Starting phenix.real_space_refine on Sat Feb 17 08:00:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u8o_26385/02_2024/7u8o_26385.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u8o_26385/02_2024/7u8o_26385.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u8o_26385/02_2024/7u8o_26385.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u8o_26385/02_2024/7u8o_26385.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u8o_26385/02_2024/7u8o_26385.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u8o_26385/02_2024/7u8o_26385.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.026 sd= 0.135 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: 4 Type Number sf(0) Gaussians S 351 5.16 5 C 43795 2.51 5 N 11743 2.21 5 O 12743 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 44": "NH1" <-> "NH2" Residue "A ARG 56": "NH1" <-> "NH2" Residue "A ARG 81": "NH1" <-> "NH2" Residue "A ARG 104": "NH1" <-> "NH2" Residue "A ARG 120": "NH1" <-> "NH2" Residue "A ARG 129": "NH1" <-> "NH2" Residue "A ARG 142": "NH1" <-> "NH2" Residue "A ARG 165": "NH1" <-> "NH2" Residue "A ARG 171": "NH1" <-> "NH2" Residue "A ARG 173": "NH1" <-> "NH2" Residue "A ARG 212": "NH1" <-> "NH2" Residue "A ARG 215": "NH1" <-> "NH2" Residue "A ARG 232": "NH1" <-> "NH2" Residue "A ARG 280": "NH1" <-> "NH2" Residue "A ARG 289": "NH1" <-> "NH2" Residue "A ARG 308": "NH1" <-> "NH2" Residue "A ARG 323": "NH1" <-> "NH2" Residue "A ARG 338": "NH1" <-> "NH2" Residue "A ARG 353": "NH1" <-> "NH2" Residue "A ARG 359": "NH1" <-> "NH2" Residue "A ARG 364": "NH1" <-> "NH2" Residue "A ARG 381": "NH1" <-> "NH2" Residue "A ARG 388": "NH1" <-> "NH2" Residue "A ARG 391": "NH1" <-> "NH2" Residue "A ARG 400": "NH1" <-> "NH2" Residue "A ARG 442": "NH1" <-> "NH2" Residue "A ARG 459": "NH1" <-> "NH2" Residue "A ARG 476": "NH1" <-> "NH2" Residue "A ARG 530": "NH1" <-> "NH2" Residue "A ARG 552": "NH1" <-> "NH2" Residue "A ARG 553": "NH1" <-> "NH2" Residue "A ARG 571": "NH1" <-> "NH2" Residue "A ARG 613": "NH1" <-> "NH2" Residue "B ARG 44": "NH1" <-> "NH2" Residue "B ARG 56": "NH1" <-> "NH2" Residue "B ARG 81": "NH1" <-> "NH2" Residue "B ARG 104": "NH1" <-> "NH2" Residue "B ARG 120": "NH1" <-> "NH2" Residue "B ARG 129": "NH1" <-> "NH2" Residue "B ARG 142": "NH1" <-> "NH2" Residue "B ARG 165": "NH1" <-> "NH2" Residue "B ARG 171": "NH1" <-> "NH2" Residue "B ARG 173": "NH1" <-> "NH2" Residue "B ARG 212": "NH1" <-> "NH2" Residue "B ARG 215": "NH1" <-> "NH2" Residue "B ARG 232": "NH1" <-> "NH2" Residue "B ARG 280": "NH1" <-> "NH2" Residue "B ARG 289": "NH1" <-> "NH2" Residue "B ARG 308": "NH1" <-> "NH2" Residue "B ARG 323": "NH1" <-> "NH2" Residue "B ARG 338": "NH1" <-> "NH2" Residue "B ARG 353": "NH1" <-> "NH2" Residue "B ARG 359": "NH1" <-> "NH2" Residue "B ARG 364": "NH1" <-> "NH2" Residue "B ARG 381": "NH1" <-> "NH2" Residue "B GLU 387": "OE1" <-> "OE2" Residue "B ARG 388": "NH1" <-> "NH2" Residue "B ARG 391": "NH1" <-> "NH2" Residue "B ARG 400": "NH1" <-> "NH2" Residue "B ARG 442": "NH1" <-> "NH2" Residue "B TYR 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 459": "NH1" <-> "NH2" Residue "B ARG 476": "NH1" <-> "NH2" Residue "B ARG 530": "NH1" <-> "NH2" Residue "B ARG 552": "NH1" <-> "NH2" Residue "B ARG 553": "NH1" <-> "NH2" Residue "B ARG 571": "NH1" <-> "NH2" Residue "B ARG 613": "NH1" <-> "NH2" Residue "C ARG 44": "NH1" <-> "NH2" Residue "C ARG 56": "NH1" <-> "NH2" Residue "C GLU 69": "OE1" <-> "OE2" Residue "C ARG 81": "NH1" <-> "NH2" Residue "C ARG 104": "NH1" <-> "NH2" Residue "C ARG 120": "NH1" <-> "NH2" Residue "C ARG 129": "NH1" <-> "NH2" Residue "C ARG 142": "NH1" <-> "NH2" Residue "C ARG 165": "NH1" <-> "NH2" Residue "C ARG 171": "NH1" <-> "NH2" Residue "C ARG 173": "NH1" <-> "NH2" Residue "C GLU 195": "OE1" <-> "OE2" Residue "C ARG 212": "NH1" <-> "NH2" Residue "C ARG 215": "NH1" <-> "NH2" Residue "C ARG 232": "NH1" <-> "NH2" Residue "C ARG 280": "NH1" <-> "NH2" Residue "C ARG 289": "NH1" <-> "NH2" Residue "C ARG 308": "NH1" <-> "NH2" Residue "C ARG 323": "NH1" <-> "NH2" Residue "C ARG 338": "NH1" <-> "NH2" Residue "C ARG 353": "NH1" <-> "NH2" Residue "C ARG 359": "NH1" <-> "NH2" Residue "C ARG 364": "NH1" <-> "NH2" Residue "C ARG 381": "NH1" <-> "NH2" Residue "C ARG 388": "NH1" <-> "NH2" Residue "C ARG 391": "NH1" <-> "NH2" Residue "C ARG 400": "NH1" <-> "NH2" Residue "C ARG 442": "NH1" <-> "NH2" Residue "C ARG 459": "NH1" <-> "NH2" Residue "C ARG 476": "NH1" <-> "NH2" Residue "C ARG 530": "NH1" <-> "NH2" Residue "C ARG 552": "NH1" <-> "NH2" Residue "C ARG 553": "NH1" <-> "NH2" Residue "C ARG 571": "NH1" <-> "NH2" Residue "C ARG 613": "NH1" <-> "NH2" Residue "D ARG 38": "NH1" <-> "NH2" Residue "D ARG 42": "NH1" <-> "NH2" Residue "D ARG 76": "NH1" <-> "NH2" Residue "D GLU 94": "OE1" <-> "OE2" Residue "D ARG 114": "NH1" <-> "NH2" Residue "D ARG 124": "NH1" <-> "NH2" Residue "D ARG 157": "NH1" <-> "NH2" Residue "D GLU 161": "OE1" <-> "OE2" Residue "D ARG 179": "NH1" <-> "NH2" Residue "D ARG 202": "NH1" <-> "NH2" Residue "D PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 236": "NH1" <-> "NH2" Residue "D ARG 265": "NH1" <-> "NH2" Residue "D ARG 270": "NH1" <-> "NH2" Residue "D ARG 302": "NH1" <-> "NH2" Residue "D ARG 308": "NH1" <-> "NH2" Residue "D ARG 314": "NH1" <-> "NH2" Residue "D ARG 315": "NH1" <-> "NH2" Residue "D ARG 331": "NH1" <-> "NH2" Residue "D ARG 334": "NH1" <-> "NH2" Residue "D GLU 336": "OE1" <-> "OE2" Residue "D ARG 338": "NH1" <-> "NH2" Residue "D ARG 375": "NH1" <-> "NH2" Residue "D ARG 380": "NH1" <-> "NH2" Residue "D TYR 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 394": "NH1" <-> "NH2" Residue "D GLU 402": "OE1" <-> "OE2" Residue "D ARG 406": "NH1" <-> "NH2" Residue "D ASP 408": "OD1" <-> "OD2" Residue "D ARG 454": "NH1" <-> "NH2" Residue "D ARG 465": "NH1" <-> "NH2" Residue "D PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 479": "NH1" <-> "NH2" Residue "D ARG 488": "NH1" <-> "NH2" Residue "E ARG 38": "NH1" <-> "NH2" Residue "E ARG 42": "NH1" <-> "NH2" Residue "E ARG 76": "NH1" <-> "NH2" Residue "E ARG 114": "NH1" <-> "NH2" Residue "E ARG 124": "NH1" <-> "NH2" Residue "E ARG 157": "NH1" <-> "NH2" Residue "E ARG 179": "NH1" <-> "NH2" Residue "E ARG 202": "NH1" <-> "NH2" Residue "E ARG 236": "NH1" <-> "NH2" Residue "E ARG 265": "NH1" <-> "NH2" Residue "E ARG 270": "NH1" <-> "NH2" Residue "E TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 302": "NH1" <-> "NH2" Residue "E ARG 308": "NH1" <-> "NH2" Residue "E ARG 314": "NH1" <-> "NH2" Residue "E ARG 315": "NH1" <-> "NH2" Residue "E GLU 330": "OE1" <-> "OE2" Residue "E ARG 331": "NH1" <-> "NH2" Residue "E ARG 334": "NH1" <-> "NH2" Residue "E ARG 338": "NH1" <-> "NH2" Residue "E ARG 375": "NH1" <-> "NH2" Residue "E ARG 380": "NH1" <-> "NH2" Residue "E ARG 394": "NH1" <-> "NH2" Residue "E ARG 406": "NH1" <-> "NH2" Residue "E ARG 454": "NH1" <-> "NH2" Residue "E ARG 465": "NH1" <-> "NH2" Residue "E ARG 479": "NH1" <-> "NH2" Residue "E ARG 488": "NH1" <-> "NH2" Residue "F ARG 38": "NH1" <-> "NH2" Residue "F ARG 42": "NH1" <-> "NH2" Residue "F ARG 76": "NH1" <-> "NH2" Residue "F ARG 114": "NH1" <-> "NH2" Residue "F ARG 124": "NH1" <-> "NH2" Residue "F PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 157": "NH1" <-> "NH2" Residue "F ARG 179": "NH1" <-> "NH2" Residue "F ARG 202": "NH1" <-> "NH2" Residue "F ARG 236": "NH1" <-> "NH2" Residue "F ARG 265": "NH1" <-> "NH2" Residue "F ARG 270": "NH1" <-> "NH2" Residue "F ARG 302": "NH1" <-> "NH2" Residue "F ARG 308": "NH1" <-> "NH2" Residue "F ARG 314": "NH1" <-> "NH2" Residue "F ARG 315": "NH1" <-> "NH2" Residue "F ARG 331": "NH1" <-> "NH2" Residue "F ARG 334": "NH1" <-> "NH2" Residue "F ARG 338": "NH1" <-> "NH2" Residue "F ASP 361": "OD1" <-> "OD2" Residue "F ARG 375": "NH1" <-> "NH2" Residue "F ARG 380": "NH1" <-> "NH2" Residue "F ARG 394": "NH1" <-> "NH2" Residue "F ARG 406": "NH1" <-> "NH2" Residue "F ARG 454": "NH1" <-> "NH2" Residue "F ARG 465": "NH1" <-> "NH2" Residue "F ARG 479": "NH1" <-> "NH2" Residue "F ARG 488": "NH1" <-> "NH2" Residue "H ARG 6": "NH1" <-> "NH2" Residue "H ARG 13": "NH1" <-> "NH2" Residue "H ARG 22": "NH1" <-> "NH2" Residue "H ARG 30": "NH1" <-> "NH2" Residue "H ARG 43": "NH1" <-> "NH2" Residue "H ARG 45": "NH1" <-> "NH2" Residue "H ARG 63": "NH1" <-> "NH2" Residue "H ARG 95": "NH1" <-> "NH2" Residue "H GLU 114": "OE1" <-> "OE2" Residue "H TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 126": "NH1" <-> "NH2" Residue "H ARG 136": "NH1" <-> "NH2" Residue "H ARG 167": "NH1" <-> "NH2" Residue "H ARG 168": "NH1" <-> "NH2" Residue "H ARG 179": "NH1" <-> "NH2" Residue "H ARG 182": "NH1" <-> "NH2" Residue "H GLU 193": "OE1" <-> "OE2" Residue "H ARG 194": "NH1" <-> "NH2" Residue "H ARG 196": "NH1" <-> "NH2" Residue "H PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 201": "NH1" <-> "NH2" Residue "I ARG 80": "NH1" <-> "NH2" Residue "I ARG 85": "NH1" <-> "NH2" Residue "I ARG 87": "NH1" <-> "NH2" Residue "I ARG 101": "NH1" <-> "NH2" Residue "I ARG 111": "NH1" <-> "NH2" Residue "I ARG 131": "NH1" <-> "NH2" Residue "I ARG 135": "NH1" <-> "NH2" Residue "I ARG 137": "NH1" <-> "NH2" Residue "I ARG 161": "NH1" <-> "NH2" Residue "I ARG 188": "NH1" <-> "NH2" Residue "I ARG 199": "NH1" <-> "NH2" Residue "I ARG 212": "NH1" <-> "NH2" Residue "I ARG 222": "NH1" <-> "NH2" Residue "J ARG 80": "NH1" <-> "NH2" Residue "J ARG 85": "NH1" <-> "NH2" Residue "J ARG 87": "NH1" <-> "NH2" Residue "J ARG 101": "NH1" <-> "NH2" Residue "J ARG 111": "NH1" <-> "NH2" Residue "J ARG 131": "NH1" <-> "NH2" Residue "J ARG 135": "NH1" <-> "NH2" Residue "J ARG 137": "NH1" <-> "NH2" Residue "J ARG 161": "NH1" <-> "NH2" Residue "J ARG 188": "NH1" <-> "NH2" Residue "J ARG 199": "NH1" <-> "NH2" Residue "J ARG 212": "NH1" <-> "NH2" Residue "J ARG 222": "NH1" <-> "NH2" Residue "K ARG 44": "NH1" <-> "NH2" Residue "K ARG 50": "NH1" <-> "NH2" Residue "K ARG 80": "NH1" <-> "NH2" Residue "K ARG 85": "NH1" <-> "NH2" Residue "K ARG 87": "NH1" <-> "NH2" Residue "K ARG 101": "NH1" <-> "NH2" Residue "K ARG 111": "NH1" <-> "NH2" Residue "K ARG 131": "NH1" <-> "NH2" Residue "K ARG 135": "NH1" <-> "NH2" Residue "K ARG 137": "NH1" <-> "NH2" Residue "K ARG 161": "NH1" <-> "NH2" Residue "K ARG 188": "NH1" <-> "NH2" Residue "K ARG 199": "NH1" <-> "NH2" Residue "K GLU 210": "OE1" <-> "OE2" Residue "K ARG 212": "NH1" <-> "NH2" Residue "K ARG 222": "NH1" <-> "NH2" Residue "L ARG 32": "NH1" <-> "NH2" Residue "L ARG 53": "NH1" <-> "NH2" Residue "L ARG 58": "NH1" <-> "NH2" Residue "L ARG 75": "NH1" <-> "NH2" Residue "L ARG 83": "NH1" <-> "NH2" Residue "L ASP 103": "OD1" <-> "OD2" Residue "L ARG 107": "NH1" <-> "NH2" Residue "L ARG 108": "NH1" <-> "NH2" Residue "M ARG 89": "NH1" <-> "NH2" Residue "M ARG 92": "NH1" <-> "NH2" Residue "M ARG 107": "NH1" <-> "NH2" Residue "M GLU 109": "OE1" <-> "OE2" Residue "M ARG 115": "NH1" <-> "NH2" Residue "N ARG 89": "NH1" <-> "NH2" Residue "N ARG 92": "NH1" <-> "NH2" Residue "N ARG 107": "NH1" <-> "NH2" Residue "N ARG 115": "NH1" <-> "NH2" Residue "O ARG 32": "NH1" <-> "NH2" Residue "O ARG 89": "NH1" <-> "NH2" Residue "O ARG 92": "NH1" <-> "NH2" Residue "O ARG 107": "NH1" <-> "NH2" Residue "O ARG 115": "NH1" <-> "NH2" Residue "Q ARG 31": "NH1" <-> "NH2" Residue "Q ARG 46": "NH1" <-> "NH2" Residue "Q ARG 61": "NH1" <-> "NH2" Residue "Q ARG 83": "NH1" <-> "NH2" Residue "Q ARG 84": "NH1" <-> "NH2" Residue "Q ARG 93": "NH1" <-> "NH2" Residue "Q ARG 153": "NH1" <-> "NH2" Residue "R ARG 31": "NH1" <-> "NH2" Residue "R ARG 46": "NH1" <-> "NH2" Residue "R ARG 61": "NH1" <-> "NH2" Residue "R ARG 83": "NH1" <-> "NH2" Residue "R ARG 84": "NH1" <-> "NH2" Residue "R ARG 93": "NH1" <-> "NH2" Residue "R ARG 153": "NH1" <-> "NH2" Residue "S ARG 31": "NH1" <-> "NH2" Residue "S ARG 46": "NH1" <-> "NH2" Residue "S ARG 61": "NH1" <-> "NH2" Residue "S ARG 83": "NH1" <-> "NH2" Residue "S ARG 84": "NH1" <-> "NH2" Residue "S ARG 93": "NH1" <-> "NH2" Residue "S ARG 153": "NH1" <-> "NH2" Residue "S GLU 214": "OE1" <-> "OE2" Residue "U ARG 263": "NH1" <-> "NH2" Residue "U ARG 265": "NH1" <-> "NH2" Residue "U ARG 267": "NH1" <-> "NH2" Residue "U ARG 285": "NH1" <-> "NH2" Residue "U ARG 289": "NH1" <-> "NH2" Residue "U TYR 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 402": "NH1" <-> "NH2" Residue "U ARG 444": "NH1" <-> "NH2" Residue "U ARG 450": "NH1" <-> "NH2" Residue "a ARG 6": "NH1" <-> "NH2" Residue "a GLU 8": "OE1" <-> "OE2" Residue "a ARG 38": "NH1" <-> "NH2" Residue "a ARG 49": "NH1" <-> "NH2" Residue "a ARG 56": "NH1" <-> "NH2" Residue "a ARG 57": "NH1" <-> "NH2" Residue "a ARG 63": "NH1" <-> "NH2" Residue "a ARG 66": "NH1" <-> "NH2" Residue "a ARG 73": "NH1" <-> "NH2" Residue "a ARG 92": "NH1" <-> "NH2" Residue "a ARG 291": "NH1" <-> "NH2" Residue "a ARG 298": "NH1" <-> "NH2" Residue "a ARG 338": "NH1" <-> "NH2" Residue "a ARG 339": "NH1" <-> "NH2" Residue "a ARG 354": "NH1" <-> "NH2" Residue "a ARG 387": "NH1" <-> "NH2" Residue "a GLU 388": "OE1" <-> "OE2" Residue "a ARG 426": "NH1" <-> "NH2" Residue "a ARG 429": "NH1" <-> "NH2" Residue "a ARG 447": "NH1" <-> "NH2" Residue "a PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 482": "NH1" <-> "NH2" Residue "a ARG 496": "NH1" <-> "NH2" Residue "a ARG 565": "NH1" <-> "NH2" Residue "a ARG 660": "NH1" <-> "NH2" Residue "a ARG 665": "NH1" <-> "NH2" Residue "a ARG 666": "NH1" <-> "NH2" Residue "a ARG 741": "NH1" <-> "NH2" Residue "a ARG 805": "NH1" <-> "NH2" Residue "a ARG 832": "NH1" <-> "NH2" Residue "b PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 34": "NH1" <-> "NH2" Residue "b PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 85": "NH1" <-> "NH2" Residue "b ARG 129": "NH1" <-> "NH2" Residue "b ARG 200": "NH1" <-> "NH2" Residue "c ARG 265": "NH1" <-> "NH2" Residue "c ARG 280": "NH1" <-> "NH2" Residue "c PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 329": "NH1" <-> "NH2" Residue "c ARG 336": "NH1" <-> "NH2" Residue "c PHE 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 343": "NH1" <-> "NH2" Residue "c GLU 345": "OE1" <-> "OE2" Residue "c PHE 368": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 409": "OE1" <-> "OE2" Residue "c ARG 410": "NH1" <-> "NH2" Residue "c ARG 454": "NH1" <-> "NH2" Residue "d ARG 21": "NH1" <-> "NH2" Residue "d ARG 73": "NH1" <-> "NH2" Residue "d ARG 83": "NH1" <-> "NH2" Residue "d ARG 86": "NH1" <-> "NH2" Residue "d PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 120": "NH1" <-> "NH2" Residue "d ARG 182": "NH1" <-> "NH2" Residue "d ARG 218": "NH1" <-> "NH2" Residue "d ARG 219": "NH1" <-> "NH2" Residue "d ARG 237": "NH1" <-> "NH2" Residue "d ARG 246": "NH1" <-> "NH2" Residue "d GLU 250": "OE1" <-> "OE2" Residue "d ARG 257": "NH1" <-> "NH2" Residue "d ARG 293": "NH1" <-> "NH2" Residue "d ARG 327": "NH1" <-> "NH2" Residue "d ARG 339": "NH1" <-> "NH2" Residue "d ARG 341": "NH1" <-> "NH2" Residue "e ARG 34": "NH1" <-> "NH2" Residue "f ARG 88": "NH1" <-> "NH2" Residue "g ARG 48": "NH1" <-> "NH2" Residue "g ARG 119": "NH1" <-> "NH2" Residue "g ARG 126": "NH1" <-> "NH2" Residue "h ARG 48": "NH1" <-> "NH2" Residue "h ARG 119": "NH1" <-> "NH2" Residue "h ARG 126": "NH1" <-> "NH2" Residue "i ARG 119": "NH1" <-> "NH2" Residue "i ARG 126": "NH1" <-> "NH2" Residue "j ARG 48": "NH1" <-> "NH2" Residue "j ARG 119": "NH1" <-> "NH2" Residue "j ARG 126": "NH1" <-> "NH2" Residue "k ARG 48": "NH1" <-> "NH2" Residue "k ARG 119": "NH1" <-> "NH2" Residue "k ARG 126": "NH1" <-> "NH2" Residue "l ARG 48": "NH1" <-> "NH2" Residue "l ARG 119": "NH1" <-> "NH2" Residue "l ARG 126": "NH1" <-> "NH2" Residue "m ARG 48": "NH1" <-> "NH2" Residue "m ARG 119": "NH1" <-> "NH2" Residue "m ARG 126": "NH1" <-> "NH2" Residue "n ARG 48": "NH1" <-> "NH2" Residue "n ARG 119": "NH1" <-> "NH2" Residue "n ARG 126": "NH1" <-> "NH2" Residue "o ARG 48": "NH1" <-> "NH2" Residue "o ARG 119": "NH1" <-> "NH2" Residue "o ARG 126": "NH1" <-> "NH2" Residue "p ARG 342": "NH1" <-> "NH2" Time to flip residues: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 68632 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 4661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4661 Classifications: {'peptide': 600} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 569} Chain: "B" Number of atoms: 4579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 588, 4579 Classifications: {'peptide': 588} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 560} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 4577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 587, 4577 Classifications: {'peptide': 587} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 557} Chain breaks: 2 Chain: "D" Number of atoms: 3590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3590 Classifications: {'peptide': 458} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 431} Chain breaks: 1 Chain: "E" Number of atoms: 3572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3572 Classifications: {'peptide': 456} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 429} Chain breaks: 1 Chain: "F" Number of atoms: 3572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3572 Classifications: {'peptide': 456} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 429} Chain breaks: 1 Chain: "G" Number of atoms: 1791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 1791 Classifications: {'peptide': 360} Incomplete info: {'truncation_to_alanine': 324} Link IDs: {'PTRANS': 9, 'TRANS': 350} Chain breaks: 1 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 1200 Unresolved non-hydrogen angles: 1534 Unresolved non-hydrogen dihedrals: 1003 Unresolved non-hydrogen chiralities: 106 Planarities with less than four sites: {'GLN:plan1': 16, 'ARG:plan': 15, 'TYR:plan': 16, 'ASN:plan1': 23, 'TRP:plan': 6, 'HIS:plan': 5, 'PHE:plan': 14, 'GLU:plan': 25, 'ASP:plan': 24} Unresolved non-hydrogen planarities: 655 Chain: "H" Number of atoms: 1717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1717 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 3, 'TRANS': 209} Chain: "I" Number of atoms: 1614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1614 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 5, 'TRANS': 211} Unresolved non-hydrogen bonds: 155 Unresolved non-hydrogen angles: 189 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 5, 'ARG:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 9, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 92 Chain: "J" Number of atoms: 1608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1608 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 5, 'TRANS': 212} Unresolved non-hydrogen bonds: 169 Unresolved non-hydrogen angles: 208 Unresolved non-hydrogen dihedrals: 139 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 5, 'ARG:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 10, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 103 Chain: "K" Number of atoms: 1707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1707 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 5, 'TRANS': 211} Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 3, 'PHE:plan': 1, 'GLU:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "L" Number of atoms: 865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 865 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 4, 'TRANS': 104} Chain: "M" Number of atoms: 682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 682 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 1, 'TRANS': 108} Unresolved non-hydrogen bonds: 227 Unresolved non-hydrogen angles: 275 Unresolved non-hydrogen dihedrals: 186 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 8, 'ASP:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 13, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 143 Chain: "N" Number of atoms: 661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 661 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PTRANS': 1, 'TRANS': 108} Unresolved non-hydrogen bonds: 248 Unresolved non-hydrogen angles: 301 Unresolved non-hydrogen dihedrals: 202 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 9, 'ASP:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 13, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 147 Chain: "O" Number of atoms: 679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 679 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PTRANS': 1, 'TRANS': 106} Unresolved non-hydrogen bonds: 217 Unresolved non-hydrogen angles: 260 Unresolved non-hydrogen dihedrals: 178 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 8, 'ASP:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 13, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 131 Chain: "Q" Number of atoms: 1824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1824 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 9, 'TRANS': 214} Chain: "R" Number of atoms: 1685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1685 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 8, 'TRANS': 197} Chain: "S" Number of atoms: 1832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1832 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 216} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "T" Number of atoms: 2124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 2124 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 384} Link IDs: {'PTRANS': 7, 'TRANS': 419} Chain breaks: 1 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 1454 Unresolved non-hydrogen angles: 1852 Unresolved non-hydrogen dihedrals: 1226 Unresolved non-hydrogen chiralities: 113 Planarities with less than four sites: {'GLN:plan1': 33, 'HIS:plan': 11, 'TYR:plan': 17, 'ASN:plan1': 20, 'TRP:plan': 8, 'ASP:plan': 18, 'PHE:plan': 17, 'GLU:plan': 38, 'ARG:plan': 22} Unresolved non-hydrogen planarities: 856 Chain: "U" Number of atoms: 2400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 2400 Classifications: {'peptide': 383} Incomplete info: {'truncation_to_alanine': 175} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 364} Chain breaks: 5 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 636 Unresolved non-hydrogen angles: 811 Unresolved non-hydrogen dihedrals: 522 Unresolved non-hydrogen chiralities: 61 Planarities with less than four sites: {'GLN:plan1': 9, 'ASP:plan': 11, 'TYR:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 2, 'HIS:plan': 7, 'PHE:plan': 9, 'GLU:plan': 18, 'ARG:plan': 18} Unresolved non-hydrogen planarities: 355 Chain: "a" Number of atoms: 5635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 5635 Classifications: {'peptide': 750} Incomplete info: {'truncation_to_alanine': 128} Link IDs: {'PTRANS': 30, 'TRANS': 719} Chain breaks: 2 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 485 Unresolved non-hydrogen angles: 615 Unresolved non-hydrogen dihedrals: 396 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 10, 'TRP:plan': 1, 'ASP:plan': 6, 'PHE:plan': 9, 'GLU:plan': 15, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 292 Chain: "b" Number of atoms: 1498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1498 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 5, 'TRANS': 197} Chain: "c" Number of atoms: 1661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1661 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 7, 'TRANS': 197} Chain: "d" Number of atoms: 2835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2835 Classifications: {'peptide': 350} Link IDs: {'PTRANS': 13, 'TRANS': 336} Chain: "e" Number of atoms: 652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 652 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 7, 'TRANS': 72} Chain: "f" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 653 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 3, 'TRANS': 80} Chain: "g" Number of atoms: 1058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1058 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "h" Number of atoms: 1058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1058 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "i" Number of atoms: 1052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1052 Classifications: {'peptide': 150} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "j" Number of atoms: 1058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1058 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "k" Number of atoms: 1058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1058 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "l" Number of atoms: 1058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1058 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "m" Number of atoms: 1058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1058 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "n" Number of atoms: 1058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1058 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "o" Number of atoms: 1058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1058 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "p" Number of atoms: 442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 442 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Time building chain proxies: 27.04, per 1000 atoms: 0.39 Number of scatterers: 68632 At special positions: 0 Unit cell: (185.15, 197.053, 285.66, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 351 16.00 O 12743 8.00 N 11743 7.00 C 43795 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 21.67 Conformation dependent library (CDL) restraints added in 10.8 seconds 18488 Ramachandran restraints generated. 9244 Oldfield, 0 Emsley, 9244 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 17340 Finding SS restraints... Secondary structure from input PDB file: 347 helices and 44 sheets defined 63.3% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.77 Creating SS restraints... Processing helix chain 'A' and resid 105 through 114 Processing helix chain 'A' and resid 231 through 236 Processing helix chain 'A' and resid 255 through 267 removed outlier: 4.189A pdb=" N ILE A 259 " --> pdb=" O GLY A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 291 Processing helix chain 'A' and resid 319 through 325 Processing helix chain 'A' and resid 325 through 338 Processing helix chain 'A' and resid 350 through 365 Processing helix chain 'A' and resid 370 through 374 Processing helix chain 'A' and resid 375 through 376 No H-bonds generated for 'chain 'A' and resid 375 through 376' Processing helix chain 'A' and resid 377 through 389 removed outlier: 4.177A pdb=" N ALA A 389 " --> pdb=" O PHE A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 416 Processing helix chain 'A' and resid 419 through 429 Processing helix chain 'A' and resid 436 through 442 Processing helix chain 'A' and resid 457 through 468 removed outlier: 4.537A pdb=" N GLU A 463 " --> pdb=" O ARG A 459 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N TYR A 464 " --> pdb=" O ALA A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 497 removed outlier: 4.609A pdb=" N GLU A 491 " --> pdb=" O GLU A 487 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ILE A 492 " --> pdb=" O ASP A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 519 Processing helix chain 'A' and resid 533 through 559 Processing helix chain 'A' and resid 566 through 584 removed outlier: 6.748A pdb=" N GLU A 576 " --> pdb=" O GLU A 572 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ILE A 577 " --> pdb=" O HIS A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 587 No H-bonds generated for 'chain 'A' and resid 585 through 587' Processing helix chain 'A' and resid 593 through 616 Processing helix chain 'B' and resid 105 through 114 Processing helix chain 'B' and resid 256 through 263 removed outlier: 3.886A pdb=" N SER B 260 " --> pdb=" O LYS B 256 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLN B 261 " --> pdb=" O THR B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 291 Processing helix chain 'B' and resid 319 through 340 removed outlier: 3.575A pdb=" N GLU B 324 " --> pdb=" O VAL B 320 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE B 327 " --> pdb=" O ARG B 323 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N TYR B 328 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASP B 339 " --> pdb=" O GLU B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 365 Processing helix chain 'B' and resid 377 through 388 removed outlier: 3.820A pdb=" N ARG B 388 " --> pdb=" O SER B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 429 removed outlier: 3.649A pdb=" N ILE B 428 " --> pdb=" O ALA B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 469 removed outlier: 5.508A pdb=" N GLU B 463 " --> pdb=" O ARG B 459 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N TYR B 464 " --> pdb=" O ALA B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 494 Processing helix chain 'B' and resid 502 through 519 Processing helix chain 'B' and resid 526 through 531 removed outlier: 4.815A pdb=" N PHE B 531 " --> pdb=" O PRO B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 558 Processing helix chain 'B' and resid 566 through 584 removed outlier: 6.399A pdb=" N GLU B 576 " --> pdb=" O GLU B 572 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ILE B 577 " --> pdb=" O HIS B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 585 through 587 No H-bonds generated for 'chain 'B' and resid 585 through 587' Processing helix chain 'B' and resid 593 through 616 Processing helix chain 'C' and resid 105 through 114 Processing helix chain 'C' and resid 231 through 238 Processing helix chain 'C' and resid 260 through 265 removed outlier: 4.336A pdb=" N SER C 264 " --> pdb=" O GLN C 261 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS C 265 " --> pdb=" O SER C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 291 Processing helix chain 'C' and resid 319 through 338 removed outlier: 3.985A pdb=" N ILE C 327 " --> pdb=" O ARG C 323 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N TYR C 328 " --> pdb=" O GLU C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 365 removed outlier: 3.569A pdb=" N TRP C 354 " --> pdb=" O SER C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 387 Processing helix chain 'C' and resid 419 through 427 Processing helix chain 'C' and resid 436 through 442 Processing helix chain 'C' and resid 461 through 469 Processing helix chain 'C' and resid 471 through 497 removed outlier: 4.590A pdb=" N GLU C 491 " --> pdb=" O GLU C 487 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N ILE C 492 " --> pdb=" O ASP C 488 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LEU C 495 " --> pdb=" O GLU C 491 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 519 Processing helix chain 'C' and resid 533 through 558 Processing helix chain 'C' and resid 566 through 583 removed outlier: 5.862A pdb=" N GLU C 576 " --> pdb=" O GLU C 572 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N ILE C 577 " --> pdb=" O HIS C 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 584 through 586 No H-bonds generated for 'chain 'C' and resid 584 through 586' Processing helix chain 'C' and resid 593 through 616 Processing helix chain 'D' and resid 118 through 122 removed outlier: 3.594A pdb=" N MET D 121 " --> pdb=" O SER D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 155 No H-bonds generated for 'chain 'D' and resid 153 through 155' Processing helix chain 'D' and resid 168 through 174 Processing helix chain 'D' and resid 192 through 204 Processing helix chain 'D' and resid 231 through 244 Processing helix chain 'D' and resid 246 through 249 removed outlier: 3.831A pdb=" N GLY D 249 " --> pdb=" O GLY D 246 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 246 through 249' Processing helix chain 'D' and resid 262 through 281 Proline residue: D 269 - end of helix Processing helix chain 'D' and resid 293 through 308 Processing helix chain 'D' and resid 313 through 317 Processing helix chain 'D' and resid 318 through 319 No H-bonds generated for 'chain 'D' and resid 318 through 319' Processing helix chain 'D' and resid 320 through 331 Processing helix chain 'D' and resid 351 through 354 Processing helix chain 'D' and resid 357 through 367 Processing helix chain 'D' and resid 374 through 380 Processing helix chain 'D' and resid 395 through 400 Processing helix chain 'D' and resid 408 through 434 Processing helix chain 'D' and resid 439 through 456 Processing helix chain 'D' and resid 466 