-85) cc_final: 0.5508 (mtm-85) REVERT: L 105 PHE cc_start: 0.6519 (m-80) cc_final: 0.6011 (m-80) REVERT: L 106 ARG cc_start: 0.4632 (ttt180) cc_final: 0.4168 (tpt90) REVERT: M 10 LYS cc_start: 0.6334 (tttt) cc_final: 0.5813 (tttm) REVERT: M 40 THR cc_start: 0.8009 (t) cc_final: 0.7398 (p) REVERT: M 43 LYS cc_start: 0.7455 (ptpt) cc_final: 0.6980 (pttt) REVERT: M 49 LEU cc_start: 0.7473 (mt) cc_final: 0.7083 (mm) REVERT: M 64 THR cc_start: 0.8164 (m) cc_final: 0.7727 (p) REVERT: M 88 LYS cc_start: 0.7079 (OUTLIER) cc_final: 0.6184 (tttt) REVERT: M 109 ASP cc_start: 0.6917 (OUTLIER) cc_final: 0.6636 (m-30) REVERT: M 111 LYS cc_start: 0.7324 (mmmt) cc_final: 0.7072 (mmtm) REVERT: N 13 LYS cc_start: 0.5907 (OUTLIER) cc_final: 0.5584 (mtmt) REVERT: N 52 GLN cc_start: 0.5289 (OUTLIER) cc_final: 0.5076 (mt0) REVERT: N 78 LYS cc_start: 0.5634 (tttm) cc_final: 0.4914 (ptpt) REVERT: N 81 MET cc_start: 0.7279 (mtm) cc_final: 0.6652 (mtm) REVERT: N 93 ARG cc_start: 0.5836 (mmt-90) cc_final: 0.5080 (mmp80) REVERT: N 110 LYS cc_start: 0.7383 (OUTLIER) cc_final: 0.6756 (mttm) REVERT: N 113 ARG cc_start: 0.5223 (OUTLIER) cc_final: 0.4581 (mmm-85) REVERT: O 39 GLU cc_start: 0.4993 (tm-30) cc_final: 0.4511 (tp30) REVERT: P 61 SER cc_start: 0.7316 (m) cc_final: 0.7018 (p) REVERT: Q 1 MET cc_start: 0.6769 (pmm) cc_final: 0.6124 (pmm) REVERT: R 6 ARG cc_start: 0.4878 (OUTLIER) cc_final: 0.4201 (mtm-85) REVERT: R 11 ARG cc_start: 0.6553 (ttm110) cc_final: 0.6000 (mmt-90) REVERT: R 40 ARG cc_start: 0.6604 (OUTLIER) cc_final: 0.6028 (mtp180) REVERT: S 16 GLU cc_start: 0.4123 (OUTLIER) cc_final: 0.3757 (tm-30) REVERT: T 44 MET cc_start: 0.6070 (mtt) cc_final: 0.5652 (mtt) REVERT: U 24 ARG cc_start: 0.7203 (mmm160) cc_final: 0.6853 (mmm160) REVERT: U 55 GLN cc_start: 0.7088 (tt0) cc_final: 0.6871 (tt0) REVERT: V 21 ARG cc_start: 0.4755 (ttt90) cc_final: 0.4266 (mmm160) REVERT: V 33 ARG cc_start: 0.5412 (mtt90) cc_final: 0.4895 (mmm160) REVERT: V 36 GLU cc_start: 0.6925 (OUTLIER) cc_final: 0.6604 (mt-10) REVERT: V 47 ARG cc_start: 0.5817 (ptt90) cc_final: 0.5427 (ptt-90) REVERT: V 49 LYS cc_start: 0.6454 (tptp) cc_final: 0.6177 (tptp) REVERT: W 143 ARG cc_start: 0.5700 (OUTLIER) cc_final: 0.5153 (mpp-170) REVERT: W 146 VAL cc_start: 0.6392 (m) cc_final: 0.6153 (t) REVERT: W 155 GLU cc_start: 0.5990 (tp30) cc_final: 0.5514 (mt-10) REVERT: W 169 ASP cc_start: 0.4747 (t0) cc_final: 0.4323 (m-30) REVERT: W 269 LYS cc_start: 0.7684 (tptp) cc_final: 0.7375 (tptm) REVERT: W 285 LYS cc_start: 0.6001 (tttp) cc_final: 0.5595 (ttpt) REVERT: W 287 GLN cc_start: 0.5396 (mt0) cc_final: 0.4893 (tm130) REVERT: W 318 THR cc_start: 0.7870 (OUTLIER) cc_final: 0.7644 (m) REVERT: W 330 ASP cc_start: 0.5410 (m-30) cc_final: 0.4827 (p0) REVERT: W 331 GLU cc_start: 0.6317 (mm-30) cc_final: 0.5445 (mp0) REVERT: W 336 LYS cc_start: 0.6457 (mttt) cc_final: 0.6022 (mmmt) REVERT: W 341 ILE cc_start: 0.7038 (mt) cc_final: 0.6766 (mm) REVERT: W 346 GLN cc_start: 0.5880 (OUTLIER) cc_final: 0.5467 (mp10) REVERT: c 5 LYS cc_start: 0.7156 (tttp) cc_final: 0.6401 (tptp) REVERT: c 97 LYS cc_start: 0.7334 (mtpp) cc_final: 0.6574 (mmpt) REVERT: c 111 LYS cc_start: 0.6681 (OUTLIER) cc_final: 0.6094 (ptpt) REVERT: c 181 MET cc_start: 0.8186 (tpp) cc_final: 0.7729 (mmm) REVERT: c 182 ARG cc_start: 0.8516 (OUTLIER) cc_final: 0.7964 (ttt90) REVERT: c 203 ARG cc_start: 0.7679 (ptt90) cc_final: 0.7273 (ptp-110) REVERT: c 269 ARG cc_start: 0.7281 (ttp-170) cc_final: 0.6841 (ttp80) REVERT: d 1 MET cc_start: 0.4047 (OUTLIER) cc_final: 0.2979 (mtt) REVERT: d 7 LYS cc_start: 0.8053 (ttmt) cc_final: 0.7352 (ttpp) REVERT: d 70 LYS cc_start: 0.7036 (tttt) cc_final: 0.6647 (tttt) REVERT: d 128 ARG cc_start: 0.8035 (OUTLIER) cc_final: 0.7365 (mtp180) REVERT: e 21 ARG cc_start: 0.6157 (OUTLIER) cc_final: 0.5698 (ptm160) REVERT: e 22 ASP cc_start: 0.6846 (p0) cc_final: 0.6194 (m-30) REVERT: e 132 LYS cc_start: 0.6967 (tttm) cc_final: 0.6731 (ttpt) REVERT: e 140 ASP cc_start: 0.5664 (m-30) cc_final: 0.5328 (m-30) REVERT: e 191 ASP cc_start: 0.5961 (t0) cc_final: 0.5711 (t0) REVERT: f 30 ARG cc_start: 0.6085 (mpp80) cc_final: 0.5540 (mtm-85) REVERT: f 88 LYS cc_start: 0.7563 (OUTLIER) cc_final: 0.7229 (ptpt) REVERT: f 125 ARG cc_start: 0.5251 (tpp-160) cc_final: 0.4871 (mmp-170) REVERT: f 129 SER cc_start: 0.7445 (m) cc_final: 0.7072 (t) REVERT: g 9 VAL cc_start: 0.4160 (m) cc_final: 0.3840 (p) REVERT: g 25 THR cc_start: 0.5607 (m) cc_final: 0.5226 (p) REVERT: g 51 THR cc_start: 0.5536 (m) cc_final: 0.5090 (p) REVERT: g 74 SER cc_start: 0.6822 (m) cc_final: 0.6552 (t) REVERT: g 95 ARG cc_start: 0.6103 (mtm110) cc_final: 0.5527 (mtm-85) REVERT: i 34 ARG cc_start: 0.7666 (ttt-90) cc_final: 0.7246 (mtp85) REVERT: i 61 LYS cc_start: 0.7108 (mttt) cc_final: 0.6676 (mmtm) REVERT: i 95 ARG cc_start: 0.6205 (ttt180) cc_final: 0.5398 (mpt-90) REVERT: i 96 ARG cc_start: 0.6639 (ptt-90) cc_final: 0.4833 (mmm-85) REVERT: i 118 MET cc_start: 0.8395 (mtt) cc_final: 0.8153 (mtt) REVERT: i 128 ASN cc_start: 0.7796 (t0) cc_final: 0.7594 (t0) REVERT: j 17 ARG cc_start: 0.7160 (mmt90) cc_final: 0.6670 (mmm160) REVERT: j 29 HIS cc_start: 0.7274 (m-70) cc_final: 0.6916 (m-70) REVERT: j 45 GLU cc_start: 0.7238 (mt-10) cc_final: 0.6979 (mt-10) REVERT: j 51 LYS cc_start: 0.7436 (mtpp) cc_final: 0.6977 (mtmt) REVERT: j 53 LYS cc_start: 0.6906 (mptm) cc_final: 0.6135 (tttm) REVERT: j 89 ASN cc_start: 0.6451 (m-40) cc_final: 0.5877 (t0) REVERT: j 98 ARG cc_start: 0.7043 (mmt-90) cc_final: 0.6497 (mtm180) REVERT: j 105 ARG cc_start: 0.5961 (OUTLIER) cc_final: 0.5440 (mtt-85) REVERT: j 114 LYS cc_start: 0.6233 (mppt) cc_final: 0.5802 (mmpt) REVERT: k 106 GLU cc_start: 0.7858 (mt-10) cc_final: 0.7003 (mm-30) REVERT: k 141 LYS cc_start: 0.6591 (tmtm) cc_final: 0.5742 (mtmt) REVERT: l 1 MET cc_start: 0.5983 (OUTLIER) cc_final: 0.5583 (ttp) REVERT: l 6 ARG cc_start: 0.6782 (mtt180) cc_final: 0.5794 (ttt-90) REVERT: l 136 MET cc_start: 0.5811 (ttp) cc_final: 0.5609 (ttp) REVERT: m 18 GLN cc_start: 0.8097 (tt0) cc_final: 0.7770 (tt0) REVERT: m 72 ASP cc_start: 0.7642 (t0) cc_final: 0.7245 (t70) REVERT: n 13 ARG cc_start: 0.6524 (tpp-160) cc_final: 0.5659 (ttp80) REVERT: n 19 GLN cc_start: 0.7349 (tt0) cc_final: 0.6485 (tt0) REVERT: n 20 GLU cc_start: 0.6091 (pt0) cc_final: 0.5661 (mt-10) REVERT: n 104 GLN cc_start: 0.7737 (tt0) cc_final: 0.7402 (tt0) REVERT: o 6 LYS cc_start: 0.6118 (ttpp) cc_final: 0.5757 (tmmt) REVERT: o 7 GLN cc_start: 0.6521 (tp40) cc_final: 0.6194 (tt0) REVERT: o 10 GLN cc_start: 0.7013 (mm-40) cc_final: 0.6217 (mt0) REVERT: o 11 GLU cc_start: 0.7386 (pt0) cc_final: 0.6846 (pt0) REVERT: o 63 LYS cc_start: 0.7627 (ptmm) cc_final: 0.7203 (pttt) REVERT: o 68 GLU cc_start: 0.5960 (mm-30) cc_final: 0.5650 (mp0) REVERT: o 89 ARG cc_start: 0.7192 (mtm180) cc_final: 0.6071 (mmt180) REVERT: o 112 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7582 (mt-10) REVERT: p 9 ILE cc_start: 0.7797 (OUTLIER) cc_final: 0.7554 (mp) REVERT: p 11 ARG cc_start: 0.6939 (tpm170) cc_final: 0.6265 (ttm110) REVERT: p 85 LYS cc_start: 0.7236 (mttt) cc_final: 0.6987 (mmtm) REVERT: p 104 VAL cc_start: 0.6541 (t) cc_final: 0.6253 (m) REVERT: p 112 LYS cc_start: 0.6847 (OUTLIER) cc_final: 0.6488 (tppp) REVERT: q 48 LYS cc_start: 0.7508 (mttm) cc_final: 0.7288 (mttp) REVERT: q 60 LYS cc_start: 0.7160 (mtmt) cc_final: 0.6531 (mttt) REVERT: q 73 LYS cc_start: 0.7902 (mmtp) cc_final: 0.7313 (mmpt) REVERT: r 28 LYS cc_start: 0.7120 (mtpt) cc_final: 0.6135 (mmtm) REVERT: r 68 ASP cc_start: 0.6779 (m-30) cc_final: 0.6519 (m-30) REVERT: r 73 LYS cc_start: 0.7631 (mttm) cc_final: 0.7293 (mtpm) REVERT: r 86 MET cc_start: 0.8074 (tpp) cc_final: 0.7286 (ttp) REVERT: s 5 GLU cc_start: 0.6615 (mt-10) cc_final: 0.5711 (pp20) REVERT: s 9 LYS cc_start: 0.6837 (mmtt) cc_final: 0.6404 (mtpt) REVERT: s 18 GLU cc_start: 0.7153 (mt-10) cc_final: 0.5992 (mp0) REVERT: s 33 LYS cc_start: 0.7434 (tttt) cc_final: 0.6675 (mttp) REVERT: s 50 LEU cc_start: 0.7351 (mt) cc_final: 0.7129 (mp) REVERT: s 51 PHE cc_start: 0.7041 (m-10) cc_final: 0.6657 (m-10) REVERT: s 69 ARG cc_start: 0.6530 (mtt-85) cc_final: 0.5877 (mtm-85) REVERT: t 7 ARG cc_start: 0.6401 (ttt180) cc_final: 0.5547 (ttm110) REVERT: t 10 GLU cc_start: 0.7041 (OUTLIER) cc_final: 0.5644 (pm20) REVERT: t 37 GLU cc_start: 0.6420 (pp20) cc_final: 0.6034 (tm-30) REVERT: t 43 LYS cc_start: 0.7211 (mtmm) cc_final: 0.6908 (mttp) REVERT: t 72 ILE cc_start: 0.7398 (tp) cc_final: 0.7078 (tt) REVERT: t 86 ARG cc_start: 0.7509 (mtm-85) cc_final: 0.7015 (mtm-85) REVERT: u 10 LYS cc_start: 0.6365 (mttp) cc_final: 0.5632 (mmmt) REVERT: u 43 ASP cc_start: 0.7400 (t0) cc_final: 0.6873 (t0) REVERT: v 44 LYS cc_start: 0.8014 (ttpt) cc_final: 0.7808 (ttpp) REVERT: v 70 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.7371 (mp0) REVERT: v 83 GLU cc_start: 0.6641 (mm-30) cc_final: 0.6102 (mt-10) REVERT: w 54 LYS cc_start: 0.7597 (OUTLIER) cc_final: 0.7029 (tttp) REVERT: x 24 GLU cc_start: 0.6844 (tt0) cc_final: 0.6613 (tt0) REVERT: x 44 LYS cc_start: 0.7029 (ttmt) cc_final: 0.6809 (ttmm) REVERT: y 56 LYS cc_start: 0.7398 (pttt) cc_final: 0.7073 (ptmt) outliers start: 216 outliers final: 114 residues processed: 1049 average time/residue: 2.4443 time to fit residues: 3563.6205 Evaluate side-chains 1047 residues out of total 4889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 892 time to evaluate : 5.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 28 ARG Chi-restraints excluded: chain 1 residue 41 ARG Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 105 LYS Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain D residue 88 ARG Chi-restraints excluded: chain D residue 132 ARG Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 177 LYS Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain F residue 14 LYS Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain G residue 37 HIS Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain G residue 98 GLU Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 75 VAL Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 106 GLU Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 149 LYS Chi-restraints excluded: chain I residue 76 GLN Chi-restraints excluded: chain I residue 90 ASP Chi-restraints excluded: chain J residue 27 LYS Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 67 VAL Chi-restraints excluded: chain J residue 73 SER Chi-restraints excluded: chain J residue 85 ARG Chi-restraints excluded: chain J residue 88 MET Chi-restraints excluded: chain K residue 7 ARG Chi-restraints excluded: chain K residue 71 LEU Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 75 ASP Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 129 VAL Chi-restraints excluded: chain M residue 3 THR Chi-restraints excluded: chain M residue 86 ARG Chi-restraints excluded: chain M residue 88 LYS Chi-restraints excluded: chain M residue 109 ASP Chi-restraints excluded: chain N residue 11 ASP Chi-restraints excluded: chain N residue 13 LYS Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 27 LYS Chi-restraints excluded: chain N residue 52 GLN Chi-restraints excluded: chain N residue 68 ASP Chi-restraints excluded: chain N residue 73 ILE Chi-restraints excluded: chain N residue 95 LEU Chi-restraints excluded: chain N residue 110 LYS Chi-restraints excluded: chain N residue 113 ARG Chi-restraints excluded: chain O residue 5 SER Chi-restraints excluded: chain O residue 23 LYS Chi-restraints excluded: chain O residue 83 LYS Chi-restraints excluded: chain P residue 83 GLU Chi-restraints excluded: chain R residue 6 ARG Chi-restraints excluded: chain R residue 29 VAL Chi-restraints excluded: chain R residue 39 LYS Chi-restraints excluded: chain R residue 40 ARG Chi-restraints excluded: chain R residue 42 THR Chi-restraints excluded: chain R residue 67 LEU Chi-restraints excluded: chain R residue 72 SER Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain S residue 16 GLU Chi-restraints excluded: chain T residue 11 ILE Chi-restraints excluded: chain T residue 70 LYS Chi-restraints excluded: chain U residue 23 SER Chi-restraints excluded: chain U residue 69 LYS Chi-restraints excluded: chain V residue 3 VAL Chi-restraints excluded: chain V residue 36 GLU Chi-restraints excluded: chain V residue 63 GLU Chi-restraints excluded: chain W residue 109 ARG Chi-restraints excluded: chain W residue 143 ARG Chi-restraints excluded: chain W residue 162 ILE Chi-restraints excluded: chain W residue 318 THR Chi-restraints excluded: chain W residue 325 THR Chi-restraints excluded: chain W residue 346 GLN Chi-restraints excluded: chain W residue 356 LEU Chi-restraints excluded: chain c residue 111 LYS Chi-restraints excluded: chain c residue 129 THR Chi-restraints excluded: chain c residue 165 VAL Chi-restraints excluded: chain c residue 182 ARG Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 91 THR Chi-restraints excluded: chain d residue 128 ARG Chi-restraints excluded: chain e residue 12 LEU Chi-restraints excluded: chain e residue 21 ARG Chi-restraints excluded: chain e residue 126 VAL Chi-restraints excluded: chain e residue 144 GLU Chi-restraints excluded: chain e residue 197 GLU Chi-restraints excluded: chain f residue 35 THR Chi-restraints excluded: chain f residue 88 LYS Chi-restraints excluded: chain f residue 120 LYS Chi-restraints excluded: chain g residue 15 VAL Chi-restraints