Starting phenix.real_space_refine on Fri Mar 15 16:28:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qsl_14133/03_2024/7qsl_14133_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qsl_14133/03_2024/7qsl_14133.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qsl_14133/03_2024/7qsl_14133_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qsl_14133/03_2024/7qsl_14133_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qsl_14133/03_2024/7qsl_14133_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qsl_14133/03_2024/7qsl_14133.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qsl_14133/03_2024/7qsl_14133.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qsl_14133/03_2024/7qsl_14133_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qsl_14133/03_2024/7qsl_14133_updated.pdb" } resolution = 2.76 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= 0.938 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: 9 Type Number sf(0) Gaussians K 1 8.98 5 Fe 28 7.16 5 Zn 1 6.06 5 P 55 5.49 5 Mg 1 5.21 5 S 473 5.16 5 C 44472 2.51 5 N 11320 2.21 5 O 13382 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 42": "OD1" <-> "OD2" Residue "A PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 27": "OE1" <-> "OE2" Residue "B ASP 35": "OD1" <-> "OD2" Residue "B PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 71": "NH1" <-> "NH2" Residue "B PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 109": "OE1" <-> "OE2" Residue "B ARG 111": "NH1" <-> "NH2" Residue "B TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 154": "OE1" <-> "OE2" Residue "B TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 172": "NH1" <-> "NH2" Residue "B ARG 179": "NH1" <-> "NH2" Residue "C ARG 8": "NH1" <-> "NH2" Residue "C ARG 12": "NH1" <-> "NH2" Residue "C ARG 14": "NH1" <-> "NH2" Residue "C PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 77": "OD1" <-> "OD2" Residue "C ASP 147": "OD1" <-> "OD2" Residue "C ARG 149": "NH1" <-> "NH2" Residue "C PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 158": "OE1" <-> "OE2" Residue "D ARG 2": "NH1" <-> "NH2" Residue "D GLU 67": "OE1" <-> "OE2" Residue "D TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 123": "OE1" <-> "OE2" Residue "D PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 221": "NH1" <-> "NH2" Residue "D ARG 233": "NH1" <-> "NH2" Residue "D GLU 343": "OE1" <-> "OE2" Residue "D PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 425": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 427": "OE1" <-> "OE2" Residue "D ASP 429": "OD1" <-> "OD2" Residue "E PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 26": "OE1" <-> "OE2" Residue "E ARG 30": "NH1" <-> "NH2" Residue "E GLU 71": "OE1" <-> "OE2" Residue "E GLU 82": "OE1" <-> "OE2" Residue "E TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 168": "OD1" <-> "OD2" Residue "E GLU 170": "OE1" <-> "OE2" Residue "E ARG 190": "NH1" <-> "NH2" Residue "E GLU 204": "OE1" <-> "OE2" Residue "F PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 32": "NH1" <-> "NH2" Residue "F GLU 99": "OE1" <-> "OE2" Residue "F ARG 112": "NH1" <-> "NH2" Residue "F ARG 132": "NH1" <-> "NH2" Residue "F ARG 139": "NH1" <-> "NH2" Residue "F GLU 189": "OE1" <-> "OE2" Residue "F ARG 249": "NH1" <-> "NH2" Residue "F GLU 278": "OE1" <-> "OE2" Residue "F ARG 349": "NH1" <-> "NH2" Residue "F ASP 370": "OD1" <-> "OD2" Residue "F ARG 429": "NH1" <-> "NH2" Residue "F PHE 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 10": "OE1" <-> "OE2" Residue "G PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 21": "OE1" <-> "OE2" Residue "G ARG 39": "NH1" <-> "NH2" Residue "G ARG 53": "NH1" <-> "NH2" Residue "G GLU 60": "OE1" <-> "OE2" Residue "G ASP 180": "OD1" <-> "OD2" Residue "G ARG 218": "NH1" <-> "NH2" Residue "G ARG 243": "NH1" <-> "NH2" Residue "G GLU 246": "OE1" <-> "OE2" Residue "G ARG 253": "NH1" <-> "NH2" Residue "G GLU 260": "OE1" <-> "OE2" Residue "G TYR 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 285": "NH1" <-> "NH2" Residue "G ARG 302": "NH1" <-> "NH2" Residue "G ASP 314": "OD1" <-> "OD2" Residue "G GLU 346": "OE1" <-> "OE2" Residue "G GLU 347": "OE1" <-> "OE2" Residue "G ARG 385": "NH1" <-> "NH2" Residue "G ARG 418": "NH1" <-> "NH2" Residue "G GLU 512": "OE1" <-> "OE2" Residue "G PHE 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 540": "OD1" <-> "OD2" Residue "G TYR 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 625": "OE1" <-> "OE2" Residue "G GLU 637": "OE1" <-> "OE2" Residue "G PHE 642": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 675": "OD1" <-> "OD2" Residue "H ARG 25": "NH1" <-> "NH2" Residue "H ARG 34": "NH1" <-> "NH2" Residue "H PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 62": "NH1" <-> "NH2" Residue "H ASP 199": "OD1" <-> "OD2" Residue "H GLU 204": "OE1" <-> "OE2" Residue "H PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 214": "OE1" <-> "OE2" Residue "H PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 227": "OE1" <-> "OE2" Residue "H GLU 253": "OE1" <-> "OE2" Residue "I TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 95": "OE1" <-> "OE2" Residue "I ARG 108": "NH1" <-> "NH2" Residue "J GLU 81": "OE1" <-> "OE2" Residue "J GLU 100": "OE1" <-> "OE2" Residue "J PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 170": "OE1" <-> "OE2" Residue "J ARG 173": "NH1" <-> "NH2" Residue "K GLU 70": "OE1" <-> "OE2" Residue "L GLU 102": "OE1" <-> "OE2" Residue "L PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 161": "NH1" <-> "NH2" Residue "L ASP 163": "OD1" <-> "OD2" Residue "L ASP 179": "OD1" <-> "OD2" Residue "L ARG 262": "NH1" <-> "NH2" Residue "L GLU 268": "OE1" <-> "OE2" Residue "L GLU 353": "OE1" <-> "OE2" Residue "L PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 368": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 397": "OE1" <-> "OE2" Residue "L TYR 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 559": "OE1" <-> "OE2" Residue "L PHE 588": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 606": "OE1" <-> "OE2" Residue "M GLU 87": "OE1" <-> "OE2" Residue "M PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 222": "OE1" <-> "OE2" Residue "M TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 419": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 432": "NH1" <-> "NH2" Residue "N GLU 54": "OE1" <-> "OE2" Residue "N GLU 117": "OE1" <-> "OE2" Residue "N PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 295": "NH1" <-> "NH2" Residue "N PHE 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 20": "OE1" <-> "OE2" Residue "O GLU 53": "OE1" <-> "OE2" Residue "O ASP 85": "OD1" <-> "OD2" Residue "O ASP 131": "OD1" <-> "OD2" Residue "O TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 302": "NH1" <-> "NH2" Residue "O ARG 305": "NH1" <-> "NH2" Residue "O TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 40": "NH1" <-> "NH2" Residue "P ARG 50": "NH1" <-> "NH2" Residue "P GLU 52": "OE1" <-> "OE2" Residue "P ASP 79": "OD1" <-> "OD2" Residue "P ARG 82": "NH1" <-> "NH2" Residue "P ARG 97": "NH1" <-> "NH2" Residue "P GLU 98": "OE1" <-> "OE2" Residue "P GLU 107": "OE1" <-> "OE2" Residue "P GLU 127": "OE1" <-> "OE2" Residue "P PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 147": "NH1" <-> "NH2" Residue "P GLU 155": "OE1" <-> "OE2" Residue "P ARG 157": "NH1" <-> "NH2" Residue "P GLU 158": "OE1" <-> "OE2" Residue "P PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 175": "OE1" <-> "OE2" Residue "P ARG 177": "NH1" <-> "NH2" Residue "P PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 224": "NH1" <-> "NH2" Residue "P ARG 235": "NH1" <-> "NH2" Residue "P PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 251": "NH1" <-> "NH2" Residue "P TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 282": "OD1" <-> "OD2" Residue "P GLU 285": "OE1" <-> "OE2" Residue "P GLU 306": "OE1" <-> "OE2" Residue "P ARG 325": "NH1" <-> "NH2" Residue "Q PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 104": "OD1" <-> "OD2" Residue "R TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 31": "NH1" <-> "NH2" Residue "R GLU 78": "OE1" <-> "OE2" Residue "S ARG 25": "NH1" <-> "NH2" Residue "S ASP 59": "OD1" <-> "OD2" Residue "T GLU 9": "OE1" <-> "OE2" Residue "T ASP 23": "OD1" <-> "OD2" Residue "T ASP 26": "OD1" <-> "OD2" Residue "T GLU 28": "OE1" <-> "OE2" Residue "T GLU 68": "OE1" <-> "OE2" Residue "T ASP 78": "OD1" <-> "OD2" Residue "T TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 39": "OD1" <-> "OD2" Residue "U ASP 43": "OD1" <-> "OD2" Residue "U GLU 49": "OE1" <-> "OE2" Residue "U GLU 55": "OE1" <-> "OE2" Residue "U GLU 61": "OE1" <-> "OE2" Residue "U GLU 68": "OE1" <-> "OE2" Residue "U TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 21": "OE1" <-> "OE2" Residue "V ARG 22": "NH1" <-> "NH2" Residue "V ASP 32": "OD1" <-> "OD2" Residue "V GLU 78": "OE1" <-> "OE2" Residue "V GLU 104": "OE1" <-> "OE2" Residue "W GLU 27": "OE1" <-> "OE2" Residue "W ARG 31": "NH1" <-> "NH2" Residue "W TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 42": "OE1" <-> "OE2" Residue "W ASP 53": "OD1" <-> "OD2" Residue "W GLU 111": "OE1" <-> "OE2" Residue "W ARG 114": "NH1" <-> "NH2" Residue "X GLU 16": "OE1" <-> "OE2" Residue "X GLU 41": "OE1" <-> "OE2" Residue "X GLU 48": "OE1" <-> "OE2" Residue "X GLU 49": "OE1" <-> "OE2" Residue "X ARG 54": "NH1" <-> "NH2" Residue "X PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 97": "NH1" <-> "NH2" Residue "X ARG 118": "NH1" <-> "NH2" Residue "X ASP 133": "OD1" <-> "OD2" Residue "X ARG 134": "NH1" <-> "NH2" Residue "X ARG 144": "NH1" <-> "NH2" Residue "X ARG 146": "NH1" <-> "NH2" Residue "X GLU 148": "OE1" <-> "OE2" Residue "Y ARG 6": "NH1" <-> "NH2" Residue "Y GLU 13": "OE1" <-> "OE2" Residue "Y TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 57": "NH1" <-> "NH2" Residue "Y ARG 80": "NH1" <-> "NH2" Residue "Y ARG 103": "NH1" <-> "NH2" Residue "Y GLU 130": "OE1" <-> "OE2" Residue "Y GLU 137": "OE1" <-> "OE2" Residue "Z TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 64": "OD1" <-> "OD2" Residue "Z ARG 68": "NH1" <-> "NH2" Residue "Z GLU 78": "OE1" <-> "OE2" Residue "Z ARG 82": "NH1" <-> "NH2" Residue "Z GLU 89": "OE1" <-> "OE2" Residue "Z GLU 108": "OE1" <-> "OE2" Residue "Z ARG 128": "NH1" <-> "NH2" Residue "Z GLU 132": "OE1" <-> "OE2" Residue "a ARG 53": "NH1" <-> "NH2" Residue "a ASP 70": "OD1" <-> "OD2" Residue "b ARG 3": "NH1" <-> "NH2" Residue "b ARG 46": "NH1" <-> "NH2" Residue "b ARG 57": "NH1" <-> "NH2" Residue "b GLU 78": "OE1" <-> "OE2" Residue "b ARG 82": "NH1" <-> "NH2" Residue "c PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 41": "OE1" <-> "OE2" Residue "c ARG 44": "NH1" <-> "NH2" Residue "d ARG 51": "NH1" <-> "NH2" Residue "d TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 99": "OE1" <-> "OE2" Residue "d ASP 105": "OD1" <-> "OD2" Residue "d GLU 111": "OE1" <-> "OE2" Residue "d GLU 114": "OE1" <-> "OE2" Residue "e ARG 8": "NH1" <-> "NH2" Residue "e ARG 50": "NH1" <-> "NH2" Residue "e GLU 60": "OE1" <-> "OE2" Residue "e ARG 63": "NH1" <-> "NH2" Residue "e ARG 79": "NH1" <-> "NH2" Residue "e ARG 82": "NH1" <-> "NH2" Residue "f ASP 9": "OD1" <-> "OD2" Residue "f PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 28": "NH1" <-> "NH2" Residue "f ASP 31": "OD1" <-> "OD2" Residue "f GLU 32": "OE1" <-> "OE2" Residue "f PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 46": "NH1" <-> "NH2" Residue "f GLU 47": "OE1" <-> "OE2" Residue "g GLU 28": "OE1" <-> "OE2" Residue "g ASP 29": "OD1" <-> "OD2" Residue "g GLU 31": "OE1" <-> "OE2" Residue "g ASP 34": "OD1" <-> "OD2" Residue "g GLU 39": "OE1" <-> "OE2" Residue "g GLU 92": "OE1" <-> "OE2" Residue "g TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ARG 20": "NH1" <-> "NH2" Residue "h ARG 26": "NH1" <-> "NH2" Residue "h GLU 51": "OE1" <-> "OE2" Residue "h GLU 54": "OE1" <-> "OE2" Residue "h TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 65": "OE1" <-> "OE2" Residue "h ARG 77": "NH1" <-> "NH2" Residue "h TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 88": "OE1" <-> "OE2" Residue "h GLU 102": "OE1" <-> "OE2" Residue "h ARG 112": "NH1" <-> "NH2" Residue "h GLU 131": "OE1" <-> "OE2" Residue "i ARG 15": "NH1" <-> "NH2" Residue "i ARG 18": "NH1" <-> "NH2" Residue "i GLU 26": "OE1" <-> "OE2" Residue "i ARG 44": "NH1" <-> "NH2" Residue "i PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i GLU 111": "OE1" <-> "OE2" Residue "i GLU 114": "OE1" <-> "OE2" Residue "i GLU 121": "OE1" <-> "OE2" Residue "j PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j GLU 26": "OE1" <-> "OE2" Residue "j GLU 62": "OE1" <-> "OE2" Residue "j GLU 63": "OE1" <-> "OE2" Residue "j GLU 71": "OE1" <-> "OE2" Residue "k ASP 17": "OD1" <-> "OD2" Residue "k GLU 24": "OE1" <-> "OE2" Residue "k GLU 33": "OE1" <-> "OE2" Residue "k ARG 38": "NH1" <-> "NH2" Residue "k ARG 41": "NH1" <-> "NH2" Residue "l TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 19": "OE1" <-> "OE2" Residue "l ARG 30": "NH1" <-> "NH2" Residue "l GLU 32": "OE1" <-> "OE2" Residue "l GLU 35": "OE1" <-> "OE2" Residue "l TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ARG 142": "NH1" <-> "NH2" Residue "l GLU 151": "OE1" <-> "OE2" Residue "m TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m GLU 21": "OE1" <-> "OE2" Residue "m TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ARG 39": "NH1" <-> "NH2" Residue "m GLU 45": "OE1" <-> "OE2" Residue "m ARG 56": "NH1" <-> "NH2" Residue "m GLU 60": "OE1" <-> "OE2" Residue "m ARG 71": "NH1" <-> "NH2" Residue "m TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m GLU 112": "OE1" <-> "OE2" Residue "n ARG 21": "NH1" <-> "NH2" Residue "n GLU 27": "OE1" <-> "OE2" Residue "n ARG 64": "NH1" <-> "NH2" Residue "n GLU 68": "OE1" <-> "OE2" Residue "n GLU 69": "OE1" <-> "OE2" Residue "n PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n GLU 91": "OE1" <-> "OE2" Residue "n ARG 92": "NH1" <-> "NH2" Residue "n GLU 94": "OE1" <-> "OE2" Residue "n TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ARG 134": "NH1" <-> "NH2" Residue "n ARG 149": "NH1" <-> "NH2" Residue "n GLU 151": "OE1" <-> "OE2" Residue "n ASP 161": "OD1" <-> "OD2" Residue "o ARG 6": "NH1" <-> "NH2" Residue "o ARG 20": "NH1" <-> "NH2" Residue "o ASP 27": "OD1" <-> "OD2" Residue "o TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o GLU 32": "OE1" <-> "OE2" Residue "o ARG 36": "NH1" <-> "NH2" Residue "o ARG 64": "NH1" <-> "NH2" Residue "o ARG 97": "NH1" <-> "NH2" Residue "o ARG 103": "NH1" <-> "NH2" Residue "o ARG 105": "NH1" <-> "NH2" Residue "o ARG 106": "NH1" <-> "NH2" Residue "o ARG 114": "NH1" <-> "NH2" Residue "p TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ARG 53": "NH1" <-> "NH2" Residue "p ARG 92": "NH1" <-> "NH2" Residue "p GLU 116": "OE1" <-> "OE2" Residue "q ARG 21": "NH1" <-> "NH2" Residue "q PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ARG 29": "NH1" <-> "NH2" Residue "q TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q GLU 50": "OE1" <-> "OE2" Residue "q ARG 88": "NH1" <-> "NH2" Residue "q TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ARG 59": "NH1" <-> "NH2" Residue "r GLU 90": "OE1" <-> "OE2" Residue "r GLU 109": "OE1" <-> "OE2" Residue "r TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.24s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 69733 Number of models: 1 Model: "" Number of chains: 109 Chain: "A" Number of atoms: 921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 921 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 1241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1241 Classifications: {'peptide': 155} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 144} Chain: "C" Number of atoms: 1738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1738 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 16, 'TRANS': 192} Chain: "D" Number of atoms: 3459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3459 Classifications: {'peptide': 430} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 401} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'2MR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 1659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1659 Classifications: {'peptide': 214} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 192} Chain: "F" Number of atoms: 3336 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 432, 3326 Classifications: {'peptide': 432} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 410} Conformer: "B" Number of residues, atoms: 432, 3326 Classifications: {'peptide': 432} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 410} bond proxies already assigned to first conformer: 3389 Chain: "G" Number of atoms: 5366 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 699, 5355 Classifications: {'peptide': 699} Link IDs: {'PTRANS': 33, 'TRANS': 665} Conformer: "B" Number of residues, atoms: 699, 5355 Classifications: {'peptide': 699} Link IDs: {'PTRANS': 33, 'TRANS': 665} bond proxies already assigned to first conformer: 5432 Chain: "H" Number of atoms: 2517 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 318, 2509 Classifications: {'peptide': 318} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 295} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 318, 2509 Classifications: {'peptide': 318} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 295} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 2572 Chain: "I" Number of atoms: 1414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1414 Classifications: {'peptide': 176} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 165} Chain: "J" Number of atoms: 1345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1345 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 3, 'TRANS': 171} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "K" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 745 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 1, 'TRANS': 96} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 4802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4802 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 27, 'TRANS': 578} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 3654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3654 Classifications: {'peptide': 459} Link IDs: {'PCIS': 3, 'PTRANS': 17, 'TRANS': 438} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 2733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2733 Classifications: {'peptide': 347} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 325} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 2589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2589 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 15, 'TRANS': 304} Chain: "P" Number of atoms: 2768 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 342, 2754 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 22, 'TRANS': 319} Conformer: "B" Number of residues, atoms: 342, 2754 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 22, 'TRANS': 319} bond proxies already assigned to first conformer: 2814 Chain: "Q" Number of atoms: 1049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1049 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 6, 'TRANS': 122} Chain: "R" Number of atoms: 740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 740 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "S" Number of atoms: 700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 700 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 4, 'TRANS': 82} Chain: "T" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 688 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 4, 'TRANS': 80} Chain: "U" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 693 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 5, 'TRANS': 80} Chain: "V" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 928 Classifications: {'peptide': 115} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 106} Chain: "W" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 976 Classifications: {'peptide': 115} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 108} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "X" Number of atoms: 1402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1402 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 12, 'TRANS': 158} Chain: "Y" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1030 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 5, 'TRANS': 134} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'AYA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "Z" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1152 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 7, 'TRANS': 133} Chain: "a" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 569 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "b" Number of atoms: 651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 651 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 11, 'TRANS': 71} Chain: "c" Number of atoms: 