through 479 Processing helix chain 'D' and resid 482 through 486 Processing helix chain 'D' and resid 490 through 498 removed outlier: 3.515A pdb=" N GLU D 496 " --> pdb=" O SER D 492 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 122 Processing helix chain 'E' and resid 153 through 157 Processing helix chain 'E' and resid 168 through 173 Processing helix chain 'E' and resid 192 through 204 Processing helix chain 'E' and resid 231 through 245 Processing helix chain 'E' and resid 247 through 249 No H-bonds generated for 'chain 'E' and resid 247 through 249' Processing helix chain 'E' and resid 263 through 283 removed outlier: 3.865A pdb=" N ILE E 267 " --> pdb=" O ILE E 263 " (cutoff:3.500A) Proline residue: E 269 - end of helix Processing helix chain 'E' and resid 293 through 308 removed outlier: 3.657A pdb=" N TYR E 297 " --> pdb=" O ASP E 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 313 through 317 Processing helix chain 'E' and resid 318 through 319 No H-bonds generated for 'chain 'E' and resid 318 through 319' Processing helix chain 'E' and resid 320 through 331 removed outlier: 3.721A pdb=" N ARG E 331 " --> pdb=" O THR E 327 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 354 Processing helix chain 'E' and resid 357 through 367 Processing helix chain 'E' and resid 374 through 380 Processing helix chain 'E' and resid 395 through 400 Processing helix chain 'E' and resid 408 through 434 removed outlier: 3.785A pdb=" N VAL E 432 " --> pdb=" O ALA E 428 " (cutoff:3.500A) Processing helix chain 'E' and resid 439 through 456 Processing helix chain 'E' and resid 466 through 479 Processing helix chain 'E' and resid 480 through 481 No H-bonds generated for 'chain 'E' and resid 480 through 481' Processing helix chain 'E' and resid 482 through 486 removed outlier: 3.601A pdb=" N MET E 485 " --> pdb=" O PRO E 482 " (cutoff:3.500A) Processing helix chain 'E' and resid 490 through 498 removed outlier: 3.721A pdb=" N PHE E 497 " --> pdb=" O MET E 493 " (cutoff:3.500A) Processing helix chain 'F' and resid 118 through 123 Processing helix chain 'F' and resid 153 through 155 No H-bonds generated for 'chain 'F' and resid 153 through 155' Processing helix chain 'F' and resid 168 through 175 Processing helix chain 'F' and resid 192 through 204 Processing helix chain 'F' and resid 231 through 245 Processing helix chain 'F' and resid 246 through 249 removed outlier: 3.850A pdb=" N GLY F 249 " --> pdb=" O GLY F 246 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 246 through 249' Processing helix chain 'F' and resid 261 through 282 Proline residue: F 269 - end of helix Processing helix chain 'F' and resid 293 through 308 Processing helix chain 'F' and resid 320 through 330 Processing helix chain 'F' and resid 351 through 354 Processing helix chain 'F' and resid 357 through 367 Processing helix chain 'F' and resid 374 through 380 Processing helix chain 'F' and resid 395 through 400 Processing helix chain 'F' and resid 408 through 434 removed outlier: 3.730A pdb=" N VAL F 432 " --> pdb=" O ALA F 428 " (cutoff:3.500A) Processing helix chain 'F' and resid 435 through 438 Processing helix chain 'F' and resid 439 through 456 Processing helix chain 'F' and resid 466 through 479 Processing helix chain 'F' and resid 490 through 498 removed outlier: 3.512A pdb=" N ILE F 494 " --> pdb=" O PRO F 490 " (cutoff:3.500A) Processing helix chain 'G' and resid 15 through 20 Processing helix chain 'G' and resid 23 through 27 Processing helix chain 'G' and resid 47 through 80 Processing helix chain 'G' and resid 97 through 104 Processing helix chain 'G' and resid 117 through 158 Processing helix chain 'G' and resid 171 through 175 Processing helix chain 'G' and resid 193 through 202 removed outlier: 4.376A pdb=" N GLU G 202 " --> pdb=" O ILE G 198 " (cutoff:3.500A) Processing helix chain 'G' and resid 233 through 244 Processing helix chain 'G' and resid 254 through 310 Proline residue: G 278 - end of helix Processing helix chain 'G' and resid 327 through 340 removed outlier: 3.647A pdb=" N LEU G 331 " --> pdb=" O THR G 327 " (cutoff:3.500A) Processing helix chain 'H' and resid 12 through 77 removed outlier: 4.876A pdb=" N ILE H 18 " --> pdb=" O MET H 14 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N ALA H 21 " --> pdb=" O THR H 17 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 86 Processing helix chain 'H' and resid 127 through 175 Processing helix chain 'H' and resid 175 through 217 Processing helix chain 'I' and resid 10 through 108 Processing helix chain 'I' and resid 108 through 128 Processing helix chain 'I' and resid 140 through 159 Proline residue: I 153 - end of helix Processing helix chain 'I' and resid 196 through 207 Processing helix chain 'I' and resid 207 through 217 Processing helix chain 'J' and resid 9 through 108 Processing helix chain 'J' and resid 108 through 128 Processing helix chain 'J' and resid 137 through 139 No H-bonds generated for 'chain 'J' and resid 137 through 139' Processing helix chain 'J' and resid 140 through 160 Proline residue: J 153 - end of helix Processing helix chain 'J' and resid 196 through 217 Proline residue: J 209 - end of helix removed outlier: 3.638A pdb=" N GLY J 213 " --> pdb=" O PRO J 209 " (cutoff:3.500A) Processing helix chain 'K' and resid 14 through 108 Processing helix chain 'K' and resid 108 through 128 Processing helix chain 'K' and resid 137 through 139 No H-bonds generated for 'chain 'K' and resid 137 through 139' Processing helix chain 'K' and resid 140 through 160 Proline residue: K 153 - end of helix Processing helix chain 'K' and resid 196 through 216 Proline residue: K 209 - end of helix Processing helix chain 'L' and resid 14 through 24 Processing helix chain 'L' and resid 44 through 58 Processing helix chain 'L' and resid 68 through 74 removed outlier: 3.660A pdb=" N MET L 73 " --> pdb=" O TYR L 69 " (cutoff:3.500A) Processing helix chain 'L' and resid 74 through 81 removed outlier: 3.597A pdb=" N ALA L 80 " --> pdb=" O HIS L 76 " (cutoff:3.500A) Processing helix chain 'L' and resid 103 through 109 removed outlier: 3.704A pdb=" N ALA L 109 " --> pdb=" O ILE L 105 " (cutoff:3.500A) Processing helix chain 'M' and resid 8 through 105 removed outlier: 4.833A pdb=" N ASP M 93 " --> pdb=" O ARG M 89 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N GLU M 94 " --> pdb=" O GLN M 90 " (cutoff:3.500A) Processing helix chain 'N' and resid 8 through 105 removed outlier: 5.038A pdb=" N ASP N 93 " --> pdb=" O ARG N 89 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N GLU N 94 " --> pdb=" O GLN N 90 " (cutoff:3.500A) Processing helix chain 'O' and resid 10 through 105 removed outlier: 5.257A pdb=" N ASP O 93 " --> pdb=" O ARG O 89 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N GLU O 94 " --> pdb=" O GLN O 90 " (cutoff:3.500A) Processing helix chain 'Q' and resid 14 through 37 Processing helix chain 'Q' and resid 42 through 49 Processing helix chain 'Q' and resid 49 through 54 Processing helix chain 'Q' and resid 63 through 71 Processing helix chain 'Q' and resid 77 through 97 Processing helix chain 'Q' and resid 104 through 118 Processing helix chain 'Q' and resid 120 through 123 Processing helix chain 'Q' and resid 124 through 142 removed outlier: 4.238A pdb=" N ASN Q 142 " --> pdb=" O ASP Q 138 " (cutoff:3.500A) Processing helix chain 'Q' and resid 146 through 167 Processing helix chain 'Q' and resid 172 through 188 Processing helix chain 'Q' and resid 192 through 206 Processing helix chain 'Q' and resid 218 through 234 Processing helix chain 'R' and resid 14 through 37 Processing helix chain 'R' and resid 42 through 54 removed outlier: 4.950A pdb=" N ASP R 51 " --> pdb=" O GLU R 47 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N VAL R 52 " --> pdb=" O ASP R 48 " (cutoff:3.500A) Processing helix chain 'R' and resid 63 through 72 Processing helix chain 'R' and resid 77 through 98 Processing helix chain 'R' and resid 104 through 117 Processing helix chain 'R' and resid 124 through 141 Processing helix chain 'R' and resid 146 through 166 Processing helix chain 'R' and resid 172 through 188 Processing helix chain 'R' and resid 192 through 207 Processing helix chain 'S' and resid 14 through 37 removed outlier: 3.506A pdb=" N ASP S 37 " --> pdb=" O MET S 33 " (cutoff:3.500A) Processing helix chain 'S' and resid 42 through 49 Processing helix chain 'S' and resid 49 through 54 Processing helix chain 'S' and resid 61 through 71 Processing helix chain 'S' and resid 77 through 98 Processing helix chain 'S' and resid 104 through 117 Processing helix chain 'S' and resid 124 through 141 Processing helix chain 'S' and resid 146 through 167 Processing helix chain 'S' and resid 172 through 188 Processing helix chain 'S' and resid 192 through 207 Processing helix chain 'S' and resid 219 through 234 removed outlier: 3.541A pdb=" N LYS S 223 " --> pdb=" O ALA S 219 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N MET S 229 " --> pdb=" O LEU S 225 " (cutoff:3.500A) Processing helix chain 'T' and resid 18 through 29 removed outlier: 3.622A pdb=" N ASN T 29 " --> pdb=" O GLU T 25 " (cutoff:3.500A) Processing helix chain 'T' and resid 32 through 37 removed outlier: 3.780A pdb=" N LEU T 37 " --> pdb=" O GLN T 34 " (cutoff:3.500A) Processing helix chain 'T' and resid 43 through 49 Processing helix chain 'T' and resid 58 through 69 removed outlier: 3.796A pdb=" N LYS T 62 " --> pdb=" O SER T 58 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N MET T 65 " --> pdb=" O GLU T 61 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU T 66 " --> pdb=" O LYS T 62 " (cutoff:3.500A) Processing helix chain 'T' and resid 74 through 84 Processing helix chain 'T' and resid 86 through 104 removed outlier: 3.954A pdb=" N THR T 100 " --> pdb=" O MET T 96 " (cutoff:3.500A) Processing helix chain 'T' and resid 115 through 117 No H-bonds generated for 'chain 'T' and resid 115 through 117' Processing helix chain 'T' and resid 118 through 123 removed outlier: 4.397A pdb=" N TRP T 123 " --> pdb=" O LYS T 119 " (cutoff:3.500A) Processing helix chain 'T' and resid 136 through 145 Processing helix chain 'T' and resid 145 through 150 Processing helix chain 'T' and resid 157 through 162 removed outlier: 3.735A pdb=" N LEU T 161 " --> pdb=" O GLU T 157 " (cutoff:3.500A) Processing helix chain 'T' and resid 195 through 209 removed outlier: 3.741A pdb=" N CYS T 200 " --> pdb=" O GLN T 196 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLY T 203 " --> pdb=" O GLN T 199 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N CYS T 204 " --> pdb=" O CYS T 200 " (cutoff:3.500A) Processing helix chain 'T' and resid 211 through 221 Processing helix chain 'T' and resid 222 through 233 Processing helix chain 'T' and resid 236 through 252 Processing helix chain 'T' and resid 253 through 261 removed outlier: 3.856A pdb=" N GLU T 258 " --> pdb=" O PRO T 254 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N HIS T 259 " --> pdb=" O GLN T 255 " (cutoff:3.500A) Processing helix chain 'T' and resid 264 through 276 removed outlier: 3.613A pdb=" N VAL T 268 " --> pdb=" O ASN T 264 " (cutoff:3.500A) Processing helix chain 'T' and resid 280 through 296 removed outlier: 3.992A pdb=" N SER T 296 " --> pdb=" O PHE T 292 " (cutoff:3.500A) Processing helix chain 'T' and resid 303 through 310 Processing helix chain 'T' and resid 313 through 324 Processing helix chain 'T' and resid 328 through 350 Processing helix chain 'T' and resid 351 through 362 Processing helix chain 'T' and resid 372 through 379 Processing helix chain 'T' and resid 379 through 384 Processing helix chain 'T' and resid 385 through 387 No H-bonds generated for 'chain 'T' and resid 385 through 387' Processing helix chain 'T' and resid 388 through 401 Processing helix chain 'T' and resid 403 through 421 Processing helix chain 'T' and resid 423 through 432 removed outlier: 4.266A pdb=" N VAL T 427 " --> pdb=" O ARG T 423 " (cutoff:3.500A) Processing helix chain 'T' and resid 432 through 441 Processing helix chain 'T' and resid 445 through 459 Processing helix chain 'U' and resid 19 through 31 removed outlier: 4.245A pdb=" N GLU U 23 " --> pdb=" O GLU U 19 " (cutoff:3.500A) Processing helix chain 'U' and resid 48 through 58 removed outlier: 3.587A pdb=" N GLY U 55 " --> pdb=" O SER U 52 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N GLU U 56 " --> pdb=" O HIS U 53 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LEU U 58 " --> pdb=" O GLY U 55 " (cutoff:3.500A) Processing helix chain 'U' and resid 59 through 72 Processing helix chain 'U' and resid 88 through 102 removed outlier: 4.016A pdb=" N SER U 102 " --> pdb=" O LEU U 98 " (cutoff:3.500A) Processing helix chain 'U' and resid 122 through 144 Processing helix chain 'U' and resid 161 through 172 removed outlier: 3.835A pdb=" N GLU U 172 " --> pdb=" O GLN U 168 " (cutoff:3.500A) Processing helix chain 'U' and resid 192 through 203 Processing helix chain 'U' and resid 203 through 218 removed outlier: 3.982A pdb=" N ALA U 207 " --> pdb=" O ALA U 203 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE U 218 " --> pdb=" O ILE U 214 " (cutoff:3.500A) Processing helix chain 'U' and resid 224 through 229 removed outlier: 4.168A pdb=" N ALA U 228 " --> pdb=" O LEU U 225 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N THR U 229 " --> pdb=" O ASP U 226 " (cutoff:3.500A) Processing helix chain 'U' and resid 238 through 240 No H-bonds generated for 'chain 'U' and resid 238 through 240' Processing helix chain 'U' and resid 247 through 258 removed outlier: 3.508A pdb=" N HIS U 257 " --> pdb=" O TYR U 253 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU U 258 " --> pdb=" O ILE U 254 " (cutoff:3.500A) Processing helix chain 'U' and resid 278 through 286 removed outlier: 3.611A pdb=" N ILE U 286 " --> pdb=" O LEU U 282 " (cutoff:3.500A) Processing helix chain 'U' and resid 430 through 441 Processing helix chain 'a' and resid 19 through 33 removed outlier: 4.151A pdb=" N TYR a 23 " --> pdb=" O SER a 19 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N CYS a 24 " --> pdb=" O GLU a 20 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N SER a 27 " --> pdb=" O TYR a 23 " (cutoff:3.500A) Processing helix chain 'a' and resid 45 through 49 Processing helix chain 'a' and resid 52 through 76 Processing helix chain 'a' and resid 84 through 88 removed outlier: 3.632A pdb=" N GLU a 87 " --> pdb=" O GLU a 84 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N VAL a 88 " --> pdb=" O ASN a 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 84 through 88' Processing helix chain 'a' and resid 92 through 132 removed outlier: 4.113A pdb=" N ALA a 99 " --> pdb=" O ILE a 95 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ASN a 100 " --> pdb=" O ASP a 96 " (cutoff:3.500A) Processing helix chain 'a' and resid 179 through 191 Processing helix chain 'a' and resid 226 through 240 Processing helix chain 'a' and resid 252 through 308 removed outlier: 3.833A pdb=" N ASN a 289 " --> pdb=" O ALA a 285 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N VAL a 292 " --> pdb=" O LYS a 288 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ILE a 295 " --> pdb=" O ARG a 291 " (cutoff:3.500A) Processing helix chain 'a' and resid 326 through 328 No H-bonds generated for 'chain 'a' and resid 326 through 328' Processing helix chain 'a' and resid 329 through 344 Processing helix chain 'a' and resid 368 through 380 removed outlier: 4.511A pdb=" N GLY a 373 " --> pdb=" O LYS a 369 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N PHE a 374 " --> pdb=" O PHE a 370 " (cutoff:3.500A) Processing helix chain 'a' and resid 391 through 407 removed outlier: 4.190A pdb=" N ILE a 397 " --> pdb=" O PRO a 393 " (cutoff:3.500A) Proline residue: a 400 - end of helix Processing helix chain 'a' and resid 409 through 426 Processing helix chain 'a' and resid 426 through 432 Processing helix chain 'a' and resid 437 through 446 Processing helix chain 'a' and resid 446 through 464 Processing helix chain 'a' and resid 483 through 488 Processing helix chain 'a' and resid 493 through 498 Processing helix chain 'a' and resid 520 through 526 removed outlier: 4.119A pdb=" N ASN a 524 " --> pdb=" O ASP a 520 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE a 525 " --> pdb=" O PRO a 521 " (cutoff:3.500A) Processing helix chain 'a' and resid 528 through 563 removed outlier: 3.867A pdb=" N PHE a 532 " --> pdb=" O ASN a 528 " (cutoff:3.500A) Processing helix chain 'a' and resid 566 through 571 Processing helix chain 'a' and resid 572 through 598 removed outlier: 4.307A pdb=" N TYR a 586 " --> pdb=" O SER a 582 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LEU a 587 " --> pdb=" O LEU a 583 " (cutoff:3.500A) Processing helix chain 'a' and resid 599 through 603 Processing helix chain 'a' and resid 608 through 619 Processing helix chain 'a' and resid 632 through 667 Proline residue: a 649 - end of helix removed outlier: 4.333A pdb=" N LYS a 655 " --> pdb=" O MET a 651 " (cutoff:3.500A) Proline residue: a 656 - end of helix Processing helix chain 'a' and resid 713 through 739 Processing helix chain 'a' and resid 739 through 760 removed outlier: 4.159A pdb=" N TRP a 743 " --> pdb=" O TYR a 739 " (cutoff:3.500A) Processing helix chain 'a' and resid 760 through 766 Processing helix chain 'a' and resid 771 through 791 removed outlier: 4.354A pdb=" N PHE a 777 " --> pdb=" O GLY a 773 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N PHE a 778 " --> pdb=" O LEU a 774 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ILE a 779 " --> pdb=" O ALA a 775 " (cutoff:3.500A) Processing helix chain 'a' and resid 793 through 810 removed outlier: 3.829A pdb=" N LEU a 806 " --> pdb=" O HIS a 802 " (cutoff:3.500A) Processing helix chain 'a' and resid 811 through 815 Processing helix chain 'b' and resid 3 through 29 Processing helix chain 'b' and resid 30 through 34 removed outlier: 3.635A pdb=" N PHE b 33 " --> pdb=" O ASP b 30 " (cutoff:3.500A) Processing helix chain 'b' and resid 36 through 43 removed outlier: 3.996A pdb=" N PHE b 40 " --> pdb=" O ASP b 36 " (cutoff:3.500A) Processing helix chain 'b' and resid 45 through 81 removed outlier: 3.789A pdb=" N TRP b 49 " --> pdb=" O SER b 45 " (cutoff:3.500A) Processing helix chain 'b' and resid 82 through 84 No H-bonds generated for 'chain 'b' and resid 82 through 84' Processing helix chain 'b' and resid 85 through 90 removed outlier: 4.026A pdb=" N LYS b 89 " --> pdb=" O ARG b 85 " (cutoff:3.500A) Processing helix chain 'b' and resid 90 through 113 removed outlier: 4.185A pdb=" N ILE b 94 " --> pdb=" O ASN b 90 " (cutoff:3.500A) Processing helix chain 'b' and resid 128 through 169 removed outlier: 3.572A pdb=" N ALA b 133 " --> pdb=" O ARG b 129 " (cutoff:3.500A) Processing helix chain 'b' and resid 172 through 177 Processing helix chain 'b' and resid 177 through 198 Processing helix chain 'c' and resid 283 through 288 removed outlier: 3.863A pdb=" N LEU c 287 " --> pdb=" O ASP c 283 " (cutoff:3.500A) Processing helix chain 'c' and resid 422 through 448 Processing helix chain 'd' and resid 4 through 9 removed outlier: 4.057A pdb=" N TYR d 8 " --> pdb=" O PHE d 4 " (cutoff:3.500A) Processing helix chain 'd' and resid 10 through 12 No H-bonds generated for 'chain 'd' and resid 10 through 12' Processing helix chain 'd' and resid 13 through 26 Processing helix chain 'd' and resid 29 through 40 removed outlier: 4.483A pdb=" N GLU d 40 " --> pdb=" O LEU d 36 " (cutoff:3.500A) Processing helix chain 'd' and resid 41 through 52 Processing helix chain 'd' and resid 54 through 59 removed outlier: 3.784A pdb=" N PHE d 57 " --> pdb=" O TYR d 54 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N LEU d 58 " --> pdb=" O GLY d 55 " (cutoff:3.500A) Processing helix chain 'd' and resid 66 through 89 Processing helix chain 'd' and resid 90 through 113 removed outlier: 3.605A pdb=" N SER d 103 " --> pdb=" O PHE d 99 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N TYR d 104 " --> pdb=" O ILE d 100 " (cutoff:3.500A) Processing helix chain 'd' and resid 121 through 126 Processing helix chain 'd' and resid 127 through 129 No H-bonds generated for 'chain 'd' and resid 127 through 129' Processing helix chain 'd' and resid 139 through 143 removed outlier: 4.073A pdb=" N ILE d 143 " --> pdb=" O ALA d 140 " (cutoff:3.500A) Processing helix chain 'd' and resid 146 through 155 Processing helix chain 'd' and resid 158 through 167 removed outlier: 3.845A pdb=" N GLN d 165 " --> pdb=" O ALA d 162 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ASP d 166 " --> pdb=" O PHE d 163 " (cutoff:3.500A) Processing helix chain 'd' and resid 170 through 175 Processing helix chain 'd' and resid 177 through 200 Processing helix chain 'd' and resid 202 through 227 Proline residue: d 210 - end of helix Processing helix chain 'd' and resid 233 through 241 Processing helix chain 'd' and resid 250 through 258 Processing helix chain 'd' and resid 260 through 270 removed outlier: 3.653A pdb=" N VAL d 264 " --> pdb=" O ASP d 260 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N TYR d 270 " --> pdb=" O ASN d 266 " (cutoff:3.500A) Processing helix chain 'd' and resid 271 through 280 Processing helix chain 'd' and resid 289 through 306 Processing helix chain 'd' and resid 312 through 338 removed outlier: 3.700A pdb=" N TYR d 316 " --> pdb=" O PHE d 312 " (cutoff:3.500A) Processing helix chain 'd' and resid 340 through 347 removed outlier: 4.674A pdb=" N ASP d 345 " --> pdb=" O ALA d 342 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN d 346 " --> pdb=" O LYS d 343 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N TYR d 347 " --> pdb=" O ILE d 344 " (cutoff:3.500A) Processing helix chain 'e' and resid 6 through 23 removed outlier: 3.565A pdb=" N LEU e 23 " --> pdb=" O PHE e 19 " (cutoff:3.500A) Processing helix chain 'e' and resid 24 through 27 Processing helix chain 'e' and resid 33 through 58 Processing helix chain 'e' and resid 70 through 80 removed outlier: 4.165A pdb=" N TYR e 78 " --> pdb=" O TRP e 74 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N TRP e 80 " --> pdb=" O LEU e 76 " (cutoff:3.500A) Processing helix chain 'f' and resid 8 through 35 Processing helix chain 'f' and resid 37 through 44 removed outlier: 5.620A pdb=" N GLU f 42 " --> pdb=" O VAL f 39 " (cutoff:3.500A) Processing helix chain 'f' and resid 55 through 90 Processing helix chain 'g' and resid 10 through 46 removed outlier: 4.308A pdb=" N PHE g 14 " --> pdb=" O TYR g 10 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ALA g 15 " --> pdb=" O ALA g 11 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL g 46 " --> pdb=" O ALA g 42 " (cutoff:3.500A) Processing helix chain 'g' and resid 52 through 55 Processing helix chain 'g' and resid 56 through 80 Processing helix chain 'g' and resid 87 through 123 removed outlier: 3.846A pdb=" N ILE g 112 " --> pdb=" O PHE g 108 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL g 113 " --> pdb=" O ALA g 109 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N ASP g 115 " --> pdb=" O GLY g 111 " (cutoff:3.500A) Processing helix chain 'g' and resid 124 through 126 No H-bonds generated for 'chain 'g' and resid 124 through 126' Processing helix chain 'g' and resid 127 through 155 removed outlier: 3.948A pdb=" N GLY g 142 " --> pdb=" O ALA g 138 " (cutoff:3.500A) Processing helix chain 'h' and resid 11 through 46 removed outlier: 3.599A pdb=" N ALA h 15 " --> pdb=" O ALA h 11 " (cutoff:3.500A) Processing helix chain 'h' and resid 48 through 52 removed outlier: 3.959A pdb=" N LEU h 51 " --> pdb=" O ARG h 48 " (cutoff:3.500A) Processing helix chain 'h' and resid 56 through 79 Processing helix chain 'h' and resid 87 through 124 removed outlier: 3.541A pdb=" N GLN h 123 " --> pdb=" O ARG h 119 " (cutoff:3.500A) Processing helix chain 'h' and resid 126 through 155 removed outlier: 4.306A pdb=" N GLY h 130 " --> pdb=" O ARG h 126 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU h 141 " --> pdb=" O PHE h 137 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLY h 142 " --> pdb=" O ALA h 138 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS h 155 " --> pdb=" O ILE h 151 " (cutoff:3.500A) Processing helix chain 'i' and resid 10 through 46 removed outlier: 4.178A pdb=" N VAL i 46 " --> pdb=" O ALA i 42 " (cutoff:3.500A) Processing helix chain 'i' and resid 48 through 55 removed outlier: 4.429A pdb=" N MET i 53 " --> pdb=" O GLU i 50 " (cutoff:3.500A) Processing helix chain 'i' and resid 56 through 79 Processing helix chain 'i' and resid 85 through 124 Processing helix chain 'i' and resid 127 through 155 Processing helix chain 'j' and resid 10 through 46 removed outlier: 3.531A pdb=" N PHE j 14 " --> pdb=" O TYR j 10 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N SER j 26 " --> pdb=" O ALA j 22 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL j 46 " --> pdb=" O ALA j 42 " (cutoff:3.500A) Processing helix chain 'j' and resid 47 through 52 removed outlier: 6.658A pdb=" N GLU j 50 " --> pdb=" O MET j 47 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU j 51 " --> pdb=" O ARG j 48 " (cutoff:3.500A) Processing helix chain 'j' and resid 53 through 55 No H-bonds generated for 'chain 'j' and resid 53 through 55' Processing helix chain 'j' and resid 56 through 80 Processing helix chain 'j' and resid 86 through 124 Processing helix chain 'j' and resid 126 through 155 removed outlier: 4.557A pdb=" N GLY j 130 " --> pdb=" O ARG j 126 " (cutoff:3.500A) Processing helix chain 'k' and resid 12 through 46 removed outlier: 3.859A pdb=" N VAL k 46 " --> pdb=" O ALA k 42 " (cutoff:3.500A) Processing helix chain 'k' and resid 48 through 52 removed outlier: 3.688A pdb=" N LEU k 51 " --> pdb=" O ARG k 48 " (cutoff:3.500A) Processing helix chain 'k' and resid 53 through 54 No H-bonds generated for 'chain 'k' and resid 53 through 54' Processing helix chain 'k' and resid 55 through 79 removed outlier: 4.684A pdb=" N VAL k 59 " --> pdb=" O SER k 55 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA k 66 " --> pdb=" O ALA k 62 " (cutoff:3.500A) Processing helix chain 'k' and resid 86 through 124 removed outlier: 3.548A pdb=" N PHE k 90 " --> pdb=" O LEU k 86 " (cutoff:3.500A) Processing helix chain 'k' and resid 127 through 155 removed outlier: 3.685A pdb=" N GLY k 142 " --> pdb=" O ALA k 138 " (cutoff:3.500A) Processing helix chain 'l' and resid 10 through 46 removed outlier: 3.562A pdb=" N PHE l 14 " --> pdb=" O TYR l 10 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL l 46 " --> pdb=" O ALA l 42 " (cutoff:3.500A) Processing helix chain 'l' and resid 47 through 50 removed outlier: 6.197A pdb=" N GLU l 50 " --> pdb=" O MET l 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 47 through 50' Processing helix chain 'l' and resid 51 through 56 Processing helix chain 'l' and resid 56 through 80 removed outlier: 3.583A pdb=" N VAL l 60 " --> pdb=" O ILE l 56 " (cutoff:3.500A) Processing helix chain 'l' and resid 87 through 124 Processing helix chain 'l' and resid 127 through 155 removed outlier: 3.745A pdb=" N GLY l 142 " --> pdb=" O ALA l 138 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS l 155 " --> pdb=" O ILE l 151 " (cutoff:3.500A) Processing helix chain 'm' and resid 8 through 48 removed outlier: 4.160A pdb=" N ALA m 12 " --> pdb=" O PRO m 8 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N PHE m 13 " --> pdb=" O GLU m 9 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N MET m 23 " --> pdb=" O ALA m 19 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N SER m 26 " --> pdb=" O ALA m 22 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL m 46 " --> pdb=" O ALA m 42 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N MET m 47 " --> pdb=" O ALA m 43 " (cutoff:3.500A) Processing helix chain 'm' and resid 49 through 55 removed outlier: 4.240A pdb=" N MET m 53 " --> pdb=" O GLU m 50 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYS m 54 " --> pdb=" O LEU m 51 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER m 55 " --> pdb=" O ILE m 52 " (cutoff:3.500A) Processing helix chain 'm' and resid 56 through 79 removed outlier: 3.629A pdb=" N ILE m 65 " --> pdb=" O MET m 61 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA m 66 " --> pdb=" O ALA m 62 " (cutoff:3.500A) Processing helix chain 'm' and resid 85 through 124 removed outlier: 3.644A pdb=" N GLN m 123 " --> pdb=" O ARG m 119 " (cutoff:3.500A) Processing helix chain 'm' and resid 126 through 155 removed outlier: 4.179A pdb=" N GLY m 130 " --> pdb=" O ARG m 126 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA m 138 " --> pdb=" O ILE m 134 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS m 155 " --> pdb=" O ILE m 151 " (cutoff:3.500A) Processing helix chain 'n' and resid 10 through 48 removed outlier: 3.760A pdb=" N PHE n 14 " --> pdb=" O TYR n 10 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER n 37 " --> pdb=" O GLY n 33 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL n 46 " --> pdb=" O ALA n 42 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N MET n 47 " --> pdb=" O ALA n 43 " (cutoff:3.500A) Processing helix chain 'n' and resid 51 through 56 Processing helix chain 'n' and resid 56 through 80 removed outlier: 3.727A pdb=" N ALA n 66 " --> pdb=" O ALA n 62 " (cutoff:3.500A) Processing helix chain 'n' and resid 86 through 124 removed outlier: 3.628A pdb=" N PHE n 90 " --> pdb=" O LEU n 86 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLN n 123 " --> pdb=" O ARG n 119 " (cutoff:3.500A) Processing helix chain 'n' and resid 126 through 155 removed outlier: 4.448A pdb=" N GLY n 130 " --> pdb=" O ARG n 126 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLY n 142 " --> pdb=" O ALA n 138 " (cutoff:3.500A) Processing helix chain 'o' and resid 10 through 48 removed outlier: 4.114A pdb=" N PHE o 14 " --> pdb=" O TYR o 10 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA o 15 " --> pdb=" O ALA o 11 " (cutoff:3.500A) Processing helix chain 'o' and resid 50 through 55 removed outlier: 4.447A pdb=" N LYS o 54 " --> pdb=" O GLU o 50 " (cutoff:3.500A) Processing helix chain 'o' and resid 56 through 80 Processing helix chain 'o' and resid 85 through 122 Processing helix chain 'o' and resid 124 through 126 No H-bonds generated for 'chain 'o' and resid 124 through 126' Processing helix chain 'o' and resid 127 through 155 removed outlier: 3.846A pdb=" N GLY o 142 " --> pdb=" O ALA o 138 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY o 145 " --> pdb=" O LEU o 141 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU o 146 " --> pdb=" O GLY o 142 " (cutoff:3.500A) Processing helix chain 'p' and resid 303 through 331 Processing helix chain 'p' and resid 337 through 345 Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 25 removed outlier: 5.689A pdb=" N VAL A 21 " --> pdb=" O CYS A 32 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N CYS A 32 " --> pdb=" O VAL A 21 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 28 through 32 current: chain 'A' and resid 50 through 58 removed outlier: 5.786A pdb=" N ILE A 54 " --> pdb=" O GLN A 65 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N GLN A 65 " --> pdb=" O ILE A 54 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 61 through 66 current: chain 'B' and resid 28 through 32 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 28 through 32 current: chain 'B' and resid 50 through 58 removed outlier: 5.787A pdb=" N ILE B 54 " --> pdb=" O GLN B 65 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N GLN B 65 " --> pdb=" O ILE B 54 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 61 through 66 current: chain 'C' and resid 28 through 32 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 28 through 32 current: chain 'C' and resid 52 through 58 removed outlier: 5.980A pdb=" N ILE C 54 " --> pdb=" O GLN C 65 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N GLN C 65 " --> pdb=" O ILE C 54 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 61 through 66 current: chain 'D' and resid 51 through 54 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 51 through 54 current: chain 'D' and resid 75 through 84 removed outlier: 5.565A pdb=" N VAL D 80 " --> pdb=" O GLN D 91 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N GLN D 91 " --> pdb=" O VAL D 80 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 87 through 92 current: chain 