excluded: chain g residue 36 THR Chi-restraints excluded: chain g residue 47 ASP Chi-restraints excluded: chain g residue 87 LEU Chi-restraints excluded: chain g residue 106 SER Chi-restraints excluded: chain g residue 122 THR Chi-restraints excluded: chain g residue 124 GLU Chi-restraints excluded: chain g residue 141 ILE Chi-restraints excluded: chain g residue 155 GLU Chi-restraints excluded: chain h residue 21 VAL Chi-restraints excluded: chain i residue 106 LYS Chi-restraints excluded: chain i residue 138 GLN Chi-restraints excluded: chain j residue 76 VAL Chi-restraints excluded: chain j residue 105 ARG Chi-restraints excluded: chain k residue 94 THR Chi-restraints excluded: chain k residue 103 ILE Chi-restraints excluded: chain l residue 1 MET Chi-restraints excluded: chain l residue 30 SER Chi-restraints excluded: chain l residue 80 VAL Chi-restraints excluded: chain m residue 15 SER Chi-restraints excluded: chain m residue 89 SER Chi-restraints excluded: chain n residue 17 LYS Chi-restraints excluded: chain n residue 81 ARG Chi-restraints excluded: chain o residue 34 GLU Chi-restraints excluded: chain o residue 70 VAL Chi-restraints excluded: chain o residue 85 SER Chi-restraints excluded: chain o residue 104 THR Chi-restraints excluded: chain o residue 112 GLU Chi-restraints excluded: chain p residue 9 ILE Chi-restraints excluded: chain p residue 22 LYS Chi-restraints excluded: chain p residue 112 LYS Chi-restraints excluded: chain q residue 33 VAL Chi-restraints excluded: chain q residue 64 VAL Chi-restraints excluded: chain q residue 99 THR Chi-restraints excluded: chain r residue 66 ILE Chi-restraints excluded: chain r residue 70 LYS Chi-restraints excluded: chain t residue 10 GLU Chi-restraints excluded: chain u residue 53 LYS Chi-restraints excluded: chain u residue 58 SER Chi-restraints excluded: chain u residue 61 LEU Chi-restraints excluded: chain u residue 62 THR Chi-restraints excluded: chain u residue 65 VAL Chi-restraints excluded: chain v residue 30 SER Chi-restraints excluded: chain v residue 70 GLU Chi-restraints excluded: chain w residue 54 LYS Chi-restraints excluded: chain x residue 4 LYS Chi-restraints excluded: chain x residue 40 SER Chi-restraints excluded: chain y residue 19 LYS Chi-restraints excluded: chain y residue 41 THR Chi-restraints excluded: chain z residue 30 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1023 random chunks: chunk 954 optimal weight: 4.9990 chunk 111 optimal weight: 4.9990 chunk 563 optimal weight: 4.9990 chunk 722 optimal weight: 4.9990 chunk 560 optimal weight: 10.0000 chunk 833 optimal weight: 6.9990 chunk 552 optimal weight: 0.9990 chunk 986 optimal weight: 4.9990 chunk 617 optimal weight: 3.9990 chunk 601 optimal weight: 9.9990 chunk 455 optimal weight: 20.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 29 GLN C 18 HIS E 198 HIS F 19 ASN F 70 ASN F 77 ASN ** F 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 3 HIS H 130 ASN J 110 GLN L 40 ASN ** L 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 37 ASN P 46 HIS R 45 HIS S 54 GLN U 68 HIS W 248 HIS c 117 GLN e 165 HIS g 64 GLN i 136 GLN k 104 GLN s 48 GLN u 12 GLN x 58 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 156812 Z= 0.353 Angle : 0.827 17.277 234226 Z= 0.428 Chirality : 0.044 0.386 29769 Planarity : 0.008 0.153 12793 Dihedral : 23.354 177.254 77640 Min Nonbonded Distance : 1.746 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.72 % Favored : 97.15 % Rotamer: Outliers : 4.01 % Allowed : 14.81 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.10), residues: 5853 helix: 0.50 (0.11), residues: 2053 sheet: -0.33 (0.14), residues: 1180 loop : -0.40 (0.11), residues: 2620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP D 201 HIS 0.013 0.002 HIS P 46 PHE 0.023 0.003 PHE m 21 TYR 0.027 0.003 TYR r 38 ARG 0.008 0.001 ARG F 93 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11706 Ramachandran restraints generated. 5853 Oldfield, 0 Emsley, 5853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11706 Ramachandran restraints generated. 5853 Oldfield, 0 Emsley, 5853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1106 residues out of total 4889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 910 time to evaluate : 6.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 33 LYS cc_start: 0.6476 (tptt) cc_final: 0.6123 (mmtp) REVERT: 2 52 LYS cc_start: 0.5951 (tttm) cc_final: 0.5549 (tppt) REVERT: 3 8 LYS cc_start: 0.7533 (mttt) cc_final: 0.6844 (mtmt) REVERT: 3 12 ARG cc_start: 0.6566 (ptt180) cc_final: 0.5689 (pmt170) REVERT: 3 15 LYS cc_start: 0.7575 (mttt) cc_final: 0.6767 (mttt) REVERT: C 16 PHE cc_start: 0.5691 (m-80) cc_final: 0.5435 (m-80) REVERT: C 49 MET cc_start: 0.4574 (mtp) cc_final: 0.4272 (mtt) REVERT: C 100 MET cc_start: 0.6621 (mtt) cc_final: 0.6334 (ttp) REVERT: C 105 LYS cc_start: 0.6847 (OUTLIER) cc_final: 0.6471 (ptpt) REVERT: C 143 LYS cc_start: 0.4297 (OUTLIER) cc_final: 0.4071 (tttt) REVERT: C 178 ASN cc_start: 0.6300 (t0) cc_final: 0.5998 (m-40) REVERT: D 27 LYS cc_start: 0.4813 (pmtt) cc_final: 0.4370 (ttpp) REVERT: D 28 GLU cc_start: 0.5997 (mt-10) cc_final: 0.5518 (mp0) REVERT: D 46 GLU cc_start: 0.5477 (tp30) cc_final: 0.4944 (mm-30) REVERT: D 88 ARG cc_start: 0.5028 (OUTLIER) cc_final: 0.4611 (ttt-90) REVERT: D 122 SER cc_start: 0.6571 (m) cc_final: 0.6240 (p) REVERT: D 129 MET cc_start: 0.5994 (mmm) cc_final: 0.5289 (mtm) REVERT: D 132 ARG cc_start: 0.5804 (OUTLIER) cc_final: 0.5504 (ptm-80) REVERT: E 20 PHE cc_start: 0.6345 (m-80) cc_final: 0.6048 (m-80) REVERT: E 29 ASP cc_start: 0.5416 (OUTLIER) cc_final: 0.4950 (p0) REVERT: E 44 ARG cc_start: 0.4580 (ttm110) cc_final: 0.4290 (tmm160) REVERT: E 73 ARG cc_start: 0.6426 (ttp80) cc_final: 0.5507 (ttm-80) REVERT: E 78 GLU cc_start: 0.6619 (tt0) cc_final: 0.6274 (tp30) REVERT: E 113 GLU cc_start: 0.7084 (tp30) cc_final: 0.6729 (tt0) REVERT: E 119 SER cc_start: 0.6639 (t) cc_final: 0.6305 (p) REVERT: E 124 MET cc_start: 0.6790 (mtm) cc_final: 0.6417 (mtt) REVERT: E 128 ARG cc_start: 0.5195 (mtt-85) cc_final: 0.4762 (mmm-85) REVERT: E 148 LYS cc_start: 0.5036 (ttpp) cc_final: 0.4060 (tptp) REVERT: E 151 LYS cc_start: 0.4349 (pptt) cc_final: 0.4065 (mttm) REVERT: E 171 LEU cc_start: 0.5912 (OUTLIER) cc_final: 0.5652 (mt) REVERT: F 45 ARG cc_start: 0.6453 (mtp-110) cc_final: 0.5825 (mmm160) REVERT: F 55 GLU cc_start: 0.6428 (mt-10) cc_final: 0.6208 (mt-10) REVERT: F 61 GLN cc_start: 0.6223 (tm-30) cc_final: 0.5718 (tm130) REVERT: F 65 GLU cc_start: 0.6190 (mt-10) cc_final: 0.5925 (mm-30) REVERT: F 116 GLU cc_start: 0.6987 (tt0) cc_final: 0.6547 (tt0) REVERT: F 156 LYS cc_start: 0.6705 (ptpp) cc_final: 0.6328 (pttt) REVERT: G 15 SER cc_start: 0.5934 (t) cc_final: 0.5389 (m) REVERT: G 56 LYS cc_start: 0.6731 (mtpt) cc_final: 0.6030 (mttp) REVERT: G 62 MET cc_start: 0.6742 (OUTLIER) cc_final: 0.6273 (ptt) REVERT: G 92 THR cc_start: 0.6046 (OUTLIER) cc_final: 0.5709 (p) REVERT: G 98 GLU cc_start: 0.3488 (OUTLIER) cc_final: 0.2821 (tm-30) REVERT: H 41 SER cc_start: 0.6152 (p) cc_final: 0.5725 (m) REVERT: H 79 ARG cc_start: 0.3677 (ttt180) cc_final: 0.3345 (mtt90) REVERT: H 92 ARG cc_start: 0.4752 (mpp-170) cc_final: 0.4415 (mpt180) REVERT: H 96 ARG cc_start: 0.5967 (mtt90) cc_final: 0.5733 (mtt180) REVERT: H 106 GLU cc_start: 0.6628 (OUTLIER) cc_final: 0.6342 (tt0) REVERT: H 119 ARG cc_start: 0.6485 (mtm180) cc_final: 0.6202 (mtt180) REVERT: H 129 GLU cc_start: 0.4425 (mm-30) cc_final: 0.3901 (mp0) REVERT: H 137 LYS cc_start: 0.5002 (ptmm) cc_final: 0.4602 (tptt) REVERT: H 139 GLU cc_start: 0.6410 (mt-10) cc_final: 0.5305 (mm-30) REVERT: H 149 LYS cc_start: 0.6128 (OUTLIER) cc_final: 0.5886 (ttpp) REVERT: I 3 MET cc_start: 0.7395 (OUTLIER) cc_final: 0.7022 (tpt) REVERT: I 26 THR cc_start: 0.7558 (m) cc_final: 0.7110 (p) REVERT: I 43 GLU cc_start: 0.7762 (mm-30) cc_final: 0.7436 (mm-30) REVERT: I 50 LYS cc_start: 0.6156 (ttpt) cc_final: 0.5716 (ttpt) REVERT: I 69 LYS cc_start: 0.6233 (mtpp) cc_final: 0.5577 (tptm) REVERT: I 76 GLN cc_start: 0.6985 (mt0) cc_final: 0.6416 (tt0) REVERT: I 89 LYS cc_start: 0.6280 (ptmt) cc_final: 0.5807 (ttpp) REVERT: I 111 MET cc_start: 0.8135 (ptp) cc_final: 0.7838 (ptp) REVERT: I 114 ARG cc_start: 0.6500 (ttm110) cc_final: 0.5843 (ttp-110) REVERT: J 27 LYS cc_start: 0.5397 (OUTLIER) cc_final: 0.5161 (pttt) REVERT: J 85 ARG cc_start: 0.6252 (OUTLIER) cc_final: 0.5835 (mtt180) REVERT: J 88 MET cc_start: 0.5664 (OUTLIER) cc_final: 0.4992 (mtt) REVERT: J 91 ASP cc_start: 0.5007 (t70) cc_final: 0.4772 (t0) REVERT: J 104 VAL cc_start: 0.7104 (t) cc_final: 0.6856 (t) REVERT: K 7 ARG cc_start: 0.5277 (OUTLIER) cc_final: 0.3916 (mtm180) REVERT: K 11 LYS cc_start: 0.7047 (mttt) cc_final: 0.6548 (mmtt) REVERT: K 75 ASP cc_start: 0.4747 (OUTLIER) cc_final: 0.3993 (p0) REVERT: L 83 GLU cc_start: 0.6543 (mt-10) cc_final: 0.6330 (mt-10) REVERT: L 98 ARG cc_start: 0.5802 (mtt-85) cc_final: 0.5492 (mtm-85) REVERT: L 105 PHE cc_start: 0.6574 (m-80) cc_final: 0.6061 (m-80) REVERT: L 106 ARG cc_start: 0.4645 (ttt180) cc_final: 0.4175 (tpt90) REVERT: M 10 LYS cc_start: 0.6338 (tttt) cc_final: 0.5848 (tttm) REVERT: M 40 THR cc_start: 0.8005 (t) cc_final: 0.7398 (p) REVERT: M 43 LYS cc_start: 0.7434 (ptpt) cc_final: 0.7003 (pttt) REVERT: M 49 LEU cc_start: 0.7485 (mt) cc_final: 0.7100 (mm) REVERT: M 64 THR cc_start: 0.8191 (m) cc_final: 0.7744 (p) REVERT: M 88 LYS cc_start: 0.7033 (OUTLIER) cc_final: 0.6082 (tttt) REVERT: M 109 ASP cc_start: 0.6956 (OUTLIER) cc_final: 0.6661 (m-30) REVERT: M 111 LYS cc_start: 0.7322 (mmmt) cc_final: 0.7070 (mmtm) REVERT: N 13 LYS cc_start: 0.5977 (OUTLIER) cc_final: 0.5659 (mtmt) REVERT: N 78 LYS cc_start: 0.5641 (tttm) cc_final: 0.4943 (ptpt) REVERT: N 81 MET cc_start: 0.7269 (mtm) cc_final: 0.6388 (mtm) REVERT: N 93 ARG cc_start: 0.5901 (mmt-90) cc_final: 0.5069 (mmp80) REVERT: N 110 LYS cc_start: 0.7328 (OUTLIER) cc_final: 0.6717 (mttm) REVERT: O 39 GLU cc_start: 0.4965 (OUTLIER) cc_final: 0.4496 (tp30) REVERT: P 61 SER cc_start: 0.7373 (m) cc_final: 0.7080 (p) REVERT: Q 1 MET cc_start: 0.6740 (pmm) cc_final: 0.6141 (pmm) REVERT: R 6 ARG cc_start: 0.4959 (OUTLIER) cc_final: 0.4269 (ttp-170) REVERT: R 11 ARG cc_start: 0.6581 (ttm110) cc_final: 0.6065 (mmt-90) REVERT: R 40 ARG cc_start: 0.6531 (OUTLIER) cc_final: 0.5981 (mtp180) REVERT: S 16 GLU cc_start: 0.4009 (OUTLIER) cc_final: 0.3769 (mm-30) REVERT: T 44 MET cc_start: 0.6125 (mtt) cc_final: 0.5729 (mtt) REVERT: U 24 ARG cc_start: 0.7186 (mmm160) cc_final: 0.6865 (mmm160) REVERT: U 55 GLN cc_start: 0.7089 (tt0) cc_final: 0.6604 (tt0) REVERT: V 33 ARG cc_start: 0.5488 (mtt90) cc_final: 0.4989 (mmm160) REVERT: V 36 GLU cc_start: 0.6880 (OUTLIER) cc_final: 0.6523 (mt-10) REVERT: V 47 ARG cc_start: 0.5779 (ptt90) cc_final: 0.5377 (ptt-90) REVERT: V 49 LYS cc_start: 0.6514 (tptp) cc_final: 0.6277 (tptp) REVERT: W 13 HIS cc_start: 0.2186 (OUTLIER) cc_final: 0.1821 (m90) REVERT: W 143 ARG cc_start: 0.5707 (OUTLIER) cc_final: 0.5144 (mpp-170) REVERT: W 155 GLU cc_start: 0.5985 (tp30) cc_final: 0.5513 (mt-10) REVERT: W 169 ASP cc_start: 0.4739 (t0) cc_final: 0.4302 (m-30) REVERT: W 269 LYS cc_start: 0.7698 (tptp) cc_final: 0.7434 (tptt) REVERT: W 287 GLN cc_start: 0.5409 (mt0) cc_final: 0.4888 (tm130) REVERT: W 317 VAL cc_start: 0.7784 (OUTLIER) cc_final: 0.7514 (p) REVERT: W 318 THR cc_start: 0.7878 (OUTLIER) cc_final: 0.7647 (m) REVERT: W 330 ASP cc_start: 0.5416 (m-30) cc_final: 0.4837 (p0) REVERT: W 336 LYS cc_start: 0.6451 (mttt) cc_final: 0.6053 (mmmt) REVERT: c 5 LYS cc_start: 0.7093 (tttp) cc_final: 0.6439 (tptp) REVERT: c 97 LYS cc_start: 0.7371 (mtpp) cc_final: 0.6614 (mmpt) REVERT: c 111 LYS cc_start: 0.6711 (OUTLIER) cc_final: 0.6128 (ptpt) REVERT: c 181 MET cc_start: 0.8201 (tpp) cc_final: 0.7727 (mmm) REVERT: c 182 ARG cc_start: 0.8442 (OUTLIER) cc_final: 0.8047 (ttt90) REVERT: c 199 GLU cc_start: 0.7460 (mt-10) cc_final: 0.6524 (pm20) REVERT: c 203 ARG cc_start: 0.7670 (ptt90) cc_final: 0.7264 (ptp-110) REVERT: c 269 ARG cc_start: 0.7329 (ttp-170) cc_final: 0.6906 (ttp80) REVERT: d 1 MET cc_start: 0.4017 (OUTLIER) cc_final: 0.2935 (mtt) REVERT: d 7 LYS cc_start: 0.8036 (ttmt) cc_final: 0.7404 (tttp) REVERT: d 17 GLU cc_start: 0.6397 (pm20) cc_final: 0.5984 (mt-10) REVERT: d 70 LYS cc_start: 0.7051 (tttt) cc_final: 0.6663 (tttt) REVERT: d 128 ARG cc_start: 0.7966 (OUTLIER) cc_final: 0.7312 (mtp180) REVERT: e 21 ARG cc_start: 0.6166 (OUTLIER) cc_final: 0.5698 (ptm160) REVERT: e 22 ASP cc_start: 0.6869 (OUTLIER) cc_final: 0.6219 (m-30) REVERT: e 132 LYS cc_start: 0.6964 (tttm) cc_final: 0.6745 (ttpt) REVERT: f 30 ARG cc_start: 0.6060 (mpp80) cc_final: 0.5486 (mtm-85) REVERT: f 60 ILE cc_start: 0.7308 (mt) cc_final: 0.6939 (mm) REVERT: f 88 LYS cc_start: 0.7559 (OUTLIER) cc_final: 0.7252 (ptpt) REVERT: f 125 ARG cc_start: 0.5298 (tpp-160) cc_final: 0.4922 (mmp-170) REVERT: f 129 SER cc_start: 0.7455 (m) cc_final: 0.7079 (t) REVERT: g 9 VAL cc_start: 0.4268 (m) cc_final: 0.3698 (p) REVERT: g 25 THR cc_start: 0.5552 (m) cc_final: 0.5132 (p) REVERT: g 51 THR cc_start: 0.5427 (m) cc_final: 0.4959 (p) REVERT: g 74 SER cc_start: 0.6863 (m) cc_final: 0.6609 (t) REVERT: g 86 LYS cc_start: 0.6969 (OUTLIER) cc_final: 0.5765 (tttm) REVERT: g 95 ARG cc_start: 0.6041 (mtm110) cc_final: 0.5465 (mtm-85) REVERT: h 21 VAL cc_start: 0.5548 (OUTLIER) cc_final: 0.5347 (t) REVERT: i 34 ARG