414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 414 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "d" Number of atoms: 999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 999 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 9, 'TRANS': 110} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'AME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "e" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 829 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 5, 'TRANS': 93} Chain: "f" Number of atoms: 492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 492 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 2, 'TRANS': 54} Chain: "g" Number of atoms: 839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 839 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 8, 'TRANS': 91} Chain: "h" Number of atoms: 1154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1154 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 10, 'TRANS': 127} Chain: "i" Number of atoms: 1097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1097 Classifications: {'peptide': 127} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 113} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'SAC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "j" Number of atoms: 580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 580 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 7, 'TRANS': 59} Chain: "k" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 653 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "l" Number of atoms: 1314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1314 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 20, 'TRANS': 135} Chain: "m" Number of atoms: 1067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1067 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 8, 'TRANS': 119} Chain: "n" Number of atoms: 1492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1492 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 15, 'TRANS': 156} Chain: "o" Number of atoms: 1048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1048 Classifications: {'peptide': 122} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 114} Chain: "p" Number of atoms: 1453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1453 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 10, 'TRANS': 162} Chain: "q" Number of atoms: 1209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1209 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 11, 'TRANS': 133} Chain: "r" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 776 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 11, 'TRANS': 83} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'AYA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "s" Number of atoms: 391 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 45, 380 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 4, 'TRANS': 40} Conformer: "B" Number of residues, atoms: 45, 380 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 4, 'TRANS': 40} bond proxies already assigned to first conformer: 380 Chain: "A" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 147 Unusual residues: {'3PE': 2, 'PC1': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 63 Chain: "B" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 49 Unusual residues: {'PC1': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'FMN': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 21 Unusual residues: {' K': 1, 'FES': 1, 'SF4': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "H" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 79 Unusual residues: {'3PE': 1, 'CDL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 72 Chain: "I" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 54 Unusual residues: {'3PE': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Chain: "K" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 69 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 31 Chain: "L" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 144 Unusual residues: {'3PE': 2, 'CDL': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 58 Chain: "M" Number of atoms: 275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 275 Unusual residues: {'3PE': 4, 'PC1': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 37 Chain: "N" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'3PE': 1, 'CDL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 43 Chain: "O" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 137 Unusual residues: {'3PE': 1, 'NDP': 1, 'PC1': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'EHZ': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "U" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'EHZ': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "X" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 73 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 27 Chain: "Y" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 157 Unusual residues: {'3PE': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 47 Chain: "Z" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 83 Unusual residues: {'3PE': 1, 'PC1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 22 Chain: "b" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 47 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "d" Number of atoms: 135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 135 Unusual residues: {'3PE': 1, 'CDL': 1, 'PC1': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 70 Chain: "h" Number of atoms: 122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 122 Unusual residues: {'CDL': 1, 'PC1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 32 Chain: "i" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'CHD': 1} Classifications: {'undetermined': 1} Chain: "m" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 80 Unusual residues: {'3PE': 1, 'PC1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 25 Chain: "o" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'MYR': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MYR:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "r" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 62 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 38 Chain: "A" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "B" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 59 Classifications: {'water': 59} Link IDs: {None: 58} Chain: "C" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 54 Classifications: {'water': 54} Link IDs: {None: 53} Chain: "D" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 123 Classifications: {'water': 123} Link IDs: {None: 122} Chain: "E" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "F" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 30 Classifications: {'water': 30} Link IDs: {None: 29} Chain: "G" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 120 Classifications: {'water': 120} Link IDs: {None: 119} Chain: "H" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 64 Classifications: {'water': 64} Link IDs: {None: 63} Chain: "I" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 64 Classifications: {'water': 64} Link IDs: {None: 63} Chain: "J" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "K" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "L" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 40 Classifications: {'water': 40} Link IDs: {None: 39} Chain: "M" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 62 Classifications: {'water': 62} Link IDs: {None: 61} Chain: "N" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 60 Classifications: {'water': 60} Link IDs: {None: 59} Chain: "O" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "P" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 44 Classifications: {'water': 44} Link IDs: {None: 43} Chain: "Q" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 51 Classifications: {'water': 51} Link IDs: {None: 50} Chain: "R" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "W" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "X" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "Y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Z" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} Chain: "a" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "b" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "d" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "e" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "g" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "h" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "i" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "k" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "l" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "m" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "n" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "p" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "q" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "r" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "s" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1668 SG CYS B 119 98.032 95.328 203.804 1.00 26.34 S ATOM 1898 SG CYS B 149 95.942 92.867 208.386 1.00 25.37 S ATOM 1164 SG CYS B 54 92.726 91.433 202.921 1.00 28.15 S ATOM 1170 SG CYS B 55 92.018 97.088 205.643 1.00 27.84 S ATOM 8167 SG CYS E 103 119.773 47.273 258.120 1.00 42.75 S ATOM 8201 SG CYS E 108 118.439 44.488 260.155 1.00 42.92 S ATOM 8481 SG CYS E 144 122.205 44.069 254.823 1.00 41.31 S ATOM 8504 SG CYS E 148 121.181 41.238 255.836 1.00 45.22 S ATOM 11739 SG CYS F 362 123.809 54.580 234.609 1.00 29.36 S ATOM 11759 SG CYS F 365 121.046 53.437 239.412 1.00 30.63 S ATOM 12083 SG CYS F 405 125.980 49.629 238.582 1.00 32.72 S ATOM 11720 SG CYS F 359 127.438 55.320 239.962 1.00 32.04 S ATOM 13180 SG CYS G 114 119.060 72.859 225.754 1.00 26.82 S ATOM 13119 SG CYS G 105 113.126 74.949 227.648 1.00 24.91 S ATOM 13140 SG CYS G 108 118.543 77.825 229.728 1.00 26.36 S ATOM 13512 SG CYS G 156 127.726 67.369 230.210 1.00 28.60 S ATOM 13489 SG CYS G 153 125.026 69.270 236.005 1.00 27.89 S ATOM 13536 SG CYS G 159 131.087 70.547 234.539 1.00 30.06 S ATOM 13866 SG CYS G 203 126.401 73.165 230.848 1.00 28.46 S ATOM 12625 SG CYS G 41 128.628 60.560 227.897 1.00 29.44 S ATOM 12711 SG CYS G 52 124.773 60.764 227.023 1.00 28.99 S ATOM 12736 SG CYS G 55 126.551 56.440 223.464 1.00 30.74 S ATOM 12837 SG CYS G 69 129.643 57.323 224.688 1.00 31.26 S ATOM 21191 SG CYS I 119 99.475 87.092 214.283 1.00 24.34 S ATOM 21165 SG CYS I 116 99.466 93.618 215.214 1.00 24.67 S ATOM 21212 SG CYS I 122 101.202 89.282 219.905 1.00 24.89 S ATOM 20939 SG CYS I 87 104.914 90.189 214.578 1.00 24.75 S ATOM 21241 SG CYS I 126 104.032 86.124 227.137 1.00 24.89 S ATOM 20870 SG CYS I 77 108.583 90.696 228.204 1.00 26.53 S ATOM 20912 SG CYS I 83 107.129 88.858 222.220 1.00 25.18 S ATOM 20889 SG CYS I 80 109.531 84.403 225.730 1.00 25.56 S ATOM 41795 SG CYS R 59 106.195 81.680 242.270 1.00 31.70 S ATOM 41973 SG CYS R 84 109.048 82.406 240.124 1.00 33.40 S ATOM 41995 SG CYS R 87 106.762 84.877 241.017 1.00 31.37 S Residues with excluded nonbonded symmetry interactions: 5 residue: pdb=" N AHIS F 356 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS F 356 " occ=0.50 residue: pdb=" N APHE G 642 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE G 642 " occ=0.50 residue: pdb=" N ALEU H 61 " occ=0.50 ... (14 atoms not shown) pdb=" CD2BLEU H 61 " occ=0.50 residue: pdb=" N ATRP P 265 " occ=0.50 ... (26 atoms not shown) pdb=" CH2BTRP P 265 " occ=0.50 residue: pdb=" N AARG s 74 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG s 74 " occ=0.50 Time building chain proxies: 34.11, per 1000 atoms: 0.49 Number of scatterers: 69733 At special positions: 0 Unit cell: (188.15, 201.642, 290.845, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Zn 1 29.99 Fe 28 26.01 K 1 19.00 S 473 16.00 P 55 15.00 Mg 1 11.99 O 13382 8.00 N 11320 7.00 C 44472 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS X 45 " - pdb=" SG CYS X 55 " distance=2.03 Simple disulfide: pdb=" SG CYS X 87 " - pdb=" SG CYS X 99 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 94 " - pdb=" SG CYS Y 114 " distance=2.03 Simple disulfide: pdb=" SG CYS e 32 " - pdb=" SG CYS e 65 " distance=2.03 Simple disulfide: pdb=" SG CYS e 42 " - pdb=" SG CYS e 55 " distance=2.04 Simple disulfide: pdb=" SG CYS o 68 " - pdb=" SG CYS o 79 " distance=2.02 Simple disulfide: pdb=" SG CYS p 112 " - pdb=" SG CYS p 124 " distance=2.03 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 23.73 Conformation dependent library (CDL) restraints added in 11.2 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 301 " pdb="FE1 FES E 301 " - pdb=" SG CYS E 108 " pdb="FE1 FES E 301 " - pdb=" SG CYS E 103 " pdb="FE2 FES E 301 " - pdb=" SG CYS E 144 " pdb="FE2 FES E 301 " - pdb=" SG CYS E 148 " pdb=" FES G 803 " pdb="FE1 FES G 803 " - pdb=" SG CYS G 52 " pdb="FE2 FES G 803 " - pdb=" SG CYS G 55 " pdb="FE2 FES G 803 " - pdb=" SG CYS G 69 " pdb="FE1 FES G 803 " - pdb=" SG CYS G 41 " pdb=" SF4 B 201 " pdb="FE1 SF4 B 201 " - pdb=" SG CYS B 119 " pdb="FE3 SF4 B 201 " - pdb=" SG CYS B 54 " pdb="FE2 SF4 B 201 " - pdb=" SG CYS B 149 " pdb="FE4 SF4 B 201 " - pdb=" SG CYS B 55 " pdb=" SF4 F 502 " pdb="FE3 SF4 F 502 " - pdb=" SG CYS F 405 " pdb="FE4 SF4 F 502 " - pdb=" SG CYS F 359 " pdb="FE2 SF4 F 502 " - pdb=" SG CYS F 365 " pdb="FE1 SF4 F 502 " - pdb=" SG CYS F 362 " pdb=" SF4 G 801 " pdb="FE3 SF4 G 801 " - pdb=" NE2 HIS G 101 " pdb="FE4 SF4 G 801 " - pdb=" SG CYS G 108 " pdb="FE1 SF4 G 801 " - pdb=" SG CYS G 114 " pdb="FE2 SF4 G 801 " - pdb=" SG CYS G 105 " pdb=" SF4 G 802 " pdb="FE3 SF4 G 802 " - pdb=" SG CYS G 159 " pdb="FE2 SF4 G 802 " - pdb=" SG CYS G 153 " pdb="FE1 SF4 G 802 " - pdb=" SG CYS G 156 " pdb="FE4 SF4 G 802 " - pdb=" SG CYS G 203 " pdb=" SF4 I 202 " pdb="FE2 SF4 I 202 " - pdb=" SG CYS I 116 " pdb="FE4 SF4 I 202 " - pdb=" SG CYS I 87 " pdb="FE3 SF4 I 202 " - pdb=" SG CYS I 122 " pdb="FE1 SF4 I 202 " - pdb=" SG CYS I 119 " pdb=" SF4 I 203 " pdb="FE1 SF4 I 203 " - pdb=" SG CYS I 126 " pdb="FE4 SF4 I 203 " - pdb=" SG CYS I 80 " pdb="FE2 SF4 I 203 " - pdb=" SG CYS I 77 " pdb="FE3 SF4 I 203 " - pdb=" SG CYS I 83 " Number of angles added : 81 Zn2+ tetrahedral coordination pdb=" ZN R 201 " pdb="ZN ZN R 201 " - pdb=" NE2 HIS R 68 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 84 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 87 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 59 " Number of angles added : 3 16390 Ramachandran restraints generated. 8195 Oldfield, 0 Emsley, 8195 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15580 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 359 helices and 30 sheets defined 53.3% alpha, 4.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.58 Creating SS restraints... Processing helix chain 'A' and resid 3 through 23 Processing helix chain 'A' and resid 31 through 34 No H-bonds generated for 'chain 'A' and resid 31 through 34' Processing helix chain 'A' and resid 56 through 80 removed outlier: 3.593A pdb=" N LEU A 64 " --> pdb=" O ILE A 60 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE A 69 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA A 70 " --> pdb=" O ASP A 66 " (cutoff:3.500A) Proline residue: A 74 - end of helix removed outlier: 5.239A pdb=" N TRP A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N GLN A 80 " --> pdb=" O PRO A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 107 Processing helix chain 'B' and resid 26 through 42 Processing helix chain 'B' and resid 54 through 63 removed outlier: 3.861A pdb=" N GLU B 58 " --> pdb=" O CYS B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 72 Processing helix chain 'B' and resid 80 through 82 No H-bonds generated for 'chain 'B' and resid 80 through 82' Processing helix chain 'B' and resid 94 through 105 Proline residue: B 98 - end of helix Processing helix chain 'B' and resid 117 through 122 Processing helix chain 'B' and resid 124 through 126 No H-bonds generated for 'chain 'B' and resid 124 through 126' Processing helix chain 'B' and resid 136 through 138 No H-bonds generated for 'chain 'B' and resid 136 through 138' Processing helix chain 'B' and resid 153 through 169 Processing helix chain 'B' and resid 172 through 177 Processing helix chain 'C' and resid 16 through 32 Processing helix chain 'C' and resid 54 through 66 removed outlier: 3.636A pdb=" N VAL C 57 " --> pdb=" O PRO C 54 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ILE C 58 " --> pdb=" O ASP C 55 " (cutoff:3.500A) Proline residue: C 59 - end of helix removed outlier: 3.650A pdb=" N THR C 62 " --> pdb=" O PRO C 59 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU C 64 " --> pdb=" O LEU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 122 No H-bonds generated for 'chain 'C' and resid 120 through 122' Processing helix chain 'C' and resid 125 through 138 removed outlier: 3.680A pdb=" N ASN C 128 " --> pdb=" O LYS C 125 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N TRP C 129 " --> pdb=" O ALA C 126 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU C 131 " --> pdb=" O ASN C 128 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N MET C 137 " --> pdb=" O ILE C 134 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N PHE C 138 " --> pdb=" O TRP C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 209 No H-bonds generated for 'chain 'C' and resid 207 through 209' Processing helix chain 'D' and resid 8 through 14 removed outlier: 3.707A pdb=" N GLN D 13 " --> pdb=" O GLU D 9 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N TYR D 14 " --> pdb=" O TRP D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 25 No H-bonds generated for 'chain 'D' and resid 23 through 25' Processing helix chain 'D' and resid 87 through 93 removed outlier: 3.855A pdb=" N GLU D 92 " --> pdb=" O GLU D 88 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N TYR D 93 " --> pdb=" O LYS D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 104 Proline residue: D 101 - end of helix removed outlier: 3.862A pdb=" N ASP D 104 " --> pdb=" O LEU D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 126 Processing helix chain 'D' and resid 132 through 161 Processing helix chain 'D' and resid 165 through 184 removed outlier: 3.555A pdb=" N GLU D 172 " --> pdb=" O PHE D 168 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLU D 173 " --> pdb=" O TRP D 169 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE D 180 " --> pdb=" O LYS D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 229 removed outlier: 3.817A pdb=" N ASN D 217 " --> pdb=" O GLU D 213 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N SER D 219 " --> pdb=" O SER D 215 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N LEU D 220 " --> pdb=" O LYS D 216 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ARG D 221 " --> pdb=" O ASN D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 239 Processing helix chain 'D' and resid 247 through 252 Processing helix chain 'D' and resid 257 through 263 removed outlier: 4.202A pdb=" N GLY D 262 " --> pdb=" O MET D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 272 No H-bonds generated for 'chain 'D' and resid 269 through 272' Processing helix chain 'D' and resid 278 through 280 No H-bonds generated for 'chain 'D' and resid 278 through 280' Processing helix chain 'D' and resid 293 through 316 Processing helix chain 'D' and resid 335 through 338 No H-bonds generated for 'chain 'D' and resid 335 through 338' Processing helix chain 'D' and resid 342 through 353 Processing helix chain 'D' and resid 394 through 405 removed outlier: 3.545A pdb=" N LEU D 402 " --> pdb=" O HIS D 398 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N ASP D 403 " --> pdb=" O LEU D 399 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N LYS D 404 " --> pdb=" O ALA D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 420 removed outlier: 3.556A pdb=" N GLY D 419 " --> pdb=" O VAL D 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 429 Processing helix chain 'E' and resid 25 through 37 removed outlier: 3.572A pdb=" N ASN E 37 " --> pdb=" O ALA E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 58 removed outlier: 4.457A pdb=" N LEU E 48 " --> pdb=" O ALA E 45 " (cutoff:3.500A) Proline residue: E 49 - end of helix removed outlier: 3.760A pdb=" N GLN E 57 " --> pdb=" O ALA E 54 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN E 58 " --> pdb=" O GLN E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 73 Processing helix chain 'E' and resid 77 through 86 removed outlier: 3.768A pdb=" N VAL E 83 " --> pdb=" O ARG E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 109 No H-bonds generated for 'chain 'E' and resid 106 through 109' Processing helix chain 'E' and resid 113 through 124 Processing helix chain 'E' and resid 168 through 178 Processing helix chain 'F' and resid 33 through 38 Processing helix chain 'F' and resid 45 through 51 removed