'E' and resid 51 through 54 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 51 through 54 current: chain 'E' and resid 75 through 80 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 75 through 80 current: chain 'F' and resid 51 through 54 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 51 through 54 current: chain 'F' and resid 75 through 84 removed outlier: 5.403A pdb=" N VAL F 80 " --> pdb=" O GLN F 91 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N GLN F 91 " --> pdb=" O VAL F 80 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 87 through 92 current: chain 'I' and resid 164 through 167 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 164 through 167 current: chain 'I' and resid 190 through 195 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 190 through 195 current: chain 'J' and resid 164 through 167 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 164 through 167 current: chain 'J' and resid 190 through 195 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 190 through 195 current: chain 'K' and resid 164 through 167 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 164 through 167 current: chain 'K' and resid 190 through 195 Processing sheet with id=AA2, first strand: chain 'A' and resid 87 through 90 Processing sheet with id=AA3, first strand: chain 'A' and resid 98 through 99 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 98 through 99 current: chain 'A' and resid 309 through 312 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 309 through 312 current: chain 'A' and resid 401 through 410 No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 165 through 167 Processing sheet with id=AA5, first strand: chain 'A' and resid 146 through 148 removed outlier: 6.538A pdb=" N GLU A 193 " --> pdb=" O THR A 177 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ILE A 179 " --> pdb=" O VAL A 191 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N VAL A 191 " --> pdb=" O ILE A 179 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 226 through 227 removed outlier: 4.583A pdb=" N CYS A 240 " --> pdb=" O LEU A 227 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 295 through 297 Processing sheet with id=AA8, first strand: chain 'B' and resid 87 through 90 Processing sheet with id=AA9, first strand: chain 'B' and resid 98 through 99 removed outlier: 6.543A pdb=" N VAL B 271 " --> pdb=" O SER B 345 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N MET B 347 " --> pdb=" O VAL B 271 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ILE B 273 " --> pdb=" O MET B 347 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ASN B 349 " --> pdb=" O ILE B 273 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N VAL B 275 " --> pdb=" O ASN B 349 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 163 through 167 removed outlier: 3.784A pdb=" N ASN B 157 " --> pdb=" O GLU B 134 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N GLU B 134 " --> pdb=" O ASN B 157 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 146 through 148 removed outlier: 3.693A pdb=" N ILE B 147 " --> pdb=" O GLY B 174 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N GLU B 193 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N ILE B 179 " --> pdb=" O VAL B 191 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N VAL B 191 " --> pdb=" O ILE B 179 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 217 through 219 Processing sheet with id=AB4, first strand: chain 'B' and resid 246 through 247 Processing sheet with id=AB5, first strand: chain 'B' and resid 295 through 297 Processing sheet with id=AB6, first strand: chain 'C' and resid 87 through 90 Processing sheet with id=AB7, first strand: chain 'C' and resid 164 through 167 Processing sheet with id=AB8, first strand: chain 'C' and resid 146 through 147 removed outlier: 6.524A pdb=" N GLU C 193 " --> pdb=" O THR C 177 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ILE C 179 " --> pdb=" O VAL C 191 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N VAL C 191 " --> pdb=" O ILE C 179 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 245 through 247 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 245 through 247 current: chain 'C' and resid 309 through 312 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 309 through 312 current: chain 'C' and resid 401 through 408 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 401 through 408 current: chain 'C' and resid 454 through 455 No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'C' and resid 295 through 297 Processing sheet with id=AC2, first strand: chain 'C' and resid 369 through 371 removed outlier: 3.918A pdb=" N ASP C 371 " --> pdb=" O TYR C 374 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 114 through 117 removed outlier: 3.524A pdb=" N LEU D 145 " --> pdb=" O THR D 115 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 125 through 126 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 125 through 126 current: chain 'D' and resid 251 through 257 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 251 through 257 current: chain 'D' and resid 341 through 350 No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'D' and resid 161 through 163 removed outlier: 3.589A pdb=" N ARG D 179 " --> pdb=" O GLU D 161 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 369 through 370 Processing sheet with id=AC7, first strand: chain 'E' and resid 114 through 117 Processing sheet with id=AC8, first strand: chain 'E' and resid 125 through 126 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 125 through 126 current: chain 'E' and resid 251 through 257 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 251 through 257 current: chain 'E' and resid 341 through 349 No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'E' and resid 177 through 178 removed outlier: 4.503A pdb=" N ILE E 177 " --> pdb=" O ILE E 164 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 369 through 370 Processing sheet with id=AD2, first strand: chain 'F' and resid 114 through 117 Processing sheet with id=AD3, first strand: chain 'F' and resid 125 through 126 removed outlier: 6.667A pdb=" N PHE F 126 " --> pdb=" O LEU F 255 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N LEU F 257 " --> pdb=" O PHE F 126 " (cutoff:3.500A) removed outlier: 9.162A pdb=" N CYS F 252 " --> pdb=" O PHE F 221 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE F 223 " --> pdb=" O CYS F 252 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N PHE F 254 " --> pdb=" O ILE F 223 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N PHE F 225 " --> pdb=" O PHE F 254 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N ASN F 256 " --> pdb=" O PHE F 225 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N ALA F 227 " --> pdb=" O ASN F 256 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 157 through 158 removed outlier: 4.011A pdb=" N ARG F 334 " --> pdb=" O ILE F 158 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 163 through 164 removed outlier: 4.489A pdb=" N ILE F 177 " --> pdb=" O ILE F 164 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 34 through 37 Processing sheet with id=AD7, first strand: chain 'G' and resid 214 through 218 removed outlier: 5.543A pdb=" N VAL G 215 " --> pdb=" O ASN G 226 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ASN G 226 " --> pdb=" O VAL G 215 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LEU G 186 " --> pdb=" O ARG G 249 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 92 through 100 Processing sheet with id=AD9, first strand: chain 'L' and resid 36 through 39 removed outlier: 6.799A pdb=" N VAL L 10 " --> pdb=" O LEU L 37 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N VAL L 39 " --> pdb=" O VAL L 10 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N GLY L 12 " --> pdb=" O VAL L 39 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N ASP L 13 " --> pdb=" O ASN L 67 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ILE L 64 " --> pdb=" O LEU L 89 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N ILE L 91 " --> pdb=" O ILE L 64 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ILE L 66 " --> pdb=" O ILE L 91 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'U' and resid 233 through 236 removed outlier: 6.006A pdb=" N GLU U 233 " --> pdb=" O TRP U 266 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N LEU U 268 " --> pdb=" O GLU U 233 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N GLN U 235 " --> pdb=" O LEU U 268 " (cutoff:3.500A) removed outlier: 8.889A pdb=" N PHE U 270 " --> pdb=" O GLN U 235 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'U' and resid 265 through 271 current: chain 'U' and resid 303 through 308 WARNING: can't find start of bonding for strands! previous: chain 'U' and resid 303 through 308 current: chain 'U' and resid 334 through 337 WARNING: can't find start of bonding for strands! previous: chain 'U' and resid 334 through 337 current: chain 'U' and resid 358 through 361 removed outlier: 5.618A pdb=" N LYS U 378 " --> pdb=" O ASP U 373 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'a' and resid 36 through 37 Processing sheet with id=AE3, first strand: chain 'a' and resid 197 through 207 removed outlier: 7.119A pdb=" N ASN a 204 " --> pdb=" O VAL a 215 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N VAL a 215 " --> pdb=" O ASN a 204 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'a' and resid 501 through 503 Processing sheet with id=AE5, first strand: chain 'c' and resid 257 through 258 removed outlier: 6.717A pdb=" N SER c 367 " --> pdb=" O SER c 415 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'c' and resid 280 through 281 removed outlier: 3.745A pdb=" N VAL c 373 " --> pdb=" O PHE c 396 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'c' and resid 307 through 312 Processing sheet with id=AE8, first strand: chain 'c' and resid 338 through 340 4604 hydrogen bonds defined for protein. 13473 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: 25.27 Time building geometry restraints manager: 23.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.29: 11585 1.29 - 1.42: 17126 1.42 - 1.55: 40498 1.55 - 1.69: 4 1.69 - 1.82: 613 Bond restraints: 69826 Sorted by residual: bond pdb=" C THR E 323 " pdb=" O THR E 323 " ideal model delta sigma weight residual 1.237 1.154 0.083 1.19e-02 7.06e+03 4.82e+01 bond pdb=" C PHE h 13 " pdb=" O PHE h 13 " ideal model delta sigma weight residual 1.236 1.162 0.075 1.15e-02 7.56e+03 4.22e+01 bond pdb=" C PRO A 169 " pdb=" O PRO A 169 " ideal model delta sigma weight residual 1.246 1.191 0.054 8.50e-03 1.38e+04 4.08e+01 bond pdb=" SD MET g 61 " pdb=" CE MET g 61 " ideal model delta sigma weight residual 1.791 1.643 0.148 2.50e-02 1.60e+03 3.51e+01 bond pdb=" CA SER D 393 " pdb=" CB SER D 393 " ideal model delta sigma weight residual 1.527 1.465 0.062 1.30e-02 5.92e+03 2.28e+01 ... (remaining 69821 not shown) Histogram of bond angle deviations from ideal: 96.12 - 103.97: 994 103.97 - 111.83: 31627 111.83 - 119.69: 28853 119.69 - 127.54: 32886 127.54 - 135.40: 427 Bond angle restraints: 94787 Sorted by residual: angle pdb=" N ILE b 126 " pdb=" CA ILE b 126 " pdb=" C ILE b 126 " ideal model delta sigma weight residual 112.90 104.80 8.10 9.60e-01 1.09e+00 7.11e+01 angle pdb=" N GLU F 142 " pdb=" CA GLU F 142 " pdb=" C GLU F 142 " ideal model delta sigma weight residual 112.45 100.96 11.49 1.39e+00 5.18e-01 6.83e+01 angle pdb=" N TYR A 336 " pdb=" CA TYR A 336 " pdb=" C TYR A 336 " ideal model delta sigma weight residual 113.12 102.97 10.15 1.25e+00 6.40e-01 6.60e+01 angle pdb=" N ILE i 67 " pdb=" CA ILE i 67 " pdb=" C ILE i 67 " ideal model delta sigma weight residual 111.45 104.34 7.11 9.30e-01 1.16e+00 5.84e+01 angle pdb=" CA THR E 323 " pdb=" C THR E 323 " pdb=" O THR E 323 " ideal model delta sigma weight residual 120.42 112.60 7.82 1.06e+00 8.90e-01 5.44e+01 ... (remaining 94782 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 37980 17.98 - 35.96: 2772 35.96 - 53.94: 774 53.94 - 71.92: 223 71.92 - 89.91: 78 Dihedral angle restraints: 41827 sinusoidal: 14882 harmonic: 26945 Sorted by residual: dihedral pdb=" C GLU f 48 " pdb=" N GLU f 48 " pdb=" CA GLU f 48 " pdb=" CB GLU f 48 " ideal model delta harmonic sigma weight residual -122.60 -142.09 19.49 0 2.50e+00 1.60e-01 6.08e+01 dihedral pdb=" C GLU N 112 " pdb=" N GLU N 112 " pdb=" CA GLU N 112 " pdb=" CB GLU N 112 " ideal model delta harmonic sigma weight residual -122.60 -140.68 18.08 0 2.50e+00 1.60e-01 5.23e+01 dihedral pdb=" N GLU f 48 " pdb=" C GLU f 48 " pdb=" CA GLU f 48 " pdb=" CB GLU f 48 " ideal model delta harmonic sigma weight residual 122.80 139.70 -16.90 0 2.50e+00 1.60e-01 4.57e+01 ... (remaining 41824 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.144: 10056 0.144 - 0.288: 939 0.288 - 0.433: 69 0.433 - 0.577: 4 0.577 - 0.721: 3 Chirality restraints: 11071 Sorted by residual: chirality pdb=" CA GLU N 112 " pdb=" N GLU N 112 " pdb=" C GLU N 112 " pdb=" CB GLU N 112 " both_signs ideal model delta sigma weight residual False 2.51 1.79 0.72 2.00e-01 2.50e+01 1.30e+01 chirality pdb=" CA GLU f 48 " pdb=" N GLU f 48 " pdb=" C GLU f 48 " pdb=" CB GLU f 48 " both_signs ideal model delta sigma weight residual False 2.51 1.83 0.68 2.00e-01 2.50e+01 1.14e+01 chirality pdb=" CA VAL L 74 " pdb=" N VAL L 74 " pdb=" C VAL L 74 " pdb=" CB VAL L 74 " both_signs ideal model delta sigma weight residual False 2.44 1.82 0.62 2.00e-01 2.50e+01 9.56e+00 ... (remaining 11068 not shown) Planarity restraints: 12263 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP e 52 " 0.161 2.00e-02 2.50e+03 8.33e-02 1.73e+02 pdb=" CG TRP e 52 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 TRP e 52 " -0.031 2.00e-02 2.50e+03 pdb=" CD2 TRP e 52 " -0.077 2.00e-02 2.50e+03 pdb=" NE1 TRP e 52 " -0.052 2.00e-02 2.50e+03 pdb=" CE2 TRP e 52 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP e 52 " -0.124 2.00e-02 2.50e+03 pdb=" CZ2 TRP e 52 " 0.081 2.00e-02 2.50e+03 pdb=" CZ3 TRP e 52 " -0.026 2.00e-02 2.50e+03 pdb=" CH2 TRP e 52 " 0.101 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP e 80 " 0.148 2.00e-02 2.50e+03 7.96e-02 1.58e+02 pdb=" CG TRP e 80 " 0.003 2.00e-02 2.50e+03 pdb=" CD1 TRP e 80 " -0.095 2.00e-02 2.50e+03 pdb=" CD2 TRP e 80 " -0.048 2.00e-02 2.50e+03 pdb=" NE1 TRP e 80 " -0.038 2.00e-02 2.50e+03 pdb=" CE2 TRP e 80 " 0.007 2.00e-02 2.50e+03 pdb=" CE3 TRP e 80 " -0.097 2.00e-02 2.50e+03 pdb=" CZ2 TRP e 80 " 0.101 2.00e-02 2.50e+03 pdb=" CZ3 TRP e 80 " -0.058 2.00e-02 2.50e+03 pdb=" CH2 TRP e 80 " 0.076 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR R 166 " -0.119 2.00e-02 2.50e+03 6.91e-02 9.56e+01 pdb=" CG TYR R 166 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 TYR R 166 " 0.055 2.00e-02 2.50e+03 pdb=" CD2 TYR R 166 " 0.053 2.00e-02 2.50e+03 pdb=" CE1 TYR R 166 " 0.043 2.00e-02 2.50e+03 pdb=" CE2 TYR R 166 " 0.046 2.00e-02 2.50e+03 pdb=" CZ TYR R 166 " 0.015 2.00e-02 2.50e+03 pdb=" OH TYR R 166 " -0.116 2.00e-02 2.50e+03 ... (remaining 12260 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 6100 2.74 - 3.28: 76350 3.28 - 3.82: 124938 3.82 - 4.36: 148484 4.36 - 4.90: 243130 Nonbonded interactions: 599002 Sorted by model distance: nonbonded pdb=" O ILE a 577 " pdb=" OG1 THR a 581 " model vdw 2.204 2.440 nonbonded pdb=" O LEU o 75 " pdb=" OG SER o 79 " model vdw 2.211 2.440 nonbonded pdb=" OD1 ASP D 354 " pdb=" OG1 THR D 356 " model vdw 2.235 2.440 nonbonded pdb=" O GLN G 275 " pdb=" N LEU G 279 " model vdw 2.237 2.520 nonbonded pdb=" O ALA g 77 " pdb=" NZ LYS h 155 " model vdw 2.252 2.520 ... (remaining 598997 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 'A' and (resid 17 through 248 or resid 258 through 411 or resid 418 throu \ gh 437 or (resid 438 and (name N or name CA or name C or name O or name CB )) or \ resid 439 through 616)) selection = (chain 'B' and (resid 17 through 248 or resid 258 through 616)) selection = (chain 'C' and (resid 17 through 248 or resid 258 through 411 or resid 418 throu \ gh 437 or (resid 438 and (name N or name CA or name C or name O or name CB )) or \ resid 439 through 616)) } ncs_group { reference = (chain 'D' and (resid 33 through 207 or resid 220 through 500)) selection = chain 'E' selection = chain 'F' } ncs_group { reference = (chain 'I' and ((resid 9 through 56 and (name N or name CA or name C or name O o \ r name CB )) or resid 57 through 225)) selection = (chain 'J' and resid 9 through 225) selection = (chain 'K' and ((resid 9 through 42 and (name N or name CA or name C or name O o \ r name CB )) or resid 43 or (resid 44 through 56 and (name N or name CA or name \ C or name O or name CB )) or resid 57 through 225)) } ncs_group { reference = (chain 'M' and ((resid 9 through 86 and (name N or name CA or name C or name O o \ r name CB )) or resid 87 through 116)) selection = (chain 'N' and resid 9 through 116) selection = (chain 'O' and ((resid 9 through 63 and (name N or name CA or name C or name O o \ r name CB )) or (resid 64 through 86 and (name N or name CA or name C or name O \ or name CB )) or resid 87 through 116)) } ncs_group { reference = (chain 'Q' and (resid 13 through 38 or (resid 39 and (name N or name CA or name \ C or name O or name CB )) or resid 40 through 218)) selection = (chain 'R' and (resid 13 through 38 or (resid 39 and (name N or name CA or name \ C or name O or name CB )) or resid 40 through 218)) selection = (chain 'S' and resid 13 through 218) } ncs_group { reference = (chain 'g' and (resid 6 through 47 or (resid 48 and (name N or name CA or name C \ or name O or name CB )) or resid 49 through 155)) selection = (chain 'h' and (resid 6 through 47 or (resid 48 and (name N or name CA or name C \ or name O or name CB )) or resid 49 through 155)) selection = chain 'i' selection = (chain 'j' and (resid 6 through 47 or (resid 48 and (name N or name CA or name C \ or name O or name CB )) or resid 49 through 155)) selection = (chain 'k' and (resid 6 through 47 or (resid 48 and (name N or name CA or name C \ or name O or name CB )) or resid 49 through 155)) selection = (chain 'l' and (resid 6 through 47 or (resid 48 and (name N or name CA or name C \ or name O or name CB )) or resid 49 through 155)) selection = (chain 'm' and (resid 6 through 47 or (resid 48 and (name N or name CA or name C \ or name O or name CB )) or resid 49 through 155)) selection = (chain 'n' and (resid 6 through 47 or (resid 48 and (name N or name CA or name C \ or name O or name CB )) or resid 49 through 155)) selection = (chain 'o' and (resid 6 through 47 or (resid 48 and (name N or name CA or name C \ or name O or name CB )) or resid 49 through 155)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 2.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.070 Extract box with map and model: 11.930 Check model and map are aligned: 0.760 Set scattering table: 0.500 Process input model: 142.610 Find NCS groups from input model: 3.220 Set up NCS constraints: 0.280 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:2.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 163.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 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 : 0.009 0.148 69826 Z= 0.575 Angle : 1.357 11.489 94787 Z= 0.944 Chirality : 0.084 0.721 11071 Planarity : 0.010 0.125 12263 Dihedral : 15.169 89.906 24487 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.46 % Favored : 95.22 % Rotamer: Outliers : 5.89 % Allowed : 5.34 % Favored : 88.77 % Cbeta Deviations : 0.33 % Peptide Plane: Cis-proline : 1.99 % 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: 0.53 (0.09), residues: 9244 helix: 1.35 (0.07), residues: 5436 sheet: -1.31 (0.19), residues: 723 loop : -0.96 (0.11), residues: 3085 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.161 0.014 TRP e 52 HIS 0.017 0.002 HIS F 409 PHE 0.081 0.008 PHE B 337 TYR 0.119 0.009 TYR R 166 ARG 0.018 0.001 ARG o 126 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18488 Ramachandran restraints generated. 9244 Oldfield, 0 Emsley, 9244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18488 Ramachandran restraints generated. 9244 Oldfield, 0 Emsley, 9244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1093 residues out of total 7883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 388 poor density : 705 time to evaluate : 6.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 ARG cc_start: 0.9391 (OUTLIER) cc_final: 0.8979 (mtp85) REVERT: A 220 LYS cc_start: 0.9493 (OUTLIER) cc_final: 0.9287 (mttm) REVERT: A 540 MET cc_start: 0.9170 (mtt) cc_final: 0.8965 (mtt) REVERT: A 573 HIS cc_start: 0.8912 (t-170) cc_final: 0.8522 (t-170) REVERT: A 574 MET cc_start: 0.8696 (pmm) cc_final: 0.8334 (pmm) REVERT: B 270 ASP cc_start: 0.8230 (OUTLIER) cc_final: 0.7987 (p0) REVERT: B 280 ARG cc_start: 0.8787 (OUTLIER) cc_final: 0.8545 (mtm-85) REVERT: B 296 MET cc_start: 0.9016 (pmm) cc_final: 0.8557 (pmm) REVERT: B 306 MET cc_start: 0.8844 (OUTLIER) cc_final: 0.8502 (mmm) REVERT: B 318 MET cc_start: 0.8645 (mtt) cc_final: 0.8373 (mtp) REVERT: B 323 ARG cc_start: 0.8871 (OUTLIER) cc_final: 0.8451 (mtm-85) REVERT: B 327 ILE cc_start: 0.9408 (OUTLIER) cc_final: 0.9184 (tt) REVERT: B 344 VAL cc_start: 0.9196 (OUTLIER) cc_final: 0.8887 (m) REVERT: B 359 ARG cc_start: 0.9016 (OUTLIER) cc_final: 0.8773 (ttm170) REVERT: B 387 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.8019 (mm-30) REVERT: B 450 TRP cc_start: 0.8489 (m-90) cc_final: 0.8206 (m-90) REVERT: B 530 ARG cc_start: 0.9043 (mtm180) cc_final: 0.8777 (mtm110) REVERT: B 540 MET cc_start: 0.8926 (mtp) cc_final: 0.8372 (mtp) REVERT: C 100 ASP cc_start: 0.7776 (OUTLIER) cc_final: 0.7522 (p0) REVERT: C 123 ASN cc_start: 0.8908 (OUTLIER) cc_final: 0.8694 (t0) REVERT: C 167 MET cc_start: 0.8486 (ptp) cc_final: 0.8210 (ptp) REVERT: C 284 MET cc_start: 0.9557 (OUTLIER) cc_final: 0.9033 (mpp) REVERT: C 291 PHE cc_start: 0.7895 (m-10) cc_final: 0.7680 (m-80) REVERT: C 361 ILE cc_start: 0.9360 (OUTLIER) cc_final: 0.9041 (mm) REVERT: C 365 LEU cc_start: 0.9438 (OUTLIER) cc_final: 0.9157 (mt) REVERT: C 392 VAL cc_start: 0.9291 (OUTLIER) cc_final: 0.8835 (m) REVERT: C 450 TRP cc_start: 0.8818 (OUTLIER) cc_final: 0.7985 (p-90) REVERT: C 487 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.6036 (mp0) REVERT: C 488 ASP cc_start: 0.8463 (m-30) cc_final: 0.7810 (m-30) REVERT: C 505 ASP cc_start: 0.9124 (m-30) cc_final: 0.8871 (m-30) REVERT: C 574 MET cc_start: 0.7796 (mmt) cc_final: 0.7581 (mmt) REVERT: D 147 ILE cc_start: 0.9199 (OUTLIER) cc_final: 0.8963 (tp) REVERT: D 202 ARG cc_start: 0.9047 (OUTLIER) cc_final: 0.8749 (mtm-85) REVERT: D 232 MET cc_start: 0.8591 (tpt) cc_final: 0.8213 (tpt) REVERT: D 402 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7632 (tp30) REVERT: D 404 MET cc_start: 0.9094 (mtt) cc_final: 0.8820 (mtt) REVERT: E 38 ARG cc_start: 0.8459 (OUTLIER) cc_final: 0.8034 (mmm-85) REVERT: E 182 LYS cc_start: 0.8831 (OUTLIER) cc_final: 0.7971 (ptpt) REVERT: E 228 MET cc_start: 0.8607 (mpp) cc_final: 0.8251 (mpp) REVERT: E 315 ARG cc_start: 0.9279 (OUTLIER) cc_final: 0.9031 (mmt-90) REVERT: E 341 SER cc_start: 0.9230 (OUTLIER) cc_final: 0.8891 (p) REVERT: E 425 ASP cc_start: 0.8874 (m-30) cc_final: 0.8601 (m-30) REVERT: E 489 ILE cc_start: 0.9384 (OUTLIER) cc_final: 0.9097 (mm) REVERT: E 493 MET cc_start: 0.9123 (tpp) cc_final: 0.8910 (tpp) REVERT: F 124 ARG cc_start: 0.8858 (OUTLIER) cc_final: 0.8655 (mtp85) REVERT: F 294 MET cc_start: 0.9024 (mmm) cc_final: 0.8600 (mmm) REVERT: F 315 ARG cc_start: 0.8718 (OUTLIER) cc_final: 0.8145 (mpt180) REVERT: F 396 MET cc_start: 0.8913 (ttt) cc_final: 0.8609 (ttt) REVERT: H 14 MET cc_start: 0.8650 (tmm) cc_final: 0.8244 (tmm) REVERT: H 112 TYR cc_start: 0.7610 (t80) cc_final: 0.7239 (t80) REVERT: H 192 ASP cc_start: 0.8454 (t0) cc_final: 0.8134 (t0) REVERT: I 72 MET cc_start: 0.8667 (tpp) cc_final: 0.8061 (tpp) REVERT: K 132 MET cc_start: 0.8329 (mtp) cc_final: 0.7897 (mtp) REVERT: K 192 VAL cc_start: 0.9256 (OUTLIER) cc_final: 0.9010 (p) REVERT: K 208 MET cc_start: 0.9339 (mmm) cc_final: 0.8936 (mmm) REVERT: L 54 GLN cc_start: 0.9159 (tp-100) cc_final: 0.8940 (tp-100) REVERT: L 59 GLU cc_start: 0.8111 (pp20) cc_final: 0.7881 (tm-30) REVERT: L 69 TYR cc_start: 0.8575 (p90) cc_final: 0.8375 (p90) REVERT: L 102 LYS cc_start: 0.8282 (OUTLIER) cc_final: 0.7849 (pttm) REVERT: Q 33 MET cc_start: 0.9244 (tpt) cc_final: 0.8990 (tpt) REVERT: Q 62 PHE cc_start: 0.8393 (OUTLIER) cc_final: 0.7543 (t80) REVERT: Q 155 MET cc_start: 0.9176 (mmp) cc_final: 0.8668 (mmm) REVERT: R 31 ARG cc_start: 0.7929 (OUTLIER) cc_final: 0.7522 (mtm-85) REVERT: R 33 MET cc_start: 0.8916 (OUTLIER) cc_final: 0.8417 (tpt) REVERT: R 83 ARG cc_start: 0.8738 (OUTLIER) cc_final: 0.8503 (ttp80) REVERT: R 122 TRP cc_start: 0.9080 (OUTLIER) cc_final: 0.8746 (t-100) REVERT: R 139 TYR cc_start: 0.8407 (t80) cc_final: 0.7944 (t80) REVERT: R 197 TYR cc_start: 0.4901 (OUTLIER) cc_final: 0.4528 (t80) REVERT: S 188 MET cc_start: 0.8870 (mtm) cc_final: 0.8521 (mtm) REVERT: S 214 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.7771 (mp0) REVERT: S 217 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8545 (pt) REVERT: S 225 LEU cc_start: 0.9295 (OUTLIER) cc_final: 0.8990 (tt) REVERT: U 345 TYR cc_start: 0.8812 (m-80) cc_final: 0.8443 (m-10) REVERT: U 365 HIS cc_start: 0.8794 (OUTLIER) cc_final: 0.7894 (m170) REVERT: U 366 ASN cc_start: 0.9299 (m-40) cc_final: 0.9047 (m-40) REVERT: U 388 THR cc_start: 0.9060 (OUTLIER) cc_final: 0.8644 (p) REVERT: a 369 LYS cc_start: 0.8708 (OUTLIER) cc_final: 0.8221 (tmtt) REVERT: a 387 ARG cc_start: 0.9315 (OUTLIER) cc_final: 0.8923 (mmm-85) REVERT: a 388 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.7889 (tt0) REVERT: a 431 LEU cc_start: 0.9635 (OUTLIER) cc_final: 0.9329 (mt) REVERT: a 549 MET cc_start: 0.9053 (mmp) cc_final: 0.8748 (mmt) REVERT: a 550 MET cc_start: 0.9057 (mmp) cc_final: 0.8732 (mmp) REVERT: a 628 MET cc_start: 0.8596 (tpp) cc_final: 0.8250 (tpp) REVERT: a 741 ARG cc_start: 0.8896 (OUTLIER) cc_final: 0.8595 (ptm160) REVERT: a 745 LEU cc_start: 0.9592 (OUTLIER) cc_final: 0.9361 (mt) REVERT: a 790 ILE cc_start: 0.9534 (pt) cc_final: 0.8861 (pt) REVERT: a 795 GLU cc_start: 0.9209 (OUTLIER) cc_final: 0.8989 (pp20) REVERT: a 824 LEU cc_start: 0.9493 (tp) cc_final: 0.9161 (pp) REVERT: b 82 LYS cc_start: 0.9099 (OUTLIER) cc_final: 0.8878 (ttpt) REVERT: b 175 LYS cc_start: 0.9011 (ptpp) cc_final: 0.8455 (tptt) REVERT: c 340 THR cc_start: 0.8962 (OUTLIER) cc_final: 0.8574 (p) REVERT: c 341 LEU cc_start: 0.9498 (OUTLIER) cc_final: 0.9154 (tt) REVERT: c 343 ARG cc_start: 0.9043 (OUTLIER) cc_final: 0.8823 (mmt90) REVERT: c 345 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.8426 (mp0) REVERT: c 366 TYR cc_start: 0.9281 (m-80) cc_final: 0.8073 (m-10) REVERT: c 438 ILE cc_start: 0.9140 (mm) cc_final: 0.8901 (mm) REVERT: d 129 CYS cc_start: 0.8664 (m) cc_final: 0.8324 (m) REVERT: d 145 GLN cc_start: 0.7912 (OUTLIER) cc_final: 0.7327 (mm-40) REVERT: d 219 ARG cc_start: 0.8987 (OUTLIER) cc_final: 0.8697 (mmt90) REVERT: d 244 CYS cc_start: 0.8327 (p) cc_final: 0.8098 (p) REVERT: d 250 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.8114 (tt0) REVERT: e 17 TRP cc_start: 0.9024 (m100) cc_final: 0.8400 (m100) REVERT: e 49 TYR cc_start: 0.8890 (t80) cc_final: 0.8621 (t80) REVERT: e 51 PHE cc_start: 0.9033 (t80) cc_final: 0.8760 (t80) REVERT: e 71 GLU cc_start: 0.9141 (mt-10) cc_final: 0.8515 (mm-30) REVERT: f 25 MET cc_start: 0.9054 (ttt) cc_final: 0.8742 (tpp) REVERT: f 46 PHE cc_start: 0.9004 (p90) cc_final: 0.8599 (p90) REVERT: g 48 ARG cc_start: 0.8547 (ptp-170) cc_final: 0.8185 (ptp90) REVERT: g 115 ASP cc_start: 0.8598 (OUTLIER) cc_final: 0.7986 (t70) REVERT: h 32 TYR cc_start: 0.9020 (t80) cc_final: 0.8473 (t80) REVERT: h 36 LYS cc_start: 0.7733 (mppt) cc_final: 0.7403 (mmtm) REVERT: h 48 ARG cc_start: 0.8523 (ttp-110) cc_final: 0.8187 (ttm110) REVERT: h 61 MET cc_start: 0.9083 (ttm) cc_final: 0.8795 (ttm) REVERT: h 68 TYR cc_start: 0.8778 (m-10) cc_final: 0.8001 (m-10) REVERT: h 115 ASP cc_start: 0.8251 (t70) cc_final: 0.8026 (t0) REVERT: h 119 ARG cc_start: 0.7925 (OUTLIER) cc_final: 0.7629 (mtm-85) REVERT: h 123 GLN cc_start: 0.9369 (mp10) cc_final: 0.9134 (mp10) REVERT: h 131 MET cc_start: 0.9201 (ttp) cc_final: 0.8999 (ttp) REVERT: h 143 LEU cc_start: 0.9682 (OUTLIER) cc_final: 0.9263 (mp) REVERT: h 144 TYR cc_start: 0.8832 (m-10) cc_final: 0.8619 (m-10) REVERT: i 23 MET cc_start: 0.8856 (tpt) cc_final: 0.8525 (tpp) REVERT: i 50 GLU cc_start: 0.8152 (pm20) cc_final: 0.7834 (pm20) REVERT: i 140 VAL cc_start: 0.9008 (t) cc_final: 0.7854 (p) REVERT: j 23 MET cc_start: 0.8947 (tmm) cc_final: 0.8613 (tmm) REVERT: j 70 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8871 (pp) REVERT: j 140 VAL cc_start: 0.9496 (OUTLIER) cc_final: 0.9245 (p) REVERT: j 155 LYS cc_start: 0.9134 (tttp) cc_final: 0.8756 (tttt) REVERT: k 32 TYR cc_start: 0.8855 (t80) cc_final: 0.8196 (t80) REVERT: k 54 LYS cc_start: 0.9504 (tttt) cc_final: 0.9229 (tttt) REVERT: k 68 TYR cc_start: 0.8999 (m-10) cc_final: 0.8781 (m-10) REVERT: k 108 PHE cc_start: 0.9462 (t80) cc_final: 0.8656 (t80) REVERT: k 123 GLN cc_start: 0.9103 (mm-40) cc_final: 0.8898 (mm-40) REVERT: k 139 GLU cc_start: 0.9137 (tp30) cc_final: 0.8798 (tp30) REVERT: k 144 TYR cc_start: 0.9464 (m-10) cc_final: 0.9135 (m-10) REVERT: l 32 TYR cc_start: 0.8493 (t80) cc_final: 0.8170 (t80) REVERT: l 54 LYS cc_start: 0.9044 (ptpp) cc_final: 0.8774 (ptpp) REVERT: l 119 ARG cc_start: 0.8391 (mmt-90) cc_final: 0.7913 (mmt-90) REVERT: l 124 GLN cc_start: 0.9214 (tp-100) cc_final: 0.8824 (tm-30) REVERT: l 131 MET cc_start: 0.9206 (OUTLIER) cc_final: 0.8964 (tmm) REVERT: m 13 PHE cc_start: 0.8896 (t80) cc_final: 0.8326 (t80) REVERT: m 14 PHE cc_start: 0.8863 (m-80) cc_final: 0.8514 (m-80) REVERT: m 17 MET cc_start: 0.8817 (mmp) cc_final: 0.8031 (mmt) REVERT: m 23 MET cc_start: 0.8849 (OUTLIER) cc_final: 0.8441 (ppp) REVERT: m 32 TYR cc_start: 0.8961 (t80) cc_final: 0.8620 (t80) REVERT: m 47 MET cc_start: 0.8466 (OUTLIER) cc_final: 0.6566 (mmt) REVERT: m 50 GLU cc_start: 0.9467 (OUTLIER) cc_final: 0.9210 (pm20) REVERT: m 70 LEU cc_start: 0.9534 (OUTLIER) cc_final: 0.9141 (mt) REVERT: m 78 ASN cc_start: 0.9245 (p0) cc_final: 0.8937 (p0) REVERT: m 108 PHE cc_start: 0.8692 (t80) cc_final: 0.8287 (t80) REVERT: m 121 THR cc_start: 0.9532 (p) cc_final: 0.9026 (p) REVERT: m 123 GLN cc_start: 0.9110 (mt0) cc_final: 0.8545 (mm-40) REVERT: m 139 GLU cc_start: 0.8399 (pm20) cc_final: 0.8148 (pm20) REVERT: n 17 MET cc_start: 0.9048 (mmp) cc_final: 0.8607 (mmp) REVERT: n 36 LYS cc_start: 0.8958 (ttmt) cc_final: 0.8060 (ttmm) REVERT: n 64 ILE cc_start: 0.9526 (mm) cc_final: 0.9298 (tt) REVERT: n 68 TYR cc_start: 0.8086 (m-10) cc_final: 0.7370 (m-10) REVERT: n 70 LEU cc_start: 0.8899 (mt) cc_final: 0.8638 (mt) REVERT: n 115 ASP cc_start: 0.9052 (t0) cc_final: 0.8234 (t0) REVERT: n 123 GLN cc_start: 0.9308 (OUTLIER) cc_final: 0.8753 (mm-40) REVERT: o 25 PHE cc_start: 0.9157 (m-80) cc_final: 0.8900 (m-80) REVERT: o 36 LYS cc_start: 0.9129 (mmtt) cc_final: 0.8620 (mmtp) REVERT: o 44 MET cc_start: 0.9010 (mmp) cc_final: 0.8736 (mmt) REVERT: o 47 MET cc_start: 0.9044 (tmm) cc_final: 0.8763 (tmm) REVERT: o 115 ASP cc_start: 0.9265 (t0) cc_final: 0.9003 (t0) REVERT: p 295 ASN cc_start: 0.9230 (OUTLIER) cc_final: 0.8091 (t0) REVERT: p 342 ARG cc_start: 0.8940 (ttp80) cc_final: 0.8548 (ttp80) outliers start: 388 outliers final: 83 residues processed: 1031 average time/residue: 0.7007 time to fit residues: 1187.3737 Evaluate side-chains 753 residues out of total 7883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 602 time to evaluate : 6.