cc_start: 0.7613 (ttt-90) cc_final: 0.7312 (mtp85) REVERT: i 61 LYS cc_start: 0.7145 (mttt) cc_final: 0.6742 (mmtm) REVERT: i 95 ARG cc_start: 0.6096 (ttt180) cc_final: 0.5466 (mpt-90) REVERT: i 96 ARG cc_start: 0.6619 (ptt-90) cc_final: 0.4833 (mmm-85) REVERT: i 118 MET cc_start: 0.8341 (mtt) cc_final: 0.8113 (mtt) REVERT: i 128 ASN cc_start: 0.7775 (t0) cc_final: 0.7509 (t0) REVERT: j 17 ARG cc_start: 0.7115 (mmt90) cc_final: 0.6655 (mmm160) REVERT: j 29 HIS cc_start: 0.7242 (m-70) cc_final: 0.6877 (m90) REVERT: j 45 GLU cc_start: 0.7312 (mt-10) cc_final: 0.7050 (mt-10) REVERT: j 51 LYS cc_start: 0.7442 (mtpp) cc_final: 0.7016 (mttt) REVERT: j 53 LYS cc_start: 0.6907 (mptm) cc_final: 0.6129 (tttm) REVERT: j 88 ASN cc_start: 0.6920 (m110) cc_final: 0.6228 (t0) REVERT: j 89 ASN cc_start: 0.6444 (m-40) cc_final: 0.5878 (t0) REVERT: j 98 ARG cc_start: 0.7029 (mmt-90) cc_final: 0.6499 (mtm180) REVERT: j 105 ARG cc_start: 0.5897 (OUTLIER) cc_final: 0.5346 (mtt-85) REVERT: j 114 LYS cc_start: 0.6132 (mppt) cc_final: 0.5743 (mmpt) REVERT: k 141 LYS cc_start: 0.6544 (tmtm) cc_final: 0.5703 (mtmt) REVERT: l 1 MET cc_start: 0.5944 (OUTLIER) cc_final: 0.5546 (ttp) REVERT: l 6 ARG cc_start: 0.6751 (mtt180) cc_final: 0.6383 (mtm110) REVERT: l 47 GLU cc_start: 0.7629 (tp30) cc_final: 0.7426 (tp30) REVERT: l 110 GLU cc_start: 0.6869 (tt0) cc_final: 0.6471 (tm-30) REVERT: m 18 GLN cc_start: 0.8115 (tt0) cc_final: 0.7805 (tt0) REVERT: m 72 ASP cc_start: 0.7652 (t0) cc_final: 0.7252 (t70) REVERT: n 13 ARG cc_start: 0.6580 (tpp-160) cc_final: 0.5684 (ttp80) REVERT: n 19 GLN cc_start: 0.7333 (tt0) cc_final: 0.6457 (tt0) REVERT: n 20 GLU cc_start: 0.6092 (pt0) cc_final: 0.5668 (mt-10) REVERT: n 56 LYS cc_start: 0.5751 (mptt) cc_final: 0.5154 (mtmt) REVERT: n 81 ARG cc_start: 0.7228 (OUTLIER) cc_final: 0.5789 (mtm-85) REVERT: n 104 GLN cc_start: 0.7760 (tt0) cc_final: 0.7422 (tt0) REVERT: o 6 LYS cc_start: 0.6129 (ttpp) cc_final: 0.5634 (tmmt) REVERT: o 7 GLN cc_start: 0.6534 (tp40) cc_final: 0.6231 (tp40) REVERT: o 10 GLN cc_start: 0.6988 (mm-40) cc_final: 0.6213 (mt0) REVERT: o 11 GLU cc_start: 0.7343 (pt0) cc_final: 0.6819 (pt0) REVERT: o 63 LYS cc_start: 0.7611 (ptmm) cc_final: 0.7086 (pttt) REVERT: o 68 GLU cc_start: 0.5886 (mm-30) cc_final: 0.5548 (mp0) REVERT: o 70 VAL cc_start: 0.7874 (OUTLIER) cc_final: 0.7575 (p) REVERT: o 89 ARG cc_start: 0.7150 (mtm180) cc_final: 0.6028 (mmt180) REVERT: o 112 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7596 (mt-10) REVERT: p 9 ILE cc_start: 0.7791 (OUTLIER) cc_final: 0.7562 (mp) REVERT: p 11 ARG cc_start: 0.6933 (tpm170) cc_final: 0.6288 (ttm110) REVERT: p 85 LYS cc_start: 0.7221 (mttt) cc_final: 0.6972 (mmtm) REVERT: p 104 VAL cc_start: 0.6541 (t) cc_final: 0.6267 (m) REVERT: p 112 LYS cc_start: 0.6910 (OUTLIER) cc_final: 0.6587 (tppp) REVERT: q 60 LYS cc_start: 0.7210 (mtmt) cc_final: 0.6500 (mtpp) REVERT: q 73 LYS cc_start: 0.7894 (mmtp) cc_final: 0.7306 (mmpt) REVERT: r 28 LYS cc_start: 0.7039 (mtpt) cc_final: 0.6064 (mmtm) REVERT: r 68 ASP cc_start: 0.6730 (m-30) cc_final: 0.6484 (m-30) REVERT: r 73 LYS cc_start: 0.7619 (mttm) cc_final: 0.7299 (mtpm) REVERT: r 86 MET cc_start: 0.8041 (tpp) cc_final: 0.7276 (ttp) REVERT: s 5 GLU cc_start: 0.6623 (mt-10) cc_final: 0.5633 (pp20) REVERT: s 9 LYS cc_start: 0.6846 (mmtt) cc_final: 0.6435 (mtpt) REVERT: s 18 GLU cc_start: 0.7030 (mt-10) cc_final: 0.5976 (mp0) REVERT: s 33 LYS cc_start: 0.7468 (tttt) cc_final: 0.6677 (mttp) REVERT: s 50 LEU cc_start: 0.7366 (mt) cc_final: 0.7156 (mp) REVERT: s 51 PHE cc_start: 0.7080 (m-10) cc_final: 0.6717 (m-10) REVERT: s 56 GLU cc_start: 0.7282 (tt0) cc_final: 0.6999 (tt0) REVERT: s 69 ARG cc_start: 0.6646 (mtt-85) cc_final: 0.5955 (mtm-85) REVERT: t 7 ARG cc_start: 0.6186 (ttt180) cc_final: 0.5447 (ttm110) REVERT: t 10 GLU cc_start: 0.7036 (OUTLIER) cc_final: 0.5714 (pm20) REVERT: t 37 GLU cc_start: 0.6362 (pp20) cc_final: 0.5958 (tm-30) REVERT: t 43 LYS cc_start: 0.7214 (mtmm) cc_final: 0.6959 (mttp) REVERT: t 72 ILE cc_start: 0.7388 (tp) cc_final: 0.7048 (tt) REVERT: t 86 ARG cc_start: 0.7524 (mtm-85) cc_final: 0.7066 (mtm-85) REVERT: u 10 LYS cc_start: 0.6367 (mttp) cc_final: 0.5645 (mmmt) REVERT: u 43 ASP cc_start: 0.7399 (t0) cc_final: 0.6788 (t0) REVERT: u 46 LYS cc_start: 0.6927 (mmtp) cc_final: 0.6470 (mttm) REVERT: v 70 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7399 (mp0) REVERT: v 83 GLU cc_start: 0.6678 (mm-30) cc_final: 0.6121 (mt-10) REVERT: w 54 LYS cc_start: 0.7537 (OUTLIER) cc_final: 0.6978 (tttp) REVERT: x 24 GLU cc_start: 0.6856 (tt0) cc_final: 0.6627 (tt0) REVERT: y 56 LYS cc_start: 0.7457 (pttt) cc_final: 0.7135 (ptmt) outliers start: 196 outliers final: 109 residues processed: 1029 average time/residue: 2.4406 time to fit residues: 3481.3717 Evaluate side-chains 1047 residues out of total 4889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 889 time to evaluate : 6.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 28 ARG Chi-restraints excluded: chain 0 residue 37 LYS Chi-restraints excluded: chain 1 residue 41 ARG Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 105 LYS Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 143 LYS Chi-restraints excluded: chain D residue 88 ARG Chi-restraints excluded: chain D residue 132 ARG Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 177 LYS Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain F residue 14 LYS Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain G residue 37 HIS Chi-restraints excluded: chain G residue 62 MET Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain G residue 98 GLU Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 75 VAL Chi-restraints excluded: chain H residue 106 GLU Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 149 LYS Chi-restraints excluded: chain I residue 3 MET Chi-restraints excluded: chain I residue 90 ASP Chi-restraints excluded: chain J residue 27 LYS Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 73 SER Chi-restraints excluded: chain J residue 85 ARG Chi-restraints excluded: chain J residue 88 MET Chi-restraints excluded: chain J residue 107 ASP Chi-restraints excluded: chain K residue 7 ARG Chi-restraints excluded: chain K residue 71 LEU Chi-restraints excluded: chain K residue 75 ASP Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 129 VAL Chi-restraints excluded: chain M residue 3 THR Chi-restraints excluded: chain M residue 86 ARG Chi-restraints excluded: chain M residue 88 LYS Chi-restraints excluded: chain M residue 109 ASP Chi-restraints excluded: chain N residue 11 ASP Chi-restraints excluded: chain N residue 13 LYS Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 27 LYS Chi-restraints excluded: chain N residue 68 ASP Chi-restraints excluded: chain N residue 73 ILE Chi-restraints excluded: chain N residue 95 LEU Chi-restraints excluded: chain N residue 110 LYS Chi-restraints excluded: chain N residue 113 ARG Chi-restraints excluded: chain O residue 5 SER Chi-restraints excluded: chain O residue 23 LYS Chi-restraints excluded: chain O residue 39 GLU Chi-restraints excluded: chain O residue 83 LYS Chi-restraints excluded: chain P residue 83 GLU Chi-restraints excluded: chain R residue 6 ARG Chi-restraints excluded: chain R residue 29 VAL Chi-restraints excluded: chain R residue 39 LYS Chi-restraints excluded: chain R residue 40 ARG Chi-restraints excluded: chain R residue 42 THR Chi-restraints excluded: chain R residue 67 LEU Chi-restraints excluded: chain R residue 72 SER Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain S residue 16 GLU Chi-restraints excluded: chain T residue 11 ILE Chi-restraints excluded: chain T residue 70 LYS Chi-restraints excluded: chain U residue 23 SER Chi-restraints excluded: chain U residue 69 LYS Chi-restraints excluded: chain V residue 3 VAL Chi-restraints excluded: chain V residue 36 GLU Chi-restraints excluded: chain W residue 13 HIS Chi-restraints excluded: chain W residue 19 VAL Chi-restraints excluded: chain W residue 77 MET Chi-restraints excluded: chain W residue 109 ARG Chi-restraints excluded: chain W residue 113 LEU Chi-restraints excluded: chain W residue 143 ARG Chi-restraints excluded: chain W residue 317 VAL Chi-restraints excluded: chain W residue 318 THR Chi-restraints excluded: chain W residue 325 THR Chi-restraints excluded: chain W residue 356 LEU Chi-restraints excluded: chain c residue 111 LYS Chi-restraints excluded: chain c residue 115 GLN Chi-restraints excluded: chain c residue 129 THR Chi-restraints excluded: chain c residue 165 VAL Chi-restraints excluded: chain c residue 182 ARG Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 91 THR Chi-restraints excluded: chain d residue 128 ARG Chi-restraints excluded: chain e residue 12 LEU Chi-restraints excluded: chain e residue 21 ARG Chi-restraints excluded: chain e residue 22 ASP Chi-restraints excluded: chain e residue 126 VAL Chi-restraints excluded: chain e residue 144 GLU Chi-restraints excluded: chain f residue 4 LEU Chi-restraints excluded: chain f residue 50 LEU Chi-restraints excluded: chain f residue 88 LYS Chi-restraints excluded: chain f residue 120 LYS Chi-restraints excluded: chain g residue 15 VAL Chi-restraints excluded: chain g residue 36 THR Chi-restraints excluded: chain g residue 47 ASP Chi-restraints excluded: chain g residue 86 LYS Chi-restraints excluded: chain g residue 87 LEU Chi-restraints excluded: chain g residue 106 SER Chi-restraints excluded: chain g residue 122 THR Chi-restraints excluded: chain g residue 155 GLU Chi-restraints excluded: chain g residue 171 THR Chi-restraints excluded: chain h residue 21 VAL Chi-restraints excluded: chain i residue 106 LYS Chi-restraints excluded: chain i residue 138 GLN Chi-restraints excluded: chain j residue 76 VAL Chi-restraints excluded: chain j residue 105 ARG Chi-restraints excluded: chain k residue 103 ILE Chi-restraints excluded: chain l residue 1 MET Chi-restraints excluded: chain l residue 30 SER Chi-restraints excluded: chain l residue 63 ILE Chi-restraints excluded: chain l residue 80 VAL Chi-restraints excluded: chain m residue 15 SER Chi-restraints excluded: chain n residue 81 ARG Chi-restraints excluded: chain o residue 34 GLU Chi-restraints excluded: chain o residue 70 VAL Chi-restraints excluded: chain o residue 85 SER Chi-restraints excluded: chain o residue 104 THR Chi-restraints excluded: chain o residue 112 GLU Chi-restraints excluded: chain p residue 9 ILE Chi-restraints excluded: chain p residue 22 LYS Chi-restraints excluded: chain p residue 112 LYS Chi-restraints excluded: chain q residue 33 VAL Chi-restraints excluded: chain q residue 64 VAL Chi-restraints excluded: chain q residue 99 THR Chi-restraints excluded: chain r residue 66 ILE Chi-restraints excluded: chain r residue 70 LYS Chi-restraints excluded: chain t residue 10 GLU Chi-restraints excluded: chain u residue 53 LYS Chi-restraints excluded: chain u residue 58 SER Chi-restraints excluded: chain u residue 61 LEU Chi-restraints excluded: chain u residue 62 THR Chi-restraints excluded: chain u residue 65 VAL Chi-restraints excluded: chain u residue 73 LYS Chi-restraints excluded: chain v residue 30 SER Chi-restraints excluded: chain v residue 70 GLU Chi-restraints excluded: chain w residue 54 LYS Chi-restraints excluded: chain x residue 4 LYS Chi-restraints excluded: chain x residue 40 SER Chi-restraints excluded: chain y residue 19 LYS Chi-restraints excluded: chain y residue 41 THR Chi-restraints excluded: chain z residue 30 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1023 random chunks: chunk 610 optimal weight: 6.9990 chunk 393 optimal weight: 0.9990 chunk 588 optimal weight: 7.9990 chunk 297 optimal weight: 10.0000 chunk 193 optimal weight: 1.9990 chunk 191 optimal weight: 0.0030 chunk 626 optimal weight: 7.9990 chunk 671 optimal weight: 10.0000 chunk 487 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 775 optimal weight: 4.9990 overall best weight: 2.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 29 GLN C 18 HIS ** C 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 198 HIS F 19 ASN F 70 ASN F 77 ASN ** F 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 3 HIS J 110 GLN L 40 ASN ** L 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 37 ASN P 46 HIS Q 63 GLN U 68 HIS W 248 HIS c 117 GLN e 165 HIS g 64 GLN i 136 GLN k 104 GLN ** q 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 40 ASN u 12 GLN x 58 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 156812 Z= 0.277 Angle : 0.734 15.687 234226 Z= 0.388 Chirality : 0.040 0.381 29769 Planarity : 0.007 0.147 12793 Dihedral : 23.273 177.200 77640 Min Nonbonded Distance : 1.775 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.70 % Favored : 97.16 % Rotamer: Outliers : 3.85 % Allowed : 15.22 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.11), residues: 5853 helix: 0.83 (0.11), residues: 2058 sheet: -0.27 (0.14), residues: 1182 loop : -0.28 (0.12), residues: 2613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 201 HIS 0.010 0.001 HIS P 46 PHE 0.020 0.002 PHE m 21 TYR 0.025 0.002 TYR r 38 ARG 0.007 0.001 ARG F 93 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11706 Ramachandran restraints generated. 5853 Oldfield, 0 Emsley, 5853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11706 Ramachandran restraints generated. 