outlier: 3.611A pdb=" N LYS F 51 " --> pdb=" O GLU F 47 " (cutoff:3.500A) Processing helix chain 'F' and resid 53 through 62 Processing helix chain 'F' and resid 75 through 80 Processing helix chain 'F' and resid 106 through 113 removed outlier: 3.512A pdb=" N ILE F 110 " --> pdb=" O LYS F 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 115 through 129 Processing helix chain 'F' and resid 143 through 158 Processing helix chain 'F' and resid 184 through 187 Processing helix chain 'F' and resid 189 through 196 Processing helix chain 'F' and resid 215 through 217 No H-bonds generated for 'chain 'F' and resid 215 through 217' Processing helix chain 'F' and resid 225 through 229 Processing helix chain 'F' and resid 231 through 237 Processing helix chain 'F' and resid 239 through 244 Processing helix chain 'F' and resid 276 through 282 Processing helix chain 'F' and resid 291 through 293 No H-bonds generated for 'chain 'F' and resid 291 through 293' Processing helix chain 'F' and resid 309 through 314 removed outlier: 3.571A pdb=" N GLU F 313 " --> pdb=" O LYS F 309 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N THR F 314 " --> pdb=" O SER F 310 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 309 through 314' Processing helix chain 'F' and resid 319 through 324 Processing helix chain 'F' and resid 343 through 357 removed outlier: 3.581A pdb=" N LEU F 350 " --> pdb=" O ALA F 346 " (cutoff:3.500A) Processing helix chain 'F' and resid 363 through 381 removed outlier: 4.262A pdb=" N ASP F 370 " --> pdb=" O ARG F 366 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG F 381 " --> pdb=" O ALA F 377 " (cutoff:3.500A) Processing helix chain 'F' and resid 386 through 399 removed outlier: 4.171A pdb=" N ASP F 390 " --> pdb=" O PRO F 386 " (cutoff:3.500A) Processing helix chain 'F' and resid 407 through 436 Proline residue: F 414 - end of helix removed outlier: 3.577A pdb=" N ARG F 423 " --> pdb=" O ILE F 419 " (cutoff:3.500A) Proline residue: F 424 - end of helix Processing helix chain 'G' and resid 26 through 32 removed outlier: 3.530A pdb=" N LYS G 32 " --> pdb=" O GLN G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 84 through 97 Processing helix chain 'G' and resid 105 through 107 No H-bonds generated for 'chain 'G' and resid 105 through 107' Processing helix chain 'G' and resid 115 through 123 Processing helix chain 'G' and resid 150 through 152 No H-bonds generated for 'chain 'G' and resid 150 through 152' Processing helix chain 'G' and resid 158 through 165 Processing helix chain 'G' and resid 178 through 180 No H-bonds generated for 'chain 'G' and resid 178 through 180' Processing helix chain 'G' and resid 196 through 202 Processing helix chain 'G' and resid 219 through 221 No H-bonds generated for 'chain 'G' and resid 219 through 221' Processing helix chain 'G' and resid 265 through 269 Processing helix chain 'G' and resid 271 through 275 Processing helix chain 'G' and resid 296 through 309 Processing helix chain 'G' and resid 312 through 314 No H-bonds generated for 'chain 'G' and resid 312 through 314' Processing helix chain 'G' and resid 325 through 337 Processing helix chain 'G' and resid 359 through 361 No H-bonds generated for 'chain 'G' and resid 359 through 361' Processing helix chain 'G' and resid 368 through 373 Processing helix chain 'G' and resid 384 through 387 No H-bonds generated for 'chain 'G' and resid 384 through 387' Processing helix chain 'G' and resid 389 through 402 Processing helix chain 'G' and resid 426 through 434 removed outlier: 3.525A pdb=" N ILE G 432 " --> pdb=" O LEU G 429 " (cutoff:3.500A) Processing helix chain 'G' and resid 438 through 445 removed outlier: 3.524A pdb=" N GLU G 445 " --> pdb=" O VAL G 442 " (cutoff:3.500A) Processing helix chain 'G' and resid 457 through 459 No H-bonds generated for 'chain 'G' and resid 457 through 459' Processing helix chain 'G' and resid 463 through 479 Processing helix chain 'G' and resid 499 through 504 Processing helix chain 'G' and resid 512 through 516 Processing helix chain 'G' and resid 534 through 536 No H-bonds generated for 'chain 'G' and resid 534 through 536' Processing helix chain 'G' and resid 554 through 556 No H-bonds generated for 'chain 'G' and resid 554 through 556' Processing helix chain 'G' and resid 566 through 568 No H-bonds generated for 'chain 'G' and resid 566 through 568' Processing helix chain 'G' and resid 596 through 606 removed outlier: 3.583A pdb=" N ILE G 600 " --> pdb=" O ASP G 596 " (cutoff:3.500A) Processing helix chain 'G' and resid 616 through 626 Processing helix chain 'G' and resid 628 through 631 removed outlier: 3.635A pdb=" N VAL G 631 " --> pdb=" O PRO G 628 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 628 through 631' Processing helix chain 'G' and resid 642 through 652 removed outlier: 3.887A pdb=" N LEU G 651 " --> pdb=" O GLU G 647 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N VAL G 652 " --> pdb=" O LEU G 648 " (cutoff:3.500A) Processing helix chain 'G' and resid 668 through 670 No H-bonds generated for 'chain 'G' and resid 668 through 670' Processing helix chain 'G' and resid 676 through 680 Processing helix chain 'G' and resid 682 through 693 Processing helix chain 'H' and resid 3 through 32 removed outlier: 3.522A pdb=" N LEU H 9 " --> pdb=" O ASN H 5 " (cutoff:3.500A) Proline residue: H 12 - end of helix removed outlier: 3.503A pdb=" N THR H 21 " --> pdb=" O VAL H 17 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU H 22 " --> pdb=" O ALA H 18 " (cutoff:3.500A) Processing helix chain 'H' and resid 42 through 44 No H-bonds generated for 'chain 'H' and resid 42 through 44' Processing helix chain 'H' and resid 47 through 56 Processing helix chain 'H' and resid 68 through 86 Proline residue: H 75 - end of helix removed outlier: 4.262A pdb=" N TRP H 86 " --> pdb=" O ALA H 82 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 123 removed outlier: 3.558A pdb=" N VAL H 113 " --> pdb=" O SER H 109 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N TYR H 114 " --> pdb=" O SER H 110 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N SER H 115 " --> pdb=" O LEU H 111 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ILE H 116 " --> pdb=" O ALA H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 126 through 154 removed outlier: 4.805A pdb=" N VAL H 144 " --> pdb=" O ILE H 140 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N THR H 145 " --> pdb=" O SER H 141 " (cutoff:3.500A) Processing helix chain 'H' and resid 162 through 168 removed outlier: 4.087A pdb=" N ILE H 166 " --> pdb=" O LEU H 162 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N THR H 167 " --> pdb=" O SER H 163 " (cutoff:3.500A) Processing helix chain 'H' and resid 174 through 177 No H-bonds generated for 'chain 'H' and resid 174 through 177' Processing helix chain 'H' and resid 179 through 192 removed outlier: 3.568A pdb=" N MET H 184 " --> pdb=" O PRO H 180 " (cutoff:3.500A) Processing helix chain 'H' and resid 204 through 207 No H-bonds generated for 'chain 'H' and resid 204 through 207' Processing helix chain 'H' and resid 210 through 212 No H-bonds generated for 'chain 'H' and resid 210 through 212' Processing helix chain 'H' and resid 217 through 242 removed outlier: 3.556A pdb=" N PHE H 223 " --> pdb=" O PRO H 219 " (cutoff:3.500A) Processing helix chain 'H' and resid 252 through 276 removed outlier: 3.545A pdb=" N SER H 276 " --> pdb=" O TRP H 272 " (cutoff:3.500A) Processing helix chain 'H' and resid 282 through 291 removed outlier: 3.741A pdb=" N MET H 286 " --> pdb=" O TYR H 282 " (cutoff:3.500A) Processing helix chain 'H' and resid 293 through 310 Proline residue: H 308 - end of helix Processing helix chain 'I' and resid 14 through 26 Processing helix chain 'I' and resid 28 through 42 removed outlier: 3.679A pdb=" N PHE I 42 " --> pdb=" O LEU I 38 " (cutoff:3.500A) Processing helix chain 'I' and resid 82 through 86 Processing helix chain 'I' and resid 121 through 125 Processing helix chain 'I' and resid 145 through 147 No H-bonds generated for 'chain 'I' and resid 145 through 147' Processing helix chain 'I' and resid 151 through 175 removed outlier: 5.378A pdb=" N ALA I 163 " --> pdb=" O ASP I 159 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N GLU I 164 " --> pdb=" O LYS I 160 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA I 167 " --> pdb=" O ALA I 163 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N LEU I 174 " --> pdb=" O GLN I 170 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N TYR I 175 " --> pdb=" O ALA I 171 " (cutoff:3.500A) Processing helix chain 'J' and resid 5 through 21 Processing helix chain 'J' and resid 26 through 46 Processing helix chain 'J' and resid 50 through 74 Processing helix chain 'J' and resid 87 through 110 Processing helix chain 'J' and resid 124 through 127 Processing helix chain 'J' and resid 138 through 146 removed outlier: 3.873A pdb=" N LEU J 146 " --> pdb=" O GLY J 142 " (cutoff:3.500A) Processing helix chain 'J' and resid 151 through 171 Processing helix chain 'K' and resid 3 through 20 removed outlier: 3.735A pdb=" N ASN K 7 " --> pdb=" O MET K 3 " (cutoff:3.500A) Processing helix chain 'K' and resid 26 through 51 Processing helix chain 'K' and resid 54 through 85 removed outlier: 3.704A pdb=" N MET K 58 " --> pdb=" O LEU K 55 " (cutoff:3.500A) Proline residue: K 60 - end of helix removed outlier: 3.729A pdb=" N CYS K 69 " --> pdb=" O PHE K 66 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA K 71 " --> pdb=" O ALA K 68 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA K 72 " --> pdb=" O CYS K 69 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU K 75 " --> pdb=" O ALA K 72 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASN K 83 " --> pdb=" O MET K 80 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N TYR K 85 " --> pdb=" O SER K 82 " (cutoff:3.500A) Processing helix chain 'K' and resid 90 through 92 No H-bonds generated for 'chain 'K' and resid 90 through 92' Processing helix chain 'K' and resid 95 through 97 No H-bonds generated for 'chain 'K' and resid 95 through 97' Processing helix chain 'L' and resid 3 through 24 removed outlier: 3.740A pdb=" N THR L 11 " --> pdb=" O LEU L 7 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU L 12 " --> pdb=" O SER L 8 " (cutoff:3.500A) Proline residue: L 18 - end of helix Processing helix chain 'L' and resid 29 through 57 Proline residue: L 33 - end of helix removed outlier: 3.520A pdb=" N VAL L 36 " --> pdb=" O PRO L 33 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR L 38 " --> pdb=" O TYR L 35 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA L 43 " --> pdb=" O ILE L 40 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR L 46 " --> pdb=" O ALA L 43 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE L 49 " --> pdb=" O THR L 46 " (cutoff:3.500A) Proline residue: L 50 - end of helix removed outlier: 3.693A pdb=" N HIS L 56 " --> pdb=" O MET L 53 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N SER L 57 " --> pdb=" O PHE L 54 " (cutoff:3.500A) Processing helix chain 'L' and resid 84 through 107 Proline residue: L 91 - end of helix removed outlier: 3.758A pdb=" N TRP L 106 " --> pdb=" O GLU L 102 " (cutoff:3.500A) Processing helix chain 'L' and resid 114 through 133 Processing helix chain 'L' and resid 137 through 155 Processing helix chain 'L' and resid 162 through 193 removed outlier: 3.520A pdb=" N ILE L 180 " --> pdb=" O ARG L 176 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLY L 181 " --> pdb=" O ILE L 177 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE L 182 " --> pdb=" O GLY L 178 " (cutoff:3.500A) Processing helix chain 'L' and resid 198 through 204 Processing helix chain 'L' and resid 210 through 223 Processing helix chain 'L' and resid 231 through 238 removed outlier: 3.578A pdb=" N SER L 235 " --> pdb=" O PRO L 231 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N MET L 237 " --> pdb=" O LEU L 233 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N GLU L 238 " --> pdb=" O PRO L 234 " (cutoff:3.500A) Processing helix chain 'L' and resid 241 through 246 Processing helix chain 'L' and resid 252 through 262 removed outlier: 4.137A pdb=" N GLY L 256 " --> pdb=" O VAL L 253 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE L 257 " --> pdb=" O VAL L 254 " (cutoff:3.500A) Processing helix chain 'L' and resid 264 through 267 No H-bonds generated for 'chain 'L' and resid 264 through 267' Processing helix chain 'L' and resid 271 through 294 removed outlier: 3.764A pdb=" N ALA L 289 " --> pdb=" O THR L 285 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU L 293 " --> pdb=" O ALA L 289 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N THR L 294 " --> pdb=" O MET L 290 " (cutoff:3.500A) Processing helix chain 'L' and resid 298 through 318 Processing helix chain 'L' and resid 322 through 349 removed outlier: 4.060A pdb=" N PHE L 334 " --> pdb=" O CYS L 330 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N PHE L 335 " --> pdb=" O THR L 331 " (cutoff:3.500A) Processing helix chain 'L' and resid 356 through 358 No H-bonds generated for 'chain 'L' and resid 356 through 358' Processing helix chain 'L' and resid 367 through 381 Processing helix chain 'L' and resid 389 through 400 removed outlier: 4.803A pdb=" N LEU L 394 " --> pdb=" O TYR L 390 " (cutoff:3.500A) Processing helix chain 'L' and resid 406 through 431 removed outlier: 3.731A pdb=" N ALA L 420 " --> pdb=" O THR L 416 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE L 421 " --> pdb=" O SER L 417 " (cutoff:3.500A) Processing helix chain 'L' and resid 448 through 469 removed outlier: 6.048A pdb=" N GLY L 465 " --> pdb=" O SER L 461 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N TYR L 466 " --> pdb=" O LEU L 462 " (cutoff:3.500A) Processing helix chain 'L' and resid 484 through 487 No H-bonds generated for 'chain 'L' and resid 484 through 487' Processing helix chain 'L' and resid 489 through 507 Processing helix chain 'L' and resid 518 through 524 Processing helix chain 'L' and resid 526 through 547 Proline residue: L 530 - end of helix removed outlier: 3.555A pdb=" N MET L 533 " --> pdb=" O PRO L 530 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N HIS L 534 " --> pdb=" O THR L 531 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU L 536 " --> pdb=" O MET L 533 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N ALA L 537 " --> pdb=" O HIS L 534 " (cutoff:3.500A) Proline residue: L 538 - end of helix removed outlier: 3.645A pdb=" N ASN L 541 " --> pdb=" O PRO L 538 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU L 542 " --> pdb=" O TYR L 539 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N SER L 543 " --> pdb=" O MET L 540 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS L 547 " --> pdb=" O MET L 544 " (cutoff:3.500A) Processing helix chain 'L' and resid 557 through 561 Processing helix chain 'L' and resid 563 through 578 Processing helix chain 'L' and resid 584 through 600 removed outlier: 3.513A pdb=" N MET L 599 " --> pdb=" O ILE L 595 " (cutoff:3.500A) Processing helix chain 'M' and resid 5 through 17 removed outlier: 4.342A pdb=" N MET M 12 " --> pdb=" O THR M 8 " (cutoff:3.500A) Proline residue: M 13 - end of helix Processing helix chain 'M' and resid 20 through 42 removed outlier: 4.197A pdb=" N ILE M 23 " --> pdb=" O ASN M 20 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N TRP M 24 " --> pdb=" O ASN M 21 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL M 25 " --> pdb=" O MET M 22 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASN M 26 " --> pdb=" O ILE M 23 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SER M 27 " --> pdb=" O TRP M 24 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR M 28 " --> pdb=" O VAL M 25 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N HIS M 30 " --> pdb=" O SER M 27 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER M 31 " --> pdb=" O THR M 28 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU M 33 " --> pdb=" O HIS M 30 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE M 34 " --> pdb=" O SER M 31 " (cutoff:3.500A) Processing helix chain 'M' and resid 60 through 80 Proline residue: M 64 - end of helix removed outlier: 3.674A pdb=" N LEU M 73 " --> pdb=" O THR M 69 " (cutoff:3.500A) Proline residue: M 74 - end of helix Processing helix chain 'M' and resid 89 through 111 Processing helix chain 'M' and resid 115 through 136 removed outlier: 4.491A pdb=" N LEU M 126 " --> pdb=" O PHE M 122 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N VAL M 127 " --> pdb=" O GLU M 123 " (cutoff:3.500A) Proline residue: M 128 - end of helix Processing helix chain 'M' and resid 142 through 171 removed outlier: 3.606A pdb=" N THR M 153 " --> pdb=" O PHE M 149 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY M 156 " --> pdb=" O TYR M 152 " (cutoff:3.500A) Proline residue: M 159 - end of helix Processing helix chain 'M' and resid 176 through 182 removed outlier: 3.771A pdb=" N TYR M 181 " --> pdb=" O LEU M 177 " (cutoff:3.500A) Processing helix chain 'M' and resid 190 through 206 removed outlier: 4.412A pdb=" N ALA M 202 " --> pdb=" O ALA M 198 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N PHE M 203 " --> pdb=" O CYS M 199 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS M 206 " --> pdb=" O ALA M 202 " (cutoff:3.500A) Processing helix chain 'M' and resid 214 through 222 removed outlier: 3.835A pdb=" N LYS M 218 " --> pdb=" O LEU M 214 " (cutoff:3.500A) Processing helix chain 'M' and resid 225 through 233 Processing helix chain 'M' and resid 237 through 250 removed outlier: 4.784A pdb=" N LEU M 248 " --> pdb=" O LEU M 244 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ILE M 249 " --> pdb=" O ARG M 245 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU M 250 " --> pdb=" O ILE M 246 " (cutoff:3.500A) Processing helix chain 'M' and resid 253 through 257 removed outlier: 3.825A pdb=" N MET M 257 " --> pdb=" O THR M 254 " (cutoff:3.500A) Processing helix chain 'M' and resid 259 through 278 removed outlier: 3.960A pdb=" N ILE M 270 " --> pdb=" O LEU M 266 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU M 277 " --> pdb=" O SER M 273 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ARG M 278 " --> pdb=" O SER M 274 " (cutoff:3.500A) Processing helix chain 'M' and resid 282 through 303 removed outlier: 3.583A pdb=" N VAL M 291 " --> pdb=" O ALA M 287 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU M 296 " --> pdb=" O SER M 292 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL M 297 " --> pdb=" O HIS M 293 " (cutoff:3.500A) Processing helix chain 'M' and resid 306 through 337 removed outlier: 3.560A pdb=" N ASN M 333 " --> pdb=" O LEU M 329 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ARG M 336 " --> pdb=" O SER M 332 " (cutoff:3.500A) Processing helix chain 'M' and resid 348 through 351 No H-bonds generated for 'chain 'M' and resid 348 through 351' Processing helix chain 'M' and resid 353 through 366 Processing helix chain 'M' and resid 373 through 388 removed outlier: 3.594A pdb=" N SER M 387 " --> pdb=" O MET M 383 " (cutoff:3.500A) Processing helix chain 'M' and resid 390 through 415 removed outlier: 3.523A pdb=" N ILE M 393 " --> pdb=" O ASN M 390 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN M 399 " --> pdb=" O MET M 396 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR M 403 " --> pdb=" O MET M 400 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N TYR M 406 " --> pdb=" O THR M 403 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N SER M 407 " --> pdb=" O ALA M 404 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU M 408 " --> pdb=" O LEU M 405 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR M 409 " --> pdb=" O TYR M 406 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N MET M 410 " --> pdb=" O SER M 407 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N MET M 413 " --> pdb=" O MET M 410 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR M 414 " --> pdb=" O LEU M 411 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLN M 415 " --> pdb=" O ILE M 412 " (cutoff:3.500A) Processing helix chain 'M' and resid 431 through 454 removed outlier: 3.592A pdb=" N HIS M 440 " --> pdb=" O LEU M 436 " (cutoff:3.500A) Proline residue: M 443 - end of helix removed outlier: 4.089A pdb=" N THR M 448 " --> pdb=" O LEU M 444 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LEU M 449 " --> pdb=" O LEU M 445 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ASN M 450 " --> pdb=" O LEU M 446 " (cutoff:3.500A) Proline residue: M 451 - end of helix removed outlier: 5.118A pdb=" N ILE M 454 " --> pdb=" O ASN M 450 " (cutoff:3.500A) Processing helix chain 'N' and resid 3 through 21 Processing helix chain 'N' and resid 26 through 47 Proline residue: N 42 - end of helix removed outlier: 5.488A pdb=" N ASN N 47 " --> pdb=" O ILE N 43 " (cutoff:3.500A) Processing helix chain 'N' and resid 50 through 81 Processing helix chain 