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 164 HIS Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 215 ARG Chi-restraints excluded: chain A residue 220 LYS Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 419 ASP Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 163 LYS Chi-restraints excluded: chain B residue 167 MET Chi-restraints excluded: chain B residue 207 GLN Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain B residue 277 CYS Chi-restraints excluded: chain B residue 280 ARG Chi-restraints excluded: chain B residue 306 MET Chi-restraints excluded: chain B residue 323 ARG Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 359 ARG Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 123 ASN Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 284 MET Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 353 ARG Chi-restraints excluded: chain C residue 361 ILE Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 392 VAL Chi-restraints excluded: chain C residue 403 SER Chi-restraints excluded: chain C residue 450 TRP Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 487 GLU Chi-restraints excluded: chain D residue 72 ASN Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 202 ARG Chi-restraints excluded: chain D residue 334 ARG Chi-restraints excluded: chain D residue 338 ARG Chi-restraints excluded: chain D residue 374 ASP Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain E residue 182 LYS Chi-restraints excluded: chain E residue 266 ILE Chi-restraints excluded: chain E residue 315 ARG Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain E residue 489 ILE Chi-restraints excluded: chain F residue 100 ASP Chi-restraints excluded: chain F residue 124 ARG Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain F residue 315 ARG Chi-restraints excluded: chain H residue 85 GLN Chi-restraints excluded: chain H residue 86 ASN Chi-restraints excluded: chain H residue 113 HIS Chi-restraints excluded: chain H residue 114 GLU Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 121 LEU Chi-restraints excluded: chain H residue 193 GLU Chi-restraints excluded: chain I residue 124 LEU Chi-restraints excluded: chain I residue 159 THR Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain J residue 191 LYS Chi-restraints excluded: chain K residue 192 VAL Chi-restraints excluded: chain L residue 25 ILE Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 40 GLU Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 56 LEU Chi-restraints excluded: chain L residue 102 LYS Chi-restraints excluded: chain M residue 110 ILE Chi-restraints excluded: chain O residue 89 ARG Chi-restraints excluded: chain O residue 109 GLU Chi-restraints excluded: chain Q residue 62 PHE Chi-restraints excluded: chain R residue 31 ARG Chi-restraints excluded: chain R residue 33 MET Chi-restraints excluded: chain R residue 83 ARG Chi-restraints excluded: chain R residue 85 SER Chi-restraints excluded: chain R residue 122 TRP Chi-restraints excluded: chain R residue 197 TYR Chi-restraints excluded: chain S residue 213 PHE Chi-restraints excluded: chain S residue 214 GLU Chi-restraints excluded: chain S residue 217 LEU Chi-restraints excluded: chain S residue 225 LEU Chi-restraints excluded: chain U residue 365 HIS Chi-restraints excluded: chain U residue 380 HIS Chi-restraints excluded: chain U residue 388 THR Chi-restraints excluded: chain a residue 9 GLU Chi-restraints excluded: chain a residue 363 THR Chi-restraints excluded: chain a residue 366 LYS Chi-restraints excluded: chain a residue 369 LYS Chi-restraints excluded: chain a residue 387 ARG Chi-restraints excluded: chain a residue 388 GLU Chi-restraints excluded: chain a residue 390 ASN Chi-restraints excluded: chain a residue 406 MET Chi-restraints excluded: chain a residue 431 LEU Chi-restraints excluded: chain a residue 442 THR Chi-restraints excluded: chain a residue 452 LEU Chi-restraints excluded: chain a residue 741 ARG Chi-restraints excluded: chain a residue 745 LEU Chi-restraints excluded: chain a residue 795 GLU Chi-restraints excluded: chain a residue 805 ARG Chi-restraints excluded: chain b residue 28 ILE Chi-restraints excluded: chain b residue 34 ARG Chi-restraints excluded: chain b residue 82 LYS Chi-restraints excluded: chain c residue 265 ARG Chi-restraints excluded: chain c residue 334 SER Chi-restraints excluded: chain c residue 336 ARG Chi-restraints excluded: chain c residue 339 PHE Chi-restraints excluded: chain c residue 340 THR Chi-restraints excluded: chain c residue 341 LEU Chi-restraints excluded: chain c residue 343 ARG Chi-restraints excluded: chain c residue 345 GLU Chi-restraints excluded: chain c residue 407 THR Chi-restraints excluded: chain d residue 120 ARG Chi-restraints excluded: chain d residue 145 GLN Chi-restraints excluded: chain d residue 149 GLU Chi-restraints excluded: chain d residue 213 GLU Chi-restraints excluded: chain d residue 219 ARG Chi-restraints excluded: chain d residue 250 GLU Chi-restraints excluded: chain d residue 314 VAL Chi-restraints excluded: chain g residue 115 ASP Chi-restraints excluded: chain h residue 16 VAL Chi-restraints excluded: chain h residue 119 ARG Chi-restraints excluded: chain h residue 140 VAL Chi-restraints excluded: chain h residue 143 LEU Chi-restraints excluded: chain j residue 70 LEU Chi-restraints excluded: chain j residue 140 VAL Chi-restraints excluded: chain j residue 143 LEU Chi-restraints excluded: chain l residue 48 ARG Chi-restraints excluded: chain l residue 115 ASP Chi-restraints excluded: chain l residue 131 MET Chi-restraints excluded: chain m residue 23 MET Chi-restraints excluded: chain m residue 47 MET Chi-restraints excluded: chain m residue 50 GLU Chi-restraints excluded: chain m residue 70 LEU Chi-restraints excluded: chain m residue 118 VAL Chi-restraints excluded: chain n residue 10 TYR Chi-restraints excluded: chain n residue 123 GLN Chi-restraints excluded: chain o residue 65 ILE Chi-restraints excluded: chain o residue 67 ILE Chi-restraints excluded: chain p residue 295 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 923 random chunks: chunk 779 optimal weight: 9.9990 chunk 699 optimal weight: 0.8980 chunk 388 optimal weight: 2.9990 chunk 238 optimal weight: 9.9990 chunk 471 optimal weight: 8.9990 chunk 373 optimal weight: 4.9990 chunk 723 optimal weight: 0.9990 chunk 279 optimal weight: 4.9990 chunk 439 optimal weight: 2.9990 chunk 538 optimal weight: 50.0000 chunk 838 optimal weight: 9.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 444 HIS A 523 ASN A 603 GLN ** B 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 65 GLN C 172 ASN C 282 ASN C 314 ASN C 317 ASN C 444 HIS ** C 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 199 GLN D 491 GLN ** E 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 370 GLN L 67 ASN S 184 HIS U 264 HIS ** a 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 69826 Z= 0.268 Angle : 0.635 9.705 94787 Z= 0.335 Chirality : 0.042 0.266 11071 Planarity : 0.004 0.061 12263 Dihedral : 7.938 96.992 10337 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.42 % Favored : 96.51 % Rotamer: Outliers : 3.05 % Allowed : 9.99 % Favored : 86.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.99 % 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: 1.21 (0.09), residues: 9244 helix: 1.92 (0.07), residues: 5559 sheet: -1.27 (0.19), residues: 710 loop : -0.79 (0.12), residues: 2975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 567 HIS 0.008 0.001 HIS L 81 PHE 0.027 0.002 PHE B 337 TYR 0.045 0.002 TYR m 144 ARG 0.010 0.001 ARG B 442 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18488 Ramachandran restraints generated. 9244 Oldfield, 0 Emsley, 9244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18488 Ramachandran restraints generated. 9244 Oldfield, 0 Emsley, 9244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 844 residues out of total 7883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 201 poor density : 643 time to evaluate : 6.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 MET cc_start: 0.8427 (mmm) cc_final: 0.8202 (mmm) REVERT: A 429 VAL cc_start: 0.9202 (OUTLIER) cc_final: 0.8879 (p) REVERT: A 540 MET cc_start: 0.8967 (mtt) cc_final: 0.8691 (mtt) REVERT: B 296 MET cc_start: 0.8972 (OUTLIER) cc_final: 0.8495 (pmm) REVERT: B 306 MET cc_start: 0.8690 (mmm) cc_final: 0.8370 (mmm) REVERT: B 318 MET cc_start: 0.8284 (mtt) cc_final: 0.8074 (mtp) REVERT: B 344 VAL cc_start: 0.9207 (OUTLIER) cc_final: 0.8889 (m) REVERT: B 359 ARG cc_start: 0.9052 (OUTLIER) cc_final: 0.8735 (ttm170) REVERT: B 451 LEU cc_start: 0.9040 (mm) cc_final: 0.8822 (pp) REVERT: B 530 ARG cc_start: 0.9036 (mtm180) cc_final: 0.8693 (mtm110) REVERT: B 540 MET cc_start: 0.8816 (mtp) cc_final: 0.8266 (mtp) REVERT: C 61 MET cc_start: 0.8212 (ttp) cc_final: 0.7983 (ttm) REVERT: C 365 LEU cc_start: 0.9441 (OUTLIER) cc_final: 0.9149 (mt) REVERT: C 392 VAL cc_start: 0.9331 (OUTLIER) cc_final: 0.8924 (m) REVERT: C 450 TRP cc_start: 0.8731 (OUTLIER) cc_final: 0.7980 (p-90) REVERT: C 488 ASP cc_start: 0.8252 (m-30) cc_final: 0.7849 (m-30) REVERT: C 505 ASP cc_start: 0.9151 (m-30) cc_final: 0.8915 (m-30) REVERT: C 553 ARG cc_start: 0.9145 (ptm160) cc_final: 0.8835 (ptm160) REVERT: D 121 MET cc_start: 0.8385 (mpp) cc_final: 0.8138 (mpp) REVERT: D 147 ILE cc_start: 0.9206 (OUTLIER) cc_final: 0.8992 (tp) REVERT: D 163 MET cc_start: 0.8787 (OUTLIER) cc_final: 0.8569 (ttm) REVERT: D 232 MET cc_start: 0.8597 (tpt) cc_final: 0.8301 (tpt) REVERT: E 163 MET cc_start: 0.7956 (tmm) cc_final: 0.7599 (tmm) REVERT: E 228 MET cc_start: 0.8519 (mpp) cc_final: 0.7878 (mpp) REVERT: E 309 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.8200 (pp20) REVERT: E 315 ARG cc_start: 0.9265 (OUTLIER) cc_final: 0.9032 (mmt-90) REVERT: E 396 MET cc_start: 0.8862 (ttm) cc_final: 0.8296 (ttp) REVERT: E 425 ASP cc_start: 0.8804 (m-30) cc_final: 0.8518 (m-30) REVERT: E 485 MET cc_start: 0.8535 (mtp) cc_final: 0.8203 (mtm) REVERT: E 493 MET cc_start: 0.8855 (tpp) cc_final: 0.8570 (tpp) REVERT: F 124 ARG cc_start: 0.8797 (OUTLIER) cc_final: 0.8592 (mtp85) REVERT: F 294 MET cc_start: 0.8783 (mmm) cc_final: 0.8084 (mmm) REVERT: F 350 MET cc_start: 0.8685 (mtp) cc_final: 0.8363 (mpp) REVERT: F 376 GLN cc_start: 0.8649 (mp-120) cc_final: 0.8306 (mp10) REVERT: F 396 MET cc_start: 0.8716 (ttt) cc_final: 0.8438 (ttt) REVERT: H 14 MET cc_start: 0.8818 (tmm) cc_final: 0.8272 (tmm) REVERT: H 112 TYR cc_start: 0.7642 (t80) cc_final: 0.7325 (t80) REVERT: H 192 ASP cc_start: 0.8398 (t0) cc_final: 0.8062 (t0) REVERT: I 72 MET cc_start: 0.8617 (tpp) cc_final: 0.7908 (tpp) REVERT: I 76 MET cc_start: 0.8669 (mmm) cc_final: 0.7913 (mmm) REVERT: I 132 MET cc_start: 0.8348 (mmt) cc_final: 0.7988 (mmp) REVERT: J 121 LEU cc_start: 0.9528 (OUTLIER) cc_final: 0.9142 (tp) REVERT: J 208 MET cc_start: 0.8887 (mmp) cc_final: 0.8611 (mmm) REVERT: K 192 VAL cc_start: 0.9118 (OUTLIER) cc_final: 0.8871 (p) REVERT: K 208 MET cc_start: 0.9349 (mmm) cc_final: 0.8973 (mmm) REVERT: L 54 GLN cc_start: 0.8918 (tp-100) cc_final: 0.8686 (tp-100) REVERT: L 69 TYR cc_start: 0.8899 (p90) cc_final: 0.8549 (p90) REVERT: L 112 MET cc_start: 0.8243 (ppp) cc_final: 0.7924 (ppp) REVERT: O 93 ASP cc_start: 0.9124 (m-30) cc_final: 0.8740 (p0) REVERT: O 105 ASP cc_start: 0.8562 (t0) cc_final: 0.8121 (p0) REVERT: Q 62 PHE cc_start: 0.8352 (OUTLIER) cc_final: 0.7883 (t80) REVERT: Q 98 ILE cc_start: 0.8020 (OUTLIER) cc_final: 0.7805 (mm) REVERT: Q 155 MET cc_start: 0.9073 (mmp) cc_final: 0.8584 (mmp) REVERT: R 33 MET cc_start: 0.8798 (tpt) cc_final: 0.8345 (tpp) REVERT: R 57 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7931 (pm20) REVERT: R 122 TRP cc_start: 0.9049 (OUTLIER) cc_final: 0.8517 (t-100) REVERT: R 139 TYR cc_start: 0.8523 (t80) cc_final: 0.8103 (t80) REVERT: R 161 MET cc_start: 0.8985 (tmm) cc_final: 0.8752 (ppp) REVERT: R 197 TYR cc_start: 0.5158 (OUTLIER) cc_final: 0.4621 (t80) REVERT: S 103 MET cc_start: 0.7171 (tpp) cc_final: 0.6805 (tpp) REVERT: S 188 MET cc_start: 0.8908 (mtm) cc_final: 0.8674 (mtp) REVERT: S 214 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.7609 (mp0) REVERT: S 225 LEU cc_start: 0.9280 (OUTLIER) cc_final: 0.8976 (tt) REVERT: U 345 TYR cc_start: 0.8833 (m-80) cc_final: 0.8357 (m-10) REVERT: U 365 HIS cc_start: 0.8798 (OUTLIER) cc_final: 0.7870 (m170) REVERT: a 4 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8454 (tp) REVERT: a 61 MET cc_start: 0.8857 (mmm) cc_final: 0.8622 (mmm) REVERT: a 381 TYR cc_start: 0.9242 (t80) cc_final: 0.8923 (t80) REVERT: a 431 LEU cc_start: 0.9608 (OUTLIER) cc_final: 0.9348 (mt) REVERT: a 484 MET cc_start: 0.8139 (ttm) cc_final: 0.7605 (tpp) REVERT: a 549 MET cc_start: 0.8749 (mmp) cc_final: 0.8546 (mmp) REVERT: a 550 MET cc_start: 0.9038 (mmp) cc_final: 0.8631 (mmm) REVERT: a 718 MET cc_start: 0.8906 (tmm) cc_final: 0.8689 (ppp) REVERT: a 745 LEU cc_start: 0.9558 (OUTLIER) cc_final: 0.9320 (mt) REVERT: a 790 ILE cc_start: 0.9491 (pt) cc_final: 0.9174 (pt) REVERT: a 795 GLU cc_start: 0.9179 (OUTLIER) cc_final: 0.8952 (pt0) REVERT: b 70 TYR cc_start: 0.9170 (p90) cc_final: 0.8828 (p90) REVERT: b 82 LYS cc_start: 0.9202 (OUTLIER) cc_final: 0.8648 (ptpp) REVERT: b 175 LYS cc_start: 0.8810 (ptpp) cc_final: 0.8509 (pttt) REVERT: c 329 ARG cc_start: 0.8194 (ppt170) cc_final: 0.7569 (ppt170) REVERT: c 341 LEU cc_start: 0.9393 (OUTLIER) cc_final: 0.9114 (tp) REVERT: c 345 GLU cc_start: 0.8949 (OUTLIER) cc_final: 0.7650 (mp0) REVERT: c 366 TYR cc_start: 0.8529 (m-80) cc_final: 0.8231 (m-80) REVERT: c 438 ILE cc_start: 0.9138 (mm) cc_final: 0.8910 (mm) REVERT: c 445 MET cc_start: 0.8828 (mmp) cc_final: 0.8405 (mmm) REVERT: d 129 CYS cc_start: 0.8690 (m) cc_final: 0.8351 (m) REVERT: d 176 MET cc_start: 0.8338 (tmm) cc_final: 0.7690 (tmm) REVERT: e 17 TRP cc_start: 0.9003 (m100) cc_final: 0.8319 (m100) REVERT: e 49 TYR cc_start: 0.8905 (t80) cc_final: 0.8681 (t80) REVERT: f 25 MET cc_start: 0.9000 (ttt) cc_final: 0.8625 (tpp) REVERT: f 28 MET cc_start: 0.9088 (mmm) cc_final: 0.8665 (mmm) REVERT: f 43 ASP cc_start: 0.9007 (OUTLIER) cc_final: 0.8757 (t0) REVERT: g 47 MET cc_start: 0.7994 (mmm) cc_final: 0.7787 (mmp) REVERT: g 115 ASP cc_start: 0.8248 (OUTLIER) cc_final: 0.7872 (t70) REVERT: h 23 MET cc_start: 0.8357 (tpp) cc_final: 0.7888 (tpp) REVERT: h 48 ARG cc_start: 0.8399 (ttp-110) cc_final: 0.8030 (ttp-110) REVERT: h 68 TYR cc_start: 0.8707 (m-10) cc_final: 0.8371 (m-10) REVERT: h 115 ASP cc_start: 0.8034 (t70) cc_final: 0.7754 (t0) REVERT: h 123 GLN cc_start: 0.9334 (mp10) cc_final: 0.8983 (mp10) REVERT: h 126 ARG cc_start: 0.8685 (OUTLIER) cc_final: 0.8376 (mtm110) REVERT: h 131 MET cc_start: 0.9158 (ttp) cc_final: 0.8916 (ttp) REVERT: i 23 MET cc_start: 0.9062 (tpt) cc_final: 0.8671 (tpp) REVERT: i 53 MET cc_start: 0.8926 (mmt) cc_final: 0.8718 (mmm) REVERT: i 115 ASP cc_start: 0.8917 (t0) cc_final: 0.8651 (m-30) REVERT: i 140 VAL cc_start: 0.9116 (t) cc_final: 0.8734 (p) REVERT: j 23 MET cc_start: 0.9185 (tmm) cc_final: 0.8814 (tmm) REVERT: j 36 LYS cc_start: 0.8966 (mmtm) cc_final: 0.8757 (mmtm) REVERT: j 44 MET cc_start: 0.8775 (tmm) cc_final: 0.8505 (tmm) REVERT: j 68 TYR cc_start: 0.8973 (m-10) cc_final: 0.8669 (m-80) REVERT: j 131 MET cc_start: 0.8867 (ppp) cc_final: 0.8621 (ppp) REVERT: j 143 LEU cc_start: 0.9379 (OUTLIER) cc_final: 0.9149 (tt) REVERT: j 155 LYS cc_start: 0.9201 (tttp) cc_final: 0.8831 (tttt) REVERT: k 32 TYR cc_start: 0.8948 (t80) cc_final: 0.8217 (t80) REVERT: k 44 MET cc_start: 0.8553 (ppp) cc_final: 0.8349 (ppp) REVERT: k 54 LYS cc_start: 0.9581 (tttt) cc_final: 0.9302 (tttt) REVERT: k 108 PHE cc_start: 0.9464 (t80) cc_final: 0.8671 (t80) REVERT: k 123 GLN cc_start: 0.9201 (mm-40) cc_final: 0.8970 (mm-40) REVERT: l 13 PHE cc_start: 0.9557 (t80) cc_final: 0.8759 (t80) REVERT: l 17 MET cc_start: 0.9003 (tpp) cc_final: 0.8648 (ptt) REVERT: l 32 TYR cc_start: 0.8590 (t80) cc_final: 0.8157 (t80) REVERT: l 54 LYS cc_start: 0.9114 (ptpp) cc_final: 0.8793 (ptpp) REVERT: l 110 ILE cc_start: 0.9153 (OUTLIER) cc_final: 0.8949 (tp) REVERT: l 115 ASP cc_start: 0.8385 (OUTLIER) cc_final: 0.8015 (m-30) REVERT: l 119 ARG cc_start: 0.8280 (mmt-90) cc_final: 0.7934 (mmt-90) REVERT: l 124 GLN cc_start: 0.8974 (tp-100) cc_final: 0.8459 (tm-30) REVERT: m 13 PHE cc_start: 0.8937 (t80) cc_final: 0.8498 (t80) REVERT: m 17 MET cc_start: 0.8949 (mmp) cc_final: 0.8534 (mmp) REVERT: m 47 MET cc_start: 0.8718 (mmm) cc_final: 0.8350 (mmp) REVERT: m 50 GLU cc_start: 0.9358 (pp20) cc_final: 0.9075 (pm20) REVERT: m 70 LEU cc_start: 0.9522 (OUTLIER) cc_final: 0.9074 (mt) REVERT: m 78 ASN cc_start: 0.9121 (p0) cc_final: 0.8856 (p0) REVERT: m 88 LYS cc_start: 0.8875 (pptt) cc_final: 0.8481 (pptt) REVERT: m 92 GLN cc_start: 0.8620 (mm-40) cc_final: 0.8248 (mm-40) REVERT: m 115 ASP cc_start: 0.8749 (p0) cc_final: 0.8531 (p0) REVERT: m 123 GLN cc_start: 0.8962 (mt0) cc_final: 0.8344 (mm-40) REVERT: m 139 GLU cc_start: 0.8832 (pm20) cc_final: 0.8484 (pm20) REVERT: n 13 PHE cc_start: 0.9381 (t80) cc_final: 0.8988 (t80) REVERT: n 17 MET cc_start: 0.9111 (mmp) cc_final: 0.8618 (mmp) REVERT: n 36 LYS cc_start: 0.8615 (ttmt) cc_final: 0.7627 (ttmm) REVERT: n 47 MET cc_start: 0.9093 (tpt) cc_final: 0.8793 (tpp) REVERT: n 115 ASP cc_start: 0.8678 (t0) cc_final: 0.8257 (t0) REVERT: n 123 GLN cc_start: 0.9087 (OUTLIER) cc_final: 0.8679 (mm-40) REVERT: o 17 MET cc_start: 0.8181 (ptm) cc_final: 0.7976 (ptp) REVERT: o 36 LYS cc_start: 0.9074 (mmtt) cc_final: 0.8850 (mmmm) REVERT: o 44 MET cc_start: 0.9059 (mmp) cc_final: 0.8701 (mmt) REVERT: o 47 MET cc_start: 0.8768 (tmm) cc_final: 0.8531 (tmm) REVERT: o 61 MET cc_start: 0.8728 (mtp) cc_final: 0.8485 (mtp) REVERT: o 115 ASP cc_start: 0.9284 (t0) cc_final: 0.9072 (t70) REVERT: o 123 GLN cc_start: 0.9352 (mp10) cc_final: 0.9100 (mp10) REVERT: o 131 MET cc_start: 0.9428 (OUTLIER) cc_final: 0.9190 (ttm) REVERT: p 303 ASP cc_start: 0.9274 (p0) cc_final: 0.8994 (p0) REVERT: p 341 TYR cc_start: 0.8076 (t80) cc_final: 0.7868 (t80) REVERT: p 342 ARG cc_start: 0.9100 (ttp80) cc_final: 0.8620 (ttp80) outliers start: 201 outliers final: 90 residues processed: 807 average time/residue: 0.6712 time to fit residues: 912.7736 Evaluate side-chains 705 residues out of total 7883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 577 time to evaluate : 6.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 HIS Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 419 ASP Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 296 MET Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 359 ARG Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 171 ARG Chi-restraints excluded: chain C residue 172 ASN Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 392 VAL Chi-restraints excluded: chain C residue 403 SER Chi-restraints excluded: chain C residue 450 TRP Chi-restraints excluded: chain C residue 514 LEU Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 163 MET Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 338 ARG Chi-restraints excluded: chain D residue 353 ASP Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain D residue 466 SER Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 293 ASP Chi-restraints excluded: chain E residue 309 GLU Chi-restraints excluded: chain E residue 315 ARG Chi-restraints excluded: chain F residue 100 ASP Chi-restraints excluded: chain F residue 124 ARG Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain F residue 315 ARG Chi-restraints excluded: chain H residue 85 GLN Chi-restraints excluded: chain H residue 86 ASN Chi-restraints excluded: chain H residue 113 HIS Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 121 LEU Chi-restraints excluded: chain H residue 193 GLU Chi-restraints excluded: chain I residue 159 THR Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain J residue 191 LYS Chi-restraints excluded: chain J residue 192 VAL Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain K residue 192 VAL Chi-restraints excluded: chain L residue 25 ILE Chi-restraints excluded: chain L residue 35 ASN Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 40 GLU Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain N residue 93 ASP Chi-restraints excluded: chain Q residue 62 PHE Chi-restraints excluded: chain Q residue 98 ILE Chi-restraints excluded: chain R residue 57 GLU Chi-restraints excluded: chain R residue 122 TRP Chi-restraints excluded: chain R residue 197 TYR Chi-restraints excluded: chain S residue 213 PHE Chi-restraints excluded: chain S residue 214 GLU Chi-restraints excluded: chain S residue 225 LEU Chi-restraints excluded: chain U residue 365 HIS Chi-restraints excluded: chain U residue 380 HIS Chi-restraints excluded: chain U residue 406 MET Chi-restraints excluded: chain a residue 4 LEU Chi-restraints excluded: chain a residue 363 THR Chi-restraints excluded: chain a residue 366 LYS Chi-restraints excluded: chain a residue 385 THR Chi-restraints excluded: chain a residue 431 LEU Chi-restraints excluded: chain a residue 452 LEU Chi-restraints excluded: chain a residue 745 LEU Chi-restraints excluded: chain a residue 795 GLU Chi-restraints excluded: chain a residue 805 ARG Chi-restraints excluded: chain b residue 24 ILE Chi-restraints excluded: chain b residue 28 ILE Chi-restraints excluded: chain b residue 30 ASP Chi-restraints excluded: chain b residue 34 ARG Chi-restraints excluded: chain b residue 82 LYS Chi-restraints excluded: chain c residue 333 VAL Chi-restraints excluded: chain c residue 336 ARG Chi-restraints excluded: chain c residue 339 PHE Chi-restraints excluded: chain c residue 341 LEU Chi-restraints excluded: chain c residue 345 GLU Chi-restraints excluded: chain c residue 407 THR Chi-restraints excluded: chain d residue 20 VAL Chi-restraints excluded: chain d residue 63 SER Chi-restraints excluded: chain d residue 110 ILE Chi-restraints excluded: chain d residue 124 GLU Chi-restraints excluded: chain d residue 145 GLN Chi-restraints excluded: chain d residue 149 GLU Chi-restraints excluded: chain d residue 213 GLU Chi-restraints excluded: chain e residue 39 THR Chi-restraints excluded: chain f residue 43 ASP Chi-restraints excluded: chain g residue 115 ASP Chi-restraints excluded: chain h residue 81 THR Chi-restraints excluded: chain h residue 126 ARG Chi-restraints excluded: chain h residue 140 VAL Chi-restraints excluded: chain j residue 143 LEU Chi-restraints excluded: chain l residue 48 ARG Chi-restraints excluded: chain l residue 110 ILE Chi-restraints excluded: chain l residue 115 ASP Chi-restraints excluded: chain m residue 46 VAL Chi-restraints excluded: chain m residue 70 LEU Chi-restraints excluded: chain m residue 81 THR Chi-restraints excluded: chain m residue 97 LEU Chi-restraints excluded: chain m residue 118 VAL Chi-restraints excluded: chain m residue 128 PHE Chi-restraints excluded: chain n residue 10 TYR Chi-restraints excluded: chain n residue 82 GLU Chi-restraints excluded: chain n residue 121 THR Chi-restraints excluded: chain n residue 123 GLN Chi-restraints excluded: chain o residue 65 ILE Chi-restraints excluded: chain o residue 97 LEU Chi-restraints excluded: chain o residue 118 VAL Chi-restraints excluded: chain o residue 131 MET Chi-restraints excluded: chain p residue 322 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 923 random chunks: chunk 465 optimal weight: 10.0000 chunk 260 optimal weight: 9.9990 chunk 697 optimal weight: 2.9990 chunk 570 optimal weight: 50.0000 chunk 231 optimal weight: 8.9990 chunk 839 optimal weight: 5.9990 chunk 907 optimal weight: 9.9990 chunk 747 optimal weight: 6.9990 chunk 832 optimal weight: 0.9990 chunk 286 optimal weight: 5.9990 chunk 673 optimal weight: 0.8980 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN ** B 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 484 GLN ** E 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 86 ASN H 152 GLN ** L 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 364 GLN ** U 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 390 ASN ** a 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 88 HIS ** d 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 69826 Z= 0.307 Angle : 0.607 9.654 94787 Z= 0.319 Chirality : 0.041 0.228 11071 Planarity : 0.004 0.051 12263 Dihedral : 6.513 92.633 10137 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.97 % Favored : 95.98 % Rotamer: Outliers : 2.85 % Allowed : 11.32 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.99 % 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: 1.43 (0.09), residues: 9244 helix: 2.10 (0.07), residues: 5553 sheet: -1.11 (0.19), residues: 735 loop : -0.73 (0.12), residues: 2956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 567 HIS 0.013 0.001 HIS L 81 PHE 0.040 0.002 PHE S 151 TYR 0.051 0.002 TYR m 144 ARG 0.009 0.001 ARG c 343 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18488 Ramachandran restraints generated. 9244 Oldfield, 0 Emsley, 9244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18488 Ramachandran restraints generated. 9244 Oldfield, 0 Emsley, 9244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 784 residues out of total 7883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 596 time to evaluate : 6.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 MET cc_start: 0.8353 (mmm) cc_final: 0.8132 (mmm) REVERT: A 429 VAL cc_start: 0.9236 (OUTLIER) cc_final: 0.8948 (p) REVERT: A 574 MET cc_start: 0.8841 (pmm) cc_final: 0.8434 (pmm) REVERT: B 163 LYS cc_start: 0.8933 (OUTLIER) cc_final: 0.8467 (mmtm) REVERT: B 296 MET cc_start: 0.8899 (OUTLIER) cc_final: 0.8453 (pmm) REVERT: B 306 MET cc_start: 0.8734 (mmm) cc_final: 0.8403 (mmm) REVERT: B 318 MET cc_start: 0.8443 (mtt) cc_final: 0.8190 (mtp) REVERT: B 344 VAL cc_start: 0.9295 (OUTLIER) cc_final: 0.8993 (m) REVERT: B 346 MET cc_start: 0.8296 (tmm) cc_final: 0.7540 (tmm) REVERT: B 359 ARG cc_start: 0.9041 (OUTLIER) cc_final: 0.8490 (ttm170) REVERT: B 451 LEU cc_start: 0.9062 (mm) cc_final: 0.8822 (pp) REVERT: B 458 MET cc_start: 0.8034 (mtp) cc_final: 0.7713 (mtp) REVERT: B 459 ARG cc_start: 0.8682 (mmp-170) cc_final: 0.8111 (mmp-170) REVERT: B 485 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.8046 (mp0) REVERT: B 530 ARG cc_start: 0.9033 (mtm180) cc_final: 0.8706 (mtm110) REVERT: C 296 MET cc_start: 0.8308 (ppp) cc_final: 0.7584 (ppp) REVERT: C 306 MET cc_start: 0.8674 (mmp) cc_final: 0.8379 (mmp) REVERT: C 365 LEU cc_start: 0.9504 (OUTLIER) cc_final: 0.9266 (mt) REVERT: C 392 VAL cc_start: 0.9320 (OUTLIER) cc_final: 0.8906 (m) REVERT: C 488 ASP cc_start: 0.8270 (m-30) cc_final: 0.7871 (m-30) REVERT: C 505 ASP cc_start: 0.9145 (m-30) cc_final: 0.8910 (m-30) REVERT: C 553 ARG cc_start: 0.9140 (ptm160) cc_final: 0.8817 (ptm160) REVERT: D 163 MET cc_start: 0.8967 (OUTLIER) cc_final: 0.8748 (ttm) REVERT: D 232 MET cc_start: 0.8618 (tpt) cc_final: 0.8337 (tpt) REVERT: D 294 MET cc_start: 0.8674 (mmm) cc_final: 0.8454 (mmm) REVERT: D 485 MET cc_start: 0.8946 (ppp) cc_final: 0.8103 (ppp) REVERT: E 163 MET cc_start: 0.8033 (tmm) cc_final: 0.7726 (tmm) REVERT: E 228 MET cc_start: 0.8560 (mpp) cc_final: 0.8001 (mpp) REVERT: E 396 MET cc_start: 0.8910 (ttm) cc_final: 0.8178 (ttp) REVERT: E 425 ASP cc_start: 0.8808 (m-30) cc_final: 0.8531 (m-30) REVERT: E 485 MET cc_start: 0.8522 (mtp) cc_final: 0.8110 (mtm) REVERT: F 124 ARG cc_start: 0.8931 (OUTLIER) cc_final: 0.8572 (mtp85) REVERT: F 294 MET cc_start: 0.8775 (mmm) cc_final: 0.8206 (mmm) REVERT: F 396 MET cc_start: 0.8746 (ttt) cc_final: 0.8443 (ttt) REVERT: H 14 MET cc_start: 0.8761 (tmm) cc_final: 0.8209 (tmm) REVERT: H 27 GLN cc_start: 0.8923 (OUTLIER) cc_final: 0.8392 (mp10) REVERT: H 112 TYR cc_start: 0.7804 (t80) cc_final: 0.7428 (t80) REVERT: H 192 ASP cc_start: 0.8346 (t0) cc_final: 0.8082 (t0) REVERT: I 72 MET cc_start: 0.8590 (tpp) cc_final: 0.8138 (tpp) REVERT: I 76 MET cc_start: 0.8800 (mmm) cc_final: 0.8205 (mmp) REVERT: I 132 MET cc_start: 0.8162 (mmt) cc_final: 0.7735 (mmm) REVERT: J 121 LEU cc_start: 0.9519 (OUTLIER) cc_final: 0.9129 (tp) REVERT: K 208 MET cc_start: 0.9353 (mmm) cc_final: 0.9052 (mmm) REVERT: L 6 LYS cc_start: 0.9319 (mptp) cc_final: 0.9072 (tppt) REVERT: L 15 ASP cc_start: 0.9087 (p0) cc_final: 0.8780 (p0) REVERT: L 54 GLN cc_start: 0.8927 (tp-100) cc_final: 0.8678 (tp-100) REVERT: L 90 GLU cc_start: 0.7936 (pt0) cc_final: 0.7703 (pt0) REVERT: L 112 MET cc_start: 0.8188 (ppp) cc_final: 0.7768 (ppp) REVERT: O 87 TYR cc_start: 0.9025 (OUTLIER) cc_final: 0.8265 (t80) REVERT: O 93 ASP cc_start: 0.9149 (OUTLIER) cc_final: 0.8758 (p0) REVERT: O 105 ASP cc_start: 0.8547 (t0) cc_final: 0.8335 (p0) REVERT: Q 62 PHE cc_start: 0.8186 (OUTLIER) cc_final: 0.7671 (t80) REVERT: Q 98 ILE cc_start: 0.8047 (OUTLIER) cc_final: 0.7738 (mm) REVERT: Q 155 MET cc_start: 0.9018 (mmp) cc_final: 0.8570 (mmp) REVERT: R 32 CYS cc_start: 0.8083 (OUTLIER) cc_final: 0.7805 (t) REVERT: R 33 MET cc_start: 0.8866 (tpt) cc_final: 0.8449 (tpp) REVERT: R 122 TRP cc_start: 0.9008 (OUTLIER) cc_final: 0.8649 (t-100) REVERT: R 139 TYR cc_start: 0.8504 (t80) cc_final: 0.8117 (t80) REVERT: R 197 TYR cc_start: 0.5170 (OUTLIER) cc_final: 0.4559 (t80) REVERT: S 103 MET cc_start: 0.7053 (tpp) cc_final: 0.6531 (tpp) REVERT: S 188 MET cc_start: 0.8981 (mtm) cc_final: 0.8551 (mtp) REVERT: S 225 LEU cc_start: 0.9293 (OUTLIER) cc_final: 0.9075 (tt) REVERT: U 345 TYR cc_start: 0.8859 (m-80) cc_final: 0.8590 (m-10) REVERT: U 365 HIS cc_start: 0.8894 (OUTLIER) cc_final: 0.7663 (m170) REVERT: a 61 MET cc_start: 0.9064 (mmm) cc_final: 0.8813 (mmm) REVERT: a 381 TYR cc_start: 0.9253 (t80) cc_final: 0.8981 (t80) REVERT: a 423 MET cc_start: 0.9545 (OUTLIER) cc_final: 0.9097 (tmm) REVERT: a 431 LEU cc_start: 0.9623 (OUTLIER) cc_final: 0.9403 (mt) REVERT: a 484 MET cc_start: 0.8092 (ttm) cc_final: 0.7452 (tpp) REVERT: a 550 MET cc_start: 0.9044 (mmp) cc_final: 0.8633 (mmm) REVERT: a 745 LEU cc_start: 0.9596 (OUTLIER) cc_final: 0.9317 (mt) REVERT: a 795 GLU cc_start: 0.9159 (OUTLIER) cc_final: 0.8884 (tt0) REVERT: b 70 TYR cc_start: 0.9209 (p90) cc_final: 0.8836 (p90) REVERT: b 98 GLU cc_start: 0.9104 (mm-30) cc_final: 0.8704 (mm-30) REVERT: b 175 LYS cc_start: 0.8788 (ptpp) cc_final: 0.8484 (pttt) REVERT: c 345 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.8301 (mp0) REVERT: c 434 PHE cc_start: 0.9044 (OUTLIER) cc_final: 0.8621 (t80) REVERT: c 438 ILE cc_start: 0.9125 (mm) cc_final: 0.8874 (mm) REVERT: d 129 CYS cc_start: 0.8753 (m) cc_final: 0.8447 (m) REVERT: d 145 GLN cc_start: 0.8011 (OUTLIER) cc_final: 0.6924 (mm110) REVERT: d 176 MET cc_start: 0.8524 (tmm) cc_final: 0.8006 (tmm) REVERT: d 213 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.7840 (mm-30) REVERT: e 17 TRP cc_start: 0.8974 (m100) cc_final: 0.8172 (m100) REVERT: e 49 TYR cc_start: 0.8926 (t80) cc_final: 0.8643 (t80) REVERT: e 75 TYR cc_start: 0.7756 (m-10) cc_final: 0.7547 (m-10) REVERT: f 25 MET cc_start: 0.8983 (ttt) cc_final: 0.8600 (tpp) REVERT: f 28 MET cc_start: 0.9087 (mmm) cc_final: 0.8665 (mmm) REVERT: f 46 PHE cc_start: 0.9026 (p90) cc_final: 0.8801 (p90) REVERT: g 47 MET cc_start: 0.8068 (mmm) cc_final: 0.7749 (mmp) REVERT: g 54 LYS cc_start: 0.9452 (tttt) cc_final: 0.9149 (tttp) REVERT: g 115 ASP cc_start: 0.8286 (OUTLIER) cc_final: 0.7983 (t70) REVERT: g 144 TYR cc_start: 0.8914 (m-80) cc_final: 0.8243 (m-80) REVERT: h 23 MET cc_start: 0.8464 (tpp) cc_final: 0.7956 (tpp) REVERT: h 32 TYR cc_start: 0.9026 (t80) cc_final: 0.8790 (t80) REVERT: h 36 LYS cc_start: 0.8304 (mppt) cc_final: 0.7476 (mmtm) REVERT: h 61 MET cc_start: 0.9000 (mtt) cc_final: 0.8649 (mmm) REVERT: h 82 GLU cc_start: 0.8893 (OUTLIER) cc_final: 0.8592 (tp30) REVERT: h 126 ARG cc_start: 0.8699 (OUTLIER) cc_final: 0.8312 (mtm110) REVERT: h 131 MET cc_start: 0.9160 (ttp) cc_final: 0.8882 (ttp) REVERT: i 23 MET cc_start: 0.9083 (tpt) cc_final: 0.8691 (tpp) REVERT: i 53 MET cc_start: 0.8950 (mmt) cc_final: 0.8732 (mmm) REVERT: i 68 TYR cc_start: 0.8100 (m-10) cc_final: 0.7784 (m-80) REVERT: i 115 ASP cc_start: 0.8918 (t0) cc_final: 0.8649 (m-30) REVERT: j 23 MET cc_start: 0.9212 (tmm) cc_final: 0.8739 (tmm) REVERT: j 36 LYS cc_start: 0.8925 (mmtm) cc_final: 0.8712 (mmtm) REVERT: j 61 MET cc_start: 0.8909 (OUTLIER) cc_final: 0.8669 (ptm) REVERT: j 68 TYR cc_start: 0.8978 (m-10) cc_final: 0.8704 (m-80) REVERT: j 143 LEU cc_start: 0.9360 (OUTLIER) cc_final: 0.9098 (tt) REVERT: j 155 LYS cc_start: 0.9185 (tttp) cc_final: 0.8805 (tttt) REVERT: k 32 TYR cc_start: 0.8948 (t80) cc_final: 0.8156 (t80) REVERT: k 54 LYS cc_start: 0.9533 (tttt) cc_final: 0.9236 (tttt) REVERT: k 68 TYR cc_start: 0.8849 (m-10) cc_final: 0.8619 (m-10) REVERT: k 123 GLN cc_start: 0.9227 (mm-40) cc_final: 0.8983 (mm-40) REVERT: k 144 TYR cc_start: 0.9347 (m-10) cc_final: 0.9128 (m-10) REVERT: l 13 PHE cc_start: 0.9600 (t80) cc_final: 0.8766 (t80) REVERT: l 17 MET cc_start: 0.9025 (tpp) cc_final: 0.8604 (ptt) REVERT: l 23 MET cc_start: 0.9486 (tpp) cc_final: 0.8839 (tpp) REVERT: l 54 LYS cc_start: 0.9140 (ptpp) cc_final: 0.8734 (ptpp) REVERT: l 68 TYR cc_start: 0.8742 (m-10) cc_final: 0.8518 (m-10) REVERT: l 115 ASP cc_start: 0.8480 (OUTLIER) cc_final: 0.7667 (m-30) REVERT: l 119 ARG cc_start: 0.8287 (mmt-90) cc_final: 0.7992 (mmt-90) REVERT: l 131 MET cc_start: 0.9168 (tmm) cc_final: 0.8776 (tmm) REVERT: m 13 PHE cc_start: 0.8991 (t80) cc_final: 0.8664 (t80) REVERT: m 17 MET cc_start: 0.8926 (mmp) cc_final: 0.8550 (mmp) REVERT: m 44 MET cc_start: 0.8183 (mmp) cc_final: 0.7759 (mmm) REVERT: m 61 MET cc_start: 0.9186 (OUTLIER) cc_final: 0.8575 (mmm) REVERT: m 70 LEU cc_start: 0.9539 (OUTLIER) cc_final: 0.9065 (mt) REVERT: m 78 ASN cc_start: 0.9046 (p0) cc_final: 0.8823 (p0) REVERT: m 123 GLN cc_start: 0.8963 (mt0) cc_final: 0.8369 (mm-40) REVERT: n 13 PHE cc_start: 0.9336 (t80) cc_final: 0.8892 (t80) REVERT: n 14 PHE cc_start: 0.9122 (m-80) cc_final: 0.8848 (m-80) REVERT: n 17 MET cc_start: 0.9114 (mmp) cc_final: 0.8595 (mmp) REVERT: n 36 LYS cc_start: 0.8793 (ttmt) cc_final: 0.7848 (ttmm) REVERT: n 48 ARG cc_start: 0.8806 (mtp85) cc_final: 0.8421 (mtp85) REVERT: n 115 ASP cc_start: 0.8890 (t0) cc_final: 0.8221 (t0) REVERT: n 123 GLN cc_start: 0.8985 (OUTLIER) cc_final: 0.8482 (mm110) REVERT: o 36 LYS cc_start: 0.9103 (mmtt) cc_final: 0.8860 (mmtp) REVERT: o 44 MET cc_start: 0.9067 (mmp) cc_final: 0.8706 (mmt) REVERT: o 47 MET cc_start: 0.8889 (tmm) cc_final: 0.8639 (tmm) REVERT: o 119 ARG cc_start: 0.8808 (mtp85) cc_final: 0.8476 (mtp85) REVERT: o 123 GLN cc_start: 0.9313 (mp10) cc_final: 0.9009 (mp10) REVERT: o 131 MET cc_start: 0.9472 (OUTLIER) cc_final: 0.9254 (ttm) REVERT: p 303 ASP cc_start: 0.9254 (p0) cc_final: 0.9024 (p0) REVERT: p 342 ARG cc_start: 0.9019 (ttp80) cc_final: 0.8770 (ttp80) REVERT: p 343 MET cc_start: 0.7141 (mtt) cc_final: 0.6764 (mtt) outliers start: 188 outliers final: 104 residues processed: 738 average time/residue: 0.6714 time to fit residues: 844.5071 Evaluate side-chains 706 residues out of total 7883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 563 time to evaluate : 6.