5853 Oldfield, 0 Emsley, 5853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1096 residues out of total 4889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 908 time to evaluate : 6.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 33 LYS cc_start: 0.6469 (tptt) cc_final: 0.6130 (mmtp) REVERT: 1 1 MET cc_start: 0.6793 (mpp) cc_final: 0.6502 (mmm) REVERT: 1 41 ARG cc_start: 0.7248 (OUTLIER) cc_final: 0.6036 (ppt170) REVERT: 2 52 LYS cc_start: 0.5922 (tttm) cc_final: 0.5520 (tppt) REVERT: 3 8 LYS cc_start: 0.7541 (mttt) cc_final: 0.6811 (mtmt) REVERT: 3 12 ARG cc_start: 0.6576 (ptt180) cc_final: 0.5700 (pmt170) REVERT: 3 15 LYS cc_start: 0.7571 (mttt) cc_final: 0.6775 (mttt) REVERT: C 49 MET cc_start: 0.4575 (mtp) cc_final: 0.4244 (mtt) REVERT: C 105 LYS cc_start: 0.6805 (OUTLIER) cc_final: 0.6453 (ptpt) REVERT: C 143 LYS cc_start: 0.4368 (OUTLIER) cc_final: 0.4105 (tttt) REVERT: C 178 ASN cc_start: 0.6116 (t0) cc_final: 0.5856 (m-40) REVERT: D 27 LYS cc_start: 0.4896 (pmtt) cc_final: 0.4695 (tmtp) REVERT: D 28 GLU cc_start: 0.5975 (mt-10) cc_final: 0.5281 (pm20) REVERT: D 46 GLU cc_start: 0.5440 (tp30) cc_final: 0.4913 (mm-30) REVERT: D 88 ARG cc_start: 0.5070 (OUTLIER) cc_final: 0.4655 (ttt-90) REVERT: D 122 SER cc_start: 0.6472 (m) cc_final: 0.6170 (p) REVERT: D 129 MET cc_start: 0.6168 (mmm) cc_final: 0.5357 (mtm) REVERT: D 132 ARG cc_start: 0.5736 (OUTLIER) cc_final: 0.5424 (ptm-80) REVERT: D 134 MET cc_start: 0.6217 (mtp) cc_final: 0.5933 (mtp) REVERT: E 20 PHE cc_start: 0.6328 (m-80) cc_final: 0.6062 (m-80) REVERT: E 29 ASP cc_start: 0.5259 (OUTLIER) cc_final: 0.4901 (p0) REVERT: E 44 ARG cc_start: 0.4668 (ttm110) cc_final: 0.4290 (tmm160) REVERT: E 73 ARG cc_start: 0.6441 (ttp80) cc_final: 0.5524 (ttm-80) REVERT: E 78 GLU cc_start: 0.6654 (tt0) cc_final: 0.6301 (tp30) REVERT: E 113 GLU cc_start: 0.7065 (tp30) cc_final: 0.6725 (tt0) REVERT: E 119 SER cc_start: 0.6615 (t) cc_final: 0.6304 (p) REVERT: E 124 MET cc_start: 0.6742 (mtm) cc_final: 0.6360 (mtt) REVERT: E 128 ARG cc_start: 0.5196 (mtt-85) cc_final: 0.4744 (mtt90) REVERT: E 148 LYS cc_start: 0.5023 (ttpp) cc_final: 0.4056 (tptp) REVERT: E 151 LYS cc_start: 0.4377 (pptt) cc_final: 0.4051 (mttm) REVERT: E 171 LEU cc_start: 0.5851 (OUTLIER) cc_final: 0.5590 (mt) REVERT: F 45 ARG cc_start: 0.6425 (mtp-110) cc_final: 0.5814 (mmm160) REVERT: F 55 GLU cc_start: 0.6389 (mt-10) cc_final: 0.6145 (mt-10) REVERT: F 61 GLN cc_start: 0.6294 (tm-30) cc_final: 0.5555 (tm130) REVERT: F 65 GLU cc_start: 0.6190 (mt-10) cc_final: 0.5757 (mm-30) REVERT: F 70 ASN cc_start: 0.5690 (m-40) cc_final: 0.5208 (m-40) REVERT: F 116 GLU cc_start: 0.6973 (tt0) cc_final: 0.6480 (tt0) REVERT: F 156 LYS cc_start: 0.6675 (ptpp) cc_final: 0.6282 (pttt) REVERT: G 15 SER cc_start: 0.5954 (t) cc_final: 0.5396 (m) REVERT: G 56 LYS cc_start: 0.6727 (mtpt) cc_final: 0.6030 (mttp) REVERT: G 62 MET cc_start: 0.6752 (OUTLIER) cc_final: 0.6537 (ptm) REVERT: G 92 THR cc_start: 0.5988 (OUTLIER) cc_final: 0.5659 (p) REVERT: H 41 SER cc_start: 0.6133 (p) cc_final: 0.5734 (m) REVERT: H 79 ARG cc_start: 0.3651 (ttt180) cc_final: 0.3322 (mtt90) REVERT: H 92 ARG cc_start: 0.4778 (mpp-170) cc_final: 0.4389 (mpt180) REVERT: H 96 ARG cc_start: 0.5975 (mtt90) cc_final: 0.5750 (mtt180) REVERT: H 106 GLU cc_start: 0.6584 (OUTLIER) cc_final: 0.6315 (tt0) REVERT: H 119 ARG cc_start: 0.6554 (mtm180) cc_final: 0.6214 (mtt180) REVERT: H 129 GLU cc_start: 0.4416 (mm-30) cc_final: 0.3895 (mp0) REVERT: H 137 LYS cc_start: 0.4914 (ptmm) cc_final: 0.4467 (tptt) REVERT: H 139 GLU cc_start: 0.6420 (mt-10) cc_final: 0.5320 (mm-30) REVERT: I 26 THR cc_start: 0.7532 (m) cc_final: 0.7066 (p) REVERT: I 43 GLU cc_start: 0.7776 (mm-30) cc_final: 0.7393 (mm-30) REVERT: I 50 LYS cc_start: 0.6117 (ttpt) cc_final: 0.5662 (ttpt) REVERT: I 69 LYS cc_start: 0.6279 (mtpp) cc_final: 0.5613 (tptm) REVERT: I 76 GLN cc_start: 0.7031 (OUTLIER) cc_final: 0.6471 (tt0) REVERT: I 89 LYS cc_start: 0.6399 (ptmt) cc_final: 0.5833 (ttpp) REVERT: I 111 MET cc_start: 0.8124 (ptp) cc_final: 0.7808 (ptp) REVERT: I 114 ARG cc_start: 0.6500 (ttm110) cc_final: 0.5827 (ttp-110) REVERT: J 27 LYS cc_start: 0.5503 (OUTLIER) cc_final: 0.5272 (pttt) REVERT: J 85 ARG cc_start: 0.6254 (OUTLIER) cc_final: 0.5868 (mtt180) REVERT: J 88 MET cc_start: 0.5574 (OUTLIER) cc_final: 0.4892 (mtt) REVERT: J 91 ASP cc_start: 0.5019 (t70) cc_final: 0.4794 (t0) REVERT: J 104 VAL cc_start: 0.7143 (t) cc_final: 0.6886 (t) REVERT: K 7 ARG cc_start: 0.5242 (OUTLIER) cc_final: 0.3929 (mtm180) REVERT: K 11 LYS cc_start: 0.7026 (mttt) cc_final: 0.6547 (mmtt) REVERT: K 75 ASP cc_start: 0.4739 (OUTLIER) cc_final: 0.3988 (p0) REVERT: L 83 GLU cc_start: 0.6512 (mt-10) cc_final: 0.6308 (mt-10) REVERT: L 98 ARG cc_start: 0.5784 (mtt-85) cc_final: 0.5458 (mtm-85) REVERT: L 105 PHE cc_start: 0.6569 (m-80) cc_final: 0.6006 (m-80) REVERT: L 106 ARG cc_start: 0.4645 (ttt180) cc_final: 0.4132 (tpt90) REVERT: M 10 LYS cc_start: 0.6336 (tttt) cc_final: 0.5855 (tttm) REVERT: M 40 THR cc_start: 0.8011 (t) cc_final: 0.7405 (p) REVERT: M 43 LYS cc_start: 0.7379 (ptpt) cc_final: 0.6962 (pttt) REVERT: M 49 LEU cc_start: 0.7480 (mt) cc_final: 0.7101 (mm) REVERT: M 54 ARG cc_start: 0.7086 (ttm-80) cc_final: 0.6126 (ttm-80) REVERT: M 64 THR cc_start: 0.8188 (m) cc_final: 0.7696 (p) REVERT: M 75 GLN cc_start: 0.7223 (OUTLIER) cc_final: 0.6797 (pm20) REVERT: M 76 GLU cc_start: 0.6128 (tt0) cc_final: 0.5551 (tt0) REVERT: M 88 LYS cc_start: 0.7061 (OUTLIER) cc_final: 0.6035 (tttt) REVERT: M 94 ARG cc_start: 0.7459 (OUTLIER) cc_final: 0.7250 (mtm180) REVERT: M 109 ASP cc_start: 0.6988 (OUTLIER) cc_final: 0.6690 (m-30) REVERT: M 111 LYS cc_start: 0.7318 (mmmt) cc_final: 0.7065 (mmtm) REVERT: M 121 ARG cc_start: 0.6547 (ttt-90) cc_final: 0.6145 (ttt180) REVERT: N 13 LYS cc_start: 0.5960 (OUTLIER) cc_final: 0.5635 (mtmt) REVERT: N 78 LYS cc_start: 0.5705 (tttm) cc_final: 0.4978 (ptpt) REVERT: N 81 MET cc_start: 0.7247 (mtm) cc_final: 0.6368 (mtm) REVERT: N 93 ARG cc_start: 0.5870 (mmt-90) cc_final: 0.5035 (mmp80) REVERT: N 110 LYS cc_start: 0.7261 (OUTLIER) cc_final: 0.6679 (mttm) REVERT: N 113 ARG cc_start: 0.5092 (OUTLIER) cc_final: 0.4438 (mmm-85) REVERT: O 39 GLU cc_start: 0.4904 (tm-30) cc_final: 0.4434 (tp30) REVERT: P 61 SER cc_start: 0.7374 (m) cc_final: 0.7081 (p) REVERT: Q 1 MET cc_start: 0.6731 (pmm) cc_final: 0.6128 (pmm) REVERT: R 6 ARG cc_start: 0.5021 (OUTLIER) cc_final: 0.4262 (mmm-85) REVERT: R 11 ARG cc_start: 0.6586 (ttm110) cc_final: 0.6081 (mmt-90) REVERT: R 40 ARG cc_start: 0.6556 (OUTLIER) cc_final: 0.5859 (mtp180) REVERT: R 44 LEU cc_start: 0.7144 (mt) cc_final: 0.6883 (mt) REVERT: S 16 GLU cc_start: 0.4096 (OUTLIER) cc_final: 0.3872 (mm-30) REVERT: S 48 ARG cc_start: 0.6473 (mtp-110) cc_final: 0.5896 (ptm-80) REVERT: T 44 MET cc_start: 0.6138 (mtt) cc_final: 0.5747 (mtt) REVERT: U 24 ARG cc_start: 0.7226 (mmm160) cc_final: 0.6943 (mmm160) REVERT: U 55 GLN cc_start: 0.7102 (tt0) cc_final: 0.6633 (tt0) REVERT: V 21 ARG cc_start: 0.4781 (ttt90) cc_final: 0.4265 (mmm160) REVERT: V 33 ARG cc_start: 0.5621 (mtt90) cc_final: 0.5059 (mmm160) REVERT: V 36 GLU cc_start: 0.6917 (OUTLIER) cc_final: 0.6530 (mt-10) REVERT: V 47 ARG cc_start: 0.5777 (ptt90) cc_final: 0.5393 (ptt-90) REVERT: V 49 LYS cc_start: 0.6561 (tptp) cc_final: 0.6337 (tptp) REVERT: W 13 HIS cc_start: 0.2375 (OUTLIER) cc_final: 0.2045 (m90) REVERT: W 143 ARG cc_start: 0.5847 (OUTLIER) cc_final: 0.5224 (mpp-170) REVERT: W 149 MET cc_start: 0.6800 (mmm) cc_final: 0.6534 (mmm) REVERT: W 155 GLU cc_start: 0.5981 (tp30) cc_final: 0.5507 (mt-10) REVERT: W 169 ASP cc_start: 0.4726 (t0) cc_final: 0.4288 (m-30) REVERT: W 269 LYS cc_start: 0.7693 (tptp) cc_final: 0.7317 (tptt) REVERT: W 285 LYS cc_start: 0.6087 (tttp) cc_final: 0.5655 (ttpt) REVERT: W 287 GLN cc_start: 0.5424 (mt0) cc_final: 0.4885 (tm130) REVERT: W 317 VAL cc_start: 0.7750 (OUTLIER) cc_final: 0.7505 (p) REVERT: W 318 THR cc_start: 0.7879 (OUTLIER) cc_final: 0.7652 (m) REVERT: W 330 ASP cc_start: 0.5385 (m-30) cc_final: 0.4827 (p0) REVERT: W 336 LYS cc_start: 0.6474 (mttt) cc_final: 0.6087 (mmmt) REVERT: W 341 ILE cc_start: 0.7015 (mt) cc_final: 0.6783 (mm) REVERT: c 5 LYS cc_start: 0.7121 (tttp) cc_final: 0.6614 (tptp) REVERT: c 97 LYS cc_start: 0.7379 (mtpp) cc_final: 0.6630 (mmpt) REVERT: c 111 LYS cc_start: 0.6760 (pttm) cc_final: 0.6158 (ptpt) REVERT: c 181 MET cc_start: 0.8088 (tpp) cc_final: 0.7543 (mmm) REVERT: c 182 ARG cc_start: 0.8393 (OUTLIER) cc_final: 0.8039 (ttt90) REVERT: c 199 GLU cc_start: 0.7476 (mt-10) cc_final: 0.6521 (pm20) REVERT: c 203 ARG cc_start: 0.7668 (ptt90) cc_final: 0.7272 (ptp-110) REVERT: c 269 ARG cc_start: 0.7366 (ttp-170) cc_final: 0.6958 (ttp80) REVERT: d 1 MET cc_start: 0.3986 (OUTLIER) cc_final: 0.2894 (mtp) REVERT: d 7 LYS cc_start: 0.7989 (ttmt) cc_final: 0.7363 (ttpp) REVERT: d 17 GLU cc_start: 0.6416 (pm20) cc_final: 0.6010 (mt-10) REVERT: d 70 LYS cc_start: 0.7040 (tttt) cc_final: 0.6658 (tttt) REVERT: d 89 GLU cc_start: 0.6960 (tp30) cc_final: 0.6524 (tt0) REVERT: d 105 LYS cc_start: 0.7755 (mmtt) cc_final: 0.7292 (mmtm) REVERT: d 128 ARG cc_start: 0.7959 (OUTLIER) cc_final: 0.7308 (mtp180) REVERT: e 21 ARG cc_start: 0.6174 (OUTLIER) cc_final: 0.5828 (ptm160) REVERT: e 22 ASP cc_start: 0.6770 (p0) cc_final: 0.6206 (m-30) REVERT: f 30 ARG cc_start: 0.6010 (mpp80) cc_final: 0.5534 (mtm-85) REVERT: f 60 ILE cc_start: 0.7287 (mt) cc_final: 0.6923 (mm) REVERT: f 83 TYR cc_start: 0.5903 (OUTLIER) cc_final: 0.5274 (m-10) REVERT: f 88 LYS cc_start: 0.7531 (OUTLIER) cc_final: 0.7271 (ptpt) REVERT: f 125 ARG cc_start: 0.5339 (tpp-160) cc_final: 0.4968 (mmp-170) REVERT: f 129 SER cc_start: 0.7460 (m) cc_final: 0.7082 (t) REVERT: g 9 VAL cc_start: 0.4361 (m) cc_final: 0.3881 (p) REVERT: g 25 THR cc_start: 0.5552 (m) cc_final: 0.5100 (p) REVERT: g 74 SER cc_start: 0.6755 (m) cc_final: 0.6493 (t) REVERT: g 86 LYS cc_start: 0.6956 (OUTLIER) cc_final: 0.5771 (tttm) REVERT: g 95 ARG cc_start: 0.5992 (mtm110) cc_final: 0.5472 (mtm-85) REVERT: h 21 VAL cc_start: 0.5671 (OUTLIER) cc_final: 0.5468 (t) REVERT: i 34 ARG cc_start: 0.7634 (ttt-90) cc_final: 0.7294 (mtp85) REVERT: i 61 LYS cc_start: 0.7145 (mttt) cc_final: 0.6761 (mmtm) REVERT: i 95 ARG cc_start: 0.6106 (ttt180) cc_final: 0.5475 (mpt-90) REVERT: i 96 ARG cc_start: 0.6602 (ptt-90) cc_final: 0.4800 (mmm-85) REVERT: i 118 MET cc_start: 0.8357 (mtt) cc_final: 0.8146 (mtt) REVERT: i 128 ASN cc_start: 0.7718 (t0) cc_final: 0.7370 (t0) REVERT: j 17 ARG cc_start: 0.7114 (mmt90) cc_final: 0.6654 (mmm160) REVERT: j 29 HIS cc_start: 0.7204 (m-70) cc_final: 0.6840 (m90) REVERT: j 45 GLU cc_start: 0.7284 (mt-10) cc_final: 0.7018 (mt-10) REVERT: j 51 LYS cc_start: 0.7446 (mtpp) cc_final: 0.7013 (mttt) REVERT: j 53 LYS cc_start: 0.6986 (mptm) cc_final: 0.6199 (tttm) REVERT: j 88 ASN cc_start: 0.6859 (OUTLIER) cc_final: 0.6132 (t0) REVERT: j 89 ASN cc_start: 0.6396 (m-40) cc_final: 0.5821 (t0) REVERT: j 98 ARG cc_start: 0.7060 (mmt-90) cc_final: 0.6561 (mtm180) REVERT: j 105 ARG cc_start: 0.5949 (OUTLIER) cc_final: 0.5407 (mtt-85) REVERT: j 114 LYS cc_start: 0.6115 (mppt) cc_final: 0.5725 (mmpt) REVERT: k 141 LYS cc_start: 0.6495 (tmtm) cc_final: 0.5661 (mtmt) REVERT: l 1 MET cc_start: 0.5965 (OUTLIER) cc_final: 0.5569 (ttp) REVERT: l 6 ARG cc_start: 0.6764 (mtt180) cc_final: 0.6380 (mtm110) REVERT: l 110 GLU cc_start: 0.6873 (tt0) cc_final: 0.6511 (tm-30) REVERT: l 136 MET cc_start: 0.5372 (ttp) cc_final: 0.5054 (ttm) REVERT: m 18 GLN cc_start: 0.8100 (tt0) cc_final: 0.7802 (tt0) REVERT: m 72 ASP cc_start: 0.7641 (t0) cc_final: 0.7226 (t70) REVERT: n 13 ARG cc_start: 0.6569 (tpp-160) cc_final: 0.5680 (ttp80) REVERT: n 19 GLN cc_start: 0.7354 (tt0) cc_final: 0.6472 (tt0) REVERT: n 20 GLU cc_start: 0.6025 (pt0) cc_final: 0.5603 (mt-10) REVERT: n 56 LYS cc_start: 0.5761 (mptt) cc_final: 0.5168 (mtmt) REVERT: n 81 ARG cc_start: 0.7176 (OUTLIER) cc_final: 0.5732 (mtm-85) REVERT: n 104 GLN cc_start: 0.7762 (tt0) cc_final: 0.7429 (tt0) REVERT: o 6 LYS cc_start: 0.6166 (ttpp) cc_final: 0.5693 (tmmt) REVERT: o 10 GLN cc_start: 0.6870 (mm-40) cc_final: 0.6121 (mt0) REVERT: o 11 GLU cc_start: 0.7325 (pt0) cc_final: 0.6817 (pt0) REVERT: o 63 LYS cc_start: 0.7636 (ptmm) cc_final: 0.7103 (pttt) REVERT: o 68 GLU cc_start: 0.5849 (mm-30) cc_final: 0.5573 (mp0) REVERT: o 70 VAL cc_start: 0.7895 (OUTLIER) cc_final: 0.7650 (p) REVERT: o 89 ARG cc_start: 0.7133 (mtm180) cc_final: 0.6003 (mmt180) REVERT: o 112 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.7659 (mt-10) REVERT: p 9 ILE cc_start: 0.7710 (OUTLIER) cc_final: 0.7486 (mp) REVERT: p 11 ARG cc_start: 0.6951 (tpm170) cc_final: 0.6335 (ttm110) REVERT: p 85 LYS cc_start: 0.7348 (mttt) cc_final: 0.6978 (mmtm) REVERT: p 104 VAL cc_start: 0.6497 (t) cc_final: 0.6239 (m) REVERT: p 112 LYS cc_start: 0.6940 (OUTLIER) cc_final: 0.6555 (tppp) REVERT: q 60 LYS cc_start: 0.7199 (mtmt) cc_final: 0.6653 (mttm) REVERT: q 73 LYS cc_start: 0.7899 (mmtp) cc_final: 0.7308 (mmpt) REVERT: r 28 LYS cc_start: 0.7087 (mtpt) cc_final: 0.6079 (mmtm) REVERT: r 68 ASP cc_start: 0.6708 (m-30) cc_final: 0.6473 (m-30) REVERT: r 73 LYS cc_start: 0.7588 (mttm) cc_final: 0.7282 (mtpm) REVERT: r 86 MET cc_start: 0.8051 (tpp) cc_final: 0.7296 (ttp) REVERT: s 9 LYS cc_start: 0.6835 (mmtt) cc_final: 0.6415 (mtpt) REVERT: s 18 GLU cc_start: 0.7033 (mt-10) cc_final: 0.5963 (mp0) REVERT: s 26 LYS cc_start: 0.6179 (ttmt) cc_final: 0.5478 (tppp) REVERT: s 33 LYS cc_start: 0.7467 (tttt) cc_final: 0.6670 (mttp) REVERT: s 50 LEU cc_start: 0.7387 (mt) cc_final: 0.7152 (mp) REVERT: s 51 PHE cc_start: 0.7064 (m-10) cc_final: 0.6690 (m-10) REVERT: s 69 ARG cc_start: 0.6681 (mtt-85) cc_final: 0.6094 (mtm110) REVERT: t 7 ARG cc_start: 0.6089 (ttt180) cc_final: 0.5311 (ttm110) REVERT: t 10 GLU cc_start: 0.7038 (OUTLIER) cc_final: 0.5774 (pm20) REVERT: t 37 GLU cc_start: 0.6394 (pp20) cc_final: 0.5992 (tm-30) REVERT: t 43 LYS cc_start: 0.7174 (mtmm) cc_final: 0.6960 (mttp) REVERT: t 72 ILE cc_start: 0.7370 (tp) cc_final: 0.7042 (tt) REVERT: t 86 ARG cc_start: 0.7553 (mtm-85) cc_final: 0.6962 (mtm180) REVERT: u 10 LYS cc_start: 0.6362 (mttp) cc_final: 0.5626 (mmmt) REVERT: u 43 ASP cc_start: 0.7375 (t0) cc_final: 0.6746 (t0) REVERT: u 46 LYS cc_start: 0.6956 (mmtp) cc_final: 0.6474 (mttm) REVERT: v 70 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.7391 (mp0) REVERT: v 83 GLU cc_start: 0.6675 (mm-30) cc_final: 0.6143 (mt-10) REVERT: w 45 ARG cc_start: 0.5857 (ptt-90) cc_final: 0.5637 (ttt-90) REVERT: w 54 LYS cc_start: 0.7535 (OUTLIER) cc_final: 0.6977 (tttp) REVERT: x 24 GLU cc_start: 0.6847 (tt0) cc_final: 0.6596 (tt0) REVERT: y 56 LYS cc_start: 0.7448 (pttt) cc_final: 0.7113 (ptmt) outliers start: 188 outliers final: 98 residues processed: 1020 average time/residue: 2.5151 time to fit residues: 3550.7544 Evaluate side-chains 1039 residues out of total 4889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 891 time to evaluate : 6.