'N' and resid 92 through 106 Processing helix chain 'N' and resid 113 through 121 removed outlier: 3.994A pdb=" N GLU N 117 " --> pdb=" O PHE N 113 " (cutoff:3.500A) Processing helix chain 'N' and resid 124 through 130 Processing helix chain 'N' and resid 133 through 148 removed outlier: 4.421A pdb=" N ALA N 137 " --> pdb=" O TRP N 133 " (cutoff:3.500A) Proline residue: N 138 - end of helix removed outlier: 3.683A pdb=" N GLN N 144 " --> pdb=" O SER N 140 " (cutoff:3.500A) Proline residue: N 147 - end of helix Processing helix chain 'N' and resid 151 through 171 removed outlier: 3.666A pdb=" N LEU N 170 " --> pdb=" O GLY N 166 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ASN N 171 " --> pdb=" O TRP N 167 " (cutoff:3.500A) Processing helix chain 'N' and resid 175 through 192 removed outlier: 3.576A pdb=" N TRP N 189 " --> pdb=" O ALA N 185 " (cutoff:3.500A) Processing helix chain 'N' and resid 198 through 222 removed outlier: 3.748A pdb=" N ASN N 222 " --> pdb=" O MET N 218 " (cutoff:3.500A) Processing helix chain 'N' and resid 227 through 235 removed outlier: 4.097A pdb=" N HIS N 232 " --> pdb=" O LEU N 228 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N THR N 233 " --> pdb=" O SER N 229 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N TRP N 234 " --> pdb=" O LEU N 230 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N ASN N 235 " --> pdb=" O SER N 231 " (cutoff:3.500A) Processing helix chain 'N' and resid 238 through 251 removed outlier: 3.556A pdb=" N VAL N 242 " --> pdb=" O PRO N 238 " (cutoff:3.500A) Processing helix chain 'N' and resid 258 through 272 Proline residue: N 262 - end of helix Processing helix chain 'N' and resid 277 through 300 removed outlier: 3.610A pdb=" N LEU N 287 " --> pdb=" O ALA N 283 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N LEU N 288 " --> pdb=" O ILE N 284 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ASN N 289 " --> pdb=" O THR N 285 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE N 292 " --> pdb=" O LEU N 288 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU N 296 " --> pdb=" O PHE N 292 " (cutoff:3.500A) Processing helix chain 'N' and resid 309 through 316 removed outlier: 3.538A pdb=" N GLN N 316 " --> pdb=" O MET N 313 " (cutoff:3.500A) Processing helix chain 'N' and resid 326 through 334 removed outlier: 3.729A pdb=" N VAL N 331 " --> pdb=" O PRO N 327 " (cutoff:3.500A) Processing helix chain 'N' and resid 337 through 345 Proline residue: N 341 - end of helix Processing helix chain 'O' and resid 5 through 10 Processing helix chain 'O' and resid 14 through 17 No H-bonds generated for 'chain 'O' and resid 14 through 17' Processing helix chain 'O' and resid 35 through 46 Processing helix chain 'O' and resid 58 through 62 removed outlier: 3.614A pdb=" N THR O 62 " --> pdb=" O TYR O 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 58 through 62' Processing helix chain 'O' and resid 71 through 74 Processing helix chain 'O' and resid 79 through 84 Processing helix chain 'O' and resid 92 through 118 Processing helix chain 'O' and resid 131 through 140 removed outlier: 4.067A pdb=" N GLU O 136 " --> pdb=" O VAL O 133 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ARG O 140 " --> pdb=" O ALA O 137 " (cutoff:3.500A) Processing helix chain 'O' and resid 146 through 162 removed outlier: 4.269A pdb=" N CYS O 161 " --> pdb=" O LYS O 157 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N GLU O 162 " --> pdb=" O VAL O 158 " (cutoff:3.500A) Processing helix chain 'O' and resid 176 through 186 Processing helix chain 'O' and resid 191 through 193 No H-bonds generated for 'chain 'O' and resid 191 through 193' Processing helix chain 'O' and resid 196 through 208 Processing helix chain 'O' and resid 210 through 217 removed outlier: 4.087A pdb=" N GLU O 216 " --> pdb=" O PRO O 212 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS O 217 " --> pdb=" O GLU O 213 " (cutoff:3.500A) Processing helix chain 'O' and resid 225 through 229 Processing helix chain 'O' and resid 231 through 240 removed outlier: 3.500A pdb=" N TYR O 240 " --> pdb=" O GLU O 236 " (cutoff:3.500A) Processing helix chain 'O' and resid 247 through 250 Processing helix chain 'O' and resid 253 through 264 Processing helix chain 'O' and resid 266 through 269 No H-bonds generated for 'chain 'O' and resid 266 through 269' Processing helix chain 'O' and resid 272 through 274 No H-bonds generated for 'chain 'O' and resid 272 through 274' Processing helix chain 'O' and resid 286 through 298 Processing helix chain 'P' and resid 29 through 40 removed outlier: 4.050A pdb=" N TYR P 33 " --> pdb=" O PHE P 29 " (cutoff:3.500A) Processing helix chain 'P' and resid 53 through 62 removed outlier: 3.610A pdb=" N MET P 57 " --> pdb=" O TYR P 54 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N HIS P 58 " --> pdb=" O ASP P 55 " (cutoff:3.500A) Proline residue: P 61 - end of helix Processing helix chain 'P' and resid 78 through 85 removed outlier: 3.603A pdb=" N ALA P 84 " --> pdb=" O SER P 80 " (cutoff:3.500A) Processing helix chain 'P' and resid 106 through 110 Processing helix chain 'P' and resid 112 through 123 Processing helix chain 'P' and resid 144 through 159 Processing helix chain 'P' and resid 179 through 188 removed outlier: 4.250A pdb=" N ARG P 186 " --> pdb=" O PHE P 182 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N TRP P 187 " --> pdb=" O ALA P 183 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N PHE P 188 " --> pdb=" O ASN P 184 " (cutoff:3.500A) Processing helix chain 'P' and resid 194 through 197 Processing helix chain 'P' and resid 207 through 219 Processing helix chain 'P' and resid 221 through 223 No H-bonds generated for 'chain 'P' and resid 221 through 223' Processing helix chain 'P' and resid 238 through 248 Processing helix chain 'P' and resid 260 through 272 removed outlier: 4.017A pdb=" N ILE P 272 " --> pdb=" O ARG P 268 " (cutoff:3.500A) Processing helix chain 'P' and resid 281 through 287 Processing helix chain 'P' and resid 300 through 303 No H-bonds generated for 'chain 'P' and resid 300 through 303' Processing helix chain 'P' and resid 310 through 321 removed outlier: 5.971A pdb=" N ILE P 315 " --> pdb=" O GLU P 311 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N GLU P 316 " --> pdb=" O LEU P 312 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N ARG P 320 " --> pdb=" O GLU P 316 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N HIS P 321 " --> pdb=" O VAL P 317 " (cutoff:3.500A) Processing helix chain 'Q' and resid 20 through 22 No H-bonds generated for 'chain 'Q' and resid 20 through 22' Processing helix chain 'Q' and resid 27 through 31 removed outlier: 4.475A pdb=" N LYS Q 31 " --> pdb=" O GLU Q 28 " (cutoff:3.500A) Processing helix chain 'Q' and resid 89 through 99 Processing helix chain 'Q' and resid 119 through 122 Processing helix chain 'R' and resid 23 through 28 Processing helix chain 'R' and resid 40 through 45 removed outlier: 3.574A pdb=" N ALA R 45 " --> pdb=" O ILE R 41 " (cutoff:3.500A) Processing helix chain 'R' and resid 64 through 66 No H-bonds generated for 'chain 'R' and resid 64 through 66' Processing helix chain 'S' and resid 27 through 38 removed outlier: 4.581A pdb=" N GLY S 31 " --> pdb=" O GLY S 28 " (cutoff:3.500A) Processing helix chain 'S' and resid 40 through 46 Processing helix chain 'S' and resid 69 through 71 No H-bonds generated for 'chain 'S' and resid 69 through 71' Processing helix chain 'S' and resid 83 through 95 Processing helix chain 'T' and resid 8 through 21 Processing helix chain 'T' and resid 44 through 57 Processing helix chain 'T' and resid 64 through 69 removed outlier: 4.541A pdb=" N LYS T 69 " --> pdb=" O ILE T 65 " (cutoff:3.500A) Processing helix chain 'T' and resid 73 through 84 Processing helix chain 'U' and resid 8 through 21 removed outlier: 3.597A pdb=" N LEU U 21 " --> pdb=" O TYR U 17 " (cutoff:3.500A) Processing helix chain 'U' and resid 44 through 58 Processing helix chain 'U' and resid 64 through 67 No H-bonds generated for 'chain 'U' and resid 64 through 67' Processing helix chain 'U' and resid 73 through 83 Processing helix chain 'V' and resid 19 through 36 removed outlier: 4.209A pdb=" N HIS V 36 " --> pdb=" O ASP V 32 " (cutoff:3.500A) Processing helix chain 'V' and resid 42 through 59 removed outlier: 3.781A pdb=" N GLN V 49 " --> pdb=" O LYS V 45 " (cutoff:3.500A) Processing helix chain 'V' and resid 64 through 71 Processing helix chain 'V' and resid 76 through 96 removed outlier: 3.802A pdb=" N GLN V 95 " --> pdb=" O ARG V 91 " (cutoff:3.500A) Processing helix chain 'W' and resid 25 through 49 removed outlier: 3.628A pdb=" N ARG W 31 " --> pdb=" O GLU W 27 " (cutoff:3.500A) Proline residue: W 44 - end of helix Processing helix chain 'W' and resid 56 through 69 Processing helix chain 'W' and resid 76 through 94 Processing helix chain 'W' and resid 100 through 106 removed outlier: 4.495A pdb=" N PHE W 106 " --> pdb=" O HIS W 102 " (cutoff:3.500A) Processing helix chain 'W' and resid 118 through 124 removed outlier: 3.508A pdb=" N VAL W 124 " --> pdb=" O SER W 120 " (cutoff:3.500A) Processing helix chain 'X' and resid 21 through 26 Processing helix chain 'X' and resid 28 through 34 removed outlier: 3.649A pdb=" N ALA X 33 " --> pdb=" O HIS X 29 " (cutoff:3.500A) Processing helix chain 'X' and resid 36 through 49 Processing helix chain 'X' and resid 52 through 76 removed outlier: 3.526A pdb=" N CYS X 55 " --> pdb=" O PRO X 52 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LEU X 56 " --> pdb=" O ARG X 53 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N GLU X 57 " --> pdb=" O ARG X 54 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU X 58 " --> pdb=" O CYS X 55 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN X 64 " --> pdb=" O LEU X 61 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU X 67 " --> pdb=" O GLN X 64 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU X 68 " --> pdb=" O CYS X 65 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE X 69 " --> pdb=" O ALA X 66 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS X 74 " --> pdb=" O ARG X 71 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG X 75 " --> pdb=" O GLN X 72 " (cutoff:3.500A) Processing helix chain 'X' and resid 78 through 90 Processing helix chain 'X' and resid 97 through 113 removed outlier: 4.257A pdb=" N ARG X 100 " --> pdb=" O ARG X 97 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N LYS X 101 " --> pdb=" O ARG X 98 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA X 104 " --> pdb=" O LYS X 101 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLU X 108 " --> pdb=" O GLN X 105 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL X 110 " --> pdb=" O ASP X 107 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASP X 112 " --> pdb=" O CYS X 109 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYS X 113 " --> pdb=" O VAL X 110 " (cutoff:3.500A) Processing helix chain 'X' and resid 123 through 125 No H-bonds generated for 'chain 'X' and resid 123 through 125' Processing helix chain 'Y' and resid 3 through 10 Processing helix chain 'Y' and resid 17 through 42 Processing helix chain 'Y' and resid 48 through 80 Processing helix chain 'Y' and resid 86 through 104 removed outlier: 3.545A pdb=" N LEU Y 90 " --> pdb=" O PRO Y 86 " (cutoff:3.500A) Processing helix chain 'Y' and resid 107 through 130 Processing helix chain 'Z' and resid 32 through 97 removed outlier: 3.501A pdb=" N ARG Z 68 " --> pdb=" O ASP Z 64 " (cutoff:3.500A) Proline residue: Z 73 - end of helix Processing helix chain 'Z' and resid 121 through 124 No H-bonds generated for 'chain 'Z' and resid 121 through 124' Processing helix chain 'Z' and resid 130 through 142 removed outlier: 5.678A pdb=" N PHE Z 140 " --> pdb=" O ALA Z 136 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N ILE Z 141 " --> pdb=" O THR Z 137 " (cutoff:3.500A) Processing helix chain 'a' and resid 2 through 30 Proline residue: a 7 - end of helix removed outlier: 3.553A pdb=" N CYS a 15 " --> pdb=" O MET a 12 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU a 16 " --> pdb=" O GLY a 13 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE a 18 " --> pdb=" O CYS a 15 " (cutoff:3.500A) Proline residue: a 19 - end of helix removed outlier: 3.609A pdb=" N ALA a 22 " --> pdb=" O PRO a 19 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR a 23 " --> pdb=" O GLY a 20 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE a 26 " --> pdb=" O THR a 23 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N HIS a 27 " --> pdb=" O ALA a 24 " (cutoff:3.500A) Processing helix chain 'a' and resid 42 through 55 Processing helix chain 'a' and resid 66 through 68 No H-bonds generated for 'chain 'a' and resid 66 through 68' Processing helix chain 'b' and resid 2 through 14 Processing helix chain 'b' and resid 16 through 34 Proline residue: b 32 - end of helix Processing helix chain 'b' and resid 38 through 47 removed outlier: 3.551A pdb=" N LEU b 42 " --> pdb=" O THR b 38 " (cutoff:3.500A) Processing helix chain 'b' and resid 78 through 82 removed outlier: 3.761A pdb=" N ARG b 82 " --> pdb=" O GLU b 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 78 through 82' Processing helix chain 'c' and resid 14 through 46 Processing helix chain 'd' and resid 16 through 20 Processing helix chain 'd' and resid 29 through 48 Processing helix chain 'd' and resid 58 through 96 removed outlier: 3.518A pdb=" N TYR d 74 " --> pdb=" O PHE d 70 " (cutoff:3.500A) Processing helix chain 'd' and resid 98 through 100 No H-bonds generated for 'chain 'd' and resid 98 through 100' Processing helix chain 'e' and resid 5 through 9 Processing helix chain 'e' and resid 15 through 17 No H-bonds generated for 'chain 'e' and resid 15 through 17' Processing helix chain 'e' and resid 25 through 27 No H-bonds generated for 'chain 'e' and resid 25 through 27' Processing helix chain 'e' and resid 33 through 42 Processing helix chain 'e' and resid 48 through 54 removed outlier: 4.045A pdb=" N LYS e 53 " --> pdb=" O ILE e 49 " (cutoff:3.500A) Processing helix chain 'e' and resid 56 through 67 Processing helix chain 'e' and resid 69 through 88 Processing helix chain 'e' and resid 95 through 98 No H-bonds generated for 'chain 'e' and resid 95 through 98' Processing helix chain 'f' and resid 3 through 33 removed outlier: 3.623A pdb=" N ASP f 9 " --> pdb=" O GLN f 5 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N HIS f 10 " --> pdb=" O VAL f 6 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N VAL f 12 " --> pdb=" O ARG f 8 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N HIS f 13 " --> pdb=" O ASP f 9 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N VAL f 14 " --> pdb=" O HIS f 10 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N LEU f 15 " --> pdb=" O TRP f 11 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N VAL f 16 " --> pdb=" O VAL f 12 " (cutoff:3.500A) Proline residue: f 17 - end of helix removed outlier: 3.614A pdb=" N GLU f 32 " --> pdb=" O ARG f 28 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS f 33 " --> pdb=" O LYS f 29 " (cutoff:3.500A) Processing helix chain 'g' and resid 37 through 40 No H-bonds generated for 'chain 'g' and resid 37 through 40' Processing helix chain 'g' and resid 51 through 65 Processing helix chain 'g' and resid 71 through 78 Processing helix chain 'g' and resid 83 through 102 removed outlier: 3.730A pdb=" N GLN g 86 " --> pdb=" O TYR g 83 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N GLU g 87 " --> pdb=" O ARG g 84 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N TRP g 88 " --> pdb=" O MET g 85 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA g 89 " --> pdb=" O GLN g 86 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU g 92 " --> pdb=" O ALA g 89 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LYS g 98 " --> pdb=" O ARG g 95 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG g 100 " --> pdb=" O VAL g 97 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU g 101 " --> pdb=" O LYS g 98 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA g 102 " --> pdb=" O TYR g 99 " (cutoff:3.500A) Processing helix chain 'g' and resid 115 through 117 No H-bonds generated for 'chain 'g' and resid 115 through 117' Processing helix chain 'h' and resid 16 through 45 removed outlier: 4.089A pdb=" N THR h 32 " --> pdb=" O TYR h 28 " (cutoff:3.500A) Proline residue: h 35 - end of helix Processing helix chain 'h' and resid 63 through 66 removed outlier: 3.586A pdb=" N TYR h 66 " --> pdb=" O HIS h 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 63 through 66' Processing helix chain 'h' and resid 70 through 79 Processing helix chain 'h' and resid 83 through 117 Processing helix chain 'h' and resid 130 through 132 No H-bonds generated for 'chain 'h' and resid 130 through 132' Processing helix chain 'i' and resid 5 through 25 removed outlier: 3.575A pdb=" N ARG i 10 " --> pdb=" O GLU i 6 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU i 16 " --> pdb=" O GLN i 12 " (cutoff:3.500A) Processing helix chain 'i' and resid 41 through 49 Processing helix chain 'i' and resid 55 through 72 removed outlier: 3.636A pdb=" N ILE i 60 " --> pdb=" O TRP i 56 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N TYR i 61 " --> pdb=" O LYS i 57 " (cutoff:3.500A) Processing helix chain 'i' and resid 75 through 87 Processing helix chain 'j' and resid 19 through 48 removed outlier: 7.360A pdb=" N ASP j 45 " --> pdb=" O TRP j 41 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N ALA j 46 " --> pdb=" O HIS j 42 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N VAL j 47 " --> pdb=" O ASP j 43 " (cutoff:3.500A) Processing helix chain 'j' and resid 56 through 58 No H-bonds generated for 'chain 'j' and resid 56 through 58' Processing helix chain 'k' and resid 27 through 38 removed outlier: 3.691A pdb=" N ARG k 38 " --> pdb=" O LYS k 34 " (cutoff:3.500A) Processing helix chain 'k' and resid 49 through 52 Processing helix chain 'k' and resid 54 through 56 No H-bonds generated for 'chain 'k' and resid 54 through 56' Processing helix chain 'k' and resid 62 through 66 Processing helix chain 'k' and resid 70 through 89 Processing helix chain 'l' and resid 6 through 8 No H-bonds generated for 'chain 'l' and resid 6 through 8' Processing helix chain 'l' and resid 17 through 26 removed outlier: 3.660A pdb=" N ALA l 21 " --> pdb=" O PRO l 17 " (cutoff:3.500A) Processing helix chain 'l' and resid 81 through 84 No H-bonds generated for 'chain 'l' and resid 81 through 84' Processing helix chain 'l' and resid 98 through 121 Processing helix chain 'l' and resid 134 through 138 Processing helix chain 'm' and resid 19 through 22 No H-bonds generated for 'chain 'm' and resid 19 through 22' Processing helix chain 'm' and resid 27 through 50 removed outlier: 3.895A pdb=" N GLN m 49 " --> pdb=" O GLU m 45 " (cutoff:3.500A) Processing helix chain 'm' and resid 62 through 70 Processing helix chain 'm' and resid 73 through 78 Proline residue: m 77 - end of helix No H-bonds generated for 'chain 'm' and resid 73 through 78' Processing helix chain 'm' and resid 83 through 92 Processing helix chain 'm' and resid 94 through 117 Processing helix chain 'n' and resid 11 through 30 removed outlier: 3.669A pdb=" N LEU n 18 " --> pdb=" O LYS n 14 " (cutoff:3.500A) Processing helix chain 'n' and resid 33 through 50 removed outlier: 3.538A pdb=" N LEU n 42 " --> pdb=" O TYR n 38 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N HIS n 50 " --> pdb=" O ARG n 46 " (cutoff:3.500A) Processing helix chain 'n' and resid 58 through 73 removed outlier: 3.703A pdb=" N HIS n 72 " --> pdb=" O GLU n 68 " (cutoff:3.500A) Processing helix chain 'n' and resid 94 through 96 No H-bonds generated for 'chain 'n' and resid 94 through 96' Processing helix chain 'n' and resid 100 through 105 removed outlier: 3.505A pdb=" N ASP n 105 " --> pdb=" O CYS n 102 " (cutoff:3.500A) Processing helix chain 'n' and resid 108 through 113 removed outlier: 3.566A pdb=" N MET n 113 " --> pdb=" O SER n 109 " (cutoff:3.500A) Processing helix chain 'n' and resid 115 through 130 removed outlier: 3.729A pdb=" N GLN n 123 " --> pdb=" O ALA n 119 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TRP n 124 " --> pdb=" O LYS n 120 " (cutoff:3.500A) Processing helix chain 'n' and resid 132 through 142 Processing helix chain 'n' and resid 167 through 170 No H-bonds generated for 'chain 'n' and resid 167 through 170' Processing helix chain 'o' and resid 3 through 9 Processing helix chain 'o' and resid 42 through 48 Processing helix chain 'o' and resid 52 through 54 No H-bonds generated for 'chain 'o' and resid 52 through 54' Processing helix chain 'o' and resid 59 through 72 Processing helix chain 'o' and resid 80 through 119 Processing helix chain 'p' and resid 28 through 39 Processing helix chain 'p' and resid 41 through 56 Processing helix chain 'p' and resid 73 through 75 No H-bonds generated for 'chain 'p' and resid 73 through 75' Processing