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 HIS Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 419 ASP Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 163 LYS Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain B residue 296 MET Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 359 ARG Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 485 GLU Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 392 VAL Chi-restraints excluded: chain C residue 514 LEU Chi-restraints excluded: chain C residue 579 TYR Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 163 MET Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 327 THR Chi-restraints excluded: chain D residue 338 ARG Chi-restraints excluded: chain D residue 353 ASP Chi-restraints excluded: chain D residue 407 LYS Chi-restraints excluded: chain D residue 466 SER Chi-restraints excluded: chain E residue 293 ASP Chi-restraints excluded: chain F residue 124 ARG Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain F residue 228 MET Chi-restraints excluded: chain F residue 315 ARG Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain H residue 27 GLN Chi-restraints excluded: chain H residue 85 GLN Chi-restraints excluded: chain H residue 86 ASN Chi-restraints excluded: chain H residue 113 HIS Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 121 LEU Chi-restraints excluded: chain H residue 193 GLU Chi-restraints excluded: chain I residue 159 THR Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain J residue 191 LYS Chi-restraints excluded: chain J residue 192 VAL Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain L residue 35 ASN Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 65 LEU Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain M residue 110 ILE Chi-restraints excluded: chain N residue 93 ASP Chi-restraints excluded: chain O residue 87 TYR Chi-restraints excluded: chain O residue 93 ASP Chi-restraints excluded: chain Q residue 62 PHE Chi-restraints excluded: chain Q residue 98 ILE Chi-restraints excluded: chain R residue 32 CYS Chi-restraints excluded: chain R residue 51 ASP Chi-restraints excluded: chain R residue 122 TRP Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain R residue 166 TYR Chi-restraints excluded: chain R residue 197 TYR Chi-restraints excluded: chain S residue 225 LEU Chi-restraints excluded: chain U residue 264 HIS Chi-restraints excluded: chain U residue 365 HIS Chi-restraints excluded: chain U residue 380 HIS Chi-restraints excluded: chain U residue 406 MET Chi-restraints excluded: chain a residue 366 LYS Chi-restraints excluded: chain a residue 385 THR Chi-restraints excluded: chain a residue 423 MET Chi-restraints excluded: chain a residue 431 LEU Chi-restraints excluded: chain a residue 556 SER Chi-restraints excluded: chain a residue 745 LEU Chi-restraints excluded: chain a residue 776 LEU Chi-restraints excluded: chain a residue 795 GLU Chi-restraints excluded: chain a residue 805 ARG Chi-restraints excluded: chain b residue 28 ILE Chi-restraints excluded: chain b residue 30 ASP Chi-restraints excluded: chain b residue 34 ARG Chi-restraints excluded: chain b residue 82 LYS Chi-restraints excluded: chain b residue 88 THR Chi-restraints excluded: chain c residue 287 LEU Chi-restraints excluded: chain c residue 325 ILE Chi-restraints excluded: chain c residue 339 PHE Chi-restraints excluded: chain c residue 340 THR Chi-restraints excluded: chain c residue 345 GLU Chi-restraints excluded: chain c residue 377 ASN Chi-restraints excluded: chain c residue 407 THR Chi-restraints excluded: chain c residue 434 PHE Chi-restraints excluded: chain d residue 20 VAL Chi-restraints excluded: chain d residue 63 SER Chi-restraints excluded: chain d residue 110 ILE Chi-restraints excluded: chain d residue 145 GLN Chi-restraints excluded: chain d residue 149 GLU Chi-restraints excluded: chain d residue 213 GLU Chi-restraints excluded: chain e residue 39 THR Chi-restraints excluded: chain f residue 78 LEU Chi-restraints excluded: chain g residue 99 VAL Chi-restraints excluded: chain g residue 115 ASP Chi-restraints excluded: chain g residue 148 VAL Chi-restraints excluded: chain h residue 81 THR Chi-restraints excluded: chain h residue 82 GLU Chi-restraints excluded: chain h residue 126 ARG Chi-restraints excluded: chain h residue 140 VAL Chi-restraints excluded: chain j residue 61 MET Chi-restraints excluded: chain j residue 143 LEU Chi-restraints excluded: chain l residue 48 ARG Chi-restraints excluded: chain l residue 59 VAL Chi-restraints excluded: chain l residue 110 ILE Chi-restraints excluded: chain l residue 115 ASP Chi-restraints excluded: chain m residue 46 VAL Chi-restraints excluded: chain m residue 61 MET Chi-restraints excluded: chain m residue 70 LEU Chi-restraints excluded: chain m residue 81 THR Chi-restraints excluded: chain m residue 97 LEU Chi-restraints excluded: chain m residue 118 VAL Chi-restraints excluded: chain m residue 139 GLU Chi-restraints excluded: chain n residue 10 TYR Chi-restraints excluded: chain n residue 64 ILE Chi-restraints excluded: chain n residue 67 ILE Chi-restraints excluded: chain n residue 82 GLU Chi-restraints excluded: chain n residue 123 GLN Chi-restraints excluded: chain o residue 67 ILE Chi-restraints excluded: chain o residue 118 VAL Chi-restraints excluded: chain o residue 131 MET Chi-restraints excluded: chain o residue 146 LEU Chi-restraints excluded: chain p residue 322 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 923 random chunks: chunk 829 optimal weight: 4.9990 chunk 631 optimal weight: 9.9990 chunk 435 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 400 optimal weight: 8.9990 chunk 563 optimal weight: 30.0000 chunk 842 optimal weight: 0.9990 chunk 892 optimal weight: 7.9990 chunk 440 optimal weight: 20.0000 chunk 798 optimal weight: 9.9990 chunk 240 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 603 GLN ** B 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 123 ASN ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 484 GLN ** E 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 152 GLN ** L 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 50 GLN S 21 GLN S 40 ASN ** a 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 69826 Z= 0.297 Angle : 0.597 10.032 94787 Z= 0.311 Chirality : 0.041 0.243 11071 Planarity : 0.004 0.053 12263 Dihedral : 6.076 86.496 10098 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.99 % Favored : 95.95 % Rotamer: Outliers : 2.87 % Allowed : 12.40 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 9244 helix: 2.18 (0.07), residues: 5553 sheet: -1.03 (0.19), residues: 742 loop : -0.75 (0.12), residues: 2949 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 567 HIS 0.012 0.001 HIS L 81 PHE 0.046 0.002 PHE S 151 TYR 0.055 0.002 TYR m 144 ARG 0.008 0.000 ARG E 315 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18488 Ramachandran restraints generated. 9244 Oldfield, 0 Emsley, 9244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18488 Ramachandran restraints generated. 9244 Oldfield, 0 Emsley, 9244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 793 residues out of total 7883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 604 time to evaluate : 6.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 368 MET cc_start: 0.8451 (tpp) cc_final: 0.7989 (tpp) REVERT: A 429 VAL cc_start: 0.9193 (OUTLIER) cc_final: 0.8935 (t) REVERT: B 163 LYS cc_start: 0.8910 (OUTLIER) cc_final: 0.8404 (mmtm) REVERT: B 296 MET cc_start: 0.8917 (OUTLIER) cc_final: 0.8528 (pmm) REVERT: B 306 MET cc_start: 0.8738 (mmm) cc_final: 0.8378 (mmm) REVERT: B 318 MET cc_start: 0.8336 (mtt) cc_final: 0.8085 (mtp) REVERT: B 344 VAL cc_start: 0.9313 (OUTLIER) cc_final: 0.9032 (m) REVERT: B 346 MET cc_start: 0.8340 (tmm) cc_final: 0.7740 (tmm) REVERT: B 359 ARG cc_start: 0.9008 (OUTLIER) cc_final: 0.8426 (ttm170) REVERT: B 458 MET cc_start: 0.8119 (mtp) cc_final: 0.7632 (mtp) REVERT: B 459 ARG cc_start: 0.8762 (mmp-170) cc_final: 0.8229 (mmp-170) REVERT: B 485 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.8038 (mp0) REVERT: B 530 ARG cc_start: 0.9020 (mtm180) cc_final: 0.8665 (mtm110) REVERT: C 296 MET cc_start: 0.8291 (ppp) cc_final: 0.7679 (ppp) REVERT: C 306 MET cc_start: 0.8557 (mmp) cc_final: 0.8298 (mmm) REVERT: C 365 LEU cc_start: 0.9522 (OUTLIER) cc_final: 0.9294 (mt) REVERT: C 392 VAL cc_start: 0.9301 (OUTLIER) cc_final: 0.8984 (p) REVERT: C 488 ASP cc_start: 0.8256 (m-30) cc_final: 0.7874 (m-30) REVERT: C 505 ASP cc_start: 0.9174 (m-30) cc_final: 0.8948 (m-30) REVERT: D 232 MET cc_start: 0.8629 (tpt) cc_final: 0.8382 (tpt) REVERT: D 331 ARG cc_start: 0.8870 (OUTLIER) cc_final: 0.6872 (mtm180) REVERT: D 407 LYS cc_start: 0.9124 (OUTLIER) cc_final: 0.8827 (mtmm) REVERT: E 163 MET cc_start: 0.8103 (tmm) cc_final: 0.7815 (tmm) REVERT: E 228 MET cc_start: 0.8504 (mpp) cc_final: 0.8008 (mpp) REVERT: E 321 MET cc_start: 0.8746 (tpp) cc_final: 0.8506 (tpp) REVERT: E 396 MET cc_start: 0.8807 (OUTLIER) cc_final: 0.7921 (ttp) REVERT: E 425 ASP cc_start: 0.8814 (m-30) cc_final: 0.8556 (m-30) REVERT: E 485 MET cc_start: 0.8497 (mtp) cc_final: 0.8134 (mtm) REVERT: E 493 MET cc_start: 0.8918 (tpp) cc_final: 0.8478 (tpp) REVERT: F 124 ARG cc_start: 0.9019 (OUTLIER) cc_final: 0.8481 (mmm-85) REVERT: H 14 MET cc_start: 0.8763 (tmm) cc_final: 0.8210 (tmm) REVERT: H 112 TYR cc_start: 0.7828 (t80) cc_final: 0.7458 (t80) REVERT: H 192 ASP cc_start: 0.8335 (t0) cc_final: 0.8103 (t0) REVERT: I 72 MET cc_start: 0.8596 (tpp) cc_final: 0.8091 (tpp) REVERT: I 76 MET cc_start: 0.8793 (mmm) cc_final: 0.8275 (mmp) REVERT: I 132 MET cc_start: 0.8152 (mmt) cc_final: 0.7710 (mmm) REVERT: J 121 LEU cc_start: 0.9530 (OUTLIER) cc_final: 0.9156 (tp) REVERT: J 207 MET cc_start: 0.8440 (tpt) cc_final: 0.8014 (mmm) REVERT: K 192 VAL cc_start: 0.9251 (OUTLIER) cc_final: 0.8963 (p) REVERT: K 208 MET cc_start: 0.9338 (mmm) cc_final: 0.9090 (mmm) REVERT: L 15 ASP cc_start: 0.9076 (p0) cc_final: 0.8814 (p0) REVERT: L 54 GLN cc_start: 0.8911 (tp-100) cc_final: 0.8664 (tp-100) REVERT: L 69 TYR cc_start: 0.8485 (p90) cc_final: 0.8185 (p90) REVERT: L 90 GLU cc_start: 0.7858 (pt0) cc_final: 0.7552 (pt0) REVERT: L 112 MET cc_start: 0.7970 (ppp) cc_final: 0.7390 (ppp) REVERT: O 93 ASP cc_start: 0.9131 (OUTLIER) cc_final: 0.8878 (p0) REVERT: Q 62 PHE cc_start: 0.8122 (OUTLIER) cc_final: 0.7526 (t80) REVERT: Q 98 ILE cc_start: 0.7989 (OUTLIER) cc_final: 0.7764 (mm) REVERT: Q 155 MET cc_start: 0.8975 (mmp) cc_final: 0.8564 (mmp) REVERT: R 32 CYS cc_start: 0.8041 (OUTLIER) cc_final: 0.7789 (t) REVERT: R 33 MET cc_start: 0.8889 (tpt) cc_final: 0.8489 (tpp) REVERT: R 122 TRP cc_start: 0.9008 (OUTLIER) cc_final: 0.8683 (t-100) REVERT: R 139 TYR cc_start: 0.8546 (t80) cc_final: 0.8190 (t80) REVERT: R 197 TYR cc_start: 0.4837 (OUTLIER) cc_final: 0.4281 (t80) REVERT: S 103 MET cc_start: 0.7105 (tpp) cc_final: 0.6523 (tpp) REVERT: S 188 MET cc_start: 0.8979 (mtm) cc_final: 0.8539 (mtp) REVERT: U 345 TYR cc_start: 0.8825 (m-80) cc_final: 0.8571 (m-10) REVERT: U 365 HIS cc_start: 0.8909 (OUTLIER) cc_final: 0.7772 (m170) REVERT: a 94 MET cc_start: 0.8023 (tpt) cc_final: 0.7694 (tmm) REVERT: a 381 TYR cc_start: 0.9262 (t80) cc_final: 0.9050 (t80) REVERT: a 406 MET cc_start: 0.9104 (mtt) cc_final: 0.8715 (mtm) REVERT: a 423 MET cc_start: 0.9516 (OUTLIER) cc_final: 0.9074 (tmm) REVERT: a 449 ILE cc_start: 0.9135 (OUTLIER) cc_final: 0.8930 (mm) REVERT: a 484 MET cc_start: 0.8124 (ttm) cc_final: 0.7731 (tpp) REVERT: a 550 MET cc_start: 0.9014 (mmp) cc_final: 0.8636 (mmm) REVERT: a 745 LEU cc_start: 0.9564 (OUTLIER) cc_final: 0.9320 (mt) REVERT: a 795 GLU cc_start: 0.9149 (OUTLIER) cc_final: 0.8854 (tt0) REVERT: b 70 TYR cc_start: 0.9199 (p90) cc_final: 0.8785 (p90) REVERT: b 98 GLU cc_start: 0.9145 (mm-30) cc_final: 0.8931 (mm-30) REVERT: b 175 LYS cc_start: 0.8759 (ptpp) cc_final: 0.8434 (pttt) REVERT: b 202 LYS cc_start: 0.8557 (tppt) cc_final: 0.8354 (tppt) REVERT: c 434 PHE cc_start: 0.9019 (OUTLIER) cc_final: 0.8647 (t80) REVERT: c 438 ILE cc_start: 0.9113 (mm) cc_final: 0.8864 (mm) REVERT: c 445 MET cc_start: 0.8850 (mmp) cc_final: 0.8324 (mmm) REVERT: d 124 GLU cc_start: 0.8949 (OUTLIER) cc_final: 0.8230 (pt0) REVERT: d 129 CYS cc_start: 0.8772 (m) cc_final: 0.8407 (m) REVERT: d 145 GLN cc_start: 0.8067 (OUTLIER) cc_final: 0.7048 (mm-40) REVERT: d 176 MET cc_start: 0.8608 (tmm) cc_final: 0.8053 (tmm) REVERT: e 17 TRP cc_start: 0.8986 (m100) cc_final: 0.8177 (m100) REVERT: e 49 TYR cc_start: 0.8949 (t80) cc_final: 0.8627 (t80) REVERT: e 75 TYR cc_start: 0.7697 (m-10) cc_final: 0.7443 (m-10) REVERT: f 25 MET cc_start: 0.8967 (ttt) cc_final: 0.8563 (tpp) REVERT: f 28 MET cc_start: 0.9099 (mmm) cc_final: 0.8671 (mmm) REVERT: f 46 PHE cc_start: 0.8996 (p90) cc_final: 0.8775 (p90) REVERT: g 17 MET cc_start: 0.8795 (tmm) cc_final: 0.8551 (tmm) REVERT: g 47 MET cc_start: 0.8106 (mmm) cc_final: 0.7724 (mmp) REVERT: g 54 LYS cc_start: 0.9429 (tttt) cc_final: 0.9103 (tttp) REVERT: g 115 ASP cc_start: 0.8259 (OUTLIER) cc_final: 0.7982 (t70) REVERT: g 144 TYR cc_start: 0.8904 (m-80) cc_final: 0.8475 (m-80) REVERT: h 23 MET cc_start: 0.8526 (tpp) cc_final: 0.8040 (tpp) REVERT: h 32 TYR cc_start: 0.9073 (t80) cc_final: 0.8753 (t80) REVERT: h 36 LYS cc_start: 0.8189 (mppt) cc_final: 0.7696 (mmtm) REVERT: h 82 GLU cc_start: 0.8907 (OUTLIER) cc_final: 0.8599 (tp30) REVERT: h 115 ASP cc_start: 0.8451 (t0) cc_final: 0.7856 (t0) REVERT: h 119 ARG cc_start: 0.8095 (mtm-85) cc_final: 0.7401 (mtm-85) REVERT: h 123 GLN cc_start: 0.9418 (mp10) cc_final: 0.9175 (mp10) REVERT: h 131 MET cc_start: 0.9147 (ttp) cc_final: 0.8852 (ttp) REVERT: i 23 MET cc_start: 0.9073 (tpt) cc_final: 0.8671 (tpp) REVERT: i 53 MET cc_start: 0.8935 (mmt) cc_final: 0.8725 (mmm) REVERT: i 68 TYR cc_start: 0.8106 (m-10) cc_final: 0.7848 (m-80) REVERT: i 115 ASP cc_start: 0.8906 (t0) cc_final: 0.8628 (m-30) REVERT: i 127 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8332 (mp) REVERT: j 23 MET cc_start: 0.9167 (tmm) cc_final: 0.8652 (tmm) REVERT: j 36 LYS cc_start: 0.8939 (mmtm) cc_final: 0.8621 (mmtt) REVERT: j 61 MET cc_start: 0.8902 (OUTLIER) cc_final: 0.8658 (ptm) REVERT: j 68 TYR cc_start: 0.9023 (m-10) cc_final: 0.8470 (m-10) REVERT: j 131 MET cc_start: 0.8831 (tmm) cc_final: 0.8482 (ppp) REVERT: j 143 LEU cc_start: 0.9371 (OUTLIER) cc_final: 0.9136 (mt) REVERT: j 155 LYS cc_start: 0.9200 (tttp) cc_final: 0.8822 (tttt) REVERT: k 32 TYR cc_start: 0.8948 (t80) cc_final: 0.8155 (t80) REVERT: k 68 TYR cc_start: 0.8841 (m-10) cc_final: 0.8616 (m-10) REVERT: k 123 GLN cc_start: 0.9215 (mm-40) cc_final: 0.8965 (mm-40) REVERT: k 144 TYR cc_start: 0.9342 (m-10) cc_final: 0.9109 (m-10) REVERT: l 17 MET cc_start: 0.9029 (tpp) cc_final: 0.8621 (ptt) REVERT: l 23 MET cc_start: 0.9452 (tpp) cc_final: 0.8641 (tpp) REVERT: l 32 TYR cc_start: 0.8551 (t80) cc_final: 0.8118 (t80) REVERT: l 54 LYS cc_start: 0.9105 (ptpp) cc_final: 0.8762 (ptpp) REVERT: l 68 TYR cc_start: 0.8706 (m-10) cc_final: 0.8435 (m-10) REVERT: l 115 ASP cc_start: 0.8383 (OUTLIER) cc_final: 0.8143 (m-30) REVERT: l 119 ARG cc_start: 0.8281 (mmt-90) cc_final: 0.8006 (mmt-90) REVERT: l 131 MET cc_start: 0.9133 (tmm) cc_final: 0.8671 (tmm) REVERT: m 13 PHE cc_start: 0.9005 (t80) cc_final: 0.8746 (t80) REVERT: m 17 MET cc_start: 0.8960 (mmp) cc_final: 0.8588 (mmp) REVERT: m 47 MET cc_start: 0.8796 (mmt) cc_final: 0.8469 (mmm) REVERT: m 61 MET cc_start: 0.9091 (OUTLIER) cc_final: 0.8340 (mmm) REVERT: m 78 ASN cc_start: 0.9033 (p0) cc_final: 0.8823 (p0) REVERT: m 115 ASP cc_start: 0.8607 (p0) cc_final: 0.8312 (p0) REVERT: m 119 ARG cc_start: 0.9515 (mmt90) cc_final: 0.9035 (mmm160) REVERT: m 123 GLN cc_start: 0.8957 (mt0) cc_final: 0.8357 (mm-40) REVERT: n 13 PHE cc_start: 0.9374 (t80) cc_final: 0.9019 (t80) REVERT: n 17 MET cc_start: 0.9106 (mmp) cc_final: 0.8585 (mmp) REVERT: n 36 LYS cc_start: 0.8866 (ttmt) cc_final: 0.7847 (ttmm) REVERT: n 48 ARG cc_start: 0.8785 (mtp85) cc_final: 0.8470 (mtp85) REVERT: n 115 ASP cc_start: 0.8858 (t0) cc_final: 0.8321 (t0) REVERT: n 123 GLN cc_start: 0.8943 (mp-120) cc_final: 0.8515 (mm110) REVERT: n 143 LEU cc_start: 0.9355 (tp) cc_final: 0.9144 (tp) REVERT: o 44 MET cc_start: 0.9076 (mmp) cc_final: 0.8697 (mmt) REVERT: o 47 MET cc_start: 0.8826 (tmm) cc_final: 0.8516 (tmm) REVERT: o 61 MET cc_start: 0.8637 (OUTLIER) cc_final: 0.8368 (mtt) REVERT: o 108 PHE cc_start: 0.8942 (m-10) cc_final: 0.8571 (t80) REVERT: o 123 GLN cc_start: 0.9316 (mp10) cc_final: 0.9020 (mp10) REVERT: o 131 MET cc_start: 0.9506 (OUTLIER) cc_final: 0.9294 (ttm) REVERT: o 139 GLU cc_start: 0.9052 (tm-30) cc_final: 0.8631 (tp30) REVERT: p 301 ASN cc_start: 0.8575 (OUTLIER) cc_final: 0.7818 (p0) REVERT: p 303 ASP cc_start: 0.9268 (p0) cc_final: 0.8903 (p0) REVERT: p 342 ARG cc_start: 0.9051 (ttp80) cc_final: 0.8783 (ttp80) outliers start: 189 outliers final: 107 residues processed: 751 average time/residue: 0.6964 time to fit residues: 899.2252 Evaluate side-chains 714 residues out of total 7883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 569 time to evaluate : 6.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 HIS Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 419 ASP Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 163 LYS Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain B residue 296 MET Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 359 ARG Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 485 GLU Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 392 VAL Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 514 LEU Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 327 THR Chi-restraints excluded: chain D residue 331 ARG Chi-restraints excluded: chain D residue 338 ARG Chi-restraints excluded: chain D residue 353 ASP Chi-restraints excluded: chain D residue 407 LYS Chi-restraints excluded: chain D residue 455 ASN Chi-restraints excluded: chain D residue 466 SER Chi-restraints excluded: chain E residue 266 ILE Chi-restraints excluded: chain E residue 293 ASP Chi-restraints excluded: chain E residue 328 ILE Chi-restraints excluded: chain E residue 396 MET Chi-restraints excluded: chain F residue 100 ASP Chi-restraints excluded: chain F residue 124 ARG Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain F residue 228 MET Chi-restraints excluded: chain F residue 315 ARG Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain H residue 27 GLN Chi-restraints excluded: chain H residue 85 GLN Chi-restraints excluded: chain H residue 86 ASN Chi-restraints excluded: chain H residue 113 HIS Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 121 LEU Chi-restraints excluded: chain H residue 193 GLU Chi-restraints excluded: chain I residue 159 THR Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain J residue 191 LYS Chi-restraints excluded: chain J residue 192 VAL Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain K residue 192 VAL Chi-restraints excluded: chain L residue 35 ASN Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 65 LEU Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain N residue 93 ASP Chi-restraints excluded: chain O residue 93 ASP Chi-restraints excluded: chain Q residue 62 PHE Chi-restraints excluded: chain Q residue 98 ILE Chi-restraints excluded: chain R residue 32 CYS Chi-restraints excluded: chain R residue 51 ASP Chi-restraints excluded: chain R residue 122 TRP Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain R residue 197 TYR Chi-restraints excluded: chain U residue 264 HIS Chi-restraints excluded: chain U residue 365 HIS Chi-restraints excluded: chain U residue 380 HIS Chi-restraints excluded: chain a residue 363 THR Chi-restraints excluded: chain a residue 366 LYS Chi-restraints excluded: chain a residue 385 THR Chi-restraints excluded: chain a residue 423 MET Chi-restraints excluded: chain a residue 449 ILE Chi-restraints excluded: chain a residue 556 SER Chi-restraints excluded: chain a residue 745 LEU Chi-restraints excluded: chain a residue 776 LEU Chi-restraints excluded: chain a residue 795 GLU Chi-restraints excluded: chain a residue 805 ARG Chi-restraints excluded: chain b residue 24 ILE Chi-restraints excluded: chain b residue 25 CYS Chi-restraints excluded: chain b residue 28 ILE Chi-restraints excluded: chain b residue 30 ASP Chi-restraints excluded: chain b residue 34 ARG Chi-restraints excluded: chain b residue 82 LYS Chi-restraints excluded: chain b residue 88 THR Chi-restraints excluded: chain c residue 287 LEU Chi-restraints excluded: chain c residue 325 ILE Chi-restraints excluded: chain c residue 339 PHE Chi-restraints excluded: chain c residue 340 THR Chi-restraints excluded: chain c residue 365 ILE Chi-restraints excluded: chain c residue 407 THR Chi-restraints excluded: chain c residue 434 PHE Chi-restraints excluded: chain d residue 20 VAL Chi-restraints excluded: chain d residue 63 SER Chi-restraints excluded: chain d residue 110 ILE Chi-restraints excluded: chain d residue 124 GLU Chi-restraints excluded: chain d residue 141 VAL Chi-restraints excluded: chain d residue 145 GLN Chi-restraints excluded: chain d residue 149 GLU Chi-restraints excluded: chain d residue 165 GLN Chi-restraints excluded: chain d residue 213 GLU Chi-restraints excluded: chain d residue 304 LEU Chi-restraints excluded: chain e residue 28 ILE Chi-restraints excluded: chain f residue 78 LEU Chi-restraints excluded: chain g residue 99 VAL Chi-restraints excluded: chain g residue 115 ASP Chi-restraints excluded: chain g residue 148 VAL Chi-restraints excluded: chain h residue 81 THR Chi-restraints excluded: chain h residue 82 GLU Chi-restraints excluded: chain h residue 140 VAL Chi-restraints excluded: chain i residue 127 LEU Chi-restraints excluded: chain j residue 61 MET Chi-restraints excluded: chain j residue 143 LEU Chi-restraints excluded: chain k residue 118 VAL Chi-restraints excluded: chain l residue 48 ARG Chi-restraints excluded: chain l residue 110 ILE Chi-restraints excluded: chain l residue 115 ASP Chi-restraints excluded: chain m residue 46 VAL Chi-restraints excluded: chain m residue 61 MET Chi-restraints excluded: chain m residue 81 THR Chi-restraints excluded: chain m residue 97 LEU Chi-restraints excluded: chain m residue 118 VAL Chi-restraints excluded: chain m residue 139 GLU Chi-restraints excluded: chain n residue 10 TYR Chi-restraints excluded: chain n residue 64 ILE Chi-restraints excluded: chain o residue 61 MET Chi-restraints excluded: chain o residue 67 ILE Chi-restraints excluded: chain o residue 118 VAL Chi-restraints excluded: chain o residue 131 MET Chi-restraints excluded: chain o residue 146 LEU Chi-restraints excluded: chain p residue 301 ASN Chi-restraints excluded: chain p residue 322 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 923 random chunks: chunk 743 optimal weight: 9.9990 chunk 506 optimal weight: 10.0000 chunk 12 optimal weight: 3.9990 chunk 664 optimal weight: 7.9990 chunk 368 optimal weight: 7.9990 chunk 761 optimal weight: 5.9990 chunk 616 optimal weight: 0.9980 chunk 1 optimal weight: 5.9990 chunk 455 optimal weight: 7.9990 chunk 800 optimal weight: 9.9990 chunk 225 optimal weight: 5.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 317 ASN ** C 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 484 GLN ** D 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 344 GLN ** E 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 86 ASN H 152 GLN ** L 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 390 ASN ** a 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 165 GLN d 302 ASN ** m 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.099 69826 Z= 0.394 Angle : 0.648 11.027 94787 Z= 0.336 Chirality : 0.042 0.229 11071 Planarity : 0.004 0.056 12263 Dihedral : 5.912 79.692 10085 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.49 % Favored : 95.48 % Rotamer: Outliers : 3.28 % Allowed : 13.05 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 1.44 (0.09), residues: 9244 helix: 2.14 (0.07), residues: 5551 sheet: -1.10 (0.19), residues: 727 loop : -0.79 (0.12), residues: 2966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP A 567 HIS 0.013 0.001 HIS L 81 PHE 0.027 0.002 PHE g 14 TYR 0.052 0.002 TYR m 144 ARG 0.008 0.001 ARG n 119 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18488 Ramachandran restraints generated. 9244 Oldfield, 0 Emsley, 9244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18488 Ramachandran restraints generated. 9244 Oldfield, 0 Emsley, 9244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 795 residues out of total 7883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 216 poor density : 579 time to evaluate : 6.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 368 MET cc_start: 0.8471 (tpp) cc_final: 0.8003 (tpp) REVERT: A 429 VAL cc_start: 0.9264 (OUTLIER) cc_final: 0.9019 (t) REVERT: A 567 TRP cc_start: 0.7992 (t60) cc_final: 0.7665 (t60) REVERT: B 163 LYS cc_start: 0.8928 (OUTLIER) cc_final: 0.8407 (mmtm) REVERT: B 296 MET cc_start: 0.8865 (OUTLIER) cc_final: 0.8542 (pmm) REVERT: B 306 MET cc_start: 0.8759 (mmm) cc_final: 0.8386 (mmm) REVERT: B 318 MET cc_start: 0.8191 (mtt) cc_final: 0.7892 (mtp) REVERT: B 344 VAL cc_start: 0.9349 (OUTLIER) cc_final: 0.9098 (m) REVERT: B 346 MET cc_start: 0.8380 (tmm) cc_final: 0.7859 (tmm) REVERT: B 359 ARG cc_start: 0.9048 (OUTLIER) cc_final: 0.8443 (ttm170) REVERT: B 450 TRP cc_start: 0.8912 (m-90) cc_final: 0.8705 (m-90) REVERT: B 458 MET cc_start: 0.8123 (mtp) cc_final: 0.7459 (mtp) REVERT: B 459 ARG cc_start: 0.8795 (mmp-170) cc_final: 0.8276 (mmp-170) REVERT: B 485 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.8070 (mp0) REVERT: C 296 MET cc_start: 0.8321 (ppp) cc_final: 0.7665 (ppp) REVERT: C 347 MET cc_start: 0.7672 (tmm) cc_final: 0.7431 (tmm) REVERT: C 365 LEU cc_start: 0.9568 (OUTLIER) cc_final: 0.9332 (mt) REVERT: C 392 VAL cc_start: 0.9316 (OUTLIER) cc_final: 0.8936 (m) REVERT: C 488 ASP cc_start: 0.8228 (m-30) cc_final: 0.7861 (m-30) REVERT: C 505 ASP cc_start: 0.9133 (m-30) cc_final: 0.8900 (m-30) REVERT: D 232 MET cc_start: 0.8683 (tpt) cc_final: 0.8463 (tpt) REVERT: D 331 ARG cc_start: 0.9025 (OUTLIER) cc_final: 0.7025 (mtm180) REVERT: D 350 MET cc_start: 0.8142 (mtp) cc_final: 0.7817 (mtp) REVERT: E 140 MET cc_start: 0.8265 (ttm) cc_final: 0.7985 (ttp) REVERT: E 163 MET cc_start: 0.8157 (tmm) cc_final: 0.7796 (tmm) REVERT: E 228 MET cc_start: 0.8519 (mpp) cc_final: 0.7983 (mpp) REVERT: E 396 MET cc_start: 0.8835 (OUTLIER) cc_final: 0.7898 (ttp) REVERT: E 425 ASP cc_start: 0.8784 (m-30) cc_final: 0.8534 (m-30) REVERT: E 485 MET cc_start: 0.8482 (mtp) cc_final: 0.8080 (mtm) REVERT: E 493 MET cc_start: 0.8990 (tpp) cc_final: 0.8429 (tpp) REVERT: F 289 VAL cc_start: 0.9544 (OUTLIER) cc_final: 0.9320 (m) REVERT: F 321 MET cc_start: 0.8652 (ttm) cc_final: 0.8371 (ttm) REVERT: H 8 GLU cc_start: 0.7395 (mp0) cc_final: 0.7114 (mp0) REVERT: H 14 MET cc_start: 0.8756 (tmm) cc_final: 0.8220 (tmm) REVERT: H 112 TYR cc_start: 0.7822 (t80) cc_final: 0.7451 (t80) REVERT: I 72 MET cc_start: 0.8627 (tpp) cc_final: 0.8046 (tpp) REVERT: I 76 MET cc_start: 0.8819 (mmm) cc_final: 0.8261 (mmp) REVERT: I 132 MET cc_start: 0.8212 (mmt) cc_final: 0.7781 (mmm) REVERT: J 132 MET cc_start: 0.8202 (OUTLIER) cc_final: 0.7595 (mmt) REVERT: K 208 MET cc_start: 0.9357 (mmm) cc_final: 0.9152 (mmm) REVERT: L 6 LYS cc_start: 0.9336 (mptp) cc_final: 0.8732 (mmmm) REVERT: L 15 ASP cc_start: 0.9090 (p0) cc_final: 0.8841 (p0) REVERT: L 47 GLU cc_start: 0.8974 (OUTLIER) cc_final: 0.8713 (pm20) REVERT: L 54 GLN cc_start: 0.8918 (tp-100) cc_final: 0.8652 (tp-100) REVERT: L 90 GLU cc_start: 0.7750 (pt0) cc_final: 0.7404 (pt0) REVERT: L 112 MET cc_start: 0.7962 (ppp) cc_final: 0.7380 (ppp) REVERT: O 87 TYR cc_start: 0.9036 (OUTLIER) cc_final: 0.8168 (t80) REVERT: Q 62 PHE cc_start: 0.8212 (OUTLIER) cc_final: 0.7589 (t80) REVERT: Q 98 ILE cc_start: 0.8151 (OUTLIER) cc_final: 0.7926 (mm) REVERT: Q 155 MET cc_start: 0.8951 (mmp) cc_final: 0.8571 (mmp) REVERT: R 32 CYS cc_start: 0.8059 (OUTLIER) cc_final: 0.7805 (t) REVERT: R 33 MET cc_start: 0.8886 (tpt) cc_final: 0.8411 (tpp) REVERT: R 122 TRP cc_start: 0.9016 (OUTLIER) cc_final: 0.8573 (t-100) REVERT: R 139 TYR cc_start: 0.8632 (t80) cc_final: 0.8315 (t80) REVERT: R 168 ILE cc_start: 0.9374 (OUTLIER) cc_final: 0.9079 (tp) REVERT: R 197 TYR cc_start: 0.4327 (OUTLIER) cc_final: 0.3844 (t80) REVERT: S 103 MET cc_start: 0.7146 (tpp) cc_final: 0.6545 (tpp) REVERT: S 188 MET cc_start: 0.8947 (mtm) cc_final: 0.8516 (mtp) REVERT: S 214 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.7551 (mp0) REVERT: U 345 TYR cc_start: 0.8838 (m-80) cc_final: 0.8594 (m-10) REVERT: U 365 HIS cc_start: 0.8897 (OUTLIER) cc_final: 0.7760 (m170) REVERT: a 381 TYR cc_start: 0.9256 (t80) cc_final: 0.9029 (t80) REVERT: a 406 MET cc_start: 0.9039 (mtt) cc_final: 0.8815 (mtm) REVERT: a 423 MET cc_start: 0.9490 (OUTLIER) cc_final: 0.9045 (tmm) REVERT: a 449 ILE cc_start: 0.9152 (OUTLIER) cc_final: 0.8939 (mm) REVERT: a 484 MET cc_start: 0.8166 (ttm) cc_final: 0.7762 (tpp) REVERT: a 550 MET cc_start: 0.9078 (mmt) cc_final: 0.8657 (mmm) REVERT: a 580 MET cc_start: 0.8197 (ppp) cc_final: 0.7876 (ppp) REVERT: a 651 MET cc_start: 0.8163 (mpp) cc_final: 0.7897 (mpp) REVERT: b 82 LYS cc_start: 0.9199 (OUTLIER) cc_final: 0.8742 (ptpp) REVERT: b 98 GLU cc_start: 0.9172 (mm-30) cc_final: 0.8946 (mm-30) REVERT: b 175 LYS cc_start: 0.8730 (ptpp) cc_final: 0.8416 (pttt) REVERT: b 180 GLU cc_start: 0.9184 (OUTLIER) cc_final: 0.8750 (pm20) REVERT: b 202 LYS cc_start: 0.8641 (tppt) cc_final: 0.8422 (tppt) REVERT: c 434 PHE cc_start: 0.9036 (OUTLIER) cc_final: 0.8667 (t80) REVERT: c 438 ILE cc_start: 0.9144 (mm) cc_final: 0.8903 (mm) REVERT: c 443 LEU cc_start: 0.9686 (OUTLIER) cc_final: 0.9475 (mm) REVERT: c 445 MET cc_start: 0.8875 (mmp) cc_final: 0.8408 (mmm) REVERT: d 124 GLU cc_start: 0.8971 (OUTLIER) cc_final: 0.8273 (pt0) REVERT: d 129 CYS cc_start: 0.8756 (m) cc_final: 0.8402 (m) REVERT: d 176 MET cc_start: 0.8573 (tmm) cc_final: 0.8017 (tmm) REVERT: e 75 TYR cc_start: 0.7736 (m-10) cc_final: 0.7520 (m-10) REVERT: f 25 MET cc_start: 0.8950 (ttt) cc_final: 0.8574 (tpp) REVERT: f 28 MET cc_start: 0.9114 (mmm) cc_final: 0.8687 (mmm) REVERT: f 46 PHE cc_start: 0.8994 (p90) cc_final: 0.8786 (p90) REVERT: g 17 MET cc_start: 0.8798 (tmm) cc_final: 0.8488 (tmm) REVERT: g 47 MET cc_start: 0.8159 (mmm) cc_final: 0.7801 (mmm) REVERT: g 54 LYS cc_start: 0.9478 (tttt) cc_final: 0.9231 (tttp) REVERT: g 115 ASP cc_start: 0.8307 (OUTLIER) cc_final: 0.8009 (t70) REVERT: g 144 TYR cc_start: 0.8920 (m-80) cc_final: 0.8508 (m-80) REVERT: h 23 MET cc_start: 0.8550 (tpp) cc_final: 0.7993 (tpp) REVERT: h 32 TYR cc_start: 0.9108 (t80) cc_final: 0.8719 (t80) REVERT: h 36 LYS cc_start: 0.8373 (mppt) cc_final: 0.7805 (mmtm) REVERT: h 68 TYR cc_start: 0.8716 (m-10) cc_final: 0.8383 (m-10) REVERT: h 82 GLU cc_start: 0.8941 (OUTLIER) cc_final: 0.8626 (tp30) REVERT: h 115 ASP cc_start: 0.8404 (t0) cc_final: 0.7777 (t0) REVERT: h 119 ARG cc_start: 0.8065 (mtm-85) cc_final: 0.7425 (mtm-85) REVERT: h 126 ARG cc_start: 0.8766 (OUTLIER) cc_final: 0.8404 (mtm110) REVERT: h 131 MET cc_start: 0.9170 (ttp) cc_final: 0.8876 (ttp) REVERT: i 53 MET cc_start: 0.8990 (mmt) cc_final: 0.8763 (mmm) REVERT: i 68 TYR cc_start: 0.8140 (m-10) cc_final: 0.7854 (m-80) REVERT: i 115 ASP cc_start: 0.8914 (t0) cc_final: 0.8635 (m-30) REVERT: i 127 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8348 (mp) REVERT: j 23 MET cc_start: 0.9175 (tmm) cc_final: 0.8658 (tmm) REVERT: j 36 LYS cc_start: 0.9003 (mmtm) cc_final: 0.8558 (mmtt) REVERT: j 61 MET cc_start: 0.8937 (OUTLIER) cc_final: 0.8674 (ptm) REVERT: j 68 TYR cc_start: 0.9039 (m-10) cc_final: 0.8755 (m-10) REVERT: k 16 VAL cc_start: 0.9065 (OUTLIER) cc_final: 0.8812 (p) REVERT: k 32 TYR cc_start: 0.8935 (t80) cc_final: 0.8123 (t80) REVERT: k 68 TYR cc_start: 0.8844 (m-10) cc_final: 0.8640 (m-10) REVERT: k 123 GLN cc_start: 0.9265 (mm-40) cc_final: 0.9026 (mm-40) REVERT: k 131 MET cc_start: 0.8925 (tpt) cc_final: 0.8674 (tpp) REVERT: k 144 TYR cc_start: 0.9321 (m-10) cc_final: 0.9101 (m-10) REVERT: l 17 MET cc_start: 0.9056 (tpp) cc_final: 0.8683 (ptt) REVERT: l 23 MET cc_start: 0.9460 (tpp) cc_final: 0.8727 (tpp) REVERT: l 44 MET cc_start: 0.8952 (ppp) cc_final: 0.8750 (ppp) REVERT: l 54 LYS cc_start: 0.9068 (ptpp) cc_final: 0.8721 (ptpp) REVERT: l 119 ARG cc_start: 0.8414 (mmt-90) cc_final: 0.8188 (mmt-90) REVERT: l 131 MET cc_start: 0.9109 (tmm) cc_final: 0.8634 (tmm) REVERT: m 13 PHE cc_start: 0.9003 (t80) cc_final: 0.8762 (t80) REVERT: m 17 MET cc_start: 0.8961 (mmp) cc_final: 0.8571 (mmp) REVERT: m 23 MET cc_start: 0.9048 (ppp) cc_final: 0.8824 (ppp) REVERT: m 47 MET cc_start: 0.8711 (mmt) cc_final: 0.8373 (mmm) REVERT: m 61 MET cc_start: 0.9138 (OUTLIER) cc_final: 0.8428 (mmm) REVERT: m 78 ASN cc_start: 0.9074 (p0) cc_final: 0.8874 (p0) REVERT: m 123 GLN cc_start: 0.8914 (mt0) cc_final: 0.8363 (mm-40) REVERT: n 13 PHE cc_start: 0.9382 (t80) cc_final: 0.9021 (t80) REVERT: n 17 MET cc_start: 0.9123 (mmp) cc_final: 0.8613 (mmp) REVERT: n 36 LYS cc_start: 0.8897 (ttmt) cc_final: 0.7890 (ttmm) REVERT: n 47 MET cc_start: 0.9152 (tpp) cc_final: 0.8832 (tpp) REVERT: n 48 ARG cc_start: 0.8786 (mtp85) cc_final: 0.8359 (mtp85) REVERT: n 115 ASP cc_start: 0.8876 (t0) cc_final: 0.8263 (t0) REVERT: n 123 GLN cc_start: 0.9003 (mp-120) cc_final: 0.8663 (mp10) REVERT: o 44 MET cc_start: 0.9107 (mmp) cc_final: 0.8740 (mmt) REVERT: o 47 MET cc_start: 0.8834 (tmm) cc_final: 0.8580 (tmm) REVERT: o 61 MET cc_start: 0.8610 (OUTLIER) cc_final: 0.8343 (mtt) REVERT: o 87 TYR cc_start: 0.8915 (t80) cc_final: 0.8526 (t80) REVERT: o 108 PHE cc_start: 0.8947 (m-10) cc_final: 0.8580 (t80) REVERT: o 115 ASP cc_start: 0.9204 (t0) cc_final: 0.8946 (m-30) REVERT: o 123 GLN cc_start: 0.9311 (mp10) cc_final: 0.9019 (mp10) REVERT: o 131 MET cc_start: 0.9477 (OUTLIER) cc_final: 0.9263 (ttm) REVERT: o 139 GLU cc_start: 0.9036 (tm-30) cc_final: 0.8741 (tp30) REVERT: p 301 ASN cc_start: 0.8620 (OUTLIER) cc_final: 0.7891 (p0) REVERT: p 303 ASP cc_start: 0.9290 (p0) cc_final: 0.8923 (p0) REVERT: p 342 ARG cc_start: 0.8982 (ttp80) cc_final: 0.8514 (ttp80) outliers start: 216 outliers final: 130 residues processed: 749 average time/residue: 0.6576 time to fit residues: 840.6647 Evaluate side-chains 727 residues out of total 7883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 558 time to evaluate : 6.