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 28 ARG Chi-restraints excluded: chain 0 residue 37 LYS Chi-restraints excluded: chain 1 residue 41 ARG Chi-restraints excluded: chain 4 residue 22 MET Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 105 LYS Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 143 LYS Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain D residue 88 ARG Chi-restraints excluded: chain D residue 132 ARG Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain F residue 14 LYS Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain G residue 37 HIS Chi-restraints excluded: chain G residue 62 MET Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 75 VAL Chi-restraints excluded: chain H residue 106 GLU Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain I residue 76 GLN Chi-restraints excluded: chain I residue 90 ASP Chi-restraints excluded: chain J residue 27 LYS Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 73 SER Chi-restraints excluded: chain J residue 85 ARG Chi-restraints excluded: chain J residue 88 MET Chi-restraints excluded: chain J residue 107 ASP Chi-restraints excluded: chain K residue 7 ARG Chi-restraints excluded: chain K residue 71 LEU Chi-restraints excluded: chain K residue 75 ASP Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 129 VAL Chi-restraints excluded: chain M residue 3 THR Chi-restraints excluded: chain M residue 75 GLN Chi-restraints excluded: chain M residue 86 ARG Chi-restraints excluded: chain M residue 88 LYS Chi-restraints excluded: chain M residue 94 ARG Chi-restraints excluded: chain M residue 109 ASP Chi-restraints excluded: chain N residue 11 ASP Chi-restraints excluded: chain N residue 13 LYS Chi-restraints excluded: chain N residue 16 VAL Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 27 LYS Chi-restraints excluded: chain N residue 68 ASP Chi-restraints excluded: chain N residue 110 LYS Chi-restraints excluded: chain N residue 113 ARG Chi-restraints excluded: chain O residue 5 SER Chi-restraints excluded: chain O residue 23 LYS Chi-restraints excluded: chain O residue 83 LYS Chi-restraints excluded: chain P residue 83 GLU Chi-restraints excluded: chain R residue 6 ARG Chi-restraints excluded: chain R residue 29 VAL Chi-restraints excluded: chain R residue 39 LYS Chi-restraints excluded: chain R residue 40 ARG Chi-restraints excluded: chain R residue 42 THR Chi-restraints excluded: chain R residue 67 LEU Chi-restraints excluded: chain R residue 72 SER Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain S residue 16 GLU Chi-restraints excluded: chain T residue 11 ILE Chi-restraints excluded: chain T residue 70 LYS Chi-restraints excluded: chain U residue 23 SER Chi-restraints excluded: chain U residue 69 LYS Chi-restraints excluded: chain V residue 3 VAL Chi-restraints excluded: chain V residue 36 GLU Chi-restraints excluded: chain W residue 13 HIS Chi-restraints excluded: chain W residue 19 VAL Chi-restraints excluded: chain W residue 109 ARG Chi-restraints excluded: chain W residue 113 LEU Chi-restraints excluded: chain W residue 143 ARG Chi-restraints excluded: chain W residue 162 ILE Chi-restraints excluded: chain W residue 317 VAL Chi-restraints excluded: chain W residue 318 THR Chi-restraints excluded: chain W residue 325 THR Chi-restraints excluded: chain W residue 356 LEU Chi-restraints excluded: chain c residue 115 GLN Chi-restraints excluded: chain c residue 129 THR Chi-restraints excluded: chain c residue 165 VAL Chi-restraints excluded: chain c residue 182 ARG Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 91 THR Chi-restraints excluded: chain d residue 128 ARG Chi-restraints excluded: chain e residue 12 LEU Chi-restraints excluded: chain e residue 21 ARG Chi-restraints excluded: chain e residue 126 VAL Chi-restraints excluded: chain e residue 144 GLU Chi-restraints excluded: chain f residue 4 LEU Chi-restraints excluded: chain f residue 83 TYR Chi-restraints excluded: chain f residue 88 LYS Chi-restraints excluded: chain g residue 15 VAL Chi-restraints excluded: chain g residue 36 THR Chi-restraints excluded: chain g residue 43 VAL Chi-restraints excluded: chain g residue 86 LYS Chi-restraints excluded: chain g residue 87 LEU Chi-restraints excluded: chain g residue 106 SER Chi-restraints excluded: chain g residue 122 THR Chi-restraints excluded: chain g residue 155 GLU Chi-restraints excluded: chain g residue 171 THR Chi-restraints excluded: chain h residue 21 VAL Chi-restraints excluded: chain i residue 106 LYS Chi-restraints excluded: chain j residue 76 VAL Chi-restraints excluded: chain j residue 88 ASN Chi-restraints excluded: chain j residue 105 ARG Chi-restraints excluded: chain k residue 103 ILE Chi-restraints excluded: chain l residue 1 MET Chi-restraints excluded: chain l residue 80 VAL Chi-restraints excluded: chain m residue 15 SER Chi-restraints excluded: chain n residue 81 ARG Chi-restraints excluded: chain o residue 34 GLU Chi-restraints excluded: chain o residue 70 VAL Chi-restraints excluded: chain o residue 85 SER Chi-restraints excluded: chain o residue 104 THR Chi-restraints excluded: chain o residue 112 GLU Chi-restraints excluded: chain p residue 9 ILE Chi-restraints excluded: chain p residue 22 LYS Chi-restraints excluded: chain p residue 112 LYS Chi-restraints excluded: chain q residue 33 VAL Chi-restraints excluded: chain q residue 64 VAL Chi-restraints excluded: chain r residue 66 ILE Chi-restraints excluded: chain r residue 70 LYS Chi-restraints excluded: chain t residue 10 GLU Chi-restraints excluded: chain u residue 53 LYS Chi-restraints excluded: chain u residue 58 SER Chi-restraints excluded: chain u residue 62 THR Chi-restraints excluded: chain u residue 65 VAL Chi-restraints excluded: chain u residue 73 LYS Chi-restraints excluded: chain v residue 30 SER Chi-restraints excluded: chain v residue 70 GLU Chi-restraints excluded: chain w residue 54 LYS Chi-restraints excluded: chain x residue 4 LYS Chi-restraints excluded: chain x residue 40 SER Chi-restraints excluded: chain y residue 19 LYS Chi-restraints excluded: chain y residue 41 THR Chi-restraints excluded: chain z residue 30 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1023 random chunks: chunk 896 optimal weight: 5.9990 chunk 944 optimal weight: 9.9990 chunk 861 optimal weight: 3.9990 chunk 918 optimal weight: 6.9990 chunk 553 optimal weight: 6.9990 chunk 400 optimal weight: 6.9990 chunk 721 optimal weight: 10.0000 chunk 281 optimal weight: 4.9990 chunk 830 optimal weight: 5.9990 chunk 869 optimal weight: 4.9990 chunk 915 optimal weight: 10.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 29 GLN C 18 HIS ** C 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 198 HIS F 19 ASN F 77 ASN ** F 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 3 HIS J 110 GLN ** L 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 46 HIS Q 63 GLN S 54 GLN U 68 HIS W 248 HIS c 117 GLN e 165 HIS g 64 GLN k 104 GLN u 12 GLN x 27 ASN x 58 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.093 156812 Z= 0.438 Angle : 0.916 18.805 234226 Z= 0.465 Chirality : 0.048 0.389 29769 Planarity : 0.008 0.159 12793 Dihedral : 23.395 177.257 77640 Min Nonbonded Distance : 1.723 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.02 % Favored : 96.84 % Rotamer: Outliers : 3.81 % Allowed : 15.65 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.10), residues: 5853 helix: 0.43 (0.11), residues: 2050 sheet: -0.37 (0.14), residues: 1164 loop : -0.41 (0.11), residues: 2639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP C 23 HIS 0.014 0.002 HIS P 46 PHE 0.028 0.003 PHE q 53 TYR 0.029 0.003 TYR r 38 ARG 0.010 0.001 ARG F 93 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11706 Ramachandran restraints generated. 5853 Oldfield, 0 Emsley, 5853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11706 Ramachandran restraints generated. 5853 Oldfield, 0 Emsley, 5853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1083 residues out of total 4889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 897 time to evaluate : 6.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 33 LYS cc_start: 0.6498 (mptt) cc_final: 0.6187 (mmtp) REVERT: 2 52 LYS cc_start: 0.5979 (tttm) cc_final: 0.5572 (tppt) REVERT: 3 8 LYS cc_start: 0.7529 (mttt) cc_final: 0.6833 (mtmt) REVERT: 3 12 ARG cc_start: 0.6543 (ptt180) cc_final: 0.5650 (pmt170) REVERT: 3 15 LYS cc_start: 0.7655 (mttt) cc_final: 0.6824 (mttt) REVERT: C 49 MET cc_start: 0.4576 (mtp) cc_final: 0.4289 (mtt) REVERT: C 74 ARG cc_start: 0.3353 (ptp90) cc_final: 0.2698 (mmt180) REVERT: C 105 LYS cc_start: 0.6791 (OUTLIER) cc_final: 0.6442 (ptpt) REVERT: C 143 LYS cc_start: 0.4454 (OUTLIER) cc_final: 0.4198 (tttt) REVERT: C 178 ASN cc_start: 0.6275 (t0) cc_final: 0.5970 (m-40) REVERT: D 27 LYS cc_start: 0.4760 (pmtt) cc_final: 0.4316 (ttpp) REVERT: D 28 GLU cc_start: 0.6027 (mt-10) cc_final: 0.5526 (mp0) REVERT: D 46 GLU cc_start: 0.5481 (tp30) cc_final: 0.4887 (mm-30) REVERT: D 122 SER cc_start: 0.6603 (m) cc_final: 0.6270 (p) REVERT: D 129 MET cc_start: 0.6034 (mmm) cc_final: 0.5275 (mtt) REVERT: D 132 ARG cc_start: 0.5738 (OUTLIER) cc_final: 0.5368 (ptm-80) REVERT: E 20 PHE cc_start: 0.6345 (m-80) cc_final: 0.5713 (m-80) REVERT: E 29 ASP cc_start: 0.5355 (OUTLIER) cc_final: 0.4905 (p0) REVERT: E 44 ARG cc_start: 0.4749 (ttm110) cc_final: 0.4305 (tmm160) REVERT: E 73 ARG cc_start: 0.6422 (ttp80) cc_final: 0.5508 (ttm-80) REVERT: E 78 GLU cc_start: 0.6607 (tt0) cc_final: 0.6273 (tp30) REVERT: E 113 GLU cc_start: 0.7068 (tp30) cc_final: 0.6734 (tt0) REVERT: E 119 SER cc_start: 0.6695 (t) cc_final: 0.6339 (p) REVERT: E 124 MET cc_start: 0.6813 (mtm) cc_final: 0.6460 (mtt) REVERT: E 128 ARG cc_start: 0.5212 (mtt-85) cc_final: 0.4741 (mmm-85) REVERT: E 148 LYS cc_start: 0.5052 (ttpp) cc_final: 0.4127 (tptp) REVERT: E 151 LYS cc_start: 0.4372 (pptt) cc_final: 0.4063 (mttm) REVERT: E 171 LEU cc_start: 0.5922 (OUTLIER) cc_final: 0.5659 (mt) REVERT: F 45 ARG cc_start: 0.6451 (mtp-110) cc_final: 0.5830 (mmm160) REVERT: F 55 GLU cc_start: 0.6434 (mt-10) cc_final: 0.6202 (mt-10) REVERT: F 61 GLN cc_start: 0.6286 (tm-30) cc_final: 0.5769 (tm130) REVERT: F 65 GLU cc_start: 0.6287 (mt-10) cc_final: 0.6027 (mm-30) REVERT: F 116 GLU cc_start: 0.7050 (tt0) cc_final: 0.6550 (tt0) REVERT: F 156 LYS cc_start: 0.6703 (ptpp) cc_final: 0.6307 (pttt) REVERT: G 15 SER cc_start: 0.5942 (t) cc_final: 0.5384 (m) REVERT: G 56 LYS cc_start: 0.6717 (mtpt) cc_final: 0.6017 (mttp) REVERT: G 62 MET cc_start: 0.6751 (OUTLIER) cc_final: 0.6329 (ptt) REVERT: G 92 THR cc_start: 0.5966 (OUTLIER) cc_final: 0.5603 (p) REVERT: H 41 SER cc_start: 0.6171 (p) cc_final: 0.5696 (m) REVERT: H 79 ARG cc_start: 0.3651 (ttt180) cc_final: 0.3339 (mtt90) REVERT: H 92 ARG cc_start: 0.4769 (mpp-170) cc_final: 0.4418 (mpt180) REVERT: H 96 ARG cc_start: 0.5940 (mtt90) cc_final: 0.5726 (mtt180) REVERT: H 106 GLU cc_start: 0.6647 (OUTLIER) cc_final: 0.6352 (tt0) REVERT: H 119 ARG cc_start: 0.6496 (mtm180) cc_final: 0.6231 (mtt180) REVERT: H 129 GLU cc_start: 0.4533 (mm-30) cc_final: 0.3987 (mp0) REVERT: H 137 LYS cc_start: 0.5001 (ptmm) cc_final: 0.4616 (tptt) REVERT: H 139 GLU cc_start: 0.6473 (mt-10) cc_final: 0.5362 (mm-30) REVERT: I 26 THR cc_start: 0.7550 (m) cc_final: 0.7126 (p) REVERT: I 43 GLU cc_start: 0.7781 (mm-30) cc_final: 0.7414 (mm-30) REVERT: I 48 ASP cc_start: 0.6578 (t70) cc_final: 0.6000 (m-30) REVERT: I 50 LYS cc_start: 0.6160 (ttpt) cc_final: 0.5704 (ttpt) REVERT: I 69 LYS cc_start: 0.6248 (mtpp) cc_final: 0.5587 (tptm) REVERT: I 76 GLN cc_start: 0.7021 (OUTLIER) cc_final: 0.6433 (tt0) REVERT: I 89 LYS cc_start: 0.6289 (ptmt) cc_final: 0.5697 (ttpp) REVERT: I 111 MET cc_start: 0.8136 (ptp) cc_final: 0.7838 (ptp) REVERT: I 114 ARG cc_start: 0.6513 (ttm110) cc_final: 0.5860 (ttp-110) REVERT: J 27 LYS cc_start: 0.5466 (OUTLIER) cc_final: 0.5226 (pttt) REVERT: J 85 ARG cc_start: 0.6276 (OUTLIER) cc_final: 0.5863 (mtt180) REVERT: J 88 MET cc_start: 0.5736 (OUTLIER) cc_final: 0.5082 (mtt) REVERT: J 91 ASP cc_start: 0.5015 (t70) cc_final: 0.4773 (t0) REVERT: J 104 VAL cc_start: 0.7087 (t) cc_final: 0.6856 (t) REVERT: K 7 ARG cc_start: 0.5272 (OUTLIER) cc_final: 0.3900 (mtm180) REVERT: K 11 LYS cc_start: 0.7034 (mttt) cc_final: 0.6499 (mmtt) REVERT: K 75 ASP cc_start: 0.4770 (OUTLIER) cc_final: 0.4067 (p0) REVERT: K 88 MET cc_start: 0.4778 (ttm) cc_final: 0.4232 (mtt) REVERT: L 83 GLU cc_start: 0.6534 (mt-10) cc_final: 0.6168 (mt-10) REVERT: L 98 ARG cc_start: 0.5781 (mtt-85) cc_final: 0.5492 (mtm-85) REVERT: L 105 PHE cc_start: 0.6540 (m-80) cc_final: 0.6014 (m-80) REVERT: L 106 ARG cc_start: 0.4630 (ttt180) cc_final: 0.4131 (tpt90) REVERT: M 10 LYS cc_start: 0.6405 (tttt) cc_final: 0.5954 (tttm) REVERT: M 40 THR cc_start: 0.7967 (t) cc_final: 0.7353 (p) REVERT: M 43 LYS cc_start: 0.7462 (ptpt) cc_final: 0.7005 (pttt) REVERT: M 49 LEU cc_start: 0.7476 (mt) cc_final: 0.7093 (mm) REVERT: M 64 THR cc_start: 0.8180 (m) cc_final: 0.7731 (p) REVERT: M 75 GLN cc_start: 0.7261 (OUTLIER) cc_final: 0.6831 (pm20) REVERT: M 88 LYS cc_start: 0.7078 (OUTLIER) cc_final: 0.6188 (tttt) REVERT: M 94 ARG cc_start: 0.7441 (OUTLIER) cc_final: 0.7203 (mtp85) REVERT: M 109 ASP cc_start: 0.6940 (OUTLIER) cc_final: 0.6556 (m-30) REVERT: M 111 LYS cc_start: 0.7319 (mmmt) cc_final: 0.7001 (mmtm) REVERT: N 13 LYS cc_start: 0.5904 (OUTLIER) cc_final: 0.5592 (mtmt) REVERT: N 68 ASP cc_start: 0.5290 (OUTLIER) cc_final: 0.4566 (t0) REVERT: N 78 LYS cc_start: 0.5601 (tttm) cc_final: 0.4930 (ptpt) REVERT: N 81 MET cc_start: 0.7268 (mtm) cc_final: 0.6634 (mtm) REVERT: N 93 ARG cc_start: 0.5812 (mmt-90) cc_final: 0.5041 (mmp80) REVERT: N 110 LYS cc_start: 0.7396 (OUTLIER) cc_final: 0.6771 (mttm) REVERT: N 113 ARG cc_start: 0.5189 (OUTLIER) cc_final: 0.4577 (mmm-85) REVERT: O 39 GLU cc_start: 0.4979 (OUTLIER) cc_final: 0.4524 (tp30) REVERT: P 61 SER cc_start: 0.7381 (m) cc_final: 0.7089 (p) REVERT: Q 1 MET cc_start: 0.6731 (pmm) cc_final: 0.6072 (pmm) REVERT: R 6 ARG cc_start: 0.4870 (OUTLIER) cc_final: 0.4190 (ttp-170) REVERT: R 11 ARG cc_start: 0.6599 (ttm110) cc_final: 0.6082 (mmt-90) REVERT: R 40 ARG cc_start: 0.6612 (OUTLIER) cc_final: 0.5981 (mtp180) REVERT: S 16 GLU cc_start: 0.4064 (OUTLIER) cc_final: 0.3832 (mm-30) REVERT: T 44 MET cc_start: 0.6129 (mtt) cc_final: 0.5716 (mtt) REVERT: U 24 ARG cc_start: 0.7197 (mmm160) cc_final: 0.6931 (mmm160) REVERT: U 55 GLN cc_start: 0.7073 (tt0) cc_final: 0.6824 (tt0) REVERT: V 21 ARG cc_start: 0.4761 (ttt90) cc_final: 0.4287 (mmm160) REVERT: V 33 ARG cc_start: 0.5507 (mtt90) cc_final: 0.4995 (mmm160) REVERT: V 36 GLU cc_start: 0.6876 (OUTLIER) cc_final: 0.6534 (mt-10) REVERT: V 47 ARG cc_start: 0.5751 (ptt90) cc_final: 0.5370 (ptt-90) REVERT: V 49 LYS cc_start: 0.6549 (tptp) cc_final: 0.6264 (tptp) REVERT: W 143 ARG cc_start: 0.5749 (OUTLIER) cc_final: 0.5172 (mpp-170) REVERT: W 155 GLU cc_start: 0.5948 (tp30) cc_final: 0.5466 (mt-10) REVERT: W 169 ASP cc_start: 0.4738 (t0) cc_final: 0.4297 (m-30) REVERT: W 269 LYS cc_start: 0.7672 (tptp) cc_final: 0.7296 (tptt) REVERT: W 287 GLN cc_start: 0.5395 (mt0) cc_final: 0.4878 (tm-30) REVERT: W 318 THR cc_start: 0.7909 (OUTLIER) cc_final: 0.7669 (m) REVERT: W 330 ASP cc_start: 0.5416 (m-30) cc_final: 0.4840 (p0) REVERT: W 336 LYS cc_start: 0.6419 (mttt) cc_final: 0.6049 (mmmt) REVERT: W 341 ILE cc_start: 0.7037 (mt) cc_final: 0.6805 (mm) REVERT: c 5 LYS cc_start: 0.7134 (tttp) cc_final: 0.6458 (tptp) REVERT: c 18 LYS cc_start: 0.7899 (OUTLIER) cc_final: 0.7563 (mtmt) REVERT: c 97 LYS cc_start: 0.7361 (mtpp) cc_final: 0.6586 (mmpt) REVERT: c 111 LYS cc_start: 0.6735 (OUTLIER) cc_final: 0.6117 (ptpt) REVERT: c 181 MET cc_start: 0.8087 (tpp) cc_final: 0.7668 (mmm) REVERT: c 182 ARG cc_start: 0.8459 (OUTLIER) cc_final: 0.7970 (ttt90) REVERT: c 199 GLU cc_start: 0.7451 (mt-10) cc_final: 0.6544 (pm20) REVERT: c 203 ARG cc_start: 0.7676 (ptt90) cc_final: 0.7270 (ptp-110) REVERT: c 269 ARG cc_start: 0.7384 (ttp-170) cc_final: 0.6968 (ttp80) REVERT: d 1 MET cc_start: 0.4035 (OUTLIER) cc_final: 0.2945 (mtt) REVERT: d 7 LYS cc_start: 0.7976 (ttmt) cc_final: 0.7324 (ttpp) REVERT: d 70 LYS cc_start: 0.7069 (tttt) cc_final: 0.6675 (tttt) REVERT: d 128 ARG cc_start: 0.8000 (OUTLIER) cc_final: 0.7344 (mtp180) REVERT: e 21 ARG cc_start: 0.6155 (OUTLIER) cc_final: 0.5693 (ptm160) REVERT: e 22 ASP cc_start: 0.6848 (OUTLIER) cc_final: 0.6196 (m-30) REVERT: f 30 ARG cc_start: 0.6067 (mpp80) cc_final: 0.5496 (mtm-85) REVERT: f 60 ILE cc_start: 0.7348 (mt) cc_final: 0.6980 (mm) REVERT: f 83 TYR cc_start: 0.5853 (OUTLIER) cc_final: 0.5192 (m-10) REVERT: f 88 LYS cc_start: 0.7526 (OUTLIER) cc_final: 0.7221 (ptpt) REVERT: f 125 ARG cc_start: 0.5254 (tpp-160) cc_final: 0.4951 (mmm160) REVERT: f 129 SER cc_start: 0.7458 (m) cc_final: 0.7072 (t) REVERT: g 25 THR cc_start: 0.5561 (m) cc_final: 0.5155 (p) REVERT: g 51 THR cc_start: 0.5390 (m) cc_final: 0.4851 (p) REVERT: g 74 SER cc_start: 0.6718 (m) cc_final: 0.6461 (t) REVERT: g 95 ARG cc_start: 0.6015 (mtm110) cc_final: 0.5383 (mtm-85) REVERT: i 34 ARG cc_start: 0.7657 (ttt-90) cc_final: 0.7414 (mtp85) REVERT: i 61 LYS cc_start: 0.7140 (mttt) cc_final: 0.6738 (mmtm) REVERT: i 91 GLU cc_start: 0.7339 (mt-10) cc_final: 0.7112 (mt-10) REVERT: i 95 ARG cc_start: 0.6146 (ttt180) cc_final: 0.5453 (mpt-90) REVERT: i 96 ARG cc_start: 0.6630 (ptt-90) cc_final: 0.4816 (mmm-85) REVERT: i 118 MET cc_start: 0.8390 (mtt) cc_final: 0.8169 (mtt) REVERT: i 128 ASN cc_start: 0.7702 (t0) cc_final: 0.7372 (t0) REVERT: j 17 ARG cc_start: 0.7168 (mmt90) cc_final: 0.6718 (mmm160) REVERT: j 29 HIS cc_start: 0.7241 (m-70) cc_final: 0.6871 (m90) REVERT: j 45 GLU cc_start: 0.7264 (mt-10) cc_final: 0.6996 (mt-10) REVERT: j 51 LYS cc_start: 0.7443 (mtpp) cc_final: 0.6979 (mtmt) REVERT: j 53 LYS cc_start: 0.6867 (mptm) cc_final: 0.6111 (tttm) REVERT: j 88 ASN cc_start: 0.6963 (OUTLIER) cc_final: 0.6252 (t0) REVERT: j 89 ASN cc_start: 0.6458 (m-40) cc_final: 0.5870 (t0) REVERT: j 98 ARG cc_start: 0.7031 (mmt-90) cc_final: 0.6517 (mtm180) REVERT: j 105 ARG cc_start: 0.5964 (OUTLIER) cc_final: 0.5450 (mtt-85) REVERT: j 114 LYS cc_start: 0.6182 (mppt) cc_final: 0.5756 (mmpt) REVERT: k 106 GLU cc_start: 0.7859 (mt-10) cc_final: 0.7005 (mm-30) REVERT: k 141 LYS cc_start: 0.6579 (tmtm) cc_final: 0.5749 (mtmt) REVERT: l 1 MET cc_start: 0.5950 (OUTLIER) cc_final: 0.5594 (ttp) REVERT: l 6 ARG cc_start: 0.6767 (mtt180) cc_final: 0.5776 (ttt-90) REVERT: l 110 GLU cc_start: 0.6909 (tt0) cc_final: 0.6483 (tt0) REVERT: l 136 MET cc_start: 0.5578 (ttp) cc_final: 0.5168 (ttm) REVERT: m 18 GLN cc_start: 0.8124 (tt0) cc_final: 0.7789 (tt0) REVERT: m 72 ASP cc_start: 0.7634 (t0) cc_final: 0.7237 (t70) REVERT: n 13 ARG cc_start: 0.6528 (tpp-160) cc_final: 0.5654 (ttp80) REVERT: n 19 GLN cc_start: 0.7325 (tt0) cc_final: 0.6449 (tt0) REVERT: n 20 GLU cc_start: 0.6117 (pt0) cc_final: 0.5705 (mt-10) REVERT: n 56 LYS cc_start: 0.5749 (mptt) cc_final: 0.5145 (mtmt) REVERT: n 81 ARG cc_start: 0.7215 (OUTLIER) cc_final: 0.5719 (mtm-85) REVERT: n 104 GLN cc_start: 0.7742 (tt0) cc_final: 0.7417 (tt0) REVERT: o 6 LYS cc_start: 0.6163 (ttpp) cc_final: 0.5702 (tmmt) REVERT: o 10 GLN cc_start: 0.6923 (mm-40) cc_final: 0.6131 (mt0) REVERT: o 11 GLU cc_start: 0.7342 (pt0) cc_final: 0.6833 (pt0) REVERT: o 63 LYS cc_start: 0.7612 (ptmm) cc_final: 0.7184 (pttt) REVERT: o 68 GLU cc_start: 0.5878 (mm-30) cc_final: 0.5555 (mp0) REVERT: o 89 ARG cc_start: 0.7220 (mtm180) cc_final: 0.6086 (mmt180) REVERT: o 112 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7596 (mt-10) REVERT: p 9 ILE cc_start: 0.7790 (OUTLIER) cc_final: 0.7552 (mp) REVERT: p 11 ARG cc_start: 0.6939 (tpm170) cc_final: 0.6258 (ttm110) REVERT: p 85 LYS cc_start: 0.7313 (mttt) cc_final: 0.7030 (mmtm) REVERT: p 104 VAL cc_start: 0.6576 (t) cc_final: 0.6298 (m) REVERT: p 112 LYS cc_start: 0.6882 (OUTLIER) cc_final: 0.6552 (tppp) REVERT: q 60 LYS cc_start: 0.7196 (mtmt) cc_final: 0.6587 (mttm) REVERT: q 73 LYS cc_start: 0.7912 (mmtp) cc_final: 0.7314 (mmpt) REVERT: r 28 LYS cc_start: 0.7056 (mtpt) cc_final: 0.6069 (mmtm) REVERT: r 68 ASP cc_start: 0.6617 (m-30) cc_final: 0.6372 (m-30) REVERT: r 73 LYS cc_start: 0.7616 (mttm) cc_final: 0.7309 (mtpm) REVERT: r 86 MET cc_start: 0.8052 (tpp) cc_final: 0.7281 (ttp) REVERT: s 5 GLU cc_start: 0.6594 (mt-10) cc_final: 0.5576 (pp20) REVERT: s 9 LYS cc_start: 0.6827 (mmtt) cc_final: 0.6332 (mppt) REVERT: s 18 GLU cc_start: 0.7108 (mt-10) cc_final: 0.5997 (mp0) REVERT: s 33 LYS cc_start: 0.7431 (tttt) cc_final: 0.6665 (mttp) REVERT: s 50 LEU cc_start: 0.7364 (mt) cc_final: 0.7138 (mp) REVERT: s 51 PHE cc_start: 0.7087 (m-10) cc_final: 0.6713 (m-10) REVERT: s 69 ARG cc_start: 0.6627 (mtt-85) cc_final: 0.6109 (mtm110) REVERT: t 7 ARG cc_start: 0.6239 (ttt180) cc_final: 0.5486 (ttm110) REVERT: t 10 GLU cc_start: 0.7027 (OUTLIER) cc_final: 0.5696 (pm20) REVERT: t 37 GLU cc_start: 0.6407 (pp20) cc_final: 0.6018 (tm-30) REVERT: t 43 LYS cc_start: 0.7226 (mtmm) cc_final: 0.6952 (mttp) REVERT: t 72 ILE cc_start: 0.7375 (tp) cc_final: 0.7051 (tt) REVERT: t 86 ARG cc_start: 0.7494 (mtm-85) cc_final: 0.7003 (mtm-85) REVERT: u 10 LYS cc_start: 0.6370 (mttp) cc_final: 0.5631 (mmmt) REVERT: u 43 ASP cc_start: 0.7408 (t0) cc_final: 0.6782 (t0) REVERT: u 46 LYS cc_start: 0.6929 (mmtp) cc_final: 0.6482 (mttm) REVERT: v 70 GLU cc_start: 0.7669 (OUTLIER) cc_final: 0.7384 (mp0) REVERT: v 83 GLU cc_start: 0.6658 (mm-30) cc_final: 0.6110 (mt-10) REVERT: w 45 ARG cc_start: 0.5775 (ptt-90) cc_final: 0.5560 (ttt-90) REVERT: w 54 LYS cc_start: 0.7545 (OUTLIER) cc_final: 0.6979 (tttp) REVERT: x 24 GLU cc_start: 0.6819 (tt0) cc_final: 0.6567 (tt0) REVERT: y 56 LYS cc_start: 0.7456 (pttt) cc_final: 0.7135 (ptmt) outliers start: 186 outliers final: 104 residues processed: 1005 average time/residue: 2.6047 time to fit residues: 3625.7714 Evaluate side-chains 1034 residues out of total 4889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 882 time to evaluate : 5.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 28 ARG Chi-restraints excluded: chain 1 residue 41 ARG Chi-restraints excluded: chain 4 residue 22 MET Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 87 CYS Chi-restraints excluded: chain C residue 105 LYS Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 143 LYS Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain D residue 88 ARG Chi-restraints excluded: chain D residue 132 ARG Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain F residue 14 LYS Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain G residue 62 MET Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 75 VAL Chi-restraints excluded: chain H residue 106 GLU Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain I residue 76 GLN Chi-restraints excluded: chain I residue 90 ASP Chi-restraints excluded: chain J residue 27 LYS Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 73 SER Chi-restraints excluded: chain J residue 85 ARG Chi-restraints excluded: chain J residue 88 MET Chi-restraints excluded: chain K residue 7 ARG Chi-restraints excluded: chain K residue 71 LEU Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 75 ASP Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 129 VAL Chi-restraints excluded: chain M residue 3 THR Chi-restraints excluded: chain M residue 75 GLN Chi-restraints excluded: chain M residue 86 ARG Chi-restraints excluded: chain M residue 88 LYS Chi-restraints excluded: chain M residue 94 ARG Chi-restraints excluded: chain M residue 109 ASP Chi-restraints excluded: chain N residue 11 ASP Chi-restraints excluded: chain N residue 13 LYS Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 27 LYS Chi-restraints excluded: chain N residue 68 ASP Chi-restraints excluded: chain N residue 110 LYS Chi-restraints excluded: chain N residue 113 ARG Chi-restraints excluded: chain O residue 5 SER Chi-restraints excluded: chain O residue 23 LYS Chi-restraints excluded: chain O residue 39 GLU Chi-restraints excluded: chain O residue 83 LYS Chi-restraints excluded: chain P residue 83 GLU Chi-restraints excluded: chain R residue 6 ARG Chi-restraints excluded: chain R residue 29 VAL Chi-restraints excluded: chain R residue 39 LYS Chi-restraints excluded: chain R residue 40 ARG Chi-restraints excluded: chain R residue 42 THR Chi-restraints excluded: chain R residue 67 LEU Chi-restraints excluded: chain R residue 72 SER Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain S residue 16 GLU Chi-restraints excluded: chain T residue 11 ILE Chi-restraints excluded: chain T residue 70 LYS Chi-restraints excluded: chain U residue 23 SER Chi-restraints excluded: chain U residue 69 LYS Chi-restraints excluded: chain V residue 3 VAL Chi-restraints excluded: chain V residue 36 GLU Chi-restraints excluded: chain W residue 19 VAL Chi-restraints excluded: chain W residue 109 ARG Chi-restraints excluded: chain W residue 113 LEU Chi-restraints excluded: chain W residue 143 ARG Chi-restraints excluded: chain W residue 318 THR Chi-restraints excluded: chain W residue 325 THR Chi-restraints excluded: chain W residue 356 LEU Chi-restraints excluded: chain c residue 18 LYS Chi-restraints excluded: chain c