helix chain 'p' and resid 81 through 115 removed outlier: 3.545A pdb=" N GLU p 86 " --> pdb=" O LEU p 82 " (cutoff:3.500A) Processing helix chain 'p' and resid 117 through 123 removed outlier: 5.074A pdb=" N ARG p 121 " --> pdb=" O GLU p 118 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN p 123 " --> pdb=" O HIS p 120 " (cutoff:3.500A) Processing helix chain 'p' and resid 125 through 142 Processing helix chain 'p' and resid 151 through 173 Processing helix chain 'q' and resid 2 through 16 removed outlier: 3.959A pdb=" N VAL q 14 " --> pdb=" O GLY q 10 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER q 15 " --> pdb=" O LEU q 11 " (cutoff:3.500A) Processing helix chain 'q' and resid 20 through 30 removed outlier: 3.613A pdb=" N VAL q 26 " --> pdb=" O GLY q 22 " (cutoff:3.500A) Processing helix chain 'q' and resid 79 through 81 No H-bonds generated for 'chain 'q' and resid 79 through 81' Processing helix chain 'q' and resid 84 through 90 removed outlier: 3.556A pdb=" N ARG q 88 " --> pdb=" O PRO q 84 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N TRP q 89 " --> pdb=" O GLU q 85 " (cutoff:3.500A) Processing helix chain 'r' and resid 5 through 15 Processing helix chain 'r' and resid 19 through 22 Processing helix chain 'r' and resid 53 through 55 No H-bonds generated for 'chain 'r' and resid 53 through 55' Processing helix chain 'r' and resid 58 through 61 No H-bonds generated for 'chain 'r' and resid 58 through 61' Processing helix chain 's' and resid 42 through 45 Processing helix chain 's' and resid 50 through 61 removed outlier: 4.447A pdb=" N LYS s 60 " --> pdb=" O LEU s 56 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N PHE s 61 " --> pdb=" O ASP s 57 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 85 through 89 removed outlier: 6.679A pdb=" N TYR B 112 " --> pdb=" O MET B 86 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N VAL B 88 " --> pdb=" O TYR B 112 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N VAL B 114 " --> pdb=" O VAL B 88 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N ILE B 144 " --> pdb=" O SER B 115 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'C' and resid 74 through 82 removed outlier: 6.666A pdb=" N ASN C 95 " --> pdb=" O ALA C 76 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LEU C 78 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N VAL C 93 " --> pdb=" O LEU C 78 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ALA C 80 " --> pdb=" O GLU C 91 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N GLU C 91 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N LEU C 48 " --> pdb=" O ARG C 104 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N TYR C 110 " --> pdb=" O ILE C 52 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 172 through 177 Processing sheet with id= D, first strand: chain 'D' and resid 47 through 51 removed outlier: 3.520A pdb=" N LYS D 75 " --> pdb=" O GLU D 67 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N SER D 69 " --> pdb=" O VAL D 73 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N VAL D 73 " --> pdb=" O SER D 69 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 361 through 369 removed outlier: 3.512A pdb=" N ARG D 388 " --> pdb=" O VAL D 379 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'E' and resid 137 through 142 removed outlier: 6.638A pdb=" N TYR E 98 " --> pdb=" O THR E 138 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N ILE E 140 " --> pdb=" O TYR E 98 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ILE E 100 " --> pdb=" O ILE E 140 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N VAL E 142 " --> pdb=" O ILE E 100 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N VAL E 102 " --> pdb=" O VAL E 142 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'F' and resid 219 through 224 removed outlier: 6.604A pdb=" N ALA F 133 " --> pdb=" O LEU F 93 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N VAL F 95 " --> pdb=" O ALA F 133 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N TYR F 135 " --> pdb=" O VAL F 95 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N ALA F 97 " --> pdb=" O TYR F 135 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N TYR F 137 " --> pdb=" O ALA F 97 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ASP F 174 " --> pdb=" O ALA F 134 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N ILE F 136 " --> pdb=" O ASP F 174 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N PHE F 176 " --> pdb=" O ILE F 136 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N ILE F 138 " --> pdb=" O PHE F 176 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N VAL F 178 " --> pdb=" O ILE F 138 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'F' and resid 266 through 271 Processing sheet with id= I, first strand: chain 'G' and resid 9 through 13 Processing sheet with id= J, first strand: chain 'G' and resid 146 through 148 Processing sheet with id= K, first strand: chain 'G' and resid 173 through 175 Processing sheet with id= L, first strand: chain 'G' and resid 223 through 228 removed outlier: 3.547A pdb=" N ARG G 249 " --> pdb=" O SER G 241 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ARG G 243 " --> pdb=" O VAL G 247 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N VAL G 247 " --> pdb=" O ARG G 243 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 283 through 285 Processing sheet with id= N, first strand: chain 'G' and resid 343 through 345 removed outlier: 8.311A pdb=" N CYS G 344 " --> pdb=" O VAL G 315 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ALA G 317 " --> pdb=" O CYS G 344 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N MET G 521 " --> pdb=" O ALA G 316 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N ILE G 318 " --> pdb=" O MET G 521 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N PHE G 523 " --> pdb=" O ILE G 318 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N PHE G 542 " --> pdb=" O LEU G 522 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N LEU G 524 " --> pdb=" O PHE G 542 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL G 544 " --> pdb=" O LEU G 524 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N VAL G 559 " --> pdb=" O TYR G 545 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N GLY G 547 " --> pdb=" O VAL G 559 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N LEU G 561 " --> pdb=" O GLY G 547 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'G' and resid 490 through 493 removed outlier: 8.437A pdb=" N ASN G 491 " --> pdb=" O PRO G 449 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N VAL G 451 " --> pdb=" O ASN G 491 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N LEU G 493 " --> pdb=" O VAL G 451 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N LEU G 453 " --> pdb=" O LEU G 493 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N VAL G 376 " --> pdb=" O MET G 450 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N ILE G 452 " --> pdb=" O VAL G 376 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N LEU G 378 " --> pdb=" O ILE G 452 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N GLY G 454 " --> pdb=" O LEU G 378 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N VAL G 380 " --> pdb=" O GLY G 454 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N LYS G 405 " --> pdb=" O VAL G 377 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N LEU G 379 " --> pdb=" O LYS G 405 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ALA G 407 " --> pdb=" O LEU G 379 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ASP G 420 " --> pdb=" O LEU G 408 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'G' and resid 572 through 574 Processing sheet with id= Q, first strand: chain 'I' and resid 65 through 67 Processing sheet with id= R, first strand: chain 'I' and resid 92 through 98 removed outlier: 6.107A pdb=" N GLU I 97 " --> pdb=" O THR I 106 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N THR I 106 " --> pdb=" O GLU I 97 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'J' and resid 112 through 115 Processing sheet with id= T, first strand: chain 'L' and resid 69 through 71 Processing sheet with id= U, first strand: chain 'L' and resid 61 through 67 removed outlier: 6.744A pdb=" N LEU L 78 " --> pdb=" O ASN L 65 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'O' and resid 219 through 224 removed outlier: 6.277A pdb=" N VAL O 122 " --> pdb=" O ILE O 25 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N VAL O 27 " --> pdb=" O VAL O 122 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LEU O 124 " --> pdb=" O VAL O 27 " (cutoff:3.500A) removed outlier: 8.680A pdb=" N GLY O 29 " --> pdb=" O LEU O 124 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LYS O 49 " --> pdb=" O VAL O 123 " (cutoff:3.500A) removed outlier: 8.295A pdb=" N GLU O 125 " --> pdb=" O LYS O 49 " (cutoff:3.500A) removed outlier: 8.520A pdb=" N PHE O 51 " --> pdb=" O GLU O 125 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'P' and resid 227 through 230 removed outlier: 6.624A pdb=" N ILE P 165 " --> pdb=" O PHE P 228 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N PHE P 230 " --> pdb=" O ILE P 165 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LYS P 167 " --> pdb=" O PHE P 230 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE P 132 " --> pdb=" O ASN P 93 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N GLN P 44 " --> pdb=" O ALA P 21 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N VAL P 23 " --> pdb=" O GLN P 44 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ILE P 46 " --> pdb=" O VAL P 23 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'P' and resid 191 through 193 Processing sheet with id= Y, first strand: chain 'Q' and resid 102 through 105 Processing sheet with id= Z, first strand: chain 'Q' and resid 64 through 66 Processing sheet with id= AA, first strand: chain 'R' and resid 50 through 52 Processing sheet with id= AB, first strand: chain 'R' and resid 56 through 59 Processing sheet with id= AC, first strand: chain 'S' and resid 51 through 56 removed outlier: 3.675A pdb=" N LEU S 22 " --> pdb=" O ARG S 55 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'q' and resid 60 through 63 removed outlier: 3.585A pdb=" N GLY q 40 " --> pdb=" O TYR q 48 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N GLU q 50 " --> pdb=" O LEU q 38 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N LEU q 38 " --> pdb=" O GLU q 50 " (cutoff:3.500A) 2849 hydrogen bonds defined for protein. 7907 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 22.08 Time building geometry restraints manager: 25.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.39: 27753 1.39 - 1.62: 41706 1.62 - 1.85: 878 1.85 - 2.07: 0 2.07 - 2.30: 80 Bond restraints: 70417 Sorted by residual: bond pdb=" C15 CHD i 201 " pdb=" C16 CHD i 201 " ideal model delta sigma weight residual 1.541 1.732 -0.191 2.00e-02 2.50e+03 9.10e+01 bond pdb=" C5 GTP O 401 " pdb=" N7 GTP O 401 " ideal model delta sigma weight residual 1.350 1.519 -0.169 2.00e-02 2.50e+03 7.12e+01 bond pdb=" C6 GTP O 401 " pdb=" O6 GTP O 401 " ideal model delta sigma weight residual 1.230 1.393 -0.163 2.00e-02 2.50e+03 6.65e+01 bond pdb=" C11 CHD i 201 " pdb=" C12 CHD i 201 " ideal model delta sigma weight residual 1.533 1.682 -0.149 2.00e-02 2.50e+03 5.59e+01 bond pdb=" CA7 CDL L 702 " pdb=" OA8 CDL L 702 " ideal model delta sigma weight residual 1.334 1.405 -0.071 1.10e-02 8.26e+03 4.18e+01 ... (remaining 70412 not shown) Histogram of bond angle deviations from ideal: 72.74 - 85.09: 76 85.09 - 97.44: 2 97.44 - 109.79: 11134 109.79 - 122.14: 74162 122.14 - 134.49: 9829 Bond angle restraints: 95203 Sorted by residual: angle pdb=" C51 CDL H 602 " pdb=" CB5 CDL H 602 " pdb=" OB6 CDL H 602 " ideal model delta sigma weight residual 111.33 121.78 -10.45 1.32e+00 5.72e-01 6.24e+01 angle pdb=" C11 CDL h 201 " pdb=" CA5 CDL h 201 " pdb=" OA6 CDL h 201 " ideal model delta sigma weight residual 111.33 121.46 -10.13 1.32e+00 5.72e-01 5.87e+01 angle pdb=" CA 2MR D 85 " pdb=" C 2MR D 85 " pdb=" O 2MR D 85 " ideal model delta sigma weight residual 120.80 107.78 13.02 1.70e+00 3.46e-01 5.87e+01 angle pdb=" C51 CDL h 201 " pdb=" CB5 CDL h 201 " pdb=" OB6 CDL h 201 " ideal model delta sigma weight residual 111.33 121.04 -9.71 1.32e+00 5.72e-01 5.40e+01 angle pdb=" C51 CDL X 201 " pdb=" CB5 CDL X 201 " pdb=" OB6 CDL X 201 " ideal model delta sigma weight residual 111.33 120.69 -9.36 1.32e+00 5.72e-01 5.01e+01 ... (remaining 95198 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.70: 41711 35.70 - 71.41: 947 71.41 - 107.11: 142 107.11 - 142.82: 11 142.82 - 178.52: 5 Dihedral angle restraints: 42816 sinusoidal: 18642 harmonic: 24174 Sorted by residual: dihedral pdb=" CB CYS X 87 " pdb=" SG CYS X 87 " pdb=" SG CYS X 99 " pdb=" CB CYS X 99 " ideal model delta sinusoidal sigma weight residual 93.00 154.82 -61.82 1 1.00e+01 1.00e-02 5.07e+01 dihedral pdb=" O3B GTP O 401 " pdb=" O3A GTP O 401 " pdb=" PB GTP O 401 " pdb=" PA GTP O 401 " ideal model delta sinusoidal sigma weight residual -68.92 109.60 -178.52 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C10 FMN F 501 " pdb=" C1' FMN F 501 " pdb=" N10 FMN F 501 " pdb=" C2' FMN F 501 " ideal model delta sinusoidal sigma weight residual 257.59 80.97 176.63 1 2.00e+01 2.50e-03 4.80e+01 ... (remaining 42813 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.257: 10244 4.257 - 8.515: 0 8.515 - 12.772: 0 12.772 - 17.029: 0 17.029 - 21.287: 16 Chirality restraints: 10260 Sorted by residual: chirality pdb="FE1 SF4 I 202 " pdb=" S2 SF4 I 202 " pdb=" S3 SF4 I 202 " pdb=" S4 SF4 I 202 " both_signs ideal model delta sigma weight residual False -10.55 10.73 -21.29 2.00e-01 2.50e+01 1.13e+04 chirality pdb="FE1 SF4 G 802 " pdb=" S2 SF4 G 802 " pdb=" S3 SF4 G 802 " pdb=" S4 SF4 G 802 " both_signs ideal model delta sigma weight residual False -10.55 10.71 -21.27 2.00e-01 2.50e+01 1.13e+04 chirality pdb="FE3 SF4 I 202 " pdb=" S1 SF4 I 202 " pdb=" S2 SF4 I 202 " pdb=" S4 SF4 I 202 " both_signs ideal model delta sigma weight residual False -10.55 10.70 -21.25 2.00e-01 2.50e+01 1.13e+04 ... (remaining 10257 not shown) Planarity restraints: 11878 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD 2MR D 85 " 0.136 2.00e-02 2.50e+03 1.50e-01 3.95e+02 pdb=" NE 2MR D 85 " -0.061 2.00e-02 2.50e+03 pdb=" CZ 2MR D 85 " -0.116 2.00e-02 2.50e+03 pdb=" NH1 2MR D 85 " -0.141 2.00e-02 2.50e+03 pdb=" NH2 2MR D 85 " -0.184 2.00e-02 2.50e+03 pdb=" CQ1 2MR D 85 " 0.161 2.00e-02 2.50e+03 pdb=" CQ2 2MR D 85 " 0.206 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 125 " 0.052 2.00e-02 2.50e+03 4.55e-02 4.14e+01 pdb=" CG TYR B 125 " -0.108 2.00e-02 2.50e+03 pdb=" CD1 TYR B 125 " 0.038 2.00e-02 2.50e+03 pdb=" CD2 TYR B 125 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR B 125 " -0.017 2.00e-02 2.50e+03 pdb=" CE2 TYR B 125 " 0.017 2.00e-02 2.50e+03 pdb=" CZ TYR B 125 " 0.009 2.00e-02 2.50e+03 pdb=" OH TYR B 125 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP P 73 " 0.041 2.00e-02 2.50e+03 3.83e-02 3.68e+01 pdb=" CG TRP P 73 " -0.100 2.00e-02 2.50e+03 pdb=" CD1 TRP P 73 " 0.052 2.00e-02 2.50e+03 pdb=" CD2 TRP P 73 " -0.007 2.00e-02 2.50e+03 pdb=" NE1 TRP P 73 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TRP P 73 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP P 73 " 0.012 2.00e-02 2.50e+03 pdb=" CZ2 TRP P 73 " 0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP P 73 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP P 73 " 0.004 2.00e-02 2.50e+03 ... (remaining 11875 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.40: 262 2.40 - 3.08: 50099 3.08 - 3.77: 128967 3.77 - 4.45: 225125 4.45 - 5.14: 342556 Nonbonded interactions: 747009 Sorted by model distance: nonbonded pdb=" OE1 GLU Z 93 " pdb=" OH TYR e 91 " model vdw 1.710 2.440 nonbonded pdb=" OG SER O 36 " pdb="MG MG O 402 " model vdw 1.809 2.170 nonbonded pdb=" O SER X 91 " pdb=" O HOH X 301 " model vdw 1.824 2.440 nonbonded pdb=" O HOH B 328 " pdb=" O HOH C 326 " model vdw 1.833 2.440 nonbonded pdb=" OE2 GLU G 260 " pdb=" O HOH G 901 " model vdw 1.840 2.440 ... (remaining 747004 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'T' selection = (chain 'U' and (resid 4 through 88 or resid 101)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 14.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 52.850 Check model and map are aligned: 0.820 Set scattering table: 0.500 Process input model: 177.320 Find NCS groups from input model: 2.360 Set up NCS constraints: 0.270 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: 0.010 Load rotamer database and sin/cos tables:10.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 259.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 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 : 0.010 0.191 70417 Z= 0.630 Angle : 0.956 15.646 95203 Z= 0.460 Chirality : 0.840 21.287 10260 Planarity : 0.005 0.150 11878 Dihedral : 15.279 178.520 27215 Min Nonbonded Distance : 1.710 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.14 % Favored : 96.82 % Rotamer: Outliers : 0.06 % Allowed : 0.21 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.63 % 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: -0.57 (0.09), residues: 8195 helix: -0.35 (0.07), residues: 4317 sheet: -0.29 (0.25), residues: 390 loop : -0.19 (0.10), residues: 3488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.100 0.002 TRP P 73 HIS 0.025 0.002 HIS G 255 PHE 0.048 0.003 PHE D 171 TYR 0.108 0.003 TYR B 125 ARG 0.025 0.002 ARG G 285 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16390 Ramachandran restraints generated. 8195 Oldfield, 0 Emsley, 8195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16390 Ramachandran restraints generated. 8195 Oldfield, 0 Emsley, 8195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1281 residues out of total 7219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1277 time to evaluate : 6.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 87 GLN cc_start: 0.8190 (pt0) cc_final: 0.7954 (pt0) REVERT: D 170 MET cc_start: 0.8689 (mmm) cc_final: 0.8299 (mmm) REVERT: D 208 MET cc_start: 0.8589 (mtm) cc_final: 0.8343 (mtp) REVERT: D 259 MET cc_start: 0.9103 (mmm) cc_final: 0.8858 (mmm) REVERT: D 334 LYS cc_start: 0.8389 (mttm) cc_final: 0.8147 (mttt) REVERT: H 8 MET cc_start: 0.8193 (mmm) cc_final: 0.7755 (mtp) REVERT: H 234 MET cc_start: 0.8766 (mmp) cc_final: 0.8300 (mmt) REVERT: M 255 ASP cc_start: 0.7898 (m-30) cc_final: 0.7593 (m-30) REVERT: N 104 MET cc_start: 0.8311 (mtp) cc_final: 0.8083 (mtt) REVERT: N 294 MET cc_start: 0.8348 (mmm) cc_final: 0.8128 (mmp) REVERT: N 311 MET cc_start: 0.8151 (tpt) cc_final: 0.7815 (tpp) REVERT: N 335 MET cc_start: 0.8845 (mtt) cc_final: 0.8584 (mtp) REVERT: T 26 ASP cc_start: 0.7530 (t70) cc_final: 0.7188 (t0) REVERT: T 37 MET cc_start: 0.7881 (mmm) cc_final: 0.7660 (mmm) REVERT: T 80 ILE cc_start: 0.9149 (mt) cc_final: 0.8889 (mt) REVERT: U 88 GLU cc_start: 0.7549 (mm-30) cc_final: 0.7228 (mm-30) REVERT: X 105 GLN cc_start: 0.8483 (mm110) cc_final: 0.8283 (mm-40) REVERT: Y 139 LYS cc_start: 0.8042 (mmtm) cc_final: 0.7434 (mtmm) REVERT: a 59 ARG cc_start: 0.7904 (mpt-90) cc_final: 0.7615 (mmt-90) REVERT: c 34 GLN cc_start: 0.8350 (tp40) cc_final: 0.7968 (tp-100) REVERT: k 48 GLU cc_start: 0.8182 (mm-30) cc_final: 0.7929 (mm-30) REVERT: p 20 SER cc_start: 0.8871 (t) cc_final: 0.8659 (t) REVERT: q 132 LYS cc_start: 0.8564 (ttpt) cc_final: 0.8320 (ttmt) REVERT: r 17 ARG cc_start: 0.7421 (mtt90) cc_final: 0.7113 (mtt90) REVERT: r 104 GLU cc_start: 0.7914 (mm-30) cc_final: 0.7516 (mp0) outliers start: 4 outliers final: 4 residues processed: 1280 average time/residue: 1.6827 time to fit residues: 2753.0471 Evaluate side-chains 982 residues out of total 7219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 978 time to evaluate : 6.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 614 ASP Chi-restraints excluded: chain L residue 198 LEU Chi-restraints excluded: chain U residue 44 SER Chi-restraints excluded: chain j residue 66 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 807 random chunks: chunk 681 optimal weight: 3.9990 chunk 611 optimal weight: 0.6980 chunk 339 optimal weight: 9.9990 chunk 208 optimal weight: 6.9990 chunk 412 optimal weight: 0.0970 chunk 326 optimal weight: 0.7980 chunk 632 optimal weight: 4.9990 chunk 244 optimal weight: 0.9990 chunk 384 optimal weight: 0.9990 chunk 470 optimal weight: 0.7980 chunk 732 optimal weight: 0.6980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 55 HIS D 114 ASN E 121 GLN F 257 ASN F 398 GLN H 171 GLN H 235 ASN J 46 ASN L 135 ASN L 199 GLN L 446 ASN L 603 ASN ** M 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 304 GLN O 2 GLN O 147 GLN O 294 GLN P 2 HIS P 87 HIS P 102 GLN S 75 ASN S 79 ASN T 47 GLN Y 18 HIS a 27 HIS b 10 ASN c 46 ASN e 20 GLN e 44 HIS k 90 GLN o 53 GLN q 135 GLN r 8 GLN s 35 ASN ** s 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.266 70417 Z= 0.433 Angle : 1.298 50.611 95203 Z= 0.833 Chirality : 0.255 6.465 10260 Planarity : 0.004 0.055 11878 Dihedral : 13.899 178.072 10843 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.77 % Favored : 98.20 % Rotamer: Outliers : 1.19 % Allowed : 7.04 % Favored : 91.