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 HIS Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 419 ASP Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 450 TRP Chi-restraints excluded: chain A residue 487 GLU Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 163 LYS Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain B residue 296 MET Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 359 ARG Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 485 GLU Chi-restraints excluded: chain B residue 574 MET Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 171 ARG Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 392 VAL Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 514 LEU Chi-restraints excluded: chain C residue 518 ASP Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 327 THR Chi-restraints excluded: chain D residue 331 ARG Chi-restraints excluded: chain D residue 338 ARG Chi-restraints excluded: chain D residue 353 ASP Chi-restraints excluded: chain D residue 455 ASN Chi-restraints excluded: chain D residue 466 SER Chi-restraints excluded: chain E residue 293 ASP Chi-restraints excluded: chain E residue 328 ILE Chi-restraints excluded: chain E residue 396 MET Chi-restraints excluded: chain F residue 100 ASP Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 228 MET Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain H residue 27 GLN Chi-restraints excluded: chain H residue 85 GLN Chi-restraints excluded: chain H residue 86 ASN Chi-restraints excluded: chain H residue 113 HIS Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 121 LEU Chi-restraints excluded: chain H residue 193 GLU Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain I residue 159 THR Chi-restraints excluded: chain I residue 221 ASN Chi-restraints excluded: chain J residue 132 MET Chi-restraints excluded: chain J residue 191 LYS Chi-restraints excluded: chain J residue 192 VAL Chi-restraints excluded: chain L residue 25 ILE Chi-restraints excluded: chain L residue 35 ASN Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain L residue 47 GLU Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 65 LEU Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain N residue 93 ASP Chi-restraints excluded: chain O residue 87 TYR Chi-restraints excluded: chain O residue 93 ASP Chi-restraints excluded: chain Q residue 62 PHE Chi-restraints excluded: chain Q residue 98 ILE Chi-restraints excluded: chain R residue 32 CYS Chi-restraints excluded: chain R residue 51 ASP Chi-restraints excluded: chain R residue 122 TRP Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain R residue 168 ILE Chi-restraints excluded: chain R residue 197 TYR Chi-restraints excluded: chain S residue 214 GLU Chi-restraints excluded: chain U residue 264 HIS Chi-restraints excluded: chain U residue 365 HIS Chi-restraints excluded: chain U residue 380 HIS Chi-restraints excluded: chain U residue 406 MET Chi-restraints excluded: chain a residue 363 THR Chi-restraints excluded: chain a residue 366 LYS Chi-restraints excluded: chain a residue 385 THR Chi-restraints excluded: chain a residue 423 MET Chi-restraints excluded: chain a residue 449 ILE Chi-restraints excluded: chain a residue 452 LEU Chi-restraints excluded: chain a residue 530 LEU Chi-restraints excluded: chain a residue 556 SER Chi-restraints excluded: chain a residue 745 LEU Chi-restraints excluded: chain a residue 776 LEU Chi-restraints excluded: chain a residue 795 GLU Chi-restraints excluded: chain b residue 24 ILE Chi-restraints excluded: chain b residue 25 CYS Chi-restraints excluded: chain b residue 28 ILE Chi-restraints excluded: chain b residue 30 ASP Chi-restraints excluded: chain b residue 34 ARG Chi-restraints excluded: chain b residue 82 LYS Chi-restraints excluded: chain b residue 180 GLU Chi-restraints excluded: chain c residue 287 LEU Chi-restraints excluded: chain c residue 325 ILE Chi-restraints excluded: chain c residue 339 PHE Chi-restraints excluded: chain c residue 340 THR Chi-restraints excluded: chain c residue 365 ILE Chi-restraints excluded: chain c residue 377 ASN Chi-restraints excluded: chain c residue 407 THR Chi-restraints excluded: chain c residue 434 PHE Chi-restraints excluded: chain c residue 443 LEU Chi-restraints excluded: chain d residue 20 VAL Chi-restraints excluded: chain d residue 63 SER Chi-restraints excluded: chain d residue 110 ILE Chi-restraints excluded: chain d residue 124 GLU Chi-restraints excluded: chain d residue 141 VAL Chi-restraints excluded: chain d residue 145 GLN Chi-restraints excluded: chain d residue 149 GLU Chi-restraints excluded: chain d residue 165 GLN Chi-restraints excluded: chain d residue 304 LEU Chi-restraints excluded: chain e residue 28 ILE Chi-restraints excluded: chain f residue 78 LEU Chi-restraints excluded: chain g residue 99 VAL Chi-restraints excluded: chain g residue 115 ASP Chi-restraints excluded: chain g residue 123 GLN Chi-restraints excluded: chain g residue 148 VAL Chi-restraints excluded: chain h residue 81 THR Chi-restraints excluded: chain h residue 82 GLU Chi-restraints excluded: chain h residue 126 ARG Chi-restraints excluded: chain h residue 140 VAL Chi-restraints excluded: chain i residue 127 LEU Chi-restraints excluded: chain j residue 24 VAL Chi-restraints excluded: chain j residue 61 MET Chi-restraints excluded: chain k residue 16 VAL Chi-restraints excluded: chain k residue 118 VAL Chi-restraints excluded: chain l residue 48 ARG Chi-restraints excluded: chain l residue 110 ILE Chi-restraints excluded: chain m residue 28 LEU Chi-restraints excluded: chain m residue 46 VAL Chi-restraints excluded: chain m residue 61 MET Chi-restraints excluded: chain m residue 81 THR Chi-restraints excluded: chain m residue 97 LEU Chi-restraints excluded: chain m residue 118 VAL Chi-restraints excluded: chain m residue 139 GLU Chi-restraints excluded: chain n residue 10 TYR Chi-restraints excluded: chain n residue 64 ILE Chi-restraints excluded: chain n residue 82 GLU Chi-restraints excluded: chain n residue 121 THR Chi-restraints excluded: chain o residue 61 MET Chi-restraints excluded: chain o residue 67 ILE Chi-restraints excluded: chain o residue 118 VAL Chi-restraints excluded: chain o residue 131 MET Chi-restraints excluded: chain p residue 301 ASN Chi-restraints excluded: chain p residue 322 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 923 random chunks: chunk 300 optimal weight: 0.6980 chunk 803 optimal weight: 6.9990 chunk 176 optimal weight: 6.9990 chunk 523 optimal weight: 10.0000 chunk 220 optimal weight: 0.8980 chunk 893 optimal weight: 1.9990 chunk 741 optimal weight: 3.9990 chunk 413 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 295 optimal weight: 1.9990 chunk 468 optimal weight: 40.0000 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 349 ASN C 468 HIS E 344 GLN ** E 409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 86 ASN H 152 GLN ** L 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 14 GLN ** a 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 165 GLN d 302 ASN ** m 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 69826 Z= 0.211 Angle : 0.586 12.076 94787 Z= 0.299 Chirality : 0.040 0.271 11071 Planarity : 0.004 0.054 12263 Dihedral : 5.556 78.938 10064 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.85 % Favored : 96.12 % Rotamer: Outliers : 2.53 % Allowed : 14.24 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.99 % 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: 1.59 (0.09), residues: 9244 helix: 2.26 (0.07), residues: 5536 sheet: -1.03 (0.19), residues: 741 loop : -0.72 (0.12), residues: 2967 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 567 HIS 0.008 0.001 HIS L 81 PHE 0.021 0.001 PHE g 14 TYR 0.054 0.001 TYR m 144 ARG 0.011 0.000 ARG n 126 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18488 Ramachandran restraints generated. 9244 Oldfield, 0 Emsley, 9244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18488 Ramachandran restraints generated. 9244 Oldfield, 0 Emsley, 9244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 762 residues out of total 7883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 595 time to evaluate : 6.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 368 MET cc_start: 0.8435 (tpp) cc_final: 0.7920 (tpp) REVERT: A 429 VAL cc_start: 0.9223 (OUTLIER) cc_final: 0.8949 (t) REVERT: B 296 MET cc_start: 0.8816 (OUTLIER) cc_final: 0.8509 (pmm) REVERT: B 306 MET cc_start: 0.8736 (mmm) cc_final: 0.8340 (mmm) REVERT: B 318 MET cc_start: 0.8280 (mtt) cc_final: 0.8008 (mtp) REVERT: B 344 VAL cc_start: 0.9332 (OUTLIER) cc_final: 0.9117 (m) REVERT: B 346 MET cc_start: 0.8327 (tmm) cc_final: 0.7900 (tmm) REVERT: B 359 ARG cc_start: 0.9004 (OUTLIER) cc_final: 0.8414 (ttm170) REVERT: B 458 MET cc_start: 0.8143 (mtp) cc_final: 0.7424 (mtp) REVERT: B 459 ARG cc_start: 0.8741 (mmp-170) cc_final: 0.8260 (mmp-170) REVERT: B 485 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7996 (mp0) REVERT: B 530 ARG cc_start: 0.9018 (mtm180) cc_final: 0.8642 (mtm110) REVERT: C 296 MET cc_start: 0.8351 (ppp) cc_final: 0.7693 (ppp) REVERT: C 347 MET cc_start: 0.7703 (tmm) cc_final: 0.7491 (tmm) REVERT: C 365 LEU cc_start: 0.9529 (OUTLIER) cc_final: 0.9311 (mt) REVERT: C 368 MET cc_start: 0.8393 (tpp) cc_final: 0.8153 (tpp) REVERT: C 392 VAL cc_start: 0.9282 (OUTLIER) cc_final: 0.8977 (p) REVERT: C 505 ASP cc_start: 0.9120 (m-30) cc_final: 0.8886 (m-30) REVERT: C 584 MET cc_start: 0.8763 (tmm) cc_final: 0.8498 (tmm) REVERT: D 232 MET cc_start: 0.8586 (tpt) cc_final: 0.8326 (tpt) REVERT: D 331 ARG cc_start: 0.8931 (OUTLIER) cc_final: 0.8365 (mtp180) REVERT: D 350 MET cc_start: 0.8092 (mtp) cc_final: 0.7799 (mtp) REVERT: E 163 MET cc_start: 0.8153 (tmm) cc_final: 0.7783 (tmm) REVERT: E 228 MET cc_start: 0.8447 (mpp) cc_final: 0.8107 (mpp) REVERT: E 321 MET cc_start: 0.8710 (tpp) cc_final: 0.8366 (tpp) REVERT: E 396 MET cc_start: 0.8822 (OUTLIER) cc_final: 0.7927 (ttp) REVERT: E 425 ASP cc_start: 0.8744 (m-30) cc_final: 0.8487 (m-30) REVERT: E 485 MET cc_start: 0.8418 (mtp) cc_final: 0.8076 (mtm) REVERT: E 493 MET cc_start: 0.8933 (tpp) cc_final: 0.8304 (tpp) REVERT: F 289 VAL cc_start: 0.9530 (OUTLIER) cc_final: 0.9309 (m) REVERT: F 321 MET cc_start: 0.8623 (ttm) cc_final: 0.8304 (ttm) REVERT: H 8 GLU cc_start: 0.7334 (mp0) cc_final: 0.7033 (mp0) REVERT: H 14 MET cc_start: 0.8665 (tmm) cc_final: 0.8119 (tmm) REVERT: H 112 TYR cc_start: 0.7786 (t80) cc_final: 0.7439 (t80) REVERT: I 72 MET cc_start: 0.8577 (tpp) cc_final: 0.7962 (tpp) REVERT: I 76 MET cc_start: 0.8775 (mmm) cc_final: 0.8038 (mmp) REVERT: I 132 MET cc_start: 0.8207 (mmt) cc_final: 0.7781 (mmm) REVERT: J 132 MET cc_start: 0.8196 (OUTLIER) cc_final: 0.7593 (mmt) REVERT: K 82 LYS cc_start: 0.9184 (OUTLIER) cc_final: 0.8946 (pttt) REVERT: K 192 VAL cc_start: 0.9261 (OUTLIER) cc_final: 0.8958 (p) REVERT: K 208 MET cc_start: 0.9325 (mmm) cc_final: 0.9104 (mmm) REVERT: L 6 LYS cc_start: 0.9317 (mptp) cc_final: 0.8609 (mmmm) REVERT: L 15 ASP cc_start: 0.9037 (p0) cc_final: 0.8760 (p0) REVERT: L 36 PHE cc_start: 0.9378 (p90) cc_final: 0.9110 (p90) REVERT: L 54 GLN cc_start: 0.8888 (tp-100) cc_final: 0.8611 (tp-100) REVERT: L 59 GLU cc_start: 0.8890 (mp0) cc_final: 0.8407 (pp20) REVERT: L 90 GLU cc_start: 0.7791 (pt0) cc_final: 0.7456 (pt0) REVERT: Q 62 PHE cc_start: 0.8291 (OUTLIER) cc_final: 0.7561 (t80) REVERT: Q 155 MET cc_start: 0.8949 (mmp) cc_final: 0.8570 (mmp) REVERT: R 33 MET cc_start: 0.8912 (tpt) cc_final: 0.8485 (tpp) REVERT: R 122 TRP cc_start: 0.9007 (OUTLIER) cc_final: 0.8523 (t-100) REVERT: R 139 TYR cc_start: 0.8522 (t80) cc_final: 0.8222 (t80) REVERT: R 168 ILE cc_start: 0.9347 (OUTLIER) cc_final: 0.9058 (tp) REVERT: R 197 TYR cc_start: 0.4052 (OUTLIER) cc_final: 0.3618 (t80) REVERT: S 103 MET cc_start: 0.7090 (tpp) cc_final: 0.6467 (tpp) REVERT: S 188 MET cc_start: 0.8952 (mtm) cc_final: 0.8528 (mtp) REVERT: U 345 TYR cc_start: 0.8808 (m-80) cc_final: 0.8565 (m-10) REVERT: a 406 MET cc_start: 0.9039 (mtt) cc_final: 0.8717 (mtm) REVERT: a 423 MET cc_start: 0.9509 (OUTLIER) cc_final: 0.9062 (tmm) REVERT: a 439 MET cc_start: 0.8733 (mpp) cc_final: 0.8429 (mpp) REVERT: a 453 MET cc_start: 0.9010 (ptm) cc_final: 0.8763 (ptm) REVERT: a 484 MET cc_start: 0.8129 (ttm) cc_final: 0.7732 (tpp) REVERT: a 550 MET cc_start: 0.9067 (mmt) cc_final: 0.8643 (mmm) REVERT: a 580 MET cc_start: 0.8149 (ppp) cc_final: 0.7907 (ppp) REVERT: a 745 LEU cc_start: 0.9528 (OUTLIER) cc_final: 0.9212 (mp) REVERT: b 82 LYS cc_start: 0.9098 (OUTLIER) cc_final: 0.8707 (ptpp) REVERT: b 98 GLU cc_start: 0.9134 (mm-30) cc_final: 0.8840 (mm-30) REVERT: b 175 LYS cc_start: 0.8729 (ptpp) cc_final: 0.8459 (pttt) REVERT: b 180 GLU cc_start: 0.9162 (OUTLIER) cc_final: 0.8682 (pm20) REVERT: c 366 TYR cc_start: 0.8358 (m-80) cc_final: 0.8120 (m-80) REVERT: c 434 PHE cc_start: 0.8997 (OUTLIER) cc_final: 0.8626 (t80) REVERT: c 438 ILE cc_start: 0.9127 (mm) cc_final: 0.8884 (mm) REVERT: c 443 LEU cc_start: 0.9677 (OUTLIER) cc_final: 0.9463 (mm) REVERT: c 445 MET cc_start: 0.8825 (mmp) cc_final: 0.8334 (mmm) REVERT: d 124 GLU cc_start: 0.8988 (OUTLIER) cc_final: 0.8391 (pt0) REVERT: d 129 CYS cc_start: 0.8734 (m) cc_final: 0.8419 (m) REVERT: d 176 MET cc_start: 0.8583 (OUTLIER) cc_final: 0.8002 (tmm) REVERT: f 25 MET cc_start: 0.8951 (ttt) cc_final: 0.8560 (tpp) REVERT: f 28 MET cc_start: 0.9080 (mmm) cc_final: 0.8693 (mmm) REVERT: g 17 MET cc_start: 0.8798 (tmm) cc_final: 0.8459 (tmm) REVERT: g 47 MET cc_start: 0.8141 (mmm) cc_final: 0.7735 (mmm) REVERT: g 54 LYS cc_start: 0.9445 (tttt) cc_final: 0.8887 (tmtp) REVERT: g 115 ASP cc_start: 0.8273 (OUTLIER) cc_final: 0.7979 (t70) REVERT: g 144 TYR cc_start: 0.8818 (m-80) cc_final: 0.8318 (m-80) REVERT: h 23 MET cc_start: 0.8492 (tpp) cc_final: 0.7944 (tpp) REVERT: h 32 TYR cc_start: 0.9076 (t80) cc_final: 0.8557 (t80) REVERT: h 36 LYS cc_start: 0.8406 (mppt) cc_final: 0.7807 (mmtm) REVERT: h 68 TYR cc_start: 0.8591 (m-10) cc_final: 0.8290 (m-10) REVERT: h 82 GLU cc_start: 0.8909 (OUTLIER) cc_final: 0.8590 (tp30) REVERT: h 115 ASP cc_start: 0.8274 (t0) cc_final: 0.7626 (t0) REVERT: h 119 ARG cc_start: 0.7879 (mtm-85) cc_final: 0.7282 (mtm-85) REVERT: h 126 ARG cc_start: 0.8689 (OUTLIER) cc_final: 0.8306 (mtm110) REVERT: h 131 MET cc_start: 0.9156 (ttp) cc_final: 0.8842 (ttp) REVERT: h 144 TYR cc_start: 0.9016 (m-10) cc_final: 0.8795 (m-10) REVERT: i 53 MET cc_start: 0.8953 (mmt) cc_final: 0.8738 (mmm) REVERT: i 115 ASP cc_start: 0.8879 (t0) cc_final: 0.8577 (m-30) REVERT: i 127 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8348 (mp) REVERT: j 23 MET cc_start: 0.9127 (tmm) cc_final: 0.8612 (tmm) REVERT: j 36 LYS cc_start: 0.8955 (mmtm) cc_final: 0.8456 (mmtt) REVERT: j 44 MET cc_start: 0.8627 (tmm) cc_final: 0.8263 (tmm) REVERT: j 61 MET cc_start: 0.8900 (OUTLIER) cc_final: 0.8648 (ptm) REVERT: j 68 TYR cc_start: 0.9014 (m-10) cc_final: 0.8427 (m-10) REVERT: j 143 LEU cc_start: 0.9349 (tp) cc_final: 0.9126 (mt) REVERT: k 16 VAL cc_start: 0.9065 (OUTLIER) cc_final: 0.8811 (p) REVERT: k 32 TYR cc_start: 0.8875 (t80) cc_final: 0.8124 (t80) REVERT: k 123 GLN cc_start: 0.9202 (mm-40) cc_final: 0.8940 (mm-40) REVERT: k 131 MET cc_start: 0.8946 (tpt) cc_final: 0.8635 (tpt) REVERT: l 17 MET cc_start: 0.9032 (tpp) cc_final: 0.8682 (ptt) REVERT: l 23 MET cc_start: 0.9433 (tpp) cc_final: 0.8709 (tpp) REVERT: l 32 TYR cc_start: 0.8389 (t80) cc_final: 0.8009 (t80) REVERT: l 54 LYS cc_start: 0.9028 (ptpp) cc_final: 0.8670 (ptpp) REVERT: l 68 TYR cc_start: 0.8641 (m-10) cc_final: 0.8336 (m-10) REVERT: l 119 ARG cc_start: 0.8341 (mmt-90) cc_final: 0.8043 (mmt-90) REVERT: l 131 MET cc_start: 0.9119 (tmm) cc_final: 0.8637 (tmm) REVERT: m 13 PHE cc_start: 0.9001 (t80) cc_final: 0.8748 (t80) REVERT: m 17 MET cc_start: 0.8970 (mmp) cc_final: 0.8555 (mmp) REVERT: m 23 MET cc_start: 0.8950 (ppp) cc_final: 0.8663 (ppp) REVERT: m 47 MET cc_start: 0.8691 (mmt) cc_final: 0.8319 (mmm) REVERT: n 13 PHE cc_start: 0.9374 (t80) cc_final: 0.9031 (t80) REVERT: n 17 MET cc_start: 0.9117 (mmp) cc_final: 0.8599 (mmp) REVERT: n 36 LYS cc_start: 0.8822 (ttmt) cc_final: 0.7669 (ttmm) REVERT: n 47 MET cc_start: 0.9190 (tpp) cc_final: 0.8843 (tpp) REVERT: n 48 ARG cc_start: 0.8852 (mtp85) cc_final: 0.8594 (mtp85) REVERT: n 61 MET cc_start: 0.8660 (mtp) cc_final: 0.8169 (ttm) REVERT: n 115 ASP cc_start: 0.8778 (t0) cc_final: 0.8212 (t0) REVERT: o 44 MET cc_start: 0.9110 (mmp) cc_final: 0.8727 (mmt) REVERT: o 47 MET cc_start: 0.8818 (tmm) cc_final: 0.8562 (tmm) REVERT: o 61 MET cc_start: 0.8668 (OUTLIER) cc_final: 0.8190 (mtp) REVERT: o 108 PHE cc_start: 0.8906 (m-10) cc_final: 0.8574 (t80) REVERT: o 115 ASP cc_start: 0.9186 (t0) cc_final: 0.8928 (m-30) REVERT: o 123 GLN cc_start: 0.9298 (mp10) cc_final: 0.9005 (mp10) REVERT: o 131 MET cc_start: 0.9485 (OUTLIER) cc_final: 0.9237 (ttm) REVERT: o 139 GLU cc_start: 0.8973 (tm-30) cc_final: 0.8719 (tp30) REVERT: p 301 ASN cc_start: 0.8381 (OUTLIER) cc_final: 0.7600 (p0) REVERT: p 303 ASP cc_start: 0.9284 (p0) cc_final: 0.8861 (p0) REVERT: p 342 ARG cc_start: 0.9030 (ttp80) cc_final: 0.8735 (ttp80) outliers start: 167 outliers final: 102 residues processed: 720 average time/residue: 0.6668 time to fit residues: 818.5505 Evaluate side-chains 705 residues out of total 7883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 569 time to evaluate : 6.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 HIS Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 419 ASP Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 450 TRP Chi-restraints excluded: chain A residue 487 GLU Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 296 MET Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 359 ARG Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 485 GLU Chi-restraints excluded: chain B residue 574 MET Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 171 ARG Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 392 VAL Chi-restraints excluded: chain C residue 514 LEU Chi-restraints excluded: chain D residue 331 ARG Chi-restraints excluded: chain D residue 338 ARG Chi-restraints excluded: chain D residue 353 ASP Chi-restraints excluded: chain D residue 455 ASN Chi-restraints excluded: chain E residue 266 ILE Chi-restraints excluded: chain E residue 293 ASP Chi-restraints excluded: chain E residue 328 ILE Chi-restraints excluded: chain E residue 396 MET Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain F residue 228 MET Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain F residue 493 MET Chi-restraints excluded: chain H residue 27 GLN Chi-restraints excluded: chain H residue 85 GLN Chi-restraints excluded: chain H residue 113 HIS Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 121 LEU Chi-restraints excluded: chain H residue 193 GLU Chi-restraints excluded: chain I residue 159 THR Chi-restraints excluded: chain J residue 132 MET Chi-restraints excluded: chain J residue 191 LYS Chi-restraints excluded: chain J residue 192 VAL Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain K residue 82 LYS Chi-restraints excluded: chain K residue 192 VAL Chi-restraints excluded: chain L residue 28 LEU Chi-restraints excluded: chain L residue 35 ASN Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 65 LEU Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain N residue 93 ASP Chi-restraints excluded: chain O residue 93 ASP Chi-restraints excluded: chain Q residue 62 PHE Chi-restraints excluded: chain R residue 51 ASP Chi-restraints excluded: chain R residue 122 TRP Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain R residue 168 ILE Chi-restraints excluded: chain R residue 197 TYR Chi-restraints excluded: chain U residue 264 HIS Chi-restraints excluded: chain U residue 380 HIS Chi-restraints excluded: chain a residue 366 LYS Chi-restraints excluded: chain a residue 385 THR Chi-restraints excluded: chain a residue 423 MET Chi-restraints excluded: chain a residue 452 LEU Chi-restraints excluded: chain a residue 556 SER Chi-restraints excluded: chain a residue 745 LEU Chi-restraints excluded: chain a residue 776 LEU Chi-restraints excluded: chain a residue 795 GLU Chi-restraints excluded: chain a residue 805 ARG Chi-restraints excluded: chain b residue 28 ILE Chi-restraints excluded: chain b residue 30 ASP Chi-restraints excluded: chain b residue 34 ARG Chi-restraints excluded: chain b residue 82 LYS Chi-restraints excluded: chain b residue 180 GLU Chi-restraints excluded: chain c residue 339 PHE Chi-restraints excluded: chain c residue 340 THR Chi-restraints excluded: chain c residue 365 ILE Chi-restraints excluded: chain c residue 377 ASN Chi-restraints excluded: chain c residue 407 THR Chi-restraints excluded: chain c residue 434 PHE Chi-restraints excluded: chain c residue 443 LEU Chi-restraints excluded: chain d residue 20 VAL Chi-restraints excluded: chain d residue 63 SER Chi-restraints excluded: chain d residue 110 ILE Chi-restraints excluded: chain d residue 124 GLU Chi-restraints excluded: chain d residue 145 GLN Chi-restraints excluded: chain d residue 149 GLU Chi-restraints excluded: chain d residue 176 MET Chi-restraints excluded: chain d residue 185 LEU Chi-restraints excluded: chain d residue 304 LEU Chi-restraints excluded: chain e residue 28 ILE Chi-restraints excluded: chain g residue 99 VAL Chi-restraints excluded: chain g residue 115 ASP Chi-restraints excluded: chain g residue 148 VAL Chi-restraints excluded: chain h residue 81 THR Chi-restraints excluded: chain h residue 82 GLU Chi-restraints excluded: chain h residue 126 ARG Chi-restraints excluded: chain h residue 140 VAL Chi-restraints excluded: chain i residue 127 LEU Chi-restraints excluded: chain j residue 24 VAL Chi-restraints excluded: chain j residue 61 MET Chi-restraints excluded: chain k residue 16 VAL Chi-restraints excluded: chain k residue 118 VAL Chi-restraints excluded: chain l residue 48 ARG Chi-restraints excluded: chain l residue 110 ILE Chi-restraints excluded: chain m residue 46 VAL Chi-restraints excluded: chain m residue 81 THR Chi-restraints excluded: chain m residue 97 LEU Chi-restraints excluded: chain m residue 118 VAL Chi-restraints excluded: chain n residue 10 TYR Chi-restraints excluded: chain n residue 64 ILE Chi-restraints excluded: chain n residue 67 ILE Chi-restraints excluded: chain n residue 82 GLU Chi-restraints excluded: chain o residue 61 MET Chi-restraints excluded: chain o residue 67 ILE Chi-restraints excluded: chain o residue 118 VAL Chi-restraints excluded: chain o residue 131 MET Chi-restraints excluded: chain o residue 146 LEU Chi-restraints excluded: chain p residue 301 ASN Chi-restraints excluded: chain p residue 322 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 923 random chunks: chunk 861 optimal weight: 10.0000 chunk 100 optimal weight: 5.9990 chunk 508 optimal weight: 3.9990 chunk 652 optimal weight: 0.9990 chunk 505 optimal weight: 2.9990 chunk 751 optimal weight: 8.9990 chunk 498 optimal weight: 7.9990 chunk 889 optimal weight: 9.9990 chunk 556 optimal weight: 50.0000 chunk 542 optimal weight: 40.0000 chunk 410 optimal weight: 50.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 484 GLN ** D 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 220 ASN ** E 409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 152 GLN ** K 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 14 GLN ** a 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 69826 Z= 0.377 Angle : 0.647 13.284 94787 Z= 0.333 Chirality : 0.042 0.260 11071 Planarity : 0.004 0.055 12263 Dihedral : 5.529 80.607 10060 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 15.95 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.72 % Favored : 95.25 % Rotamer: Outliers : 2.96 % Allowed : 14.83 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.99 % 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: 9244 helix: 2.25 (0.07), residues: 5494 sheet: -1.14 (0.19), residues: 720 loop : -0.76 (0.12), residues: 3030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 567 HIS 0.011 0.001 HIS L 81 PHE 0.044 0.002 PHE A 337 TYR 0.054 0.002 TYR m 144 ARG 0.011 0.001 ARG i 126 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18488 Ramachandran restraints generated. 9244 Oldfield, 0 Emsley, 9244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18488 Ramachandran restraints generated. 9244 Oldfield, 0 Emsley, 9244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 767 residues out of total 7883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 195 poor density : 572 time to evaluate : 6.