residue 111 LYS Chi-restraints excluded: chain c residue 115 GLN Chi-restraints excluded: chain c residue 129 THR Chi-restraints excluded: chain c residue 165 VAL Chi-restraints excluded: chain c residue 182 ARG Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 91 THR Chi-restraints excluded: chain d residue 128 ARG Chi-restraints excluded: chain e residue 12 LEU Chi-restraints excluded: chain e residue 21 ARG Chi-restraints excluded: chain e residue 22 ASP Chi-restraints excluded: chain e residue 126 VAL Chi-restraints excluded: chain e residue 144 GLU Chi-restraints excluded: chain f residue 4 LEU Chi-restraints excluded: chain f residue 35 THR Chi-restraints excluded: chain f residue 83 TYR Chi-restraints excluded: chain f residue 88 LYS Chi-restraints excluded: chain g residue 15 VAL Chi-restraints excluded: chain g residue 36 THR Chi-restraints excluded: chain g residue 43 VAL Chi-restraints excluded: chain g residue 47 ASP Chi-restraints excluded: chain g residue 87 LEU Chi-restraints excluded: chain g residue 106 SER Chi-restraints excluded: chain g residue 122 THR Chi-restraints excluded: chain g residue 155 GLU Chi-restraints excluded: chain g residue 171 THR Chi-restraints excluded: chain i residue 106 LYS Chi-restraints excluded: chain i residue 138 GLN Chi-restraints excluded: chain j residue 88 ASN Chi-restraints excluded: chain j residue 105 ARG Chi-restraints excluded: chain k residue 103 ILE Chi-restraints excluded: chain l residue 1 MET Chi-restraints excluded: chain l residue 63 ILE Chi-restraints excluded: chain l residue 80 VAL Chi-restraints excluded: chain m residue 15 SER Chi-restraints excluded: chain n residue 81 ARG Chi-restraints excluded: chain o residue 34 GLU Chi-restraints excluded: chain o residue 70 VAL Chi-restraints excluded: chain o residue 85 SER Chi-restraints excluded: chain o residue 104 THR Chi-restraints excluded: chain o residue 112 GLU Chi-restraints excluded: chain p residue 9 ILE Chi-restraints excluded: chain p residue 22 LYS Chi-restraints excluded: chain p residue 112 LYS Chi-restraints excluded: chain q residue 33 VAL Chi-restraints excluded: chain q residue 64 VAL Chi-restraints excluded: chain q residue 99 THR Chi-restraints excluded: chain r residue 66 ILE Chi-restraints excluded: chain r residue 70 LYS Chi-restraints excluded: chain t residue 10 GLU Chi-restraints excluded: chain u residue 53 LYS Chi-restraints excluded: chain u residue 58 SER Chi-restraints excluded: chain u residue 62 THR Chi-restraints excluded: chain u residue 65 VAL Chi-restraints excluded: chain u residue 73 LYS Chi-restraints excluded: chain v residue 30 SER Chi-restraints excluded: chain v residue 70 GLU Chi-restraints excluded: chain w residue 54 LYS Chi-restraints excluded: chain x residue 4 LYS Chi-restraints excluded: chain x residue 40 SER Chi-restraints excluded: chain y residue 19 LYS Chi-restraints excluded: chain y residue 41 THR Chi-restraints excluded: chain z residue 30 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1023 random chunks: chunk 603 optimal weight: 10.0000 chunk 971 optimal weight: 0.7980 chunk 593 optimal weight: 5.9990 chunk 460 optimal weight: 7.9990 chunk 675 optimal weight: 6.9990 chunk 1019 optimal weight: 1.9990 chunk 938 optimal weight: 0.7980 chunk 811 optimal weight: 8.9990 chunk 84 optimal weight: 9.9990 chunk 626 optimal weight: 6.9990 chunk 497 optimal weight: 8.9990 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 29 GLN ** C 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 198 HIS F 19 ASN F 77 ASN ** F 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 3 HIS J 110 GLN ** L 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 46 HIS Q 63 GLN U 68 HIS W 248 HIS c 117 GLN e 165 HIS g 64 GLN k 104 GLN s 48 GLN u 12 GLN x 58 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 156812 Z= 0.301 Angle : 0.763 16.060 234226 Z= 0.401 Chirality : 0.042 0.386 29769 Planarity : 0.007 0.150 12793 Dihedral : 23.319 177.027 77638 Min Nonbonded Distance : 1.766 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.56 % Favored : 97.30 % Rotamer: Outliers : 3.29 % Allowed : 16.28 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.10), residues: 5853 helix: 0.70 (0.11), residues: 2053 sheet: -0.28 (0.14), residues: 1188 loop : -0.33 (0.12), residues: 2612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 201 HIS 0.011 0.002 HIS P 46 PHE 0.021 0.002 PHE m 21 TYR 0.025 0.002 TYR r 38 ARG 0.007 0.001 ARG L 69 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11706 Ramachandran restraints generated. 5853 Oldfield, 0 Emsley, 5853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11706 Ramachandran restraints generated. 5853 Oldfield, 0 Emsley, 5853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1054 residues out of total 4889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 893 time to evaluate : 6.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 33 LYS cc_start: 0.6500 (mptt) cc_final: 0.6174 (mmtp) REVERT: 1 1 MET cc_start: 0.6801 (mpp) cc_final: 0.6521 (mmm) REVERT: 2 52 LYS cc_start: 0.5923 (tttm) cc_final: 0.5540 (tppt) REVERT: 3 8 LYS cc_start: 0.7529 (mttt) cc_final: 0.6797 (mtmt) REVERT: 3 12 ARG cc_start: 0.6572 (ptt180) cc_final: 0.5693 (pmt170) REVERT: 3 15 LYS cc_start: 0.7610 (mttt) cc_final: 0.6787 (mttt) REVERT: C 49 MET cc_start: 0.4662 (mtp) cc_final: 0.4335 (mtt) REVERT: C 74 ARG cc_start: 0.3275 (ptp90) cc_final: 0.2639 (mmt180) REVERT: C 105 LYS cc_start: 0.6894 (OUTLIER) cc_final: 0.6552 (ptpt) REVERT: C 143 LYS cc_start: 0.4341 (OUTLIER) cc_final: 0.4095 (tttt) REVERT: C 178 ASN cc_start: 0.6184 (t0) cc_final: 0.5916 (m-40) REVERT: D 28 GLU cc_start: 0.5974 (mt-10) cc_final: 0.5281 (pm20) REVERT: D 46 GLU cc_start: 0.5469 (tp30) cc_final: 0.4902 (mm-30) REVERT: D 88 ARG cc_start: 0.5090 (OUTLIER) cc_final: 0.4653 (ttt-90) REVERT: D 122 SER cc_start: 0.6491 (m) cc_final: 0.6176 (p) REVERT: D 129 MET cc_start: 0.6171 (mmm) cc_final: 0.5384 (mtt) REVERT: D 132 ARG cc_start: 0.5624 (OUTLIER) cc_final: 0.5316 (ptm-80) REVERT: D 134 MET cc_start: 0.6161 (mtp) cc_final: 0.5869 (mtp) REVERT: E 29 ASP cc_start: 0.5311 (OUTLIER) cc_final: 0.4849 (p0) REVERT: E 44 ARG cc_start: 0.4675 (ttm110) cc_final: 0.4286 (tmm160) REVERT: E 73 ARG cc_start: 0.6438 (ttp80) cc_final: 0.5520 (ttm-80) REVERT: E 78 GLU cc_start: 0.6669 (tt0) cc_final: 0.6320 (tp30) REVERT: E 113 GLU cc_start: 0.7068 (tp30) cc_final: 0.6740 (tt0) REVERT: E 119 SER cc_start: 0.6624 (t) cc_final: 0.6305 (p) REVERT: E 124 MET cc_start: 0.6750 (mtm) cc_final: 0.6369 (mtt) REVERT: E 128 ARG cc_start: 0.5271 (mtt-85) cc_final: 0.4818 (mtt90) REVERT: E 148 LYS cc_start: 0.5034 (ttpp) cc_final: 0.4083 (tptp) REVERT: E 151 LYS cc_start: 0.4376 (pptt) cc_final: 0.4063 (mttm) REVERT: E 171 LEU cc_start: 0.5860 (OUTLIER) cc_final: 0.5603 (mt) REVERT: F 45 ARG cc_start: 0.6421 (mtp-110) cc_final: 0.5808 (mmm160) REVERT: F 55 GLU cc_start: 0.6429 (mt-10) cc_final: 0.6201 (mt-10) REVERT: F 61 GLN cc_start: 0.6298 (tm-30) cc_final: 0.5767 (tm130) REVERT: F 65 GLU cc_start: 0.6270 (mt-10) cc_final: 0.6005 (mm-30) REVERT: F 116 GLU cc_start: 0.6989 (tt0) cc_final: 0.6496 (tt0) REVERT: F 156 LYS cc_start: 0.6690 (ptpp) cc_final: 0.6318 (pttt) REVERT: G 15 SER cc_start: 0.5943 (t) cc_final: 0.5390 (m) REVERT: G 56 LYS cc_start: 0.6720 (mtpt) cc_final: 0.6028 (mttp) REVERT: G 92 THR cc_start: 0.5980 (OUTLIER) cc_final: 0.5653 (p) REVERT: H 41 SER cc_start: 0.6142 (p) cc_final: 0.5728 (m) REVERT: H 79 ARG cc_start: 0.3629 (ttt180) cc_final: 0.3301 (mtt90) REVERT: H 92 ARG cc_start: 0.4737 (mpp-170) cc_final: 0.4432 (mpt180) REVERT: H 96 ARG cc_start: 0.5979 (mtt90) cc_final: 0.5759 (mtt180) REVERT: H 106 GLU cc_start: 0.6624 (OUTLIER) cc_final: 0.6354 (tt0) REVERT: H 119 ARG cc_start: 0.6557 (mtm180) cc_final: 0.6220 (mtt180) REVERT: H 129 GLU cc_start: 0.4411 (mm-30) cc_final: 0.3890 (mp0) REVERT: H 137 LYS cc_start: 0.4980 (ptmm) cc_final: 0.4590 (tptt) REVERT: H 139 GLU cc_start: 0.6419 (mt-10) cc_final: 0.5320 (mm-30) REVERT: I 26 THR cc_start: 0.7559 (m) cc_final: 0.7117 (p) REVERT: I 43 GLU cc_start: 0.7778 (mm-30) cc_final: 0.7432 (mm-30) REVERT: I 48 ASP cc_start: 0.6505 (t70) cc_final: 0.6230 (t70) REVERT: I 50 LYS cc_start: 0.6123 (ttpt) cc_final: 0.5672 (ttpt) REVERT: I 69 LYS cc_start: 0.6284 (mtpp) cc_final: 0.5613 (tptm) REVERT: I 76 GLN cc_start: 0.6956 (OUTLIER) cc_final: 0.6397 (tt0) REVERT: I 89 LYS cc_start: 0.6395 (ptmt) cc_final: 0.5783 (ttpp) REVERT: I 111 MET cc_start: 0.8139 (ptp) cc_final: 0.7841 (ptp) REVERT: I 114 ARG cc_start: 0.6496 (ttm110) cc_final: 0.5846 (ttp-110) REVERT: J 27 LYS cc_start: 0.5496 (OUTLIER) cc_final: 0.5274 (pttt) REVERT: J 85 ARG cc_start: 0.6260 (OUTLIER) cc_final: 0.5850 (mtt180) REVERT: J 88 MET cc_start: 0.5664 (OUTLIER) cc_final: 0.4985 (mtt) REVERT: J 91 ASP cc_start: 0.5043 (t70) cc_final: 0.4790 (t0) REVERT: J 104 VAL cc_start: 0.7071 (t) cc_final: 0.6833 (t) REVERT: K 7 ARG cc_start: 0.5227 (OUTLIER) cc_final: 0.4961 (mtt180) REVERT: K 11 LYS cc_start: 0.7056 (mttt) cc_final: 0.6696 (mmmt) REVERT: K 75 ASP cc_start: 0.4723 (OUTLIER) cc_final: 0.4295 (p0) REVERT: K 88 MET cc_start: 0.4678 (ttm) cc_final: 0.4088 (mtt) REVERT: L 83 GLU cc_start: 0.6505 (mt-10) cc_final: 0.6283 (mt-10) REVERT: L 98 ARG cc_start: 0.5778 (mtt-85) cc_final: 0.5489 (mtm-85) REVERT: L 105 PHE cc_start: 0.6555 (m-80) cc_final: 0.5987 (m-80) REVERT: L 106 ARG cc_start: 0.4606 (ttt180) cc_final: 0.4107 (tpt90) REVERT: M 10 LYS cc_start: 0.6357 (tttt) cc_final: 0.5886 (tttm) REVERT: M 40 THR cc_start: 0.7989 (t) cc_final: 0.7375 (p) REVERT: M 43 LYS cc_start: 0.7398 (ptpt) cc_final: 0.6975 (pttt) REVERT: M 49 LEU cc_start: 0.7478 (mt) cc_final: 0.7096 (mm) REVERT: M 64 THR cc_start: 0.8193 (m) cc_final: 0.7741 (p) REVERT: M 75 GLN cc_start: 0.7225 (OUTLIER) cc_final: 0.6790 (pm20) REVERT: M 76 GLU cc_start: 0.6283 (tt0) cc_final: 0.5584 (tt0) REVERT: M 88 LYS cc_start: 0.7028 (OUTLIER) cc_final: 0.6068 (tttt) REVERT: M 94 ARG cc_start: 0.7417 (OUTLIER) cc_final: 0.7196 (mtm180) REVERT: M 109 ASP cc_start: 0.6969 (OUTLIER) cc_final: 0.6670 (m-30) REVERT: M 111 LYS cc_start: 0.7319 (mmmt) cc_final: 0.7058 (mmtm) REVERT: N 13 LYS cc_start: 0.5951 (OUTLIER) cc_final: 0.5637 (mtmt) REVERT: N 78 LYS cc_start: 0.5654 (tttm) cc_final: 0.4949 (ptpt) REVERT: N 81 MET cc_start: 0.7253 (mtm) cc_final: 0.6373 (mtm) REVERT: N 93 ARG cc_start: 0.5874 (mmt-90) cc_final: 0.5052 (mmp80) REVERT: N 110 LYS cc_start: 0.7289 (OUTLIER) cc_final: 0.6675 (mttm) REVERT: N 113 ARG cc_start: 0.5129 (OUTLIER) cc_final: 0.4514 (mmm-85) REVERT: O 39 GLU cc_start: 0.4925 (OUTLIER) cc_final: 0.4461 (tp30) REVERT: P 61 SER cc_start: 0.7368 (m) cc_final: 0.7087 (p) REVERT: Q 1 MET cc_start: 0.6767 (pmm) cc_final: 0.6190 (pmm) REVERT: R 6 ARG cc_start: 0.4973 (OUTLIER) cc_final: 0.4286 (ttp-170) REVERT: R 11 ARG cc_start: 0.6584 (ttm110) cc_final: 0.6079 (mmt-90) REVERT: R 40 ARG cc_start: 0.6564 (OUTLIER) cc_final: 0.5964 (mtp180) REVERT: S 16 GLU cc_start: 0.4052 (OUTLIER) cc_final: 0.3811 (mm-30) REVERT: T 44 MET cc_start: 0.6132 (mtt) cc_final: 0.5744 (mtt) REVERT: U 55 GLN cc_start: 0.7094 (tt0) cc_final: 0.6790 (tt0) REVERT: V 21 ARG cc_start: 0.4766 (ttt90) cc_final: 0.4283 (mmm160) REVERT: V 33 ARG cc_start: 0.5518 (mtt90) cc_final: 0.5004 (mmm160) REVERT: V 36 GLU cc_start: 0.6907 (OUTLIER) cc_final: 0.6531 (mt-10) REVERT: V 47 ARG cc_start: 0.5757 (ptt90) cc_final: 0.5367 (ptt-90) REVERT: V 49 LYS cc_start: 0.6468 (tptp) cc_final: 0.6193 (tptp) REVERT: W 143 ARG cc_start: 0.5817 (OUTLIER) cc_final: 0.5230 (mpp-170) REVERT: W 155 GLU cc_start: 0.5979 (tp30) cc_final: 0.5489 (mt-10) REVERT: W 169 ASP cc_start: 0.4716 (t0) cc_final: 0.4307 (m-30) REVERT: W 269 LYS cc_start: 0.7692 (tptp) cc_final: 0.7315 (tptt) REVERT: W 287 GLN cc_start: 0.5416 (mt0) cc_final: 0.4885 (tm130) REVERT: W 318 THR cc_start: 0.7880 (OUTLIER) cc_final: 0.7644 (m) REVERT: W 330 ASP cc_start: 0.5387 (m-30) cc_final: 0.4827 (p0) REVERT: W 336 LYS cc_start: 0.6451 (mttt) cc_final: 0.6082 (mmmt) REVERT: c 5 LYS cc_start: 0.7112 (tttp) cc_final: 0.6377 (tptp) REVERT: c 97 LYS cc_start: 0.7347 (mtpp) cc_final: 0.6610 (mmpt) REVERT: c 111 LYS cc_start: 0.6751 (pttm) cc_final: 0.6157 (ptpt) REVERT: c 181 MET cc_start: 0.8081 (tpp) cc_final: 0.7538 (mmm) REVERT: c 182 ARG cc_start: 0.8411 (OUTLIER) cc_final: 0.8050 (ttt90) REVERT: c 199 GLU cc_start: 0.7428 (mt-10) cc_final: 0.6509 (pm20) REVERT: c 203 ARG cc_start: 0.7665 (ptt90) cc_final: 0.7271 (ptp-110) REVERT: c 269 ARG cc_start: 0.7412 (ttp-170) cc_final: 0.7002 (ttp80) REVERT: d 1 MET cc_start: 0.4006 (OUTLIER) cc_final: 0.2925 (mtt) REVERT: d 7 LYS cc_start: 0.7955 (ttmt) cc_final: 0.7299 (ttpp) REVERT: d 70 LYS cc_start: 0.7049 (tttt) cc_final: 0.6657 (tttt) REVERT: d 105 LYS cc_start: 0.7755 (mmtt) cc_final: 0.7293 (mmtm) REVERT: d 128 ARG cc_start: 0.7960 (OUTLIER) cc_final: 0.7306 (mtp180) REVERT: e 21 ARG cc_start: 0.6171 (OUTLIER) cc_final: 0.5824 (ptm160) REVERT: e 22 ASP cc_start: 0.6844 (OUTLIER) cc_final: 0.6245 (m-30) REVERT: f 26 MET cc_start: 0.7531 (mmm) cc_final: 0.7196 (mmm) REVERT: f 30 ARG cc_start: 0.6033 (mpp80) cc_final: 0.5552 (mtm-85) REVERT: f 60 ILE cc_start: 0.7340 (mt) cc_final: 0.6960 (mm) REVERT: f 83 TYR cc_start: 0.5871 (OUTLIER) cc_final: 0.5212 (m-10) REVERT: f 88 LYS cc_start: 0.7533 (OUTLIER) cc_final: 