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.63 % 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: 0.78 (0.09), residues: 8195 helix: 1.04 (0.08), residues: 4315 sheet: -0.01 (0.26), residues: 374 loop : 0.05 (0.10), residues: 3506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP P 73 HIS 0.011 0.001 HIS L 514 PHE 0.030 0.001 PHE s 33 TYR 0.048 0.001 TYR B 125 ARG 0.009 0.000 ARG g 25 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16390 Ramachandran restraints generated. 8195 Oldfield, 0 Emsley, 8195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16390 Ramachandran restraints generated. 8195 Oldfield, 0 Emsley, 8195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1157 residues out of total 7219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 1071 time to evaluate : 6.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 178 ARG cc_start: 0.8223 (OUTLIER) cc_final: 0.7700 (mtp85) REVERT: C 87 GLN cc_start: 0.8177 (pt0) cc_final: 0.7950 (pt0) REVERT: C 186 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7634 (mt-10) REVERT: D 170 MET cc_start: 0.8749 (mmm) cc_final: 0.8028 (mmt) REVERT: D 304 MET cc_start: 0.8906 (mtm) cc_final: 0.8699 (mtp) REVERT: D 334 LYS cc_start: 0.8297 (mttm) cc_final: 0.8078 (mttt) REVERT: D 427 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.6301 (pp20) REVERT: F 249 ARG cc_start: 0.7936 (ttp80) cc_final: 0.7601 (mtm110) REVERT: G 180 ASP cc_start: 0.7653 (t0) cc_final: 0.7449 (t0) REVERT: H 10 ILE cc_start: 0.8321 (pt) cc_final: 0.7918 (mm) REVERT: I 81 LYS cc_start: 0.8890 (mttp) cc_final: 0.8609 (mttp) REVERT: L 31 ASN cc_start: 0.6278 (m-40) cc_final: 0.5924 (m110) REVERT: L 48 MET cc_start: 0.8443 (mmm) cc_final: 0.8210 (mmt) REVERT: L 352 ASP cc_start: 0.8161 (m-30) cc_final: 0.7960 (m-30) REVERT: N 14 MET cc_start: 0.7799 (mtm) cc_final: 0.7505 (mtm) REVERT: N 104 MET cc_start: 0.8345 (mtp) cc_final: 0.7984 (mtt) REVERT: N 187 MET cc_start: 0.7929 (mmp) cc_final: 0.7703 (mmm) REVERT: T 66 ASP cc_start: 0.8537 (OUTLIER) cc_final: 0.8333 (m-30) REVERT: U 84 LYS cc_start: 0.8909 (OUTLIER) cc_final: 0.8238 (mttp) REVERT: Y 139 LYS cc_start: 0.7983 (mmtm) cc_final: 0.7413 (mtmm) REVERT: Z 85 GLN cc_start: 0.8410 (OUTLIER) cc_final: 0.8115 (tt0) REVERT: a 59 ARG cc_start: 0.7888 (mpt-90) cc_final: 0.7558 (mmp80) REVERT: b 64 ASP cc_start: 0.7217 (t0) cc_final: 0.7012 (t0) REVERT: c 34 GLN cc_start: 0.8295 (tp40) cc_final: 0.7877 (tp-100) REVERT: e 58 GLU cc_start: 0.8291 (mp0) cc_final: 0.7857 (mp0) REVERT: i 38 ARG cc_start: 0.6910 (mtp180) cc_final: 0.6671 (tpp-160) REVERT: i 125 GLN cc_start: 0.7095 (pm20) cc_final: 0.6865 (pt0) REVERT: k 48 GLU cc_start: 0.8058 (mm-30) cc_final: 0.7812 (mm-30) REVERT: o 80 LYS cc_start: 0.8443 (OUTLIER) cc_final: 0.8200 (mttp) REVERT: r 104 GLU cc_start: 0.7832 (mm-30) cc_final: 0.7532 (mp0) outliers start: 86 outliers final: 23 residues processed: 1107 average time/residue: 1.6327 time to fit residues: 2327.9974 Evaluate side-chains 965 residues out of total 7219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 935 time to evaluate : 6.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 178 ARG Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain D residue 427 GLU Chi-restraints excluded: chain F residue 10 THR Chi-restraints excluded: chain F residue 432 GLN Chi-restraints excluded: chain G residue 486 ASP Chi-restraints excluded: chain H residue 251 MET Chi-restraints excluded: chain J residue 157 THR Chi-restraints excluded: chain L residue 214 ILE Chi-restraints excluded: chain S residue 75 ASN Chi-restraints excluded: chain T residue 31 SER Chi-restraints excluded: chain T residue 66 ASP Chi-restraints excluded: chain U residue 44 SER Chi-restraints excluded: chain U residue 84 LYS Chi-restraints excluded: chain Y residue 50 GLU Chi-restraints excluded: chain Y residue 87 LEU Chi-restraints excluded: chain Z residue 85 GLN Chi-restraints excluded: chain d residue 3 THR Chi-restraints excluded: chain i residue 42 VAL Chi-restraints excluded: chain i residue 55 LEU Chi-restraints excluded: chain i residue 124 ASP Chi-restraints excluded: chain j residue 32 MET Chi-restraints excluded: chain k residue 31 VAL Chi-restraints excluded: chain k residue 60 VAL Chi-restraints excluded: chain k residue 90 GLN Chi-restraints excluded: chain n residue 34 ASP Chi-restraints excluded: chain n residue 48 ASP Chi-restraints excluded: chain n residue 145 VAL Chi-restraints excluded: chain n residue 175 GLU Chi-restraints excluded: chain o residue 80 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 807 random chunks: chunk 407 optimal weight: 0.7980 chunk 227 optimal weight: 7.9990 chunk 609 optimal weight: 6.9990 chunk 499 optimal weight: 0.9980 chunk 202 optimal weight: 2.9990 chunk 734 optimal weight: 0.9980 chunk 793 optimal weight: 0.7980 chunk 653 optimal weight: 8.9990 chunk 728 optimal weight: 5.9990 chunk 250 optimal weight: 5.9990 chunk 588 optimal weight: 9.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 69 ASN D 150 HIS E 37 ASN F 398 GLN ** G 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 5 ASN I 23 GLN M 175 ASN P 3 HIS P 102 GLN S 79 ASN c 46 ASN d 12 GLN l 87 ASN l 155 HIS o 53 GLN p 27 ASN q 135 GLN ** s 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.246 70417 Z= 0.443 Angle : 1.286 50.586 95203 Z= 0.828 Chirality : 0.255 6.478 10260 Planarity : 0.004 0.055 11878 Dihedral : 13.215 177.609 10837 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.25 % Favored : 97.71 % Rotamer: Outliers : 1.59 % Allowed : 8.45 % Favored : 89.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.09), residues: 8195 helix: 1.38 (0.08), residues: 4316 sheet: 0.07 (0.26), residues: 368 loop : 0.13 (0.10), residues: 3511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP L 144 HIS 0.012 0.001 HIS L 514 PHE 0.030 0.001 PHE U 60 TYR 0.040 0.001 TYR B 125 ARG 0.009 0.000 ARG q 21 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16390 Ramachandran restraints generated. 8195 Oldfield, 0 Emsley, 8195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16390 Ramachandran restraints generated. 8195 Oldfield, 0 Emsley, 8195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1088 residues out of total 7219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 973 time to evaluate : 6.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 170 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7835 (mt-10) REVERT: B 178 ARG cc_start: 0.8219 (OUTLIER) cc_final: 0.7693 (mtp85) REVERT: C 87 GLN cc_start: 0.8139 (pt0) cc_final: 0.7914 (pt0) REVERT: C 186 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7659 (mt-10) REVERT: D 47 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.7869 (tp) REVERT: D 170 MET cc_start: 0.8735 (mmm) cc_final: 0.8193 (mmm) REVERT: D 334 LYS cc_start: 0.8330 (mttm) cc_final: 0.8100 (mttt) REVERT: G 180 ASP cc_start: 0.7668 (t0) cc_final: 0.7450 (t0) REVERT: H 8 MET cc_start: 0.7697 (mtp) cc_final: 0.7241 (mtt) REVERT: H 10 ILE cc_start: 0.8304 (pt) cc_final: 0.7913 (mm) REVERT: I 15 LYS cc_start: 0.8141 (tttm) cc_final: 0.7827 (tttp) REVERT: L 31 ASN cc_start: 0.6310 (m-40) cc_final: 0.5937 (m110) REVERT: N 14 MET cc_start: 0.7749 (mtm) cc_final: 0.7462 (mtm) REVERT: N 104 MET cc_start: 0.8317 (mtp) cc_final: 0.7920 (mtt) REVERT: N 187 MET cc_start: 0.7932 (mmp) cc_final: 0.7705 (mmm) REVERT: Y 139 LYS cc_start: 0.8023 (mmtm) cc_final: 0.7549 (mppt) REVERT: a 59 ARG cc_start: 0.7948 (mpt-90) cc_final: 0.7599 (mmp80) REVERT: a 67 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.7987 (pm20) REVERT: c 34 GLN cc_start: 0.8251 (tp40) cc_final: 0.7973 (tp40) REVERT: e 80 ARG cc_start: 0.7844 (OUTLIER) cc_final: 0.7398 (mtm-85) REVERT: e 82 ARG cc_start: 0.8163 (ttp80) cc_final: 0.7680 (ttp-170) REVERT: i 38 ARG cc_start: 0.6872 (mtp180) cc_final: 0.6648 (tpp-160) REVERT: j 55 ASP cc_start: 0.8361 (t0) cc_final: 0.8013 (t0) REVERT: j 58 GLN cc_start: 0.8313 (OUTLIER) cc_final: 0.7826 (mp10) REVERT: k 48 GLU cc_start: 0.8032 (mm-30) cc_final: 0.7822 (mm-30) REVERT: o 80 LYS cc_start: 0.8375 (OUTLIER) cc_final: 0.8130 (mttp) REVERT: o 112 LYS cc_start: 0.8817 (OUTLIER) cc_final: 0.8188 (ttmt) REVERT: p 42 ARG cc_start: 0.7297 (OUTLIER) cc_final: 0.6011 (tmt90) outliers start: 115 outliers final: 35 residues processed: 1029 average time/residue: 1.6074 time to fit residues: 2136.5733 Evaluate side-chains 982 residues out of total 7219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 937 time to evaluate : 6.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 178 ARG Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain E residue 192 SER Chi-restraints excluded: chain F residue 10 THR Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain F residue 432 GLN Chi-restraints excluded: chain H residue 251 MET Chi-restraints excluded: chain J residue 107 VAL Chi-restraints excluded: chain L residue 52 MET Chi-restraints excluded: chain L residue 214 ILE Chi-restraints excluded: chain L residue 544 MET Chi-restraints excluded: chain O residue 32 CYS Chi-restraints excluded: chain Q residue 115 SER Chi-restraints excluded: chain R residue 5 SER Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain T residue 83 LYS Chi-restraints excluded: chain U residue 44 SER Chi-restraints excluded: chain W residue 22 SER Chi-restraints excluded: chain X residue 4 VAL Chi-restraints excluded: chain Y residue 87 LEU Chi-restraints excluded: chain Y residue 109 ILE Chi-restraints excluded: chain Z residue 120 MET Chi-restraints excluded: chain a residue 67 GLU Chi-restraints excluded: chain a residue 69 ILE Chi-restraints excluded: chain d residue 3 THR Chi-restraints excluded: chain d residue 107 LYS Chi-restraints excluded: chain e residue 53 LYS Chi-restraints excluded: chain e residue 80 ARG Chi-restraints excluded: chain g residue 24 LEU Chi-restraints excluded: chain i residue 42 VAL Chi-restraints excluded: chain i residue 60 ILE Chi-restraints excluded: chain i residue 124 ASP Chi-restraints excluded: chain j residue 32 MET Chi-restraints excluded: chain j residue 40 PHE Chi-restraints excluded: chain j residue 58 GLN Chi-restraints excluded: chain k residue 31 VAL Chi-restraints excluded: chain k residue 87 LEU Chi-restraints excluded: chain n residue 57 VAL Chi-restraints excluded: chain o residue 21 MET Chi-restraints excluded: chain o residue 80 LYS Chi-restraints excluded: chain o residue 112 LYS Chi-restraints excluded: chain p residue 42 ARG Chi-restraints excluded: chain p residue 112 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 807 random chunks: chunk 725 optimal weight: 0.8980 chunk 551 optimal weight: 4.9990 chunk 381 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 350 optimal weight: 5.9990 chunk 492 optimal weight: 4.9990 chunk 736 optimal weight: 9.9990 chunk 780 optimal weight: 0.8980 chunk 384 optimal weight: 0.9990 chunk 698 optimal weight: 5.9990 chunk 210 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 69 ASN F 398 GLN ** G 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 292 ASN I 23 GLN L 31 ASN L 446 ASN M 187 HIS M 390 ASN N 171 ASN c 46 ASN d 12 GLN h 63 HIS k 90 GLN l 87 ASN o 53 GLN q 135 GLN ** s 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.245 70417 Z= 0.441 Angle : 1.282 50.580 95203 Z= 0.827 Chirality : 0.254 6.465 10260 Planarity : 0.004 0.054 11878 Dihedral : 12.807 178.172 10837 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.05 % Favored : 97.91 % Rotamer: Outliers : 1.62 % Allowed : 9.64 % Favored : 88.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.09), residues: 8195 helix: 1.53 (0.08), residues: 4309 sheet: 0.04 (0.26), residues: 379 loop : 0.16 (0.10), residues: 3507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP L 144 HIS 0.011 0.001 HIS L 514 PHE 0.026 0.001 PHE U 60 TYR 0.031 0.001 TYR B 125 ARG 0.008 0.000 ARG g 25 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16390 Ramachandran restraints generated. 8195 Oldfield, 0 Emsley, 8195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16390 Ramachandran restraints generated. 8195 Oldfield, 0 Emsley, 8195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1090 residues out of total 7219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 973 time to evaluate : 6.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 178 ARG cc_start: 0.8240 (OUTLIER) cc_final: 0.7668 (mtp85) REVERT: C 87 GLN cc_start: 0.8145 (pt0) cc_final: 0.7924 (pt0) REVERT: C 186 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7641 (mt-10) REVERT: D 47 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.7854 (tp) REVERT: D 334 LYS cc_start: 0.8327 (mttm) cc_final: 0.8099 (mttm) REVERT: F 432 GLN cc_start: 0.7281 (OUTLIER) cc_final: 0.6871 (mp10) REVERT: G 180 ASP cc_start: 0.7695 (t0) cc_final: 0.7456 (t0) REVERT: H 8 MET cc_start: 0.7720 (mtp) cc_final: 0.7270 (mtt) REVERT: H 10 ILE cc_start: 0.8284 (pt) cc_final: 0.7912 (mm) REVERT: I 15 LYS cc_start: 0.8158 (tttm) cc_final: 0.7835 (tttp) REVERT: K 34 GLU cc_start: 0.7595 (mt-10) cc_final: 0.7377 (mt-10) REVERT: L 31 ASN cc_start: 0.6456 (m110) cc_final: 0.6037 (m110) REVERT: N 14 MET cc_start: 0.7736 (mtm) cc_final: 0.7439 (mtm) REVERT: N 104 MET cc_start: 0.8333 (mtp) cc_final: 0.7943 (mtt) REVERT: N 187 MET cc_start: 0.7921 (mmp) cc_final: 0.7690 (mmm) REVERT: T 43 ASP cc_start: 0.8147 (OUTLIER) cc_final: 0.7937 (p0) REVERT: U 9 GLU cc_start: 0.7731 (mp0) cc_final: 0.7437 (mp0) REVERT: U 88 GLU cc_start: 0.7065 (mm-30) cc_final: 0.6487 (mm-30) REVERT: V 6 LYS cc_start: 0.7875 (OUTLIER) cc_final: 0.7476 (ttpp) REVERT: Y 50 GLU cc_start: 0.7451 (OUTLIER) cc_final: 0.7121 (tm-30) REVERT: Y 139 LYS cc_start: 0.8061 (mmtm) cc_final: 0.7435 (mtmm) REVERT: a 59 ARG cc_start: 0.7926 (mpt-90) cc_final: 0.7603 (mmp80) REVERT: a 67 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.7937 (pm20) REVERT: c 34 GLN cc_start: 0.8181 (tp40) cc_final: 0.7947 (tp-100) REVERT: e 80 ARG cc_start: 0.7837 (OUTLIER) cc_final: 0.7444 (mtm-85) REVERT: e 82 ARG cc_start: 0.8144 (ttp80) cc_final: 0.7708 (ttp-170) REVERT: f 30 ASN cc_start: 0.8298 (t0) cc_final: 0.7824 (t0) REVERT: i 38 ARG cc_start: 0.6899 (mtp180) cc_final: 0.6648 (tpp-160) REVERT: k 48 GLU cc_start: 0.8051 (mm-30) cc_final: 0.7834 (mm-30) REVERT: l 5 THR cc_start: 0.7958 (t) cc_final: 0.7747 (t) REVERT: o 80 LYS cc_start: 0.8333 (OUTLIER) cc_final: 0.8111 (mttp) REVERT: o 112 LYS cc_start: 0.8781 (OUTLIER) cc_final: 0.8120 (ttmt) REVERT: o 121 MET cc_start: 0.7138 (mmm) cc_final: 0.6652 (pp-130) REVERT: p 42 ARG cc_start: 0.7316 (OUTLIER) cc_final: 0.5959 (tmt90) REVERT: r 5 ARG cc_start: 0.7292 (mmm-85) cc_final: 0.7010 (ptm-80) REVERT: r 104 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7349 (mp0) outliers start: 117 outliers final: 38 residues processed: 1027 average time/residue: 1.6158 time to fit residues: 2143.0957 Evaluate side-chains 994 residues out of total 7219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 943 time to evaluate : 6.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 178 ARG Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain E residue 192 SER Chi-restraints excluded: chain F residue 10 THR Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain F residue 432 GLN Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain J residue 107 VAL Chi-restraints excluded: chain J residue 118 GLU Chi-restraints excluded: chain L residue 214 ILE Chi-restraints excluded: chain L residue 544 MET Chi-restraints excluded: chain M residue 246 ILE Chi-restraints excluded: chain O residue 32 CYS Chi-restraints excluded: chain Q residue 115 SER Chi-restraints excluded: chain R residue 5 SER Chi-restraints excluded: chain R residue 19 ASP Chi-restraints excluded: chain S residue 90 LEU Chi-restraints excluded: chain T residue 7 THR Chi-restraints excluded: chain T residue 43 ASP Chi-restraints excluded: chain V residue 6 LYS Chi-restraints excluded: chain W residue 22 SER Chi-restraints excluded: chain X residue 105 GLN Chi-restraints excluded: chain Y residue 50 GLU Chi-restraints excluded: chain Y residue 78 GLN Chi-restraints excluded: chain Y residue 87 LEU Chi-restraints excluded: chain Y residue 114 CYS Chi-restraints excluded: chain Z residue 50 MET Chi-restraints excluded: chain Z residue 120 MET Chi-restraints excluded: chain a residue 67 GLU Chi-restraints excluded: chain b residue 4 VAL Chi-restraints excluded: chain d residue 3 THR Chi-restraints excluded: chain d residue 107 LYS Chi-restraints excluded: chain e residue 80 ARG Chi-restraints excluded: chain g residue 60 VAL Chi-restraints excluded: chain i residue 42 VAL Chi-restraints excluded: chain i residue 124 ASP Chi-restraints excluded: chain j residue 32 MET Chi-restraints excluded: chain j residue 40 PHE Chi-restraints excluded: chain k residue 31 VAL Chi-restraints excluded: chain k residue 87 LEU Chi-restraints excluded: chain l residue 3 HIS Chi-restraints excluded: chain n residue 145 VAL Chi-restraints excluded: chain o residue 21 MET Chi-restraints excluded: chain o residue 23 THR Chi-restraints excluded: chain o residue 80 LYS Chi-restraints excluded: chain o residue 112 LYS Chi-restraints excluded: chain p residue 42 ARG Chi-restraints excluded: chain p residue 112 CYS Chi-restraints excluded: chain r residue 104 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 807 random chunks: chunk 649 optimal weight: 0.7980 chunk 442 optimal weight: 0.3980 chunk 11 optimal weight: 0.0770 chunk 580 optimal weight: 6.9990 chunk 321 optimal weight: 0.7980 chunk 665 optimal weight: 2.9990 chunk 539 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 398 optimal weight: 4.9990 chunk 700 optimal weight: 4.9990 chunk 196 optimal weight: 3.9990 overall best weight: 1.0140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 69 ASN E 37 ASN F 261 HIS F 398 GLN G 237 ASN ** G 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 171 GLN M 187 HIS S 75 ASN c 46 ASN k 90 GLN o 53 GLN q 135 GLN ** s 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.246 70417 Z= 0.429 Angle : 1.276 50.580 95203 Z= 0.824 Chirality : 0.253 6.438 10260 Planarity : 0.004 0.057 11878 Dihedral : 12.415 178.610 10836 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.05 % Favored : 97.91 % Rotamer: Outliers : 1.69 % Allowed : 10.29 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.09), residues: 8195 helix: 1.66 (0.08), residues: 4319 sheet: 0.16 (0.26), residues: 379 loop : 0.22 (0.11), residues: 3497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP X 85 HIS 0.010 0.001 HIS L 514 PHE 0.023 0.001 PHE N 292 TYR 0.023 0.001 TYR P 263 ARG 0.010 0.000 ARG q 21 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16390 Ramachandran restraints generated. 8195 Oldfield, 0 Emsley, 8195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16390 Ramachandran restraints generated. 8195 Oldfield, 0 Emsley, 8195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1100 residues out of total 7219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 978 time to evaluate : 6.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 75 VAL cc_start: 0.8884 (t) cc_final: 0.8663 (t) REVERT: B 170 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7778 (mt-10) REVERT: B 178 ARG cc_start: 0.8233 (OUTLIER) cc_final: 0.7648 (mtp85) REVERT: C 87 GLN cc_start: 0.8141 (pt0) cc_final: 0.7925 (pt0) REVERT: D 40 LYS cc_start: 0.7715 (mmtp) cc_final: 0.7378 (mttp) REVERT: D 47 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7829 (tp) REVERT: D 334 LYS cc_start: 0.8325 (mttm) cc_final: 0.8092 (mttm) REVERT: E 98 TYR cc_start: 0.8909 (m-80) cc_final: 0.8445 (m-80) REVERT: F 432 GLN cc_start: 0.7274 (OUTLIER) cc_final: 0.6757 (mp10) REVERT: G 180 ASP cc_start: 0.7668 (t0) cc_final: 0.7429 (t0) REVERT: H 8 MET cc_start: 0.7686 (mtp) cc_final: 0.7219 (mtt) REVERT: H 10 ILE cc_start: 0.8264 (pt) cc_final: 0.7937 (mm) REVERT: I 15 LYS cc_start: 0.8154 (tttm) cc_final: 0.7891 (tttp) REVERT: I 36 MET cc_start: 0.8378 (tpp) cc_final: 0.7926 (tpp) REVERT: J 141 MET cc_start: 0.8255 (mmp) cc_final: 0.8033 (mmm) REVERT: K 34 GLU cc_start: 0.7577 (mt-10) cc_final: 0.7358 (mt-10) REVERT: L 31 ASN cc_start: 0.6413 (m110) cc_final: 0.5988 (m110) REVERT: N 14 MET cc_start: 0.7706 (mtm) cc_final: 0.7406 (mtm) REVERT: N 187 MET cc_start: 0.7921 (mmp) cc_final: 0.7712 (mmm) REVERT: T 43 ASP cc_start: 0.8116 (OUTLIER) cc_final: 0.7842 (p0) REVERT: U 9 GLU cc_start: 0.7720 (mp0) cc_final: 0.7414 (mp0) REVERT: U 88 GLU cc_start: 0.7074 (mm-30) cc_final: 0.6518 (mm-30) REVERT: V 6 LYS cc_start: 0.7860 (OUTLIER) cc_final: 0.7464 (ttpp) REVERT: Y 50 GLU cc_start: 0.7443 (OUTLIER) cc_final: 0.7062 (tm-30) REVERT: Y 139 LYS cc_start: 0.8050 (mmtm) cc_final: 0.7404 (mtmm) REVERT: Z 99 LYS cc_start: 0.7001 (ptpp) cc_final: 0.6583 (ptpp) REVERT: a 59 ARG cc_start: 0.7907 (mpt-90) cc_final: 0.7591 (mmp80) REVERT: a 67 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.7967 (pm20) REVERT: d 107 LYS cc_start: 0.8760 (OUTLIER) cc_final: 0.8549 (mtpp) REVERT: e 82 ARG cc_start: 0.8101 (ttp80) cc_final: 0.7671 (ttp-170) REVERT: f 30 ASN cc_start: 0.8369 (t0) cc_final: 0.7785 (t0) REVERT: j 58 GLN cc_start: 0.8299 (OUTLIER) cc_final: 0.8019 (mp10) REVERT: k 48 GLU cc_start: 0.8037 (mm-30) cc_final: 0.7815 (mm-30) REVERT: o 112 LYS cc_start: 0.8751 (OUTLIER) cc_final: 0.8030 (ttmt) REVERT: p 42 ARG cc_start: 0.7295 (OUTLIER) cc_final: 0.5927 (tmt90) REVERT: q 53 LYS cc_start: 0.8748 (mtmt) cc_final: 0.8537 (mtmm) REVERT: q 67 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7773 (tt0) REVERT: r 5 ARG cc_start: 0.7206 (mmm-85) cc_final: 0.6951 (ptm-80) REVERT: r 104 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7333 (mp0) outliers start: 122 outliers final: 53 residues processed: 1034 average time/residue: 1.5906 time to fit residues: 2128.2191 Evaluate side-chains 999 residues out of total 7219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 932 time to evaluate : 6.