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 429 VAL cc_start: 0.9304 (OUTLIER) cc_final: 0.9038 (t) REVERT: B 163 LYS cc_start: 0.8900 (OUTLIER) cc_final: 0.8372 (mmtm) REVERT: B 296 MET cc_start: 0.8788 (OUTLIER) cc_final: 0.8536 (pmm) REVERT: B 306 MET cc_start: 0.8769 (mmm) cc_final: 0.8372 (mmm) REVERT: B 318 MET cc_start: 0.8217 (mtt) cc_final: 0.7951 (mtt) REVERT: B 344 VAL cc_start: 0.9421 (OUTLIER) cc_final: 0.9142 (m) REVERT: B 346 MET cc_start: 0.8365 (tmm) cc_final: 0.7932 (tmm) REVERT: B 359 ARG cc_start: 0.9045 (OUTLIER) cc_final: 0.8461 (ttm170) REVERT: B 458 MET cc_start: 0.8344 (mtp) cc_final: 0.7816 (mtp) REVERT: B 485 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.8054 (mp0) REVERT: C 296 MET cc_start: 0.8271 (ppp) cc_final: 0.7613 (ppp) REVERT: C 318 MET cc_start: 0.9050 (mmm) cc_final: 0.8839 (mmp) REVERT: C 347 MET cc_start: 0.7842 (tmm) cc_final: 0.7503 (tmm) REVERT: C 365 LEU cc_start: 0.9583 (OUTLIER) cc_final: 0.9358 (mt) REVERT: C 392 VAL cc_start: 0.9321 (OUTLIER) cc_final: 0.8950 (m) REVERT: C 505 ASP cc_start: 0.9121 (m-30) cc_final: 0.8900 (m-30) REVERT: D 220 ASN cc_start: 0.8802 (OUTLIER) cc_final: 0.8581 (p0) REVERT: D 331 ARG cc_start: 0.9030 (OUTLIER) cc_final: 0.7034 (mtm180) REVERT: D 350 MET cc_start: 0.8177 (mtp) cc_final: 0.7823 (mtp) REVERT: D 493 MET cc_start: 0.8980 (ppp) cc_final: 0.8362 (ppp) REVERT: E 163 MET cc_start: 0.8156 (tmm) cc_final: 0.7771 (tmm) REVERT: E 228 MET cc_start: 0.8491 (mpp) cc_final: 0.8218 (mpp) REVERT: E 321 MET cc_start: 0.8838 (tpp) cc_final: 0.8296 (tpp) REVERT: E 374 ASP cc_start: 0.8626 (t0) cc_final: 0.8375 (t0) REVERT: E 396 MET cc_start: 0.8854 (OUTLIER) cc_final: 0.7968 (ttp) REVERT: E 425 ASP cc_start: 0.8776 (m-30) cc_final: 0.8528 (m-30) REVERT: E 485 MET cc_start: 0.8470 (mtp) cc_final: 0.8047 (mtm) REVERT: E 493 MET cc_start: 0.8972 (tpp) cc_final: 0.8414 (tpp) REVERT: F 266 ILE cc_start: 0.9376 (OUTLIER) cc_final: 0.8997 (mm) REVERT: F 289 VAL cc_start: 0.9541 (OUTLIER) cc_final: 0.9316 (m) REVERT: F 321 MET cc_start: 0.8759 (ttm) cc_final: 0.8363 (ttm) REVERT: H 14 MET cc_start: 0.8654 (tmm) cc_final: 0.8121 (tmm) REVERT: H 112 TYR cc_start: 0.7819 (t80) cc_final: 0.7434 (t80) REVERT: I 72 MET cc_start: 0.8610 (tpp) cc_final: 0.7833 (tpp) REVERT: I 76 MET cc_start: 0.8827 (mmm) cc_final: 0.8117 (mmp) REVERT: I 132 MET cc_start: 0.8210 (mmt) cc_final: 0.7772 (mmm) REVERT: J 132 MET cc_start: 0.8205 (OUTLIER) cc_final: 0.7618 (mmt) REVERT: K 82 LYS cc_start: 0.9204 (OUTLIER) cc_final: 0.8697 (pptt) REVERT: L 6 LYS cc_start: 0.9336 (mptp) cc_final: 0.8634 (mmmm) REVERT: L 15 ASP cc_start: 0.9054 (p0) cc_final: 0.8804 (p0) REVERT: L 54 GLN cc_start: 0.8924 (tp-100) cc_final: 0.8654 (tp-100) REVERT: L 59 GLU cc_start: 0.8921 (mp0) cc_final: 0.8456 (pp20) REVERT: L 90 GLU cc_start: 0.7686 (pt0) cc_final: 0.6703 (pm20) REVERT: Q 62 PHE cc_start: 0.8275 (OUTLIER) cc_final: 0.7578 (t80) REVERT: Q 155 MET cc_start: 0.8977 (mmp) cc_final: 0.8571 (mmp) REVERT: R 32 CYS cc_start: 0.8064 (OUTLIER) cc_final: 0.7800 (t) REVERT: R 33 MET cc_start: 0.8894 (tpt) cc_final: 0.8436 (tpp) REVERT: R 122 TRP cc_start: 0.9011 (OUTLIER) cc_final: 0.8501 (t-100) REVERT: R 139 TYR cc_start: 0.8694 (t80) cc_final: 0.8379 (t80) REVERT: R 168 ILE cc_start: 0.9339 (OUTLIER) cc_final: 0.9056 (tp) REVERT: R 170 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.8249 (tm-30) REVERT: R 197 TYR cc_start: 0.4095 (OUTLIER) cc_final: 0.3633 (t80) REVERT: S 103 MET cc_start: 0.7211 (tpp) cc_final: 0.6566 (tpp) REVERT: S 188 MET cc_start: 0.8933 (mtm) cc_final: 0.8516 (mtp) REVERT: S 214 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.8049 (mt-10) REVERT: U 345 TYR cc_start: 0.8781 (m-80) cc_final: 0.8511 (m-10) REVERT: U 432 GLU cc_start: 0.8514 (pp20) cc_final: 0.8291 (tm-30) REVERT: a 61 MET cc_start: 0.9063 (mmm) cc_final: 0.8797 (mmm) REVERT: a 406 MET cc_start: 0.9045 (mtt) cc_final: 0.8626 (mtm) REVERT: a 423 MET cc_start: 0.9493 (OUTLIER) cc_final: 0.9035 (tmm) REVERT: a 453 MET cc_start: 0.9033 (ptm) cc_final: 0.8742 (ptm) REVERT: a 484 MET cc_start: 0.8151 (OUTLIER) cc_final: 0.7747 (tpp) REVERT: a 550 MET cc_start: 0.9097 (mmt) cc_final: 0.8709 (mmm) REVERT: a 580 MET cc_start: 0.8149 (ppp) cc_final: 0.7914 (ppp) REVERT: a 583 LEU cc_start: 0.9324 (mt) cc_final: 0.9102 (mt) REVERT: a 616 MET cc_start: 0.8999 (ppp) cc_final: 0.8671 (ppp) REVERT: a 741 ARG cc_start: 0.8533 (OUTLIER) cc_final: 0.7995 (ttp-110) REVERT: a 745 LEU cc_start: 0.9552 (OUTLIER) cc_final: 0.9134 (mp) REVERT: a 759 MET cc_start: 0.9083 (mmm) cc_final: 0.8597 (tpp) REVERT: b 82 LYS cc_start: 0.9078 (OUTLIER) cc_final: 0.8708 (ptpp) REVERT: b 98 GLU cc_start: 0.9169 (mm-30) cc_final: 0.8891 (mm-30) REVERT: b 175 LYS cc_start: 0.8730 (ptpp) cc_final: 0.8430 (pttt) REVERT: b 180 GLU cc_start: 0.9226 (OUTLIER) cc_final: 0.8747 (pm20) REVERT: c 366 TYR cc_start: 0.8422 (m-80) cc_final: 0.8138 (m-80) REVERT: c 434 PHE cc_start: 0.9036 (OUTLIER) cc_final: 0.8666 (t80) REVERT: c 438 ILE cc_start: 0.9134 (mm) cc_final: 0.8895 (mm) REVERT: c 443 LEU cc_start: 0.9697 (OUTLIER) cc_final: 0.9481 (mm) REVERT: d 124 GLU cc_start: 0.8999 (OUTLIER) cc_final: 0.8385 (pt0) REVERT: d 129 CYS cc_start: 0.8763 (m) cc_final: 0.8403 (m) REVERT: d 157 ASP cc_start: 0.8489 (OUTLIER) cc_final: 0.8233 (t0) REVERT: d 176 MET cc_start: 0.8535 (tmm) cc_final: 0.8130 (tmm) REVERT: e 56 ILE cc_start: 0.9321 (OUTLIER) cc_final: 0.9072 (mm) REVERT: f 25 MET cc_start: 0.8950 (ttt) cc_final: 0.8554 (tpp) REVERT: f 28 MET cc_start: 0.9094 (mmm) cc_final: 0.8622 (mmm) REVERT: g 47 MET cc_start: 0.8216 (mmm) cc_final: 0.7866 (mmm) REVERT: g 54 LYS cc_start: 0.9474 (tttt) cc_final: 0.8908 (tmtp) REVERT: g 115 ASP cc_start: 0.8348 (OUTLIER) cc_final: 0.8025 (t70) REVERT: g 144 TYR cc_start: 0.8832 (m-80) cc_final: 0.8369 (m-80) REVERT: h 23 MET cc_start: 0.8539 (tpp) cc_final: 0.8006 (tpp) REVERT: h 32 TYR cc_start: 0.9062 (t80) cc_final: 0.8662 (t80) REVERT: h 36 LYS cc_start: 0.8513 (mppt) cc_final: 0.8133 (mmtm) REVERT: h 47 MET cc_start: 0.8448 (ppp) cc_final: 0.8182 (ppp) REVERT: h 68 TYR cc_start: 0.8642 (m-10) cc_final: 0.8340 (m-10) REVERT: h 82 GLU cc_start: 0.8950 (OUTLIER) cc_final: 0.8623 (tp30) REVERT: h 115 ASP cc_start: 0.8288 (t0) cc_final: 0.7644 (t0) REVERT: h 119 ARG cc_start: 0.7923 (mtm-85) cc_final: 0.7376 (mtm-85) REVERT: h 126 ARG cc_start: 0.8760 (OUTLIER) cc_final: 0.8401 (mtm110) REVERT: h 131 MET cc_start: 0.9176 (ttp) cc_final: 0.8868 (ttp) REVERT: i 53 MET cc_start: 0.9004 (mmt) cc_final: 0.8768 (mmm) REVERT: i 68 TYR cc_start: 0.7998 (m-80) cc_final: 0.7796 (m-80) REVERT: i 115 ASP cc_start: 0.8904 (t0) cc_final: 0.8608 (m-30) REVERT: i 127 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8379 (mp) REVERT: j 23 MET cc_start: 0.9159 (tmm) cc_final: 0.8625 (tmm) REVERT: j 36 LYS cc_start: 0.9020 (mmtm) cc_final: 0.8434 (mmtt) REVERT: j 44 MET cc_start: 0.8539 (tmm) cc_final: 0.8292 (tmm) REVERT: j 61 MET cc_start: 0.8984 (OUTLIER) cc_final: 0.8754 (ptm) REVERT: j 68 TYR cc_start: 0.9000 (m-10) cc_final: 0.8670 (m-10) REVERT: k 32 TYR cc_start: 0.8932 (t80) cc_final: 0.8123 (t80) REVERT: k 68 TYR cc_start: 0.8787 (m-10) cc_final: 0.8244 (m-10) REVERT: k 131 MET cc_start: 0.8889 (tpt) cc_final: 0.8588 (tpp) REVERT: l 17 MET cc_start: 0.9044 (tpp) cc_final: 0.8680 (ptt) REVERT: l 23 MET cc_start: 0.9441 (tpp) cc_final: 0.8768 (tpp) REVERT: l 54 LYS cc_start: 0.9103 (ptpp) cc_final: 0.8712 (ptpp) REVERT: l 68 TYR cc_start: 0.8699 (m-10) cc_final: 0.8462 (m-10) REVERT: l 119 ARG cc_start: 0.8427 (mmt-90) cc_final: 0.8184 (mmt-90) REVERT: l 131 MET cc_start: 0.9125 (tmm) cc_final: 0.8617 (tmm) REVERT: m 13 PHE cc_start: 0.8989 (t80) cc_final: 0.8751 (t80) REVERT: m 17 MET cc_start: 0.8976 (mmp) cc_final: 0.8565 (mmp) REVERT: m 47 MET cc_start: 0.8689 (mmt) cc_final: 0.8310 (mmm) REVERT: m 78 ASN cc_start: 0.9083 (p0) cc_final: 0.8824 (p0) REVERT: m 123 GLN cc_start: 0.8986 (mt0) cc_final: 0.8407 (mm-40) REVERT: n 13 PHE cc_start: 0.9381 (t80) cc_final: 0.9074 (t80) REVERT: n 17 MET cc_start: 0.9117 (mmp) cc_final: 0.8605 (mmp) REVERT: n 36 LYS cc_start: 0.8904 (ttmt) cc_final: 0.7842 (ttmm) REVERT: n 47 MET cc_start: 0.9288 (tpp) cc_final: 0.8931 (tpp) REVERT: n 48 ARG cc_start: 0.8865 (mtp85) cc_final: 0.8502 (mtp85) REVERT: n 61 MET cc_start: 0.8693 (mtp) cc_final: 0.8187 (ttm) REVERT: n 115 ASP cc_start: 0.8830 (t0) cc_final: 0.8358 (t0) REVERT: n 123 GLN cc_start: 0.9085 (mp10) cc_final: 0.8712 (mp10) REVERT: o 44 MET cc_start: 0.9155 (mmp) cc_final: 0.8763 (mmt) REVERT: o 47 MET cc_start: 0.8752 (tmm) cc_final: 0.8536 (tmm) REVERT: o 61 MET cc_start: 0.8673 (OUTLIER) cc_final: 0.8212 (mtp) REVERT: o 87 TYR cc_start: 0.8927 (t80) cc_final: 0.8565 (t80) REVERT: o 108 PHE cc_start: 0.8900 (m-10) cc_final: 0.8566 (t80) REVERT: o 115 ASP cc_start: 0.9183 (t0) cc_final: 0.8934 (m-30) REVERT: o 123 GLN cc_start: 0.9319 (mp10) cc_final: 0.9026 (mp10) REVERT: o 131 MET cc_start: 0.9489 (OUTLIER) cc_final: 0.9256 (ttm) REVERT: o 139 GLU cc_start: 0.8942 (tm-30) cc_final: 0.8634 (tp30) REVERT: p 301 ASN cc_start: 0.8571 (OUTLIER) cc_final: 0.7778 (p0) REVERT: p 303 ASP cc_start: 0.9271 (p0) cc_final: 0.8904 (p0) REVERT: p 342 ARG cc_start: 0.8942 (ttp80) cc_final: 0.8400 (ttp80) outliers start: 195 outliers final: 127 residues processed: 729 average time/residue: 0.6577 time to fit residues: 823.4112 Evaluate side-chains 730 residues out of total 7883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 562 time to evaluate : 6.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 HIS Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 419 ASP Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 450 TRP Chi-restraints excluded: chain A residue 487 GLU Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 163 LYS Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain B residue 296 MET Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 340 MET Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 359 ARG Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 485 GLU Chi-restraints excluded: chain B residue 574 MET Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 171 ARG Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 392 VAL Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 514 LEU Chi-restraints excluded: chain C residue 518 ASP Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 220 ASN Chi-restraints excluded: chain D residue 327 THR Chi-restraints excluded: chain D residue 331 ARG Chi-restraints excluded: chain D residue 338 ARG Chi-restraints excluded: chain D residue 353 ASP Chi-restraints excluded: chain D residue 455 ASN Chi-restraints excluded: chain E residue 293 ASP Chi-restraints excluded: chain E residue 328 ILE Chi-restraints excluded: chain E residue 396 MET Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 228 MET Chi-restraints excluded: chain F residue 266 ILE Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain F residue 493 MET Chi-restraints excluded: chain H residue 27 GLN Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 85 GLN Chi-restraints excluded: chain H residue 113 HIS Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 121 LEU Chi-restraints excluded: chain H residue 193 GLU Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain I residue 159 THR Chi-restraints excluded: chain J residue 132 MET Chi-restraints excluded: chain J residue 191 LYS Chi-restraints excluded: chain J residue 192 VAL Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain K residue 82 LYS Chi-restraints excluded: chain L residue 35 ASN Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 65 LEU Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain N residue 93 ASP Chi-restraints excluded: chain O residue 93 ASP Chi-restraints excluded: chain Q residue 62 PHE Chi-restraints excluded: chain Q residue 103 MET Chi-restraints excluded: chain R residue 32 CYS Chi-restraints excluded: chain R residue 51 ASP Chi-restraints excluded: chain R residue 122 TRP Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain R residue 168 ILE Chi-restraints excluded: chain R residue 170 GLU Chi-restraints excluded: chain R residue 197 TYR Chi-restraints excluded: chain S residue 214 GLU Chi-restraints excluded: chain U residue 264 HIS Chi-restraints excluded: chain U residue 380 HIS Chi-restraints excluded: chain a residue 363 THR Chi-restraints excluded: chain a residue 366 LYS Chi-restraints excluded: chain a residue 385 THR Chi-restraints excluded: chain a residue 423 MET Chi-restraints excluded: chain a residue 452 LEU Chi-restraints excluded: chain a residue 484 MET Chi-restraints excluded: chain a residue 556 SER Chi-restraints excluded: chain a residue 741 ARG Chi-restraints excluded: chain a residue 745 LEU Chi-restraints excluded: chain a residue 776 LEU Chi-restraints excluded: chain a residue 821 PHE Chi-restraints excluded: chain b residue 28 ILE Chi-restraints excluded: chain b residue 30 ASP Chi-restraints excluded: chain b residue 34 ARG Chi-restraints excluded: chain b residue 82 LYS Chi-restraints excluded: chain b residue 180 GLU Chi-restraints excluded: chain c residue 287 LEU Chi-restraints excluded: chain c residue 325 ILE Chi-restraints excluded: chain c residue 339 PHE Chi-restraints excluded: chain c residue 340 THR Chi-restraints excluded: chain c residue 364 SER Chi-restraints excluded: chain c residue 365 ILE Chi-restraints excluded: chain c residue 377 ASN Chi-restraints excluded: chain c residue 407 THR Chi-restraints excluded: chain c residue 434 PHE Chi-restraints excluded: chain c residue 443 LEU Chi-restraints excluded: chain d residue 20 VAL Chi-restraints excluded: chain d residue 39 CYS Chi-restraints excluded: chain d residue 63 SER Chi-restraints excluded: chain d residue 110 ILE Chi-restraints excluded: chain d residue 124 GLU Chi-restraints excluded: chain d residue 145 GLN Chi-restraints excluded: chain d residue 149 GLU Chi-restraints excluded: chain d residue 157 ASP Chi-restraints excluded: chain d residue 304 LEU Chi-restraints excluded: chain e residue 28 ILE Chi-restraints excluded: chain e residue 56 ILE Chi-restraints excluded: chain f residue 78 LEU Chi-restraints excluded: chain g residue 99 VAL Chi-restraints excluded: chain g residue 115 ASP Chi-restraints excluded: chain g residue 123 GLN Chi-restraints excluded: chain g residue 148 VAL Chi-restraints excluded: chain h residue 81 THR Chi-restraints excluded: chain h residue 82 GLU Chi-restraints excluded: chain h residue 126 ARG Chi-restraints excluded: chain h residue 140 VAL Chi-restraints excluded: chain i residue 127 LEU Chi-restraints excluded: chain j residue 17 MET Chi-restraints excluded: chain j residue 24 VAL Chi-restraints excluded: chain j residue 61 MET Chi-restraints excluded: chain j residue 99 VAL Chi-restraints excluded: chain k residue 118 VAL Chi-restraints excluded: chain k residue 140 VAL Chi-restraints excluded: chain l residue 48 ARG Chi-restraints excluded: chain l residue 110 ILE Chi-restraints excluded: chain m residue 28 LEU Chi-restraints excluded: chain m residue 45 SER Chi-restraints excluded: chain m residue 64 ILE Chi-restraints excluded: chain m residue 81 THR Chi-restraints excluded: chain m residue 97 LEU Chi-restraints excluded: chain m residue 118 VAL Chi-restraints excluded: chain n residue 10 TYR Chi-restraints excluded: chain n residue 82 GLU Chi-restraints excluded: chain o residue 61 MET Chi-restraints excluded: chain o residue 67 ILE Chi-restraints excluded: chain o residue 131 MET Chi-restraints excluded: chain o residue 143 LEU Chi-restraints excluded: chain o residue 146 LEU Chi-restraints excluded: chain p residue 301 ASN Chi-restraints excluded: chain p residue 322 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 923 random chunks: chunk 550 optimal weight: 40.0000 chunk 355 optimal weight: 5.9990 chunk 531 optimal weight: 10.0000 chunk 267 optimal weight: 0.9990 chunk 174 optimal weight: 8.9990 chunk 172 optimal weight: 9.9990 chunk 565 optimal weight: 20.0000 chunk 606 optimal weight: 10.0000 chunk 439 optimal weight: 5.9990 chunk 82 optimal weight: 0.7980 chunk 699 optimal weight: 4.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 172 ASN ** C 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 152 GLN ** K 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 90 ASN ** d 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 69826 Z= 0.335 Angle : 0.643 14.009 94787 Z= 0.328 Chirality : 0.041 0.295 11071 Planarity : 0.004 0.055 12263 Dihedral : 5.454 81.236 10053 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 15.90 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.38 % Favored : 95.59 % Rotamer: Outliers : 3.01 % Allowed : 15.06 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.99 % 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: 9244 helix: 2.25 (0.07), residues: 5466 sheet: -1.12 (0.19), residues: 721 loop : -0.74 (0.12), residues: 3057 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 567 HIS 0.010 0.001 HIS L 81 PHE 0.035 0.002 PHE A 337 TYR 0.054 0.002 TYR m 144 ARG 0.009 0.000 ARG i 126 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18488 Ramachandran restraints generated. 9244 Oldfield, 0 Emsley, 9244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18488 Ramachandran restraints generated. 9244 Oldfield, 0 Emsley, 9244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 780 residues out of total 7883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 582 time to evaluate : 6.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 429 VAL cc_start: 0.9308 (OUTLIER) cc_final: 0.9037 (t) REVERT: B 163 LYS cc_start: 0.8892 (OUTLIER) cc_final: 0.8347 (mmtm) REVERT: B 296 MET cc_start: 0.8783 (OUTLIER) cc_final: 0.8554 (pmm) REVERT: B 306 MET cc_start: 0.8763 (mmm) cc_final: 0.8366 (mmm) REVERT: B 318 MET cc_start: 0.8239 (mtt) cc_final: 0.7967 (mtp) REVERT: B 344 VAL cc_start: 0.9397 (OUTLIER) cc_final: 0.9078 (m) REVERT: B 346 MET cc_start: 0.8374 (tmm) cc_final: 0.7924 (tmm) REVERT: B 359 ARG cc_start: 0.9044 (OUTLIER) cc_final: 0.8446 (ttm170) REVERT: B 405 THR cc_start: 0.9186 (OUTLIER) cc_final: 0.8771 (p) REVERT: B 458 MET cc_start: 0.8382 (mtp) cc_final: 0.7881 (mtp) REVERT: B 485 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.8046 (mp0) REVERT: C 296 MET cc_start: 0.8258 (ppp) cc_final: 0.7585 (ppp) REVERT: C 318 MET cc_start: 0.9064 (mmm) cc_final: 0.8842 (mmp) REVERT: C 347 MET cc_start: 0.7729 (tmm) cc_final: 0.7460 (tmm) REVERT: C 365 LEU cc_start: 0.9584 (OUTLIER) cc_final: 0.9345 (mt) REVERT: C 392 VAL cc_start: 0.9322 (OUTLIER) cc_final: 0.8954 (m) REVERT: C 455 SER cc_start: 0.8667 (OUTLIER) cc_final: 0.8083 (m) REVERT: C 505 ASP cc_start: 0.9121 (m-30) cc_final: 0.8907 (m-30) REVERT: D 294 MET cc_start: 0.8632 (mmm) cc_final: 0.8380 (mmm) REVERT: D 331 ARG cc_start: 0.8997 (OUTLIER) cc_final: 0.8393 (mtp180) REVERT: D 350 MET cc_start: 0.8210 (mtp) cc_final: 0.7818 (mtp) REVERT: D 493 MET cc_start: 0.8921 (ppp) cc_final: 0.8229 (ppp) REVERT: E 163 MET cc_start: 0.8154 (tmm) cc_final: 0.7751 (tmm) REVERT: E 228 MET cc_start: 0.8460 (mpp) cc_final: 0.8231 (mpp) REVERT: E 321 MET cc_start: 0.8807 (tpp) cc_final: 0.8252 (tpp) REVERT: E 374 ASP cc_start: 0.8585 (t0) cc_final: 0.8350 (t0) REVERT: E 396 MET cc_start: 0.8855 (OUTLIER) cc_final: 0.7961 (ttp) REVERT: E 425 ASP cc_start: 0.8734 (m-30) cc_final: 0.8483 (m-30) REVERT: E 442 ASP cc_start: 0.8528 (OUTLIER) cc_final: 0.8256 (t0) REVERT: E 485 MET cc_start: 0.8441 (mtp) cc_final: 0.8025 (mtm) REVERT: E 493 MET cc_start: 0.8985 (tpp) cc_final: 0.8544 (tpp) REVERT: F 266 ILE cc_start: 0.9362 (OUTLIER) cc_final: 0.8988 (mm) REVERT: F 321 MET cc_start: 0.8749 (ttm) cc_final: 0.8339 (ttm) REVERT: H 14 MET cc_start: 0.8597 (tmm) cc_final: 0.8093 (tmm) REVERT: H 112 TYR cc_start: 0.7808 (t80) cc_final: 0.7444 (t80) REVERT: I 72 MET cc_start: 0.8596 (tpp) cc_final: 0.7784 (tpp) REVERT: I 76 MET cc_start: 0.8806 (mmm) cc_final: 0.8114 (mmp) REVERT: I 132 MET cc_start: 0.8233 (mmt) cc_final: 0.7810 (mmm) REVERT: J 127 LEU cc_start: 0.9417 (OUTLIER) cc_final: 0.8935 (mp) REVERT: J 132 MET cc_start: 0.8170 (OUTLIER) cc_final: 0.7689 (mmt) REVERT: K 82 LYS cc_start: 0.9203 (OUTLIER) cc_final: 0.8689 (pptt) REVERT: L 6 LYS cc_start: 0.9331 (mptp) cc_final: 0.8639 (mmmm) REVERT: L 15 ASP cc_start: 0.9026 (p0) cc_final: 0.8757 (p0) REVERT: L 54 GLN cc_start: 0.8931 (tp-100) cc_final: 0.8657 (tp-100) REVERT: L 59 GLU cc_start: 0.8889 (mp0) cc_final: 0.8422 (pp20) REVERT: L 90 GLU cc_start: 0.7689 (pt0) cc_final: 0.6698 (pm20) REVERT: L 112 MET cc_start: 0.7738 (ppp) cc_final: 0.7348 (ppp) REVERT: Q 62 PHE cc_start: 0.8282 (OUTLIER) cc_final: 0.7565 (t80) REVERT: Q 155 MET cc_start: 0.8975 (mmp) cc_final: 0.8572 (mmp) REVERT: Q 188 MET cc_start: 0.8623 (ptm) cc_final: 0.8196 (ppp) REVERT: R 32 CYS cc_start: 0.8052 (OUTLIER) cc_final: 0.7793 (t) REVERT: R 33 MET cc_start: 0.8903 (tpt) cc_final: 0.8439 (tpp) REVERT: R 103 MET cc_start: 0.6852 (tpp) cc_final: 0.6487 (tpp) REVERT: R 122 TRP cc_start: 0.8984 (OUTLIER) cc_final: 0.8493 (t-100) REVERT: R 139 TYR cc_start: 0.8648 (t80) cc_final: 0.8347 (t80) REVERT: R 168 ILE cc_start: 0.9345 (OUTLIER) cc_final: 0.9065 (tp) REVERT: R 170 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8250 (tm-30) REVERT: R 197 TYR cc_start: 0.3759 (OUTLIER) cc_final: 0.3361 (t80) REVERT: S 103 MET cc_start: 0.7245 (tpp) cc_final: 0.6594 (tpp) REVERT: S 188 MET cc_start: 0.8927 (mtm) cc_final: 0.8511 (mtp) REVERT: U 345 TYR cc_start: 0.8767 (m-80) cc_final: 0.8515 (m-10) REVERT: U 432 GLU cc_start: 0.8524 (pp20) cc_final: 0.8281 (tm-30) REVERT: a 61 MET cc_start: 0.9017 (mmm) cc_final: 0.8739 (mmm) REVERT: a 406 MET cc_start: 0.9089 (mtt) cc_final: 0.8232 (mtp) REVERT: a 423 MET cc_start: 0.9500 (OUTLIER) cc_final: 0.9038 (tmm) REVERT: a 453 MET cc_start: 0.9025 (ptm) cc_final: 0.8774 (ptm) REVERT: a 484 MET cc_start: 0.8165 (OUTLIER) cc_final: 0.7761 (tpp) REVERT: a 550 MET cc_start: 0.9088 (mmt) cc_final: 0.8692 (mmm) REVERT: a 580 MET cc_start: 0.8151 (ppp) cc_final: 0.7879 (ppp) REVERT: a 583 LEU cc_start: 0.9321 (mt) cc_final: 0.9092 (mt) REVERT: a 616 MET cc_start: 0.9014 (ppp) cc_final: 0.8664 (ppp) REVERT: a 741 ARG cc_start: 0.8541 (OUTLIER) cc_final: 0.7763 (ttp-170) REVERT: a 745 LEU cc_start: 0.9553 (OUTLIER) cc_final: 0.8551 (mp) REVERT: a 759 MET cc_start: 0.9106 (mmm) cc_final: 0.8601 (tpp) REVERT: a 794 MET cc_start: 0.8798 (tmm) cc_final: 0.8584 (ppp) REVERT: b 82 LYS cc_start: 0.9093 (OUTLIER) cc_final: 0.8732 (ptpp) REVERT: b 98 GLU cc_start: 0.9189 (mm-30) cc_final: 0.8933 (mm-30) REVERT: b 175 LYS cc_start: 0.8729 (ptpp) cc_final: 0.8433 (pttt) REVERT: b 180 GLU cc_start: 0.9208 (OUTLIER) cc_final: 0.8859 (pm20) REVERT: c 319 MET cc_start: 0.8405 (tpp) cc_final: 0.7506 (ttt) REVERT: c 366 TYR cc_start: 0.8417 (m-80) cc_final: 0.8137 (m-80) REVERT: c 434 PHE cc_start: 0.8978 (OUTLIER) cc_final: 0.8659 (t80) REVERT: c 438 ILE cc_start: 0.9129 (mm) cc_final: 0.8890 (mm) REVERT: c 443 LEU cc_start: 0.9695 (OUTLIER) cc_final: 0.9475 (mm) REVERT: c 445 MET cc_start: 0.8896 (mmp) cc_final: 0.8520 (mmm) REVERT: d 124 GLU cc_start: 0.9008 (OUTLIER) cc_final: 0.8384 (pt0) REVERT: d 129 CYS cc_start: 0.8763 (m) cc_final: 0.8446 (m) REVERT: d 157 ASP cc_start: 0.8537 (OUTLIER) cc_final: 0.8285 (t0) REVERT: d 176 MET cc_start: 0.8506 (OUTLIER) cc_final: 0.8092 (tmm) REVERT: e 56 ILE cc_start: 0.9398 (OUTLIER) cc_final: 0.9089 (mm) REVERT: f 25 MET cc_start: 0.8951 (ttt) cc_final: 0.8549 (tpp) REVERT: f 28 MET cc_start: 0.9095 (mmm) cc_final: 0.8614 (mmm) REVERT: g 47 MET cc_start: 0.8159 (mmm) cc_final: 0.7788 (mmm) REVERT: g 48 ARG cc_start: 0.8465 (ptp-170) cc_final: 0.7937 (ptp-170) REVERT: g 115 ASP cc_start: 0.8299 (OUTLIER) cc_final: 0.7923 (t70) REVERT: g 144 TYR cc_start: 0.8807 (m-80) cc_final: 0.8359 (m-80) REVERT: h 23 MET cc_start: 0.8535 (tpp) cc_final: 0.8006 (tpp) REVERT: h 32 TYR cc_start: 0.8984 (t80) cc_final: 0.8584 (t80) REVERT: h 36 LYS cc_start: 0.8518 (mppt) cc_final: 0.8096 (mmtm) REVERT: h 68 TYR cc_start: 0.8554 (m-10) cc_final: 0.8239 (m-10) REVERT: h 82 GLU cc_start: 0.8950 (OUTLIER) cc_final: 0.8621 (tp30) REVERT: h 115 ASP cc_start: 0.8254 (t0) cc_final: 0.7608 (t0) REVERT: h 119 ARG cc_start: 0.7897 (mtm-85) cc_final: 0.7414 (mtm-85) REVERT: h 126 ARG cc_start: 0.8730 (OUTLIER) cc_final: 0.8360 (mtm110) REVERT: h 131 MET cc_start: 0.9175 (ttp) cc_final: 0.8869 (ttp) REVERT: h 144 TYR cc_start: 0.9043 (m-10) cc_final: 0.8701 (m-10) REVERT: i 68 TYR cc_start: 0.7847 (m-10) cc_final: 0.7530 (m-80) REVERT: i 115 ASP cc_start: 0.8893 (t0) cc_final: 0.8604 (m-30) REVERT: i 127 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8347 (mp) REVERT: j 23 MET cc_start: 0.9154 (tmm) cc_final: 0.8650 (tmm) REVERT: j 36 LYS cc_start: 0.9013 (mmtm) cc_final: 0.8524 (mmtt) REVERT: j 44 MET cc_start: 0.8596 (tmm) cc_final: 0.8316 (tmm) REVERT: j 61 MET cc_start: 0.9006 (OUTLIER) cc_final: 0.8773 (ptm) REVERT: j 68 TYR cc_start: 0.9010 (m-10) cc_final: 0.8695 (m-10) REVERT: k 16 VAL cc_start: 0.9066 (OUTLIER) cc_final: 0.8812 (p) REVERT: k 32 TYR cc_start: 0.8945 (t80) cc_final: 0.8134 (t80) REVERT: k 61 MET cc_start: 0.8686 (mtp) cc_final: 0.8458 (mtp) REVERT: k 68 TYR cc_start: 0.8789 (m-10) cc_final: 0.8548 (m-10) REVERT: k 131 MET cc_start: 0.8860 (tpt) cc_final: 0.8504 (tpt) REVERT: l 17 MET cc_start: 0.9034 (tpp) cc_final: 0.8680 (ptt) REVERT: l 23 MET cc_start: 0.9453 (tpp) cc_final: 0.8909 (tpp) REVERT: l 32 TYR cc_start: 0.8466 (t80) cc_final: 0.8112 (t80) REVERT: l 54 LYS cc_start: 0.9079 (ptpp) cc_final: 0.8704 (ptpp) REVERT: l 68 TYR cc_start: 0.8691 (m-10) cc_final: 0.8478 (m-10) REVERT: l 119 ARG cc_start: 0.8422 (mmt-90) cc_final: 0.8173 (mmt-90) REVERT: l 131 MET cc_start: 0.9130 (tmm) cc_final: 0.8612 (tmm) REVERT: m 13 PHE cc_start: 0.9005 (t80) cc_final: 0.8752 (t80) REVERT: m 17 MET cc_start: 0.8980 (mmp) cc_final: 0.8563 (mmp) REVERT: m 78 ASN cc_start: 0.9089 (p0) cc_final: 0.8829 (p0) REVERT: n 13 PHE cc_start: 0.9385 (t80) cc_final: 0.9063 (t80) REVERT: n 17 MET cc_start: 0.9121 (mmp) cc_final: 0.8603 (mmp) REVERT: n 36 LYS cc_start: 0.8910 (ttmt) cc_final: 0.7860 (ttmm) REVERT: n 47 MET cc_start: 0.9331 (tpp) cc_final: 0.8948 (tpp) REVERT: n 48 ARG cc_start: 0.8878 (mtp85) cc_final: 0.8649 (mtp85) REVERT: n 61 MET cc_start: 0.8669 (mtp) cc_final: 0.8278 (ttm) REVERT: n 115 ASP cc_start: 0.8816 (t0) cc_final: 0.8387 (t0) REVERT: n 123 GLN cc_start: 0.9023 (mp10) cc_final: 0.8591 (mp10) REVERT: n 139 GLU cc_start: 0.8941 (tm-30) cc_final: 0.8680 (tm-30) REVERT: o 17 MET cc_start: 0.8506 (ptm) cc_final: 0.8161 (ptp) REVERT: o 44 MET cc_start: 0.9157 (mmp) cc_final: 0.8736 (mmt) REVERT: o 47 MET cc_start: 0.8764 (tmm) cc_final: 0.8559 (tmm) REVERT: o 61 MET cc_start: 0.8660 (OUTLIER) cc_final: 0.8393 (mtt) REVERT: o 87 TYR cc_start: 0.8893 (t80) cc_final: 0.8560 (t80) REVERT: o 108 PHE cc_start: 0.8893 (m-10) cc_final: 0.8569 (t80) REVERT: o 115 ASP cc_start: 0.9179 (t0) cc_final: 0.8927 (m-30) REVERT: o 123 GLN cc_start: 0.9313 (mp10) cc_final: 0.9023 (mp10) REVERT: o 131 MET cc_start: 0.9454 (OUTLIER) cc_final: 0.9248 (ttm) REVERT: o 139 GLU cc_start: 0.8930 (tm-30) cc_final: 0.8564 (tp30) REVERT: p 301 ASN cc_start: 0.8552 (OUTLIER) cc_final: 0.7806 (p0) REVERT: p 303 ASP cc_start: 0.9293 (p0) cc_final: 0.8867 (p0) REVERT: p 342 ARG cc_start: 0.8954 (ttp80) cc_final: 0.8495 (ttp80) outliers start: 198 outliers final: 128 residues processed: 740 average time/residue: 0.6506 time to fit residues: 827.1529 Evaluate side-chains 736 residues out of total 7883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 564 time to evaluate : 6.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 HIS Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 419 ASP Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 450 TRP Chi-restraints excluded: chain A residue 487 GLU Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 163 LYS Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain B residue 296 MET Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 359 ARG Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 485 GLU Chi-restraints excluded: chain B residue 574 MET Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 171 ARG Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 392 VAL Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 514 LEU Chi-restraints excluded: chain C residue 518 ASP Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 327 THR Chi-restraints excluded: chain D residue 331 ARG Chi-restraints excluded: chain D residue 338 ARG Chi-restraints excluded: chain D residue 353 ASP Chi-restraints excluded: chain D residue 455 ASN Chi-restraints excluded: chain D residue 466 SER Chi-restraints excluded: chain E residue 293 ASP Chi-restraints excluded: chain E residue 328 ILE Chi-restraints excluded: chain E residue 396 MET Chi-restraints excluded: chain E residue 442 ASP Chi-restraints excluded: chain F residue 100 ASP Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain F residue 228 MET Chi-restraints excluded: chain F residue 266 ILE Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain H residue 27 GLN Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 85 GLN Chi-restraints excluded: chain H residue 113 HIS Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 121 LEU Chi-restraints excluded: chain H residue 193 GLU Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain I residue 159 THR Chi-restraints excluded: chain J residue 127 LEU Chi-restraints excluded: chain J residue 132 MET Chi-restraints excluded: chain J residue 191 LYS Chi-restraints excluded: chain J residue 192 VAL Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain K residue 82 LYS Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 65 LEU Chi-restraints excluded: chain L residue 69 TYR Chi-restraints excluded: chain L residue 85 ILE Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain N residue 93 ASP Chi-restraints excluded: chain O residue 93 ASP Chi-restraints excluded: chain Q residue 62 PHE Chi-restraints excluded: chain Q residue 103 MET Chi-restraints excluded: chain R residue 32 CYS Chi-restraints excluded: chain R residue 51 ASP Chi-restraints excluded: chain R residue 88 LEU Chi-restraints excluded: chain R residue 122 TRP Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain R residue 168 ILE Chi-restraints excluded: chain R residue 170 GLU Chi-restraints excluded: chain R residue 197 TYR Chi-restraints excluded: chain U residue 264 HIS Chi-restraints excluded: chain U residue 380 HIS Chi-restraints excluded: chain a residue 363 THR Chi-restraints excluded: chain a residue 385 THR Chi-restraints excluded: chain a residue 423 MET Chi-restraints excluded: chain a residue 452 LEU Chi-restraints excluded: chain a residue 484 MET Chi-restraints excluded: chain a residue 486 ASP Chi-restraints excluded: chain a residue 556 SER Chi-restraints excluded: chain a residue 650 TRP Chi-restraints excluded: chain a residue 741 ARG Chi-restraints excluded: chain a residue 745 LEU Chi-restraints excluded: chain a residue 776 LEU Chi-restraints excluded: chain a residue 821 PHE Chi-restraints excluded: chain b residue 28 ILE Chi-restraints excluded: chain b residue 30 ASP Chi-restraints excluded: chain b residue 82 LYS Chi-restraints excluded: chain b residue 180 GLU Chi-restraints excluded: chain c residue 287 LEU Chi-restraints excluded: chain c residue 325 ILE Chi-restraints excluded: chain c residue 339 PHE Chi-restraints excluded: chain c residue 340 THR Chi-restraints excluded: chain c residue 364 SER Chi-restraints excluded: chain c residue 365 ILE Chi-restraints excluded: chain c residue 377 ASN Chi-restraints excluded: chain c residue 407 THR Chi-restraints excluded: chain c residue 434 PHE Chi-restraints excluded: chain c residue 443 LEU Chi-restraints excluded: chain d residue 20 VAL Chi-restraints excluded: chain d residue 39 CYS Chi-restraints excluded: chain d residue 63 SER Chi-restraints excluded: chain d residue 110 ILE Chi-restraints excluded: chain d residue 124 GLU Chi-restraints excluded: chain d residue 141 VAL Chi-restraints excluded: chain d residue 145 GLN Chi-restraints excluded: chain d residue 157 ASP Chi-restraints excluded: chain d residue 176 MET Chi-restraints excluded: chain d residue 185 LEU Chi-restraints excluded: chain d residue 304 LEU Chi-restraints excluded: chain e residue 28 ILE Chi-restraints excluded: chain e residue 56 ILE Chi-restraints excluded: chain f residue 78 LEU Chi-restraints excluded: chain g residue 99 VAL Chi-restraints excluded: chain g residue 115 ASP Chi-restraints excluded: chain g residue 123 GLN Chi-restraints excluded: chain g residue 148 VAL Chi-restraints excluded: chain h residue 81 THR Chi-restraints excluded: chain h residue 82 GLU Chi-restraints excluded: chain h residue 126 ARG Chi-restraints excluded: chain h residue 140 VAL Chi-restraints excluded: chain i residue 127 LEU Chi-restraints excluded: chain j residue 24 VAL Chi-restraints excluded: chain j residue 61 MET Chi-restraints excluded: chain j residue 99 VAL Chi-restraints excluded: chain k residue 16 VAL Chi-restraints excluded: chain k residue 118 VAL Chi-restraints excluded: chain k residue 140 VAL Chi-restraints excluded: chain l residue 48 ARG Chi-restraints excluded: chain l residue 110 ILE Chi-restraints excluded: chain m residue 28 LEU Chi-restraints excluded: chain m residue 45 SER Chi-restraints excluded: chain m residue 64 ILE Chi-restraints excluded: chain m residue 81 THR Chi-restraints excluded: chain m residue 97 LEU Chi-restraints excluded: chain m residue 118 VAL Chi-restraints excluded: chain n residue 10 TYR Chi-restraints excluded: chain n residue 82 GLU Chi-restraints excluded: chain o residue 61 MET Chi-restraints excluded: chain o residue 67 ILE Chi-restraints excluded: chain o residue 118 VAL Chi-restraints excluded: chain o residue 131 MET Chi-restraints excluded: chain o residue 143 LEU Chi-restraints excluded: chain p residue 301 ASN Chi-restraints excluded: chain p residue 322 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 923 random chunks: chunk 809 optimal weight: 6.9990 chunk 852 optimal weight: 10.0000 chunk 777 optimal weight: 9.9990 chunk 829 optimal weight: 0.9990 chunk 498 optimal weight: 10.0000 chunk 361 optimal weight: 2.9990 chunk 650 optimal weight: 0.9980 chunk 254 optimal weight: 4.9990 chunk 749 optimal weight: 9.9990 chunk 784 optimal weight: 3.9990 chunk 826 optimal weight: 0.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 603 GLN E 36 HIS ** E 409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 379 ASN ** d 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 69826 Z= 0.230 Angle : 0.615 13.879 94787 Z= 0.310 Chirality : 0.041 0.292 11071 Planarity : 0.004 0.054 12263 Dihedral : 5.263 79.570 10042 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 14.74 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.29 % Favored : 95.68 % Rotamer: Outliers : 2.63 % Allowed : 15.51 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.99 % 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: 9244 helix: 2.32 (0.07), residues: 5462 sheet: -0.96 (0.19), residues: 715 loop : -0.71 (0.12), residues: 3067 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP A 567 HIS 0.008 0.001 HIS L 81 PHE 0.026 0.001 PHE f 84 TYR 0.058 0.001 TYR m 144 ARG 0.009 0.000 ARG i 126 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18488 Ramachandran restraints generated. 9244 Oldfield, 0 Emsley, 9244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18488 Ramachandran restraints generated. 9244 Oldfield, 0 Emsley, 9244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 760 residues out of total 7883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 587 time to evaluate : 6.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 429 VAL cc_start: 0.9276 (OUTLIER) cc_final: 0.9006 (t) REVERT: A 584 MET cc_start: 0.8938 (ptp) cc_final: 0.8735 (mtp) REVERT: B 296 MET cc_start: 0.8751 (OUTLIER) cc_final: 0.8543 (pmm) REVERT: B 306 MET cc_start: 0.8767 (mmm) cc_final: 0.8357 (mmm) REVERT: B 318 MET cc_start: 0.8301 (mtt) cc_final: 0.8032 (mtp) REVERT: B 344 VAL cc_start: 0.9402 (OUTLIER) cc_final: 0.9144 (m) REVERT: B 346 MET cc_start: 0.8324 (tmm) cc_final: 0.7837 (tmm) REVERT: B 359 ARG cc_start: 0.8995 (OUTLIER) cc_final: 0.8296 (ttm170) REVERT: B 458 MET cc_start: 0.8249 (mtp) cc_final: 0.7750 (mtp) REVERT: B 485 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.8008 (mp0) REVERT: C 296 MET cc_start: 0.8252 (ppp) cc_final: 0.7578 (ppp) REVERT: C 392 VAL cc_start: 0.9262 (OUTLIER) cc_final: 0.8872 (m) REVERT: C 455 SER cc_start: 0.8551 (OUTLIER) cc_final: 0.7977 (m) REVERT: C 544 MET cc_start: 0.8817 (mtt) cc_final: 0.8550 (ttt) REVERT: C 584 MET cc_start: 0.8718 (tmm) cc_final: 0.8516 (tmm) REVERT: D 140 MET cc_start: 0.8346 (tpp) cc_final: 0.8099 (tpp) REVERT: D 331 ARG cc_start: 0.8945 (OUTLIER) cc_final: 0.8365 (mtp180) REVERT: D 338 ARG cc_start: 0.7606 (OUTLIER) cc_final: 0.7403 (mmm160) REVERT: D 350 MET cc_start: 0.8291 (mtp) cc_final: 0.8021 (mtp) REVERT: D 493 MET cc_start: 0.8860 (ppp) cc_final: 0.8226 (ppp) REVERT: E 163 MET cc_start: 0.8232 (tmm) cc_final: 0.7959 (tmm) REVERT: E 321 MET cc_start: 0.8760 (tpp) cc_final: 0.8173 (tpp) REVERT: E 374 ASP cc_start: 0.8594 (t0) cc_final: 0.8370 (t0) REVERT: E 396 MET cc_start: 0.8820 (OUTLIER) cc_final: 0.7873 (ttp) REVERT: E 425 ASP cc_start: 0.8723 (m-30) cc_final: 0.8468 (m-30) REVERT: E 442 ASP cc_start: 0.8574 (OUTLIER) cc_final: 0.8274 (t0) REVERT: E 485 MET cc_start: 0.8398 (mtp) cc_final: 0.7988 (mtm) REVERT: E 493 MET cc_start: 0.8966 (tpp) cc_final: 0.8576 (tpp) REVERT: F 321 MET cc_start: 0.8705 (ttm) cc_final: 0.8306 (ttm) REVERT: H 14 MET cc_start: 0.8550 (tmm) cc_final: 0.8030 (tmm) REVERT: H 112 TYR cc_start: 0.7728 (t80) cc_final: 0.7422 (t80) REVERT: I 72 MET cc_start: 0.8570 (tpp) cc_final: 0.7735 (tpp) REVERT: I 76 MET cc_start: 0.8762 (mmm) cc_final: 0.8056 (mmp) REVERT: I 132 MET cc_start: 0.8159 (mmt) cc_final: 0.7729 (mmm) REVERT: J 132 MET cc_start: 0.8192 (OUTLIER) cc_final: 0.7613 (mmt) REVERT: K 82 LYS cc_start: 0.9199 (OUTLIER) cc_final: 0.8662 (pptt) REVERT: K 192 VAL cc_start: 0.9209 (OUTLIER) cc_final: 0.8889 (p) REVERT: L 6 LYS cc_start: 0.9315 (mptp) cc_final: 0.8639 (mmmm) REVERT: L 15 ASP cc_start: 0.8954 (p0) cc_final: 0.8636 (p0) REVERT: L 54 GLN cc_start: 0.8893 (tp-100) cc_final: 0.8579 (tp-100) REVERT: L 59 GLU cc_start: 0.8871 (mp0) cc_final: 0.8471 (pp20) REVERT: L 90 GLU cc_start: 0.7558 (pt0) cc_final: 0.7197 (pt0) REVERT: L 112 MET cc_start: 0.7756 (ppp) cc_final: 0.7362 (ppp) REVERT: Q 62 PHE cc_start: 0.8390 (OUTLIER) cc_final: 0.7589 (t80) REVERT: Q 155 MET cc_start: 0.8946 (mmp) cc_final: 0.8569 (mmp) REVERT: Q 188 MET cc_start: 0.8661 (ptm) cc_final: 0.8210 (ppp) REVERT: R 33 MET cc_start: 0.8887 (tpt) cc_final: 0.8428 (tpp) REVERT: R 103 MET cc_start: 0.6692 (tpp) cc_final: 0.6410 (tpp) REVERT: R 122 TRP cc_start: 0.8959 (OUTLIER) cc_final: 0.8455 (t-100) REVERT: R 139 TYR cc_start: 0.8593 (t80) cc_final: 0.8300 (t80) REVERT: R 168 ILE cc_start: 0.9334 (OUTLIER) cc_final: 0.9094 (tt) REVERT: R 170 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.8268 (tm-30) REVERT: R 197 TYR cc_start: 0.3756 (OUTLIER) cc_final: 0.3345 (t80) REVERT: S 103 MET cc_start: 0.7334 (tpp) cc_final: 0.6674 (tpp) REVERT: S 188 MET cc_start: 0.8940 (mtm) cc_final: 0.8525 (mtp) REVERT: U 345 TYR cc_start: 0.8647 (m-80) cc_final: 0.8389 (m-10) REVERT: U 432 GLU cc_start: 0.8540 (pp20) cc_final: 0.8305 (tm-30) REVERT: a 61 MET cc_start: 0.9005 (mmm) cc_final: 0.8718 (mmm) REVERT: a 406 MET cc_start: 0.9085 (mtt) cc_final: 0.8760 (mtp) REVERT: a 423 MET cc_start: 0.9495 (OUTLIER) cc_final: 0.9060 (tmm) REVERT: a 439 MET cc_start: 0.8708 (mpp) cc_final: 0.8446 (mpp) REVERT: a 453 MET cc_start: 0.9015 (ptm) cc_final: 0.8763 (ptm) REVERT: a 484 MET cc_start: 0.8222 (OUTLIER) cc_final: 0.7798 (tpp) REVERT: a 538 MET cc_start: 0.8648 (mtm) cc_final: 0.8420 (tmm) REVERT: a 550 MET cc_start: 0.9053 (mmt) cc_final: 0.8735 (mmm) REVERT: a 580 MET cc_start: 0.8096 (ppp) cc_final: 0.7817 (ppp) REVERT: a 583 LEU cc_start: 0.9355 (mt) cc_final: 0.9130 (mt) REVERT: a 628 MET cc_start: 0.8617 (tpp) cc_final: 0.7717 (tpp) REVERT: a 759 MET cc_start: 0.9083 (mmm) cc_final: 0.8623 (tpp) REVERT: b 82 LYS cc_start: 0.9087 (OUTLIER) cc_final: 0.8736 (ptpp) REVERT: b 98 GLU cc_start: 0.9119 (mm-30) cc_final: 0.8736 (mm-30) REVERT: b 175 LYS cc_start: 0.8731 (ptpp) cc_final: 0.8493 (pttt) REVERT: b 180 GLU cc_start: 0.9148 (OUTLIER) cc_final: 0.8674 (pm20) REVERT: c 319 MET cc_start: 0.8533 (tpp) cc_final: 0.7569 (ttt) REVERT: c 366 TYR cc_start: 0.8282 (m-80) cc_final: 0.8017 (m-80) REVERT: c 434 PHE cc_start: 0.8973 (OUTLIER) cc_final: 0.8616 (t80) REVERT: c 438 ILE cc_start: 0.9134 (mm) cc_final: 0.8898 (mm) REVERT: c 443 LEU cc_start: 0.9690 (OUTLIER) cc_final: 0.9466 (mm) REVERT: c 445 MET cc_start: 0.8886 (mmp) cc_final: 0.8535 (mmm) REVERT: d 124 GLU cc_start: 0.9014 (OUTLIER) cc_final: 0.8381 (pt0) REVERT: d 129 CYS cc_start: 0.8746 (m) cc_final: 0.8416 (m) REVERT: d 145 GLN cc_start: 0.7656 (OUTLIER) cc_final: 0.5912 (mm110) REVERT: d 176 MET cc_start: 0.8523 (OUTLIER) cc_final: 0.7955 (tmm) REVERT: e 49 TYR cc_start: 0.8870 (t80) cc_final: 0.8648 (t80) REVERT: e 56 ILE cc_start: 0.9371 (OUTLIER) cc_final: 0.9079 (mm) REVERT: e 67 GLN cc_start: 0.9007 (mm110) cc_final: 0.8549 (mm-40) REVERT: e 71 GLU cc_start: 0.9317 (mt-10) cc_final: 0.8422 (mm-30) REVERT: f 28 MET cc_start: 0.9080 (mmm) cc_final: 0.8685 (mmm) REVERT: g 17 MET cc_start: 0.8711 (tmm) cc_final: 0.8189 (tmm) REVERT: g 36 LYS cc_start: 0.9149 (ttmm) cc_final: 0.8885 (ttmm) REVERT: g 47 MET cc_start: 0.8186 (mmm) cc_final: 0.7821 (mmm) REVERT: g 48 ARG cc_start: 0.8449 (ptp-170) cc_final: 0.7917 (ptp-170) REVERT: g 99 VAL cc_start: 0.8912 (OUTLIER) cc_final: 0.8701 (p) REVERT: g 115 ASP cc_start: 0.8269 (OUTLIER) cc_final: 0.7902 (t70) REVERT: g 144 TYR cc_start: 0.8805 (m-80) cc_final: 0.8302 (m-80) REVERT: h 23 MET cc_start: 0.8486 (tpp) cc_final: 0.7962 (tpp) REVERT: h 32 TYR cc_start: 0.8925 (t80) cc_final: 0.8475 (t80) REVERT: h 36 LYS cc_start: 0.8541 (mppt) cc_final: 0.7885 (mmtm) REVERT: h 68 TYR cc_start: 0.8645 (m-10) cc_final: 0.8344 (m-10) REVERT: h 82 GLU cc_start: 0.8925 (OUTLIER) cc_final: 0.8597 (tp30) REVERT: h 115 ASP cc_start: 0.8200 (t0) cc_final: 0.7518 (t0) REVERT: h 119 ARG cc_start: 0.7767 (mtm-85) cc_final: 0.7305 (mtm-85) REVERT: h 126 ARG cc_start: 0.8705 (OUTLIER) cc_final: 0.8319 (mtm110) REVERT: h 131 MET cc_start: 0.9170 (ttp) cc_final: 0.8883 (ttp) REVERT: h 144 TYR cc_start: 0.8996 (m-10) cc_final: 0.8728 (m-10) REVERT: i 23 MET cc_start: 0.8538 (tpp) cc_final: 0.7530 (tpp) REVERT: i 44 MET cc_start: 0.8250 (tmm) cc_final: 0.7977 (tpt) REVERT: i 115 ASP cc_start: 0.8878 (t0) cc_final: 0.8575 (m-30) REVERT: i 127 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8303 (mp) REVERT: j 23 MET cc_start: 0.9112 (tmm) cc_final: 0.8612 (tmm) REVERT: j 36 LYS cc_start: 0.8967 (mmtm) cc_final: 0.8543 (mmtt) REVERT: j 44 MET cc_start: 0.8602 (tmm) cc_final: 0.8390 (tmm) REVERT: j 68 TYR cc_start: 0.8986 (m-10) cc_final: 0.8451 (m-10) REVERT: j 143 LEU cc_start: 0.9348 (tp) cc_final: 0.9134 (mt) REVERT: j 144 TYR cc_start: 0.9154 (m-10) cc_final: 0.8722 (m-10) REVERT: k 16 VAL cc_start: 0.8984 (OUTLIER) cc_final: 0.8734 (p) REVERT: k 32 TYR cc_start: 0.8881 (t80) cc_final: 0.8131 (t80) REVERT: k 61 MET cc_start: 0.8689 (mtp) cc_final: 0.8453 (mtp) REVERT: k 68 TYR cc_start: 0.8822 (m-10) cc_final: 0.8603 (m-10) REVERT: k 123 GLN cc_start: 0.9280 (mm-40) cc_final: 0.9013 (mm-40) REVERT: k 131 MET cc_start: 0.8851 (tpt) cc_final: 0.8494 (tpt) REVERT: l 17 MET cc_start: 0.9024 (tpp) cc_final: 0.8681 (ptt) REVERT: l 23 MET cc_start: 0.9424 (tpp) cc_final: 0.8891 (tpp) REVERT: l 32 TYR cc_start: 0.8438 (t80) cc_final: 0.8160 (t80) REVERT: l 36 LYS cc_start: 0.9059 (ptmt) cc_final: 0.8826 (pttp) REVERT: l 54 LYS cc_start: 0.9041 (ptpp) cc_final: 0.8628 (ptpp) REVERT: l 119 ARG cc_start: 0.8360 (mmt-90) cc_final: 0.8109 (mmt-90) REVERT: l 131 MET cc_start: 0.9133 (tmm) cc_final: 0.8611 (tmm) REVERT: m 13 PHE cc_start: 0.9004 (t80) cc_final: 0.8740 (t80) REVERT: m 17 MET cc_start: 0.8983 (mmp) cc_final: 0.8551 (mmp) REVERT: m 78 ASN cc_start: 0.9067 (p0) cc_final: 0.8821 (p0) REVERT: n 13 PHE cc_start: 0.9385 (t80) cc_final: 0.9056 (t80) REVERT: n 17 MET cc_start: 0.9130 (mmp) cc_final: 0.8592 (mmp) REVERT: n 36 LYS cc_start: 0.8871 (ttmt) cc_final: 0.7705 (ttmm) REVERT: n 47 MET cc_start: 0.9298 (tpp) cc_final: 0.8943 (tpp) REVERT: n 48 ARG cc_start: 0.8888 (mtp85) cc_final: 0.8660 (mtp85) REVERT: n 115 ASP cc_start: 0.8795 (t0) cc_final: 0.8380 (t0) REVERT: n 139 GLU cc_start: 0.8924 (tm-30) cc_final: 0.8445 (tp30) REVERT: o 17 MET cc_start: 0.8493 (ptm) cc_final: 0.8140 (ptp) REVERT: o 44 MET cc_start: 0.9124 (mmp) cc_final: 0.8653 (mmt) REVERT: o 47 MET cc_start: 0.8704 (tmm) cc_final: 0.8485 (tmm) REVERT: o 61 MET cc_start: 0.8607 (OUTLIER) cc_final: 0.8207 (mtt) REVERT: o 108 PHE cc_start: 0.8882 (m-10) cc_final: 0.8554 (t80) REVERT: o 115 ASP cc_start: 0.9184 (t0) cc_final: 0.8918 (m-30) REVERT: o 123 GLN cc_start: 0.9313 (mp10) cc_final: 0.9037 (mp10) REVERT: o 131 MET cc_start: 0.9445 (OUTLIER) cc_final: 0.9218 (ttm) REVERT: o 139 GLU cc_start: 0.8887 (tm-30) cc_final: 0.8568 (tp30) REVERT: p 301 ASN cc_start: 0.8536 (OUTLIER) cc_final: 0.7792 (p0) REVERT: p 303 ASP cc_start: 0.9243 (p0) cc_final: 0.8845 (p0) REVERT: p 342 ARG cc_start: 0.8963 (ttp80) cc_final: 0.8492 (ttp80) outliers start: 173 outliers final: 116 residues processed: 724 average time/residue: 0.6539 time to fit residues: 813.9218 Evaluate side-chains 729 residues out of total 7883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 575 time to evaluate : 6.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 HIS Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 419 ASP Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 450 TRP Chi-restraints excluded: chain A residue 487 GLU Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 296 MET Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 359 ARG Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 485 GLU Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 171 ARG Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 392 VAL Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 514 LEU Chi-restraints excluded: chain C residue 518 ASP Chi-restraints excluded: chain D residue 327 THR Chi-restraints excluded: chain D residue 331 ARG Chi-restraints excluded: chain D residue 338 ARG Chi-restraints excluded: chain D residue 353 ASP Chi-restraints excluded: chain D residue 455 ASN Chi-restraints excluded: chain D residue 466 SER Chi-restraints excluded: chain E residue 266 ILE Chi-restraints excluded: chain E residue 293 ASP Chi-restraints excluded: chain E residue 328 ILE Chi-restraints excluded: chain E residue 396 MET Chi-restraints excluded: chain E residue 442 ASP Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain F residue 228 MET Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain H residue 27 GLN Chi-restraints excluded: chain H residue 85 GLN Chi-restraints excluded: chain H residue 113 HIS Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 121 LEU Chi-restraints excluded: chain H residue 193 GLU Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain I residue 159 THR Chi-restraints excluded: chain J residue 132 MET Chi-restraints excluded: chain J residue 191 LYS Chi-restraints excluded: chain J residue 192 VAL Chi-restraints excluded: chain J residue 207 MET Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain K residue 82 LYS Chi-restraints excluded: chain K residue 192 VAL Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 65 LEU Chi-restraints excluded: chain L residue 69 TYR Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain N residue 93 ASP Chi-restraints excluded: chain O residue 93 ASP Chi-restraints excluded: chain Q residue 62 PHE Chi-restraints excluded: chain Q residue 103 MET Chi-restraints excluded: chain R residue 51 ASP Chi-restraints excluded: chain R residue 122 TRP Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain R residue 166 TYR Chi-restraints excluded: chain R residue 168 ILE Chi-restraints excluded: chain R residue 170 GLU Chi-restraints excluded: chain R residue 197 TYR Chi-restraints excluded: chain U residue 264 HIS Chi-restraints excluded: chain U residue 380 HIS Chi-restraints excluded: chain a residue 385 THR Chi-restraints excluded: chain a residue 423 MET Chi-restraints excluded: chain a residue 452 LEU Chi-restraints excluded: chain a residue 484 MET Chi-restraints excluded: chain a residue 486 ASP Chi-restraints excluded: chain a residue 556 SER Chi-restraints excluded: chain a residue 650 TRP Chi-restraints excluded: chain a residue 776 LEU Chi-restraints excluded: chain a residue 805 ARG Chi-restraints excluded: chain a residue 821 PHE Chi-restraints excluded: chain b residue 28 ILE Chi-restraints excluded: chain b residue 30 ASP Chi-restraints excluded: chain b residue 82 LYS Chi-restraints excluded: chain b residue 180 GLU Chi-restraints excluded: chain c residue 287 LEU Chi-restraints excluded: chain c residue 325 ILE Chi-restraints excluded: chain c residue 339 PHE Chi-restraints excluded: chain c residue 364 SER Chi-restraints excluded: chain c residue 365 ILE Chi-restraints excluded: chain c residue 377 ASN Chi-restraints excluded: chain c residue 379 ASN Chi-restraints excluded: chain c residue 434 PHE Chi-restraints excluded: chain c residue 443 LEU Chi-restraints excluded: chain d residue 20 VAL Chi-restraints excluded: chain d residue 63 SER Chi-restraints excluded: chain d residue 110 ILE Chi-restraints excluded: chain d residue 124 GLU Chi-restraints excluded: chain d residue 141 VAL Chi-restraints excluded: chain d residue 145 GLN Chi-restraints excluded: chain d residue 176 MET Chi-restraints excluded: chain d residue 185 LEU Chi-restraints excluded: chain d residue 304 LEU Chi-restraints excluded: chain e residue 28 ILE Chi-restraints excluded: chain e residue 56 ILE Chi-restraints excluded: chain f residue 78 LEU Chi-restraints excluded: chain g residue 99 VAL Chi-restraints excluded: chain g residue 115 ASP Chi-restraints excluded: chain g residue 123 GLN Chi-restraints excluded: chain g residue 148 VAL Chi-restraints excluded: chain h residue 81 THR Chi-restraints excluded: chain h residue 82 GLU Chi-restraints excluded: chain h residue 126 ARG Chi-restraints excluded: chain h residue 140 VAL Chi-restraints excluded: chain i residue 127 LEU Chi-restraints excluded: chain j residue 24 VAL Chi-restraints excluded: chain j residue 99 VAL Chi-restraints excluded: chain k residue 16 VAL Chi-restraints excluded: chain k residue 24 VAL Chi-restraints excluded: chain k residue 118 VAL Chi-restraints excluded: chain k residue 140 VAL Chi-restraints excluded: chain l residue 48 ARG Chi-restraints excluded: chain l residue 110 ILE Chi-restraints excluded: chain m residue 24 VAL Chi-restraints excluded: chain m residue 45 SER Chi-restraints excluded: chain m residue 64 ILE Chi-restraints excluded: chain m residue 97 LEU Chi-restraints excluded: chain n residue 10 TYR Chi-restraints excluded: chain n residue 143 LEU Chi-restraints excluded: chain o residue 61 MET Chi-restraints excluded: chain o residue 67 ILE Chi-restraints excluded: chain o residue 118 VAL Chi-restraints excluded: chain o residue 131 MET Chi-restraints excluded: chain o residue 143 LEU Chi-restraints excluded: chain p residue 301 ASN Chi-restraints excluded: chain p residue 322 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 923 random chunks: chunk 544 optimal weight: 8.9990 chunk 876 optimal weight: 10.0000 chunk 535 optimal weight: 0.3980 chunk 415 optimal weight: 7.9990 chunk 609 optimal weight: 9.9990 chunk 919 optimal weight: 0.3980 chunk 846 optimal weight: 7.9990 chunk 732 optimal weight: 5.9990 chunk 76 optimal weight: 10.0000 chunk 565 optimal weight: 20.0000 chunk 448 optimal weight: 8.9990 overall best weight: 4.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 302 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.102 69826 Z= 0.399 Angle : 0.689 14.811 94787 Z= 0.350 Chirality : 0.042 0.320 11071 Planarity : 0.004 0.056 12263 Dihedral : 5.247 80.632 10035 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 16.78 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.79 % Favored : 95.18 % Rotamer: Outliers : 2.67 % Allowed : 15.80 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.99 % 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: 1.52 (0.09), residues: 9244 helix: 2.26 (0.07), residues: 5476 sheet: -1.23 (0.18), residues: 763 loop : -0.73 (0.12), residues: 3005 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP A 567 HIS 0.010 0.001 HIS L 81 PHE 0.026 0.002 PHE n 90 TYR 0.056 0.002 TYR m 144 ARG 0.010 0.001 ARG S 83 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18488 Ramachandran restraints generated. 9244 Oldfield, 0 Emsley, 9244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18488 Ramachandran restraints generated. 9244 Oldfield, 0 Emsley, 9244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 747 residues out of total 7883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 571 time to evaluate : 6.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8792 (mmm) cc_final: 0.8185 (mmm) REVERT: A 429 VAL cc_start: 0.9332 (OUTLIER) cc_final: 0.9071 (t) REVERT: B 296 MET cc_start: 0.8749 (OUTLIER) cc_final: 0.8486 (pmm) REVERT: B 306 MET cc_start: 0.8800 (mmm) cc_final: 0.8391 (mmm) REVERT: B 318 MET cc_start: 0.8240 (mtt) cc_final: 0.7974 (mtt) REVERT: B 344 VAL cc_start: 0.9442 (OUTLIER) cc_final: 0.9180 (m) REVERT: B 346 MET cc_start: 0.8369 (tmm) cc_final: 0.7951 (tmm) REVERT: B 359 ARG cc_start: 0.9032 (OUTLIER) cc_final: 0.8307 (ttm170) REVERT: B 458 MET cc_start: 0.8386 (mtp) cc_final: 0.7862 (mtp) REVERT: B 485 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.8062 (mp0) REVERT: C 296 MET cc_start: 0.8252 (ppp) cc_final: 0.7575 (ppp) REVERT: C 392 VAL cc_start: 0.9311 (OUTLIER) cc_final: 0.8943 (m) REVERT: C 455 SER cc_start: 0.8597 (OUTLIER) cc_final: 0.7994 (m) REVERT: D 331 ARG cc_start: 0.9024 (OUTLIER) cc_final: 0.7090 (mtm180) REVERT: D 350 MET cc_start: 0.8239 (mtp) cc_final: 0.7862 (mtp) REVERT: D 493 MET cc_start: 0.8899 (ppp) cc_final: 0.8205 (ppp) REVERT: E 163 MET cc_start: 0.8189 (tmm) cc_final: 0.7787 (tmm) REVERT: E 321 MET cc_start: 0.8837 (tpp) cc_final: 0.8257 (tpp) REVERT: E 374 ASP cc_start: 0.8574 (t0) cc_final: 0.8342 (t0) REVERT: E 396 MET cc_start: 0.8877 (OUTLIER) cc_final: 0.7909 (ttp) REVERT: E 425 ASP cc_start: 0.8740 (m-30) cc_final: 0.8495 (m-30) REVERT: E 442 ASP cc_start: 0.8600 (OUTLIER) cc_final: 0.8314 (t0) REVERT: E 485 MET cc_start: 0.8400 (mtp) cc_final: 0.8133 (mtm) REVERT: E 493 MET cc_start: 0.9012 (tpp) cc_final: 0.8554 (tpp) REVERT: F 140 MET cc_start: 0.8795 (ppp) cc_final: 0.8473 (ppp) REVERT: F 266 ILE cc_start: 0.9364 (OUTLIER) cc_final: 0.8977 (mm) REVERT: F 321 MET cc_start: 0.8810 (ttm) cc_final: 0.8378 (ttm) REVERT: H 8 GLU cc_start: 0.7634 (mp0) cc_final: 0.7416 (mp0) REVERT: H 14 MET cc_start: 0.8570 (tmm) cc_final: 0.7908 (tmm) REVERT: H 112 TYR cc_start: 0.7799 (t80) cc_final: 0.7452 (t80) REVERT: I 72 MET cc_start: 0.8617 (tpp) cc_final: 0.7805 (tpp) REVERT: I 76 MET cc_start: 0.8801 (mmm) cc_final: 0.8148 (mmp) REVERT: I 132 MET cc_start: 0.8173 (mmt) cc_final: 0.7759 (mmm) REVERT: J 127 LEU cc_start: 0.9429 (OUTLIER) cc_final: 0.8931 (mp) REVERT: J 132 MET cc_start: 0.8168 (OUTLIER) cc_final: 0.7689 (mmt) REVERT: K 82 LYS cc_start: 0.9212 (OUTLIER) cc_final: 0.8696 (pptt) REVERT: L 6 LYS cc_start: 0.9322 (mptp) cc_final: 0.8651 (mmmm) REVERT: L 54 GLN cc_start: 0.8952 (tp-100) cc_final: 0.8680 (tp-100) REVERT: L 59 GLU cc_start: 0.8944 (mp0) cc_final: 0.8538 (pp20) REVERT: L 90 GLU cc_start: 0.7516 (pt0) cc_final: 0.7156 (pt0) REVERT: L 112 MET cc_start: 0.7765 (ppp) cc_final: 0.7381 (ppp) REVERT: Q 62 PHE cc_start: 0.8316 (OUTLIER) cc_final: 0.7591 (t80) REVERT: Q 155 MET cc_start: 0.8977 (mmp) cc_final: 0.8596 (mmp) REVERT: Q 188 MET cc_start: 0.8635 (ptm) cc_final: 0.8187 (ppp) REVERT: R 32 CYS cc_start: 0.8075 (OUTLIER) cc_final: 0.7783 (t) REVERT: R 33 MET cc_start: 0.8921 (tpt) cc_final: 0.8457 (tpp) REVERT: R 103 MET cc_start: 0.6787 (tpp) cc_final: 0.6564 (tpp) REVERT: R 122 TRP cc_start: 0.8990 (OUTLIER) cc_final: 0.8495 (t-100) REVERT: R 139 TYR cc_start: 0.8693 (t80) cc_final: 0.8388 (t80) REVERT: R 168 ILE cc_start: 0.9343 (OUTLIER) cc_final: 0.9067 (tp) REVERT: R 170 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.8257 (tm-30) REVERT: R 197 TYR cc_start: 0.3751 (OUTLIER) cc_final: 0.3287 (t80) REVERT: S 103 MET cc_start: 0.7295 (tpp) cc_final: 0.6637 (tpp) REVERT: S 188 MET cc_start: 0.8926 (mtm) cc_final: 0.8514 (mtp) REVERT: U 345 TYR cc_start: 0.8726 (m-80) cc_final: 0.8477 (m-10) REVERT: U 432 GLU cc_start: 0.8485 (pp20) cc_final: 0.8255 (tm-30) REVERT: a 61 MET cc_start: 0.9023 (mmm) cc_final: 0.8746 (mmm) REVERT: a 423 MET cc_start: 0.9492 (OUTLIER) cc_final: 0.9032 (tmm) REVERT: a 453 MET cc_start: 0.9040 (ptm) cc_final: 0.8806 (ptm) REVERT: a 484 MET cc_start: 0.8193 (OUTLIER) cc_final: 0.7791 (tpp) REVERT: a 538 MET cc_start: 0.8750 (mtm) cc_final: 0.8474 (tmm) REVERT: a 550 MET cc_start: 0.9095 (mmt) cc_final: 0.8708 (mmm) REVERT: a 580 MET cc_start: 0.8097 (ppp) cc_final: 0.7846 (ppp) REVERT: a 583 LEU cc_start: 0.9342 (mt) cc_final: 0.9104 (mt) REVERT: a 616 MET cc_start: 0.9078 (ppp) cc_final: 0.8731 (ppp) REVERT: a 759 MET cc_start: 0.9102 (mmm) cc_final: 0.8654 (tpp) REVERT: b 82 LYS cc_start: 0.9083 (OUTLIER) cc_final: 0.8740 (ptpp) REVERT: b 98 GLU cc_start: 0.9163 (mm-30) cc_final: 0.8794 (mm-30) REVERT: b 175 LYS cc_start: 0.8729 (ptpp) cc_final: 0.8455 (pttt) REVERT: b 180 GLU cc_start: 0.9217 (OUTLIER) cc_final: 0.8701 (pm20) REVERT: c 319 MET cc_start: 0.8584 (tpp) cc_final: 0.7660 (ttt) REVERT: c 366 TYR cc_start: 0.8428 (m-80) cc_final: 0.8124 (m-80) REVERT: c 434 PHE cc_start: 0.9031 (OUTLIER) cc_final: 0.8684 (t80) REVERT: c 438 ILE cc_start: 0.9129 (mm) cc_final: 0.8892 (mm) REVERT: c 443 LEU cc_start: 0.9696 (OUTLIER) cc_final: 0.9471 (mm) REVERT: c 445 MET cc_start: 0.8907 (mmp) cc_final: 0.8532 (mmm) REVERT: d 129 CYS cc_start: 0.8763 (m) cc_final: 0.8386 (m) REVERT: d 157 ASP cc_start: 0.8568 (OUTLIER) cc_final: 0.8310 (t0) REVERT: d 176 MET cc_start: 0.8513 (OUTLIER) cc_final: 0.8106 (tmm) REVERT: e 49 TYR cc_start: 0.8877 (t80) cc_final: 0.8598 (t80) REVERT: e 56 ILE cc_start: 0.9316 (OUTLIER) cc_final: 0.9051 (mm) REVERT: e 67 GLN cc_start: 0.9011 (mm110) cc_final: 0.8540 (mm-40) REVERT: f 28 MET cc_start: 0.9082 (mmm) cc_final: 0.8689 (mmm) REVERT: g 17 MET cc_start: 0.8705 (tmm) cc_final: 0.8208 (tmm) REVERT: g 47 MET cc_start: 0.8160 (mmm) cc_final: 0.7784 (mmm) REVERT: g 115 ASP cc_start: 0.8327 (OUTLIER) cc_final: 0.7928 (t70) REVERT: g 144 TYR cc_start: 0.8827 (m-80) cc_final: 0.8290 (m-80) REVERT: h 23 MET cc_start: 0.8532 (tpp) cc_final: 0.8004 (tpp) REVERT: h 32 TYR cc_start: 0.9001 (t80) cc_final: 0.8722 (t80) REVERT: h 68 TYR cc_start: 0.8665 (m-10) cc_final: 0.8362 (m-10) REVERT: h 82 GLU cc_start: 0.8974 (OUTLIER) cc_final: 0.8641 (tp30) REVERT: h 115 ASP cc_start: 0.8250 (t0) cc_final: 0.7548 (t0) REVERT: h 119 ARG cc_start: 0.7863 (mtm-85) cc_final: 0.7359 (mtm-85) REVERT: h 126 ARG cc_start: 0.8767 (OUTLIER) cc_final: 0.8431 (mtm110) REVERT: h 131 MET cc_start: 0.9187 (ttp) cc_final: 0.8880 (ttp) REVERT: i 23 MET cc_start: 0.8849 (tpp) cc_final: 0.7806 (tpp) REVERT: i 44 MET cc_start: 0.8201 (tmm) cc_final: 0.7936 (tpt) REVERT: i 53 MET cc_start: 0.8991 (mmt) cc_final: 0.8770 (mmm) REVERT: i 115 ASP cc_start: 0.8905 (t0) cc_final: 0.8601 (m-30) REVERT: i 127 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8340 (mp) REVERT: j 23 MET cc_start: 0.9153 (tmm) cc_final: 0.8581 (tmm) REVERT: j 36 LYS cc_start: 0.8975 (mmtm) cc_final: 0.8682 (mmtt) REVERT: j 44 MET cc_start: 0.8533 (tmm) cc_final: 0.8249 (tmm) REVERT: j 68 TYR cc_start: 0.9001 (m-10) cc_final: 0.8693 (m-10) REVERT: j 144 TYR cc_start: 0.9191 (m-10) cc_final: 0.8789 (m-10) REVERT: k 32 TYR cc_start: 0.8935 (t80) cc_final: 0.8123 (t80) REVERT: k 61 MET cc_start: 0.8702 (mtp) cc_final: 0.8457 (mtp) REVERT: k 68 TYR cc_start: 0.8857 (m-10) cc_final: 0.8628 (m-10) REVERT: k 123 GLN cc_start: 0.9275 (mm-40) cc_final: 0.8997 (mm-40) REVERT: k 131 MET cc_start: 0.8849 (tpt) cc_final: 0.8492 (tpt) REVERT: l 17 MET cc_start: 0.9039 (tpp) cc_final: 0.8684 (ptt) REVERT: l 23 MET cc_start: 0.9458 (tpp) cc_final: 0.8954 (tpp) REVERT: l 32 TYR cc_start: 0.8447 (t80) cc_final: 0.8123 (t80) REVERT: l 54 LYS cc_start: 0.9039 (ptpp) cc_final: 0.8628 (ptpp) REVERT: l 119 ARG cc_start: 0.8435 (mmt-90) cc_final: 0.8190 (mmt-90) REVERT: l 131 MET cc_start: 0.9126 (tmm) cc_final: 0.8607 (tmm) REVERT: m 13 PHE cc_start: 0.8999 (t80) cc_final: 0.8757 (t80) REVERT: m 17 MET cc_start: 0.8977 (mmp) cc_final: 0.8554 (mmp) REVERT: m 47 MET cc_start: 0.8985 (tpp) cc_final: 0.8563 (tpp) REVERT: m 78 ASN cc_start: 0.9100 (p0) cc_final: 0.8850 (p0) REVERT: n 13 PHE cc_start: 0.9380 (t80) cc_final: 0.9062 (t80) REVERT: n 17 MET cc_start: 0.9128 (mmp) cc_final: 0.8607 (mmp) REVERT: n 36 LYS cc_start: 0.8945 (ttmt) cc_final: 0.7872 (ttmm) REVERT: n 47 MET cc_start: 0.9311 (tpp) cc_final: 0.8945 (tpp) REVERT: n 48 ARG cc_start: 0.8854 (mtp85) cc_final: 0.8464 (mtp85) REVERT: n 61 MET cc_start: 0.8760 (mtp) cc_final: 0.8323 (ttm) REVERT: n 115 ASP cc_start: 0.8782 (t0) cc_final: 0.8426 (t0) REVERT: n 123 GLN cc_start: 0.9103 (mp10) cc_final: 0.8692 (mp10) REVERT: o 44 MET cc_start: 0.9142 (mmp) cc_final: 0.8712 (mmt) REVERT: o 61 MET cc_start: 0.8648 (OUTLIER) cc_final: 0.8374 (mtt) REVERT: o 87 TYR cc_start: 0.8900 (t80) cc_final: 0.8539 (t80) REVERT: o 108 PHE cc_start: 0.8887 (m-10) cc_final: 0.8544 (t80) REVERT: o 115 ASP cc_start: 0.9235 (t0) cc_final: 0.8951 (m-30) REVERT: o 123 GLN cc_start: 0.9340 (mp10) cc_final: 0.9062 (mp10) REVERT: o 139 GLU cc_start: 0.8892 (tm-30) cc_final: 0.8604 (tp30) REVERT: p 301 ASN cc_start: 0.8566 (OUTLIER) cc_final: 0.7822 (p0) REVERT: p 303 ASP cc_start: 0.9278 (p0) cc_final: 0.8897 (p0) REVERT: p 342 ARG cc_start: 0.8962 (ttp80) cc_final: 0.8484 (ttp80) outliers start: 176 outliers final: 127 residues processed: 709 average time/residue: 0.6510 time to fit residues: 793.3182 Evaluate side-chains 730 residues out of total 7883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 568 time to evaluate : 6.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 HIS Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 419 ASP Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 450 TRP Chi-restraints excluded: chain A residue 487 GLU Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 296 MET Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 359 ARG Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 485 GLU Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 171 ARG Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain C residue 392 VAL Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 489 LEU Chi-restraints excluded: chain C residue 514 LEU Chi-restraints excluded: chain C residue 518 ASP Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 327 THR Chi-restraints excluded: chain D residue 331 ARG Chi-restraints excluded: chain D residue 338 ARG Chi-restraints excluded: chain D residue 353 ASP Chi-restraints excluded: chain D residue 455 ASN Chi-restraints excluded: chain D residue 466 SER Chi-restraints excluded: chain E residue 293 ASP Chi-restraints excluded: chain E residue 328 ILE Chi-restraints excluded: chain E residue 396 MET Chi-restraints excluded: chain E residue 442 ASP Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 228 MET Chi-restraints excluded: chain F residue 266 ILE Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain H residue 27 GLN Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 85 GLN Chi-restraints excluded: chain H residue 113 HIS Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 121 LEU Chi-restraints excluded: chain H residue 187 ILE Chi-restraints excluded: chain H residue 193 GLU Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain I residue 159 THR Chi-restraints excluded: chain J residue 127 LEU Chi-restraints excluded: chain J residue 132 MET Chi-restraints excluded: chain J residue 191 LYS Chi-restraints excluded: chain J residue 192 VAL Chi-restraints excluded: chain J residue 207 MET Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain K residue 82 LYS Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 65 LEU Chi-restraints excluded: chain L residue 85 ILE Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain N residue 93 ASP Chi-restraints excluded: chain O residue 93 ASP Chi-restraints excluded: chain Q residue 62 PHE Chi-restraints excluded: chain Q residue 103 MET Chi-restraints excluded: chain R residue 32 CYS Chi-restraints excluded: chain R residue 51 ASP Chi-restraints excluded: chain R residue 122 TRP Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain R residue 168 ILE Chi-restraints excluded: chain R residue 170 GLU Chi-restraints excluded: chain R residue 197 TYR Chi-restraints excluded: chain U residue 264 HIS Chi-restraints excluded: chain U residue 380 HIS Chi-restraints excluded: chain U residue 386 THR Chi-restraints excluded: chain a residue 385 THR Chi-restraints excluded: chain a residue 423 MET Chi-restraints excluded: chain a residue 452 LEU Chi-restraints excluded: chain a residue 484 MET Chi-restraints excluded: chain a residue 486 ASP Chi-restraints excluded: chain a residue 556 SER Chi-restraints excluded: chain a residue 623 ASP Chi-restraints excluded: chain a residue 650 TRP Chi-restraints excluded: chain a residue 776 LEU Chi-restraints excluded: chain a residue 821 PHE Chi-restraints excluded: chain b residue 28 ILE Chi-restraints excluded: chain b residue 30 ASP Chi-restraints excluded: chain b residue 82 LYS Chi-restraints excluded: chain b residue 180 GLU Chi-restraints excluded: chain c residue 287 LEU Chi-restraints excluded: chain c residue 325 ILE Chi-restraints excluded: chain c residue 339 PHE Chi-restraints excluded: chain c residue 364 SER Chi-restraints excluded: chain c residue 365 ILE Chi-restraints excluded: chain c residue 377 ASN Chi-restraints excluded: chain c residue 434 PHE Chi-restraints excluded: chain c residue 443 LEU Chi-restraints excluded: chain d residue 20 VAL Chi-restraints excluded: chain d residue 39 CYS Chi-restraints excluded: chain d residue 63 SER Chi-restraints excluded: chain d residue 110 ILE Chi-restraints excluded: chain d residue 141 VAL Chi-restraints excluded: chain d residue 145 GLN Chi-restraints excluded: chain d residue 157 ASP Chi-restraints excluded: chain d residue 176 MET Chi-restraints excluded: chain d residue 304 LEU Chi-restraints excluded: chain e residue 28 ILE Chi-restraints excluded: chain e residue 56 ILE Chi-restraints excluded: chain f residue 78 LEU Chi-restraints excluded: chain g residue 99 VAL Chi-restraints excluded: chain g residue 115 ASP Chi-restraints excluded: chain g residue 123 GLN Chi-restraints excluded: chain g residue 148 VAL Chi-restraints excluded: chain h residue 81 THR Chi-restraints excluded: chain h residue 82 GLU Chi-restraints excluded: chain h residue 126 ARG Chi-restraints excluded: chain h residue 140 VAL Chi-restraints excluded: chain i residue 127 LEU Chi-restraints excluded: chain j residue 24 VAL Chi-restraints excluded: chain j residue 99 VAL Chi-restraints excluded: chain k residue 24 VAL Chi-restraints excluded: chain k residue 118 VAL Chi-restraints excluded: chain k residue 140 VAL Chi-restraints excluded: chain l residue 48 ARG Chi-restraints excluded: chain l residue 110 ILE Chi-restraints excluded: chain m residue 45 SER Chi-restraints excluded: chain m residue 64 ILE Chi-restraints excluded: chain m residue 97 LEU Chi-restraints excluded: chain n residue 10 TYR Chi-restraints excluded: chain n residue 67 ILE Chi-restraints excluded: chain n residue 82 GLU Chi-restraints excluded: chain n residue 143 LEU Chi-restraints excluded: chain o residue 61 MET Chi-restraints excluded: chain o residue 67 ILE Chi-restraints excluded: chain o residue 118 VAL Chi-restraints excluded: chain o residue 143 LEU Chi-restraints excluded