0.7241 (ptpt) REVERT: f 125 ARG cc_start: 0.5348 (tpp-160) cc_final: 0.5027 (mmp-170) REVERT: f 129 SER cc_start: 0.7469 (m) cc_final: 0.7086 (t) REVERT: g 25 THR cc_start: 0.5552 (m) cc_final: 0.5117 (p) REVERT: g 74 SER cc_start: 0.6783 (m) cc_final: 0.6548 (t) REVERT: g 86 LYS cc_start: 0.6945 (OUTLIER) cc_final: 0.5756 (tttm) REVERT: g 95 ARG cc_start: 0.5929 (mtm110) cc_final: 0.5427 (mtm-85) REVERT: i 34 ARG cc_start: 0.7624 (ttt-90) cc_final: 0.7322 (mtp85) REVERT: i 61 LYS cc_start: 0.7154 (mttt) cc_final: 0.6755 (mmtm) REVERT: i 91 GLU cc_start: 0.7356 (mt-10) cc_final: 0.7134 (mt-10) REVERT: i 95 ARG cc_start: 0.6150 (ttt180) cc_final: 0.5498 (mpt-90) REVERT: i 96 ARG cc_start: 0.6663 (ptt-90) cc_final: 0.4821 (mmm-85) REVERT: i 118 MET cc_start: 0.8349 (mtt) cc_final: 0.8132 (mtt) REVERT: i 128 ASN cc_start: 0.7674 (t0) cc_final: 0.7346 (t0) REVERT: j 17 ARG cc_start: 0.7115 (mmt90) cc_final: 0.6651 (mmm160) REVERT: j 29 HIS cc_start: 0.7210 (m-70) cc_final: 0.6848 (m90) REVERT: j 45 GLU cc_start: 0.7261 (mt-10) cc_final: 0.6988 (mt-10) REVERT: j 51 LYS cc_start: 0.7453 (mtpp) cc_final: 0.7022 (mttt) REVERT: j 53 LYS cc_start: 0.6985 (mptm) cc_final: 0.6183 (tttm) REVERT: j 88 ASN cc_start: 0.6893 (OUTLIER) cc_final: 0.6181 (t0) REVERT: j 89 ASN cc_start: 0.6475 (m-40) cc_final: 0.5912 (t0) REVERT: j 98 ARG cc_start: 0.7056 (mmt-90) cc_final: 0.6558 (mtm180) REVERT: j 105 ARG cc_start: 0.5946 (OUTLIER) cc_final: 0.5401 (mtt-85) REVERT: j 114 LYS cc_start: 0.6115 (mppt) cc_final: 0.5726 (mmpt) REVERT: k 141 LYS cc_start: 0.6548 (tmtm) cc_final: 0.5700 (mtmt) REVERT: l 1 MET cc_start: 0.5919 (OUTLIER) cc_final: 0.5507 (ttp) REVERT: l 6 ARG cc_start: 0.6770 (mtt180) cc_final: 0.6394 (mtm110) REVERT: l 110 GLU cc_start: 0.6829 (tt0) cc_final: 0.6464 (tm-30) REVERT: l 133 LYS cc_start: 0.6455 (ttpt) cc_final: 0.5910 (ttmt) REVERT: l 136 MET cc_start: 0.5624 (ttp) cc_final: 0.5283 (ttm) REVERT: m 18 GLN cc_start: 0.8113 (tt0) cc_final: 0.7813 (tt0) REVERT: m 72 ASP cc_start: 0.7623 (t0) cc_final: 0.7217 (t70) REVERT: n 13 ARG cc_start: 0.6571 (tpp-160) cc_final: 0.5682 (ttp80) REVERT: n 19 GLN cc_start: 0.7346 (tt0) cc_final: 0.6501 (tt0) REVERT: n 20 GLU cc_start: 0.6126 (pt0) cc_final: 0.5703 (mt-10) REVERT: n 56 LYS cc_start: 0.5771 (mptt) cc_final: 0.5180 (mtmt) REVERT: n 81 ARG cc_start: 0.7207 (OUTLIER) cc_final: 0.5797 (mtm-85) REVERT: n 104 GLN cc_start: 0.7744 (tt0) cc_final: 0.7420 (tt0) REVERT: o 6 LYS cc_start: 0.6132 (ttpp) cc_final: 0.5665 (tmmt) REVERT: o 10 GLN cc_start: 0.6884 (mm-40) cc_final: 0.6132 (mt0) REVERT: o 11 GLU cc_start: 0.7319 (pt0) cc_final: 0.6817 (pt0) REVERT: o 63 LYS cc_start: 0.7614 (ptmm) cc_final: 0.7091 (pttt) REVERT: o 68 GLU cc_start: 0.5934 (mm-30) cc_final: 0.5672 (mp0) REVERT: o 70 VAL cc_start: 0.7904 (OUTLIER) cc_final: 0.7644 (p) REVERT: o 89 ARG cc_start: 0.7178 (mtm180) cc_final: 0.6033 (mmt180) REVERT: o 112 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7637 (mt-10) REVERT: p 9 ILE cc_start: 0.7778 (OUTLIER) cc_final: 0.7550 (mp) REVERT: p 11 ARG cc_start: 0.6928 (tpm170) cc_final: 0.6299 (ttm110) REVERT: p 85 LYS cc_start: 0.7338 (mttt) cc_final: 0.7024 (mmtm) REVERT: p 104 VAL cc_start: 0.6551 (t) cc_final: 0.6277 (m) REVERT: p 112 LYS cc_start: 0.6936 (OUTLIER) cc_final: 0.6530 (tppp) REVERT: q 60 LYS cc_start: 0.7183 (mtmt) cc_final: 0.6489 (mtpp) REVERT: q 73 LYS cc_start: 0.7900 (mmtp) cc_final: 0.7308 (mmpt) REVERT: r 28 LYS cc_start: 0.7030 (mtpt) cc_final: 0.6050 (mmtm) REVERT: r 68 ASP cc_start: 0.6625 (m-30) cc_final: 0.6391 (m-30) REVERT: r 73 LYS cc_start: 0.7587 (mttm) cc_final: 0.7301 (mtpm) REVERT: r 86 MET cc_start: 0.8039 (tpp) cc_final: 0.7282 (ttp) REVERT: s 5 GLU cc_start: 0.6591 (mt-10) cc_final: 0.5615 (pp20) REVERT: s 9 LYS cc_start: 0.6850 (mmtt) cc_final: 0.6345 (mppt) REVERT: s 18 GLU cc_start: 0.7017 (mt-10) cc_final: 0.5948 (mp0) REVERT: s 26 LYS cc_start: 0.6160 (ttmt) cc_final: 0.5471 (tppp) REVERT: s 33 LYS cc_start: 0.7488 (tttt) cc_final: 0.6681 (mttp) REVERT: s 50 LEU cc_start: 0.7364 (mt) cc_final: 0.7162 (mp) REVERT: s 51 PHE cc_start: 0.7074 (m-10) cc_final: 0.6689 (m-10) REVERT: s 69 ARG cc_start: 0.6782 (mtt-85) cc_final: 0.6018 (mtm-85) REVERT: t 7 ARG cc_start: 0.6123 (ttt180) cc_final: 0.5335 (ttm110) REVERT: t 10 GLU cc_start: 0.7031 (OUTLIER) cc_final: 0.5757 (pm20) REVERT: t 37 GLU cc_start: 0.6393 (pp20) cc_final: 0.5981 (tm-30) REVERT: t 43 LYS cc_start: 0.7208 (mtmm) cc_final: 0.6971 (mttp) REVERT: t 72 ILE cc_start: 0.7378 (tp) cc_final: 0.7042 (tt) REVERT: t 86 ARG cc_start: 0.7538 (mtm-85) cc_final: 0.6914 (mtm180) REVERT: u 10 LYS cc_start: 0.6367 (mttp) cc_final: 0.5627 (mmmt) REVERT: u 43 ASP cc_start: 0.7386 (t0) cc_final: 0.6750 (t0) REVERT: u 46 LYS cc_start: 0.6926 (mmtp) cc_final: 0.6481 (mttm) REVERT: v 70 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7423 (mp0) REVERT: v 83 GLU cc_start: 0.6670 (mm-30) cc_final: 0.6116 (mt-10) REVERT: w 54 LYS cc_start: 0.7529 (OUTLIER) cc_final: 0.6966 (tttp) REVERT: x 24 GLU cc_start: 0.6833 (tt0) cc_final: 0.6583 (tt0) REVERT: y 56 LYS cc_start: 0.7445 (pttt) cc_final: 0.7125 (ptmt) outliers start: 161 outliers final: 103 residues processed: 986 average time/residue: 2.5186 time to fit residues: 3449.5158 Evaluate side-chains 1029 residues out of total 4889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 879 time to evaluate : 6.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 28 ARG Chi-restraints excluded: chain 0 residue 37 LYS Chi-restraints excluded: chain 1 residue 41 ARG Chi-restraints excluded: chain 4 residue 22 MET Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 105 LYS Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 143 LYS Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain D residue 88 ARG Chi-restraints excluded: chain D residue 132 ARG Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain F residue 14 LYS Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 75 VAL Chi-restraints excluded: chain H residue 106 GLU Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain I residue 76 GLN Chi-restraints excluded: chain I residue 90 ASP Chi-restraints excluded: chain J residue 27 LYS Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 73 SER Chi-restraints excluded: chain J residue 85 ARG Chi-restraints excluded: chain J residue 88 MET Chi-restraints excluded: chain K residue 7 ARG Chi-restraints excluded: chain K residue 71 LEU Chi-restraints excluded: chain K residue 75 ASP Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 129 VAL Chi-restraints excluded: chain M residue 3 THR Chi-restraints excluded: chain M residue 75 GLN Chi-restraints excluded: chain M residue 86 ARG Chi-restraints excluded: chain M residue 88 LYS Chi-restraints excluded: chain M residue 94 ARG Chi-restraints excluded: chain M residue 109 ASP Chi-restraints excluded: chain N residue 11 ASP Chi-restraints excluded: chain N residue 13 LYS Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 27 LYS Chi-restraints excluded: chain N residue 68 ASP Chi-restraints excluded: chain N residue 110 LYS Chi-restraints excluded: chain N residue 113 ARG Chi-restraints excluded: chain O residue 5 SER Chi-restraints excluded: chain O residue 23 LYS Chi-restraints excluded: chain O residue 39 GLU Chi-restraints excluded: chain O residue 83 LYS Chi-restraints excluded: chain P residue 83 GLU Chi-restraints excluded: chain R residue 6 ARG Chi-restraints excluded: chain R residue 29 VAL Chi-restraints excluded: chain R residue 39 LYS Chi-restraints excluded: chain R residue 40 ARG Chi-restraints excluded: chain R residue 42 THR Chi-restraints excluded: chain R residue 67 LEU Chi-restraints excluded: chain R residue 72 SER Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain S residue 16 GLU Chi-restraints excluded: chain T residue 7 LYS Chi-restraints excluded: chain T residue 11 ILE Chi-restraints excluded: chain T residue 70 LYS Chi-restraints excluded: chain U residue 23 SER Chi-restraints excluded: chain U residue 69 LYS Chi-restraints excluded: chain V residue 3 VAL Chi-restraints excluded: chain V residue 36 GLU Chi-restraints excluded: chain W residue 19 VAL Chi-restraints excluded: chain W residue 45 LEU Chi-restraints excluded: chain W residue 109 ARG Chi-restraints excluded: chain W residue 113 LEU Chi-restraints excluded: chain W residue 143 ARG Chi-restraints excluded: chain W residue 318 THR Chi-restraints excluded: chain W residue 325 THR Chi-restraints excluded: chain W residue 356 LEU Chi-restraints excluded: chain c residue 115 GLN Chi-restraints excluded: chain c residue 129 THR Chi-restraints excluded: chain c residue 165 VAL Chi-restraints excluded: chain c residue 182 ARG Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 91 THR Chi-restraints excluded: chain d residue 128 ARG Chi-restraints excluded: chain e residue 12 LEU Chi-restraints excluded: chain e residue 21 ARG Chi-restraints excluded: chain e residue 22 ASP Chi-restraints excluded: chain e residue 126 VAL Chi-restraints excluded: chain e residue 144 GLU Chi-restraints excluded: chain f residue 4 LEU Chi-restraints excluded: chain f residue 83 TYR Chi-restraints excluded: chain f residue 88 LYS Chi-restraints excluded: chain g residue 15 VAL Chi-restraints excluded: chain g residue 36 THR Chi-restraints excluded: chain g residue 43 VAL Chi-restraints excluded: chain g residue 86 LYS Chi-restraints excluded: chain g residue 87 LEU Chi-restraints excluded: chain g residue 106 SER Chi-restraints excluded: chain g residue 122 THR Chi-restraints excluded: chain g residue 155 GLU Chi-restraints excluded: chain g residue 171 THR Chi-restraints excluded: chain h residue 21 VAL Chi-restraints excluded: chain i residue 106 LYS Chi-restraints excluded: chain i residue 138 GLN Chi-restraints excluded: chain j residue 88 ASN Chi-restraints excluded: chain j residue 105 ARG Chi-restraints excluded: chain k residue 103 ILE Chi-restraints excluded: chain l residue 1 MET Chi-restraints excluded: chain l residue 63 ILE Chi-restraints excluded: chain l residue 80 VAL Chi-restraints excluded: chain m residue 15 SER Chi-restraints excluded: chain n residue 81 ARG Chi-restraints excluded: chain o residue 34 GLU Chi-restraints excluded: chain o residue 70 VAL Chi-restraints excluded: chain o residue 85 SER Chi-restraints excluded: chain o residue 104 THR Chi-restraints excluded: chain o residue 112 GLU Chi-restraints excluded: chain p residue 9 ILE Chi-restraints excluded: chain p residue 22 LYS Chi-restraints excluded: chain p residue 112 LYS Chi-restraints excluded: chain q residue 33 VAL Chi-restraints excluded: chain q residue 51 VAL Chi-restraints excluded: chain q residue 64 VAL Chi-restraints excluded: chain r residue 66 ILE Chi-restraints excluded: chain r residue 70 LYS Chi-restraints excluded: chain t residue 10 GLU Chi-restraints excluded: chain u residue 53 LYS Chi-restraints excluded: chain u residue 58 SER Chi-restraints excluded: chain u residue 62 THR Chi-restraints excluded: chain u residue 65 VAL Chi-restraints excluded: chain u residue 73 LYS Chi-restraints excluded: chain v residue 30 SER Chi-restraints excluded: chain v residue 70 GLU Chi-restraints excluded: chain w residue 54 LYS Chi-restraints excluded: chain x residue 4 LYS Chi-restraints excluded: chain x residue 40 SER Chi-restraints excluded: chain y residue 19 LYS Chi-restraints excluded: chain y residue 41 THR Chi-restraints excluded: chain z residue 30 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1023 random chunks: chunk 644 optimal weight: 6.9990 chunk 864 optimal weight: 5.9990 chunk 248 optimal weight: 0.8980 chunk 748 optimal weight: 4.9990 chunk 119 optimal weight: 9.9990 chunk 225 optimal weight: 4.9990 chunk 812 optimal weight: 4.9990 chunk 340 optimal weight: 7.9990 chunk 834 optimal weight: 10.0000 chunk 102 optimal weight: 8.9990 chunk 149 optimal weight: 10.0000 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 29 GLN C 18 HIS ** C 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 198 HIS F 19 ASN F 77 ASN ** F 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 3 HIS J 110 GLN ** L 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 112 GLN P 46 HIS Q 63 GLN U 68 HIS W 248 HIS c 117 GLN e 165 HIS g 64 GLN k 104 GLN u 12 GLN x 58 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.164634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.145042 restraints weight = 127373.271| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 0.57 r_work: 0.3323 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 156812 Z= 0.379 Angle : 0.849 17.894 234226 Z= 0.438 Chirality : 0.045 0.387 29769 Planarity : 0.008 0.156 12793 Dihedral : 23.358 177.228 77638 Min Nonbonded Distance : 1.742 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.04 % Favored : 96.82 % Rotamer: Outliers : 3.64 % Allowed : 16.10 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.10), residues: 5853 helix: 0.53 (0.11), residues: 2052 sheet: -0.33 (0.14), residues: 1165 loop : -0.39 (0.11), residues: 2636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP C 23 HIS 0.012 0.002 HIS P 46 PHE 0.025 0.003 PHE q 53 TYR 0.027 0.003 TYR r 38 ARG 0.009 0.001 ARG L 69 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 53152.60 seconds wall clock time: 920 minutes 28.29 seconds (55228.29 seconds total)