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 178 ARG Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 66 MET Chi-restraints excluded: chain D residue 420 THR Chi-restraints excluded: chain E residue 192 SER Chi-restraints excluded: chain F residue 10 THR Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain F residue 432 GLN Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain H residue 251 MET Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain J residue 107 VAL Chi-restraints excluded: chain J residue 118 GLU Chi-restraints excluded: chain L residue 214 ILE Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain M residue 204 MET Chi-restraints excluded: chain M residue 246 ILE Chi-restraints excluded: chain M residue 385 THR Chi-restraints excluded: chain O residue 32 CYS Chi-restraints excluded: chain O residue 242 LYS Chi-restraints excluded: chain P residue 329 SER Chi-restraints excluded: chain Q residue 44 ASN Chi-restraints excluded: chain Q residue 115 SER Chi-restraints excluded: chain R residue 5 SER Chi-restraints excluded: chain R residue 19 ASP Chi-restraints excluded: chain S residue 75 ASN Chi-restraints excluded: chain T residue 7 THR Chi-restraints excluded: chain T residue 43 ASP Chi-restraints excluded: chain V residue 4 LEU Chi-restraints excluded: chain V residue 6 LYS Chi-restraints excluded: chain W residue 22 SER Chi-restraints excluded: chain X residue 4 VAL Chi-restraints excluded: chain X residue 105 GLN Chi-restraints excluded: chain Y residue 50 GLU Chi-restraints excluded: chain Y residue 78 GLN Chi-restraints excluded: chain Y residue 87 LEU Chi-restraints excluded: chain Y residue 114 CYS Chi-restraints excluded: chain Z residue 50 MET Chi-restraints excluded: chain Z residue 120 MET Chi-restraints excluded: chain a residue 67 GLU Chi-restraints excluded: chain a residue 69 ILE Chi-restraints excluded: chain b residue 4 VAL Chi-restraints excluded: chain b residue 27 LEU Chi-restraints excluded: chain d residue 3 THR Chi-restraints excluded: chain d residue 107 LYS Chi-restraints excluded: chain i residue 124 ASP Chi-restraints excluded: chain j residue 32 MET Chi-restraints excluded: chain j residue 40 PHE Chi-restraints excluded: chain j residue 48 LEU Chi-restraints excluded: chain j residue 58 GLN Chi-restraints excluded: chain k residue 31 VAL Chi-restraints excluded: chain k residue 87 LEU Chi-restraints excluded: chain k residue 90 GLN Chi-restraints excluded: chain l residue 3 HIS Chi-restraints excluded: chain n residue 34 ASP Chi-restraints excluded: chain n residue 56 MET Chi-restraints excluded: chain n residue 57 VAL Chi-restraints excluded: chain n residue 145 VAL Chi-restraints excluded: chain o residue 21 MET Chi-restraints excluded: chain o residue 112 LYS Chi-restraints excluded: chain p residue 42 ARG Chi-restraints excluded: chain p residue 112 CYS Chi-restraints excluded: chain q residue 67 GLU Chi-restraints excluded: chain r residue 104 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 807 random chunks: chunk 262 optimal weight: 5.9990 chunk 702 optimal weight: 6.9990 chunk 154 optimal weight: 0.3980 chunk 457 optimal weight: 0.8980 chunk 192 optimal weight: 0.8980 chunk 780 optimal weight: 0.9990 chunk 648 optimal weight: 4.9990 chunk 361 optimal weight: 4.9990 chunk 64 optimal weight: 0.7980 chunk 258 optimal weight: 0.9990 chunk 409 optimal weight: 5.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 69 ASN C 211 GLN F 398 GLN ** G 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 187 HIS ** N 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 72 GLN S 79 ASN c 46 ASN ** k 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 50 HIS o 53 GLN q 135 GLN ** s 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.246 70417 Z= 0.424 Angle : 1.273 50.582 95203 Z= 0.823 Chirality : 0.253 6.416 10260 Planarity : 0.004 0.054 11878 Dihedral : 12.138 176.986 10836 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.88 % Favored : 98.09 % Rotamer: Outliers : 1.62 % Allowed : 10.81 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.09), residues: 8195 helix: 1.73 (0.08), residues: 4333 sheet: 0.23 (0.26), residues: 377 loop : 0.26 (0.11), residues: 3485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP X 85 HIS 0.009 0.001 HIS L 514 PHE 0.024 0.001 PHE i 45 TYR 0.022 0.001 TYR L 422 ARG 0.008 0.000 ARG d 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16390 Ramachandran restraints generated. 8195 Oldfield, 0 Emsley, 8195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16390 Ramachandran restraints generated. 8195 Oldfield, 0 Emsley, 8195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1080 residues out of total 7219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 963 time to evaluate : 6.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 75 VAL cc_start: 0.8879 (t) cc_final: 0.8676 (t) REVERT: B 170 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7748 (mt-10) REVERT: B 178 ARG cc_start: 0.8209 (OUTLIER) cc_final: 0.7583 (mtp85) REVERT: C 87 GLN cc_start: 0.8135 (pt0) cc_final: 0.7929 (pt0) REVERT: D 40 LYS cc_start: 0.7702 (mmtp) cc_final: 0.7370 (mttp) REVERT: D 47 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7840 (tp) REVERT: D 334 LYS cc_start: 0.8320 (mttm) cc_final: 0.8085 (mttm) REVERT: D 427 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.6243 (pp20) REVERT: E 98 TYR cc_start: 0.8910 (m-80) cc_final: 0.8465 (m-80) REVERT: F 432 GLN cc_start: 0.7259 (OUTLIER) cc_final: 0.6539 (mp10) REVERT: G 180 ASP cc_start: 0.7660 (t0) cc_final: 0.7391 (t0) REVERT: H 8 MET cc_start: 0.7661 (mtp) cc_final: 0.7199 (mtt) REVERT: H 10 ILE cc_start: 0.8235 (pt) cc_final: 0.7952 (mm) REVERT: I 15 LYS cc_start: 0.8141 (tttm) cc_final: 0.7898 (tttp) REVERT: I 36 MET cc_start: 0.8361 (tpp) cc_final: 0.7929 (tpp) REVERT: K 34 GLU cc_start: 0.7547 (mt-10) cc_final: 0.7336 (mt-10) REVERT: N 14 MET cc_start: 0.7689 (mtm) cc_final: 0.7396 (mtm) REVERT: N 104 MET cc_start: 0.8319 (mtp) cc_final: 0.7942 (mtt) REVERT: S 85 GLN cc_start: 0.8368 (OUTLIER) cc_final: 0.8018 (mt0) REVERT: T 43 ASP cc_start: 0.8084 (OUTLIER) cc_final: 0.7829 (p0) REVERT: T 60 PHE cc_start: 0.7481 (p90) cc_final: 0.7259 (p90) REVERT: U 84 LYS cc_start: 0.8908 (OUTLIER) cc_final: 0.8422 (mttp) REVERT: V 6 LYS cc_start: 0.7855 (OUTLIER) cc_final: 0.7456 (ttpp) REVERT: Y 6 ARG cc_start: 0.7607 (ttp80) cc_final: 0.7355 (ttp-110) REVERT: Y 50 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.7038 (tm-30) REVERT: Y 139 LYS cc_start: 0.8045 (mmtm) cc_final: 0.7399 (mtmm) REVERT: Z 99 LYS cc_start: 0.6985 (ptpp) cc_final: 0.6543 (ptpp) REVERT: a 59 ARG cc_start: 0.7897 (mpt-90) cc_final: 0.7575 (mmp80) REVERT: a 67 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.7981 (pm20) REVERT: e 80 ARG cc_start: 0.7822 (OUTLIER) cc_final: 0.7521 (mtm-85) REVERT: e 82 ARG cc_start: 0.8098 (ttp80) cc_final: 0.7687 (ttp-170) REVERT: f 30 ASN cc_start: 0.8275 (t0) cc_final: 0.7810 (t0) REVERT: j 58 GLN cc_start: 0.8293 (OUTLIER) cc_final: 0.8000 (mp10) REVERT: k 48 GLU cc_start: 0.8001 (mm-30) cc_final: 0.7790 (mm-30) REVERT: m 112 GLU cc_start: 0.7510 (mm-30) cc_final: 0.7082 (tm-30) REVERT: o 112 LYS cc_start: 0.8731 (OUTLIER) cc_final: 0.8014 (ttmt) REVERT: o 121 MET cc_start: 0.6997 (mmm) cc_final: 0.6571 (pp-130) REVERT: p 42 ARG cc_start: 0.7289 (OUTLIER) cc_final: 0.5910 (tmt90) REVERT: r 5 ARG cc_start: 0.7189 (mmm-85) cc_final: 0.6934 (ptm-80) REVERT: r 104 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7328 (mp0) outliers start: 117 outliers final: 58 residues processed: 1023 average time/residue: 1.6339 time to fit residues: 2159.0004 Evaluate side-chains 1000 residues out of total 7219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 926 time to evaluate : 6.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 178 ARG Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 427 GLU Chi-restraints excluded: chain E residue 192 SER Chi-restraints excluded: chain F residue 10 THR Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain F residue 432 GLN Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain H residue 251 MET Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain J residue 107 VAL Chi-restraints excluded: chain J residue 118 GLU Chi-restraints excluded: chain K residue 70 GLU Chi-restraints excluded: chain L residue 52 MET Chi-restraints excluded: chain L residue 214 ILE Chi-restraints excluded: chain L residue 544 MET Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain M residue 246 ILE Chi-restraints excluded: chain M residue 255 ASP Chi-restraints excluded: chain M residue 385 THR Chi-restraints excluded: chain O residue 32 CYS Chi-restraints excluded: chain O residue 242 LYS Chi-restraints excluded: chain P residue 329 SER Chi-restraints excluded: chain Q residue 44 ASN Chi-restraints excluded: chain R residue 5 SER Chi-restraints excluded: chain R residue 19 ASP Chi-restraints excluded: chain S residue 85 GLN Chi-restraints excluded: chain S residue 90 LEU Chi-restraints excluded: chain T residue 7 THR Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain T residue 43 ASP Chi-restraints excluded: chain U residue 84 LYS Chi-restraints excluded: chain V residue 4 LEU Chi-restraints excluded: chain V residue 6 LYS Chi-restraints excluded: chain W residue 22 SER Chi-restraints excluded: chain X residue 4 VAL Chi-restraints excluded: chain X residue 105 GLN Chi-restraints excluded: chain Y residue 50 GLU Chi-restraints excluded: chain Y residue 78 GLN Chi-restraints excluded: chain Y residue 87 LEU Chi-restraints excluded: chain Y residue 109 ILE Chi-restraints excluded: chain Y residue 114 CYS Chi-restraints excluded: chain Z residue 120 MET Chi-restraints excluded: chain Z residue 130 SER Chi-restraints excluded: chain a residue 67 GLU Chi-restraints excluded: chain b residue 4 VAL Chi-restraints excluded: chain b residue 27 LEU Chi-restraints excluded: chain d residue 3 THR Chi-restraints excluded: chain e residue 80 ARG Chi-restraints excluded: chain g residue 60 VAL Chi-restraints excluded: chain i residue 124 ASP Chi-restraints excluded: chain j residue 32 MET Chi-restraints excluded: chain j residue 40 PHE Chi-restraints excluded: chain j residue 48 LEU Chi-restraints excluded: chain j residue 58 GLN Chi-restraints excluded: chain k residue 31 VAL Chi-restraints excluded: chain k residue 87 LEU Chi-restraints excluded: chain k residue 90 GLN Chi-restraints excluded: chain l residue 3 HIS Chi-restraints excluded: chain n residue 34 ASP Chi-restraints excluded: chain n residue 56 MET Chi-restraints excluded: chain n residue 145 VAL Chi-restraints excluded: chain n residue 175 GLU Chi-restraints excluded: chain o residue 21 MET Chi-restraints excluded: chain o residue 23 THR Chi-restraints excluded: chain o residue 27 ASP Chi-restraints excluded: chain o residue 112 LYS Chi-restraints excluded: chain p residue 42 ARG Chi-restraints excluded: chain p residue 112 CYS Chi-restraints excluded: chain r residue 104 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 807 random chunks: chunk 752 optimal weight: 5.9990 chunk 88 optimal weight: 0.6980 chunk 444 optimal weight: 9.9990 chunk 570 optimal weight: 1.9990 chunk 441 optimal weight: 3.9990 chunk 657 optimal weight: 6.9990 chunk 436 optimal weight: 0.0000 chunk 777 optimal weight: 8.9990 chunk 486 optimal weight: 0.0370 chunk 474 optimal weight: 0.9980 chunk 359 optimal weight: 0.9980 overall best weight: 0.5462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 69 ASN ** G 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 187 HIS ** N 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 75 ASN j 50 HIS k 90 GLN o 53 GLN q 135 GLN ** s 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.247 70417 Z= 0.419 Angle : 1.270 50.564 95203 Z= 0.821 Chirality : 0.252 6.393 10260 Planarity : 0.004 0.059 11878 Dihedral : 11.746 175.579 10836 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.94 % Favored : 98.03 % Rotamer: Outliers : 1.29 % Allowed : 11.66 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.09), residues: 8195 helix: 1.85 (0.08), residues: 4322 sheet: 0.10 (0.26), residues: 389 loop : 0.34 (0.11), residues: 3484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP L 144 HIS 0.008 0.001 HIS L 514 PHE 0.022 0.001 PHE N 292 TYR 0.022 0.001 TYR L 422 ARG 0.009 0.000 ARG r 102 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16390 Ramachandran restraints generated. 8195 Oldfield, 0 Emsley, 8195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16390 Ramachandran restraints generated. 8195 Oldfield, 0 Emsley, 8195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1061 residues out of total 7219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 968 time to evaluate : 6.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 75 VAL cc_start: 0.8889 (t) cc_final: 0.8669 (m) REVERT: B 170 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7728 (mt-10) REVERT: C 87 GLN cc_start: 0.8120 (pt0) cc_final: 0.7908 (pt0) REVERT: D 40 LYS cc_start: 0.7652 (mmtp) cc_final: 0.7334 (mtpp) REVERT: D 47 LEU cc_start: 0.8088 (OUTLIER) cc_final: 0.7820 (tp) REVERT: D 334 LYS cc_start: 0.8316 (mttm) cc_final: 0.8073 (mttm) REVERT: E 98 TYR cc_start: 0.8903 (m-80) cc_final: 0.8423 (m-80) REVERT: G 180 ASP cc_start: 0.7608 (t0) cc_final: 0.7326 (t0) REVERT: H 8 MET cc_start: 0.7640 (mtp) cc_final: 0.7194 (mtt) REVERT: I 15 LYS cc_start: 0.8133 (tttm) cc_final: 0.7899 (tttp) REVERT: I 36 MET cc_start: 0.8324 (tpp) cc_final: 0.7935 (tpp) REVERT: N 14 MET cc_start: 0.7619 (mtm) cc_final: 0.7335 (mtm) REVERT: N 104 MET cc_start: 0.8324 (mtp) cc_final: 0.7915 (mtt) REVERT: U 84 LYS cc_start: 0.8906 (OUTLIER) cc_final: 0.8467 (mttp) REVERT: V 6 LYS cc_start: 0.7849 (OUTLIER) cc_final: 0.7451 (ttpp) REVERT: Y 50 GLU cc_start: 0.7418 (OUTLIER) cc_final: 0.6965 (tm-30) REVERT: Y 139 LYS cc_start: 0.8049 (mmtm) cc_final: 0.7405 (mtmm) REVERT: Z 99 LYS cc_start: 0.6994 (ptpp) cc_final: 0.6497 (ptpp) REVERT: a 59 ARG cc_start: 0.7902 (mpt-90) cc_final: 0.7586 (mmp80) REVERT: e 80 ARG cc_start: 0.7805 (OUTLIER) cc_final: 0.7538 (mtm-85) REVERT: e 82 ARG cc_start: 0.8089 (ttp80) cc_final: 0.7690 (ttp-170) REVERT: f 29 LYS cc_start: 0.8602 (ttmm) cc_final: 0.8398 (tttt) REVERT: f 30 ASN cc_start: 0.8245 (t0) cc_final: 0.7844 (t0) REVERT: h 23 LYS cc_start: 0.8508 (OUTLIER) cc_final: 0.8301 (tmtm) REVERT: j 7 ILE cc_start: 0.8853 (mt) cc_final: 0.8630 (mt) REVERT: j 58 GLN cc_start: 0.8251 (OUTLIER) cc_final: 0.7986 (mp10) REVERT: k 48 GLU cc_start: 0.7973 (mm-30) cc_final: 0.7694 (mm-30) REVERT: l 15 LYS cc_start: 0.8659 (OUTLIER) cc_final: 0.8304 (mtpp) REVERT: m 112 GLU cc_start: 0.7515 (mm-30) cc_final: 0.7204 (tm-30) REVERT: o 112 LYS cc_start: 0.8734 (OUTLIER) cc_final: 0.8019 (ttmt) REVERT: p 42 ARG cc_start: 0.7290 (OUTLIER) cc_final: 0.5889 (tmt90) REVERT: r 5 ARG cc_start: 0.7167 (mmm-85) cc_final: 0.6919 (ptm-80) REVERT: r 104 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7314 (mp0) outliers start: 93 outliers final: 45 residues processed: 1014 average time/residue: 1.6324 time to fit residues: 2140.5405 Evaluate side-chains 991 residues out of total 7219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 934 time to evaluate : 6.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 420 THR Chi-restraints excluded: chain E residue 192 SER Chi-restraints excluded: chain F residue 10 THR Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain F residue 432 GLN Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain H residue 91 MET Chi-restraints excluded: chain J residue 87 LYS Chi-restraints excluded: chain J residue 118 GLU Chi-restraints excluded: chain J residue 139 GLU Chi-restraints excluded: chain L residue 52 MET Chi-restraints excluded: chain L residue 214 ILE Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain M residue 246 ILE Chi-restraints excluded: chain M residue 385 THR Chi-restraints excluded: chain O residue 32 CYS Chi-restraints excluded: chain O residue 242 LYS Chi-restraints excluded: chain P residue 329 SER Chi-restraints excluded: chain Q residue 44 ASN Chi-restraints excluded: chain R residue 5 SER Chi-restraints excluded: chain S residue 90 LEU Chi-restraints excluded: chain S residue 93 VAL Chi-restraints excluded: chain T residue 7 THR Chi-restraints excluded: chain U residue 84 LYS Chi-restraints excluded: chain V residue 4 LEU Chi-restraints excluded: chain V residue 6 LYS Chi-restraints excluded: chain W residue 22 SER Chi-restraints excluded: chain X residue 105 GLN Chi-restraints excluded: chain Y residue 50 GLU Chi-restraints excluded: chain Y residue 87 LEU Chi-restraints excluded: chain Y residue 109 ILE Chi-restraints excluded: chain Y residue 114 CYS Chi-restraints excluded: chain Z residue 120 MET Chi-restraints excluded: chain Z residue 130 SER Chi-restraints excluded: chain b residue 27 LEU Chi-restraints excluded: chain d residue 3 THR Chi-restraints excluded: chain e residue 80 ARG Chi-restraints excluded: chain g residue 60 VAL Chi-restraints excluded: chain h residue 23 LYS Chi-restraints excluded: chain i residue 124 ASP Chi-restraints excluded: chain j residue 23 ILE Chi-restraints excluded: chain j residue 32 MET Chi-restraints excluded: chain j residue 40 PHE Chi-restraints excluded: chain j residue 58 GLN Chi-restraints excluded: chain l residue 3 HIS Chi-restraints excluded: chain l residue 15 LYS Chi-restraints excluded: chain n residue 34 ASP Chi-restraints excluded: chain n residue 145 VAL Chi-restraints excluded: chain o residue 27 ASP Chi-restraints excluded: chain o residue 112 LYS Chi-restraints excluded: chain p residue 42 ARG Chi-restraints excluded: chain p residue 112 CYS Chi-restraints excluded: chain r residue 104 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 807 random chunks: chunk 481 optimal weight: 0.8980 chunk 310 optimal weight: 0.7980 chunk 464 optimal weight: 3.9990 chunk 234 optimal weight: 0.5980 chunk 152 optimal weight: 3.9990 chunk 150 optimal weight: 0.8980 chunk 494 optimal weight: 5.9990 chunk 529 optimal weight: 0.9980 chunk 384 optimal weight: 0.9990 chunk 72 optimal weight: 6.9990 chunk 611 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 69 ASN ** G 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 187 HIS M 399 ASN N 232 HIS ** N 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 102 GLN S 72 GLN S 75 ASN c 46 ASN k 90 GLN o 53 GLN q 46 ASN q 135 GLN ** s 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.246 70417 Z= 0.424 Angle : 1.273 50.553 95203 Z= 0.822 Chirality : 0.253 6.410 10260 Planarity : 0.004 0.060 11878 Dihedral : 11.580 174.617 10836 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.98 % Favored : 98.00 % Rotamer: Outliers : 1.40 % Allowed : 11.94 % Favored : 86.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.09), residues: 8195 helix: 1.85 (0.08), residues: 4331 sheet: 0.20 (0.26), residues: 380 loop : 0.34 (0.11), residues: 3484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP j 41 HIS 0.005 0.001 HIS R 68 PHE 0.029 0.001 PHE i 45 TYR 0.022 0.001 TYR L 422 ARG 0.011 0.000 ARG M 340 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16390 Ramachandran restraints generated. 8195 Oldfield, 0 Emsley, 8195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16390 Ramachandran restraints generated. 8195 Oldfield, 0 Emsley, 8195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1054 residues out of total 7219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 953 time to evaluate : 6.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 170 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7715 (mt-10) REVERT: C 87 GLN cc_start: 0.8122 (pt0) cc_final: 0.7860 (pt0) REVERT: D 40 LYS cc_start: 0.7649 (mmtp) cc_final: 0.7329 (mtpp) REVERT: D 47 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7808 (tp) REVERT: D 334 LYS cc_start: 0.8325 (mttm) cc_final: 0.8085 (mttm) REVERT: E 74 GLN cc_start: 0.8253 (OUTLIER) cc_final: 0.7538 (mt0) REVERT: E 98 TYR cc_start: 0.8890 (m-80) cc_final: 0.8402 (m-80) REVERT: G 180 ASP cc_start: 0.7579 (t0) cc_final: 0.7308 (t0) REVERT: G 260 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7580 (mt-10) REVERT: H 8 MET cc_start: 0.7675 (mtp) cc_final: 0.7180 (mtt) REVERT: I 36 MET cc_start: 0.8347 (tpp) cc_final: 0.7938 (tpp) REVERT: N 14 MET cc_start: 0.7620 (mtm) cc_final: 0.7340 (mtm) REVERT: N 68 MET cc_start: 0.8720 (mmp) cc_final: 0.8511 (mmp) REVERT: N 104 MET cc_start: 0.8331 (mtp) cc_final: 0.7940 (mtt) REVERT: S 25 ARG cc_start: 0.8010 (OUTLIER) cc_final: 0.7780 (mtm-85) REVERT: U 84 LYS cc_start: 0.8911 (OUTLIER) cc_final: 0.8471 (mttp) REVERT: V 6 LYS cc_start: 0.7853 (OUTLIER) cc_final: 0.7464 (ttpp) REVERT: Y 50 GLU cc_start: 0.7422 (OUTLIER) cc_final: 0.6985 (tm-30) REVERT: Y 139 LYS cc_start: 0.8094 (mmtm) cc_final: 0.7433 (mtmm) REVERT: Z 99 LYS cc_start: 0.7013 (ptpp) cc_final: 0.6514 (ptpp) REVERT: a 59 ARG cc_start: 0.7889 (mpt-90) cc_final: 0.7584 (mmp80) REVERT: e 80 ARG cc_start: 0.7807 (OUTLIER) cc_final: 0.7544 (mtm-85) REVERT: e 82 ARG cc_start: 0.8085 (ttp80) cc_final: 0.7701 (ttp-170) REVERT: f 30 ASN cc_start: 0.8242 (t0) cc_final: 0.7864 (t0) REVERT: h 23 LYS cc_start: 0.8514 (OUTLIER) cc_final: 0.8307 (tmtm) REVERT: j 58 GLN cc_start: 0.8260 (OUTLIER) cc_final: 0.7994 (mp10) REVERT: m 112 GLU cc_start: 0.7520 (mm-30) cc_final: 0.7202 (mm-30) REVERT: o 121 MET cc_start: 0.6892 (mmm) cc_final: 0.6519 (pp-130) REVERT: p 42 ARG cc_start: 0.7304 (OUTLIER) cc_final: 0.5892 (tmt90) REVERT: r 5 ARG cc_start: 0.7171 (mmm-85) cc_final: 0.6923 (ptm-80) REVERT: r 104 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7314 (mp0) outliers start: 101 outliers final: 54 residues processed: 1002 average time/residue: 1.6123 time to fit residues: 2085.2932 Evaluate side-chains 995 residues out of total 7219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 928 time to evaluate : 6.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 420 THR Chi-restraints excluded: chain E residue 74 GLN Chi-restraints excluded: chain E residue 192 SER Chi-restraints excluded: chain F residue 10 THR Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 260 GLU Chi-restraints excluded: chain H residue 91 MET Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain J residue 87 LYS Chi-restraints excluded: chain J residue 118 GLU Chi-restraints excluded: chain J residue 139 GLU Chi-restraints excluded: chain L residue 14 LEU Chi-restraints excluded: chain L residue 183 ILE Chi-restraints excluded: chain L residue 214 ILE Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain M residue 144 ASN Chi-restraints excluded: chain M residue 246 ILE Chi-restraints excluded: chain M residue 385 THR Chi-restraints excluded: chain O residue 32 CYS Chi-restraints excluded: chain O residue 242 LYS Chi-restraints excluded: chain P residue 329 SER Chi-restraints excluded: chain Q residue 44 ASN Chi-restraints excluded: chain Q residue 115 SER Chi-restraints excluded: chain R residue 5 SER Chi-restraints excluded: chain R residue 19 ASP Chi-restraints excluded: chain S residue 25 ARG Chi-restraints excluded: chain S residue 75 ASN Chi-restraints excluded: chain T residue 7 THR Chi-restraints excluded: chain T residue 30 LEU Chi-restraints excluded: chain U residue 84 LYS Chi-restraints excluded: chain V residue 4 LEU Chi-restraints excluded: chain V residue 6 LYS Chi-restraints excluded: chain W residue 22 SER Chi-restraints excluded: chain X residue 4 VAL Chi-restraints excluded: chain X residue 105 GLN Chi-restraints excluded: chain Y residue 50 GLU Chi-restraints excluded: chain Y residue 87 LEU Chi-restraints excluded: chain Y residue 109 ILE Chi-restraints excluded: chain Y residue 114 CYS Chi-restraints excluded: chain Z residue 31 SER Chi-restraints excluded: chain Z residue 120 MET Chi-restraints excluded: chain Z residue 130 SER Chi-restraints excluded: chain d residue 3 THR Chi-restraints excluded: chain e residue 80 ARG Chi-restraints excluded: chain g residue 60 VAL Chi-restraints excluded: chain h residue 23 LYS Chi-restraints excluded: chain i residue 9 LEU Chi-restraints excluded: chain i residue 124 ASP Chi-restraints excluded: chain j residue 32 MET Chi-restraints excluded: chain j residue 40 PHE Chi-restraints excluded: chain j residue 58 GLN Chi-restraints excluded: chain k residue 87 LEU Chi-restraints excluded: chain l residue 3 HIS Chi-restraints excluded: chain n residue 34 ASP Chi-restraints excluded: chain n residue 145 VAL Chi-restraints excluded: chain o residue 21 MET Chi-restraints excluded: chain o residue 23 THR Chi-restraints excluded: chain o residue 27 ASP Chi-restraints excluded: chain p residue 38 LEU Chi-restraints excluded: chain p residue 42 ARG Chi-restraints excluded: chain p residue 112 CYS Chi-restraints excluded: chain r residue 104 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 807 random chunks: chunk 707 optimal weight: 5.9990 chunk 745 optimal weight: 5.9990 chunk 679 optimal weight: 5.9990 chunk 724 optimal weight: 5.9990 chunk 744 optimal weight: 1.9990 chunk 436 optimal weight: 4.9990 chunk 315 optimal weight: 9.9990 chunk 569 optimal weight: 0.0270 chunk 222 optimal weight: 0.5980 chunk 654 optimal weight: 0.1980 chunk 685 optimal weight: 0.3980 overall best weight: 0.6440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 69 ASN ** G 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 514 HIS M 187 HIS ** N 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 72 GLN S 75 ASN T 74 GLN W 70 ASN c 46 ASN ** j 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 90 GLN o 53 GLN q 135 GLN ** s 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.247 70417 Z= 0.422 Angle : 1.274 50.540 95203 Z= 0.823 Chirality : 0.253 6.395 10260 Planarity : 0.004 0.060 11878 Dihedral : 11.402 174.121 10836 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.94 % Favored : 98.02 % Rotamer: Outliers : 1.36 % Allowed : 12.11 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.09), residues: 8195 helix: 1.90 (0.08), residues: 4317 sheet: 0.06 (0.25), residues: 409 loop : 0.42 (0.11), residues: 3469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP X 85 HIS 0.005 0.001 HIS R 68 PHE 0.025 0.001 PHE l 106 TYR 0.022 0.001 TYR L 422 ARG 0.010 0.000 ARG M 340 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16390 Ramachandran restraints generated. 8195 Oldfield, 0 Emsley, 8195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16390 Ramachandran restraints generated. 8195 Oldfield, 0 Emsley, 8195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1041 residues out of total 7219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 943 time to evaluate : 6.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 170 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7706 (mt-10) REVERT: C 87 GLN cc_start: 0.8111 (pt0) cc_final: 0.7852 (pt0) REVERT: D 40 LYS cc_start: 0.7631 (mmtp) cc_final: 0.7326 (mtpp) REVERT: D 47 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7857 (tp) REVERT: D 334 LYS cc_start: 0.8320 (mttm) cc_final: 0.8082 (mttm) REVERT: D 427 GLU cc_start: 0.7529 (OUTLIER) cc_final: 0.6488 (pp20) REVERT: E 74 GLN cc_start: 0.8243 (OUTLIER) cc_final: 0.7537 (mt0) REVERT: E 98 TYR cc_start: 0.8886 (m-80) cc_final: 0.8409 (m-80) REVERT: G 180 ASP cc_start: 0.7544 (t0) cc_final: 0.7265 (t0) REVERT: G 260 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7547 (mt-10) REVERT: H 8 MET cc_start: 0.7644 (mtp) cc_final: 0.7176 (mtt) REVERT: I 36 MET cc_start: 0.8334 (tpp) cc_final: 0.7936 (tpp) REVERT: N 14 MET cc_start: 0.7604 (mtm) cc_final: 0.7317 (mtm) REVERT: N 104 MET cc_start: 0.8334 (mtp) cc_final: 0.7920 (mtt) REVERT: S 25 ARG cc_start: 0.8015 (OUTLIER) cc_final: 0.7785 (mtm-85) REVERT: U 84 LYS cc_start: 0.8912 (OUTLIER) cc_final: 0.8416 (mttp) REVERT: V 6 LYS cc_start: 0.7860 (OUTLIER) cc_final: 0.7470 (ttpp) REVERT: Y 50 GLU cc_start: 0.7405 (OUTLIER) cc_final: 0.6951 (tm-30) REVERT: Y 139 LYS cc_start: 0.8072 (mmtm) cc_final: 0.7417 (mtmm) REVERT: Z 93 GLU cc_start: 0.7521 (mm-30) cc_final: 0.7309 (mm-30) REVERT: a 59 ARG cc_start: 0.7875 (mpt-90) cc_final: 0.7575 (mmp80) REVERT: e 7 LYS cc_start: 0.8320 (mtmt) cc_final: 0.8116 (mtpt) REVERT: e 80 ARG cc_start: 0.7804 (OUTLIER) cc_final: 0.7590 (mtm-85) REVERT: e 82 ARG cc_start: 0.8108 (ttp80) cc_final: 0.7730 (ttp-170) REVERT: f 30 ASN cc_start: 0.8209 (t0) cc_final: 0.7897 (t0) REVERT: h 23 LYS cc_start: 0.8511 (OUTLIER) cc_final: 0.8307 (tmtm) REVERT: l 15 LYS cc_start: 0.8672 (OUTLIER) cc_final: 0.8323 (mtpp) REVERT: n 159 GLN cc_start: 0.7774 (OUTLIER) cc_final: 0.7471 (tm-30) REVERT: o 121 MET cc_start: 0.6870 (mmm) cc_final: 0.6594 (pp-130) REVERT: p 42 ARG cc_start: 0.7303 (OUTLIER) cc_final: 0.5870 (tmt90) REVERT: r 5 ARG cc_start: 0.7170 (mmm-85) cc_final: 0.6926 (ptm-80) REVERT: r 104 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7309 (mp0) outliers start: 98 outliers final: 57 residues processed: 991 average time/residue: 1.6114 time to fit residues: 2067.1582 Evaluate side-chains 992 residues out of total 7219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 920 time to evaluate : 6.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 420 THR Chi-restraints excluded: chain D residue 427 GLU Chi-restraints excluded: chain E residue 74 GLN Chi-restraints excluded: chain E residue 192 SER Chi-restraints excluded: chain F residue 10 THR Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 260 GLU Chi-restraints excluded: chain H residue 91 MET Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain J residue 107 VAL Chi-restraints excluded: chain J residue 118 GLU Chi-restraints excluded: chain L residue 14 LEU Chi-restraints excluded: chain L residue 183 ILE Chi-restraints excluded: chain L residue 214 ILE Chi-restraints excluded: chain L residue 446 ASN Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain M residue 144 ASN Chi-restraints excluded: chain M residue 246 ILE Chi-restraints excluded: chain M residue 385 THR Chi-restraints excluded: chain O residue 32 CYS Chi-restraints excluded: chain O residue 242 LYS Chi-restraints excluded: chain P residue 329 SER Chi-restraints excluded: chain Q residue 44 ASN Chi-restraints excluded: chain Q residue 115 SER Chi-restraints excluded: chain R residue 5 SER Chi-restraints excluded: chain R residue 19 ASP Chi-restraints excluded: chain S residue 25 ARG Chi-restraints excluded: chain S residue 93 VAL Chi-restraints excluded: chain T residue 7 THR Chi-restraints excluded: chain U residue 84 LYS Chi-restraints excluded: chain V residue 4 LEU Chi-restraints excluded: chain V residue 6 LYS Chi-restraints excluded: chain W residue 22 SER Chi-restraints excluded: chain X residue 4 VAL Chi-restraints excluded: chain X residue 105 GLN Chi-restraints excluded: chain Y residue 50 GLU Chi-restraints excluded: chain Y residue 87 LEU Chi-restraints excluded: chain Y residue 109 ILE Chi-restraints excluded: chain Y residue 114 CYS Chi-restraints excluded: chain Z residue 31 SER Chi-restraints excluded: chain Z residue 130 SER Chi-restraints excluded: chain b residue 27 LEU Chi-restraints excluded: chain b residue 64 ASP Chi-restraints excluded: chain d residue 3 THR Chi-restraints excluded: chain e residue 80 ARG Chi-restraints excluded: chain g residue 60 VAL Chi-restraints excluded: chain h residue 23 LYS Chi-restraints excluded: chain i residue 9 LEU Chi-restraints excluded: chain i residue 124 ASP Chi-restraints excluded: chain j residue 32 MET Chi-restraints excluded: chain j residue 40 PHE Chi-restraints excluded: chain j residue 48 LEU Chi-restraints excluded: chain k residue 87 LEU Chi-restraints excluded: chain l residue 3 HIS Chi-restraints excluded: chain l residue 15 LYS Chi-restraints excluded: chain n residue 34 ASP Chi-restraints excluded: chain n residue 145 VAL Chi-restraints excluded: chain n residue 159 GLN Chi-restraints excluded: chain o residue 21 MET Chi-restraints excluded: chain o residue 23 THR Chi-restraints excluded: chain o residue 27 ASP Chi-restraints excluded: chain p residue 16 THR Chi-restraints excluded: chain p residue 38 LEU Chi-restraints excluded: chain p residue 42 ARG Chi-restraints excluded: chain p residue 112 CYS Chi-restraints excluded: chain r residue 104 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 807 random chunks: chunk 722 optimal weight: 8.9990 chunk 475 optimal weight: 5.9990 chunk 766 optimal weight: 5.9990 chunk 467 optimal weight: 1.9990 chunk 363 optimal weight: 1.9990 chunk 532 optimal weight: 6.9990 chunk 803 optimal weight: 5.9990 chunk 739 optimal weight: 2.9990 chunk 640 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 494 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 69 ASN F 398 GLN F 432 GLN F 436 GLN ** G 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 135 ASN M 304 GLN S 72 GLN T 74 GLN c 46 ASN ** h 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 90 GLN o 53 GLN q 135 GLN ** s 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.244 70417 Z= 0.525 Angle : 1.316 50.506 95203 Z= 0.838 Chirality : 0.257 6.558 10260 Planarity : 0.004 0.058 11878 Dihedral : 11.868 173.096 10836 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.32 % Favored : 97.65 % Rotamer: Outliers : 1.26 % Allowed : 12.38 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.09), residues: 8195 helix: 1.55 (0.08), residues: 4328 sheet: 0.22 (0.26), residues: 378 loop : 0.23 (0.11), residues: 3489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP f 56 HIS 0.007 0.001 HIS R 68 PHE 0.030 0.002 PHE i 45 TYR 0.026 0.002 TYR P 145 ARG 0.011 0.001 ARG c 44 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16390 Ramachandran restraints generated. 8195 Oldfield, 0 Emsley, 8195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16390 Ramachandran restraints generated. 8195 Oldfield, 0 Emsley, 8195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1016 residues out of total 7219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 925 time to evaluate : 6.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 170 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7761 (mt-10) REVERT: C 87 GLN cc_start: 0.8191 (pt0) cc_final: 0.7907 (pt0) REVERT: C 186 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7689 (mt-10) REVERT: D 47 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.7871 (tp) REVERT: D 334 LYS cc_start: 0.8359 (mttm) cc_final: 0.8128 (mttm) REVERT: D 427 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.6663 (pp20) REVERT: G 180 ASP cc_start: 0.7654 (t0) cc_final: 0.7388 (t0) REVERT: H 8 MET cc_start: 0.7790 (mtp) cc_final: 0.7290 (mtt) REVERT: N 104 MET cc_start: 0.8326 (mtp) cc_final: 0.7995 (mtt) REVERT: U 84 LYS cc_start: 0.8962 (OUTLIER) cc_final: 0.8382 (mttp) REVERT: V 6 LYS cc_start: 0.7877 (OUTLIER) cc_final: 0.7473 (ttpp) REVERT: Y 50 GLU cc_start: 0.7487 (OUTLIER) cc_final: 0.7125 (tm-30) REVERT: Y 139 LYS cc_start: 0.8103 (mmtm) cc_final: 0.7420 (mtmm) REVERT: a 59 ARG cc_start: 0.7903 (mpt-90) cc_final: 0.7542 (mmp80) REVERT: a 67 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.7930 (pm20) REVERT: e 80 ARG cc_start: 0.7850 (OUTLIER) cc_final: 0.7481 (mtm-85) REVERT: e 82 ARG cc_start: 0.8111 (ttp80) cc_final: 0.7762 (ttp-170) REVERT: f 30 ASN cc_start: 0.8332 (t0) cc_final: 0.7882 (t0) REVERT: l 15 LYS cc_start: 0.8709 (OUTLIER) cc_final: 0.8278 (mtpp) REVERT: n 159 GLN cc_start: 0.7842 (OUTLIER) cc_final: 0.7548 (tm-30) REVERT: o 121 MET cc_start: 0.6931 (mmm) cc_final: 0.6689 (pp-130) REVERT: p 42 ARG cc_start: 0.7342 (OUTLIER) cc_final: 0.5864 (tmt90) REVERT: r 5 ARG cc_start: 0.7274 (mmm-85) cc_final: 0.7019 (ptm-80) REVERT: r 104 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7280 (mp0) outliers start: 91 outliers final: 49 residues processed: 975 average time/residue: 1.6806 time to fit residues: 2107.2620 Evaluate side-chains 974 residues out of total 7219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 912 time to evaluate : 6.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 420 THR Chi-restraints excluded: chain D residue 427 GLU Chi-restraints excluded: chain E residue 192 SER Chi-restraints excluded: chain F residue 10 THR Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain J residue 87 LYS Chi-restraints excluded: chain J residue 107 VAL Chi-restraints excluded: chain J residue 118 GLU Chi-restraints excluded: chain L residue 60 GLU Chi-restraints excluded: chain L residue 214 ILE Chi-restraints excluded: chain M residue 255 ASP Chi-restraints excluded: chain M residue 385 THR Chi-restraints excluded: chain N residue 164 ILE Chi-restraints excluded: chain O residue 32 CYS Chi-restraints excluded: chain Q residue 44 ASN Chi-restraints excluded: chain Q residue 115 SER Chi-restraints excluded: chain R residue 5 SER Chi-restraints excluded: chain R residue 19 ASP Chi-restraints excluded: chain S residue 90 LEU Chi-restraints excluded: chain S residue 93 VAL Chi-restraints excluded: chain T residue 7 THR Chi-restraints excluded: chain T residue 30 LEU Chi-restraints excluded: chain U residue 54 MET Chi-restraints excluded: chain U residue 84 LYS Chi-restraints excluded: chain V residue 6 LYS Chi-restraints excluded: chain W residue 22 SER Chi-restraints excluded: chain X residue 4 VAL Chi-restraints excluded: chain Y residue 50 GLU Chi-restraints excluded: chain Y residue 87 LEU Chi-restraints excluded: chain Y residue 114 CYS Chi-restraints excluded: chain Z residue 130 SER Chi-restraints excluded: chain a residue 67 GLU Chi-restraints excluded: chain b residue 27 LEU Chi-restraints excluded: chain d residue 3 THR Chi-restraints excluded: chain d residue 107 LYS Chi-restraints excluded: chain e residue 80 ARG Chi-restraints excluded: chain g residue 60 VAL Chi-restraints excluded: chain i residue 9 LEU Chi-restraints excluded: chain i residue 124 ASP Chi-restraints excluded: chain j residue 32 MET Chi-restraints excluded: chain j residue 40 PHE Chi-restraints excluded: chain k residue 31 VAL Chi-restraints excluded: chain k residue 87 LEU Chi-restraints excluded: chain l residue 3 HIS Chi-restraints excluded: chain l residue 15 LYS Chi-restraints excluded: chain n residue 34 ASP Chi-restraints excluded: chain n residue 145 VAL Chi-restraints excluded: chain n residue 159 GLN Chi-restraints excluded: chain o residue 21 MET Chi-restraints excluded: chain o residue 23 THR Chi-restraints excluded: chain p residue 38 LEU Chi-restraints excluded: chain p residue 42 ARG Chi-restraints excluded: chain p residue 112 CYS Chi-restraints excluded: chain r residue 104 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 807 random chunks: chunk 392 optimal weight: 3.9990 chunk 508 optimal weight: 0.9980 chunk 681 optimal weight: 1.9990 chunk 196 optimal weight: 0.0980 chunk 590 optimal weight: 5.9990 chunk 94 optimal weight: 6.9990 chunk 177 optimal weight: 4.9990 chunk 641 optimal weight: 0.9990 chunk 268 optimal weight: 0.8980 chunk 658 optimal weight: 6.9990 chunk 81 optimal weight: 0.8980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 69 ASN F 398 GLN F 432 GLN ** G 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 514 HIS M 51 ASN M 187 HIS ** N 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 72 GLN S 75 ASN ** b 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 46 ASN ** j 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 90 GLN o 53 GLN q 135 GLN ** s 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.092487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.077485 restraints weight = 167947.600| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 1.76 r_work: 0.2877 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2766 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2766 r_free = 0.2766 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2766 r_free = 0.2766 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2766 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.247 70417 Z= 0.425 Angle : 1.281 50.543 95203 Z= 0.825 Chirality : 0.253 6.417 10260 Planarity : 0.004 0.059 11878 Dihedral : 11.516 173.983 10836 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.91 % Favored : 98.07 % Rotamer: Outliers : 0.91 % Allowed : 12.74 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.09), residues: 8195 helix: 1.75 (0.08), residues: 4312 sheet: 0.29 (0.26), residues: 382 loop : 0.28 (0.11), residues: 3501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP X 85 HIS 0.005 0.001 HIS R 68 PHE 0.023 0.001 PHE N 292 TYR 0.022 0.001 TYR L 422 ARG 0.015 0.000 ARG g 25 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 32150.33 seconds wall clock time: 557 minutes 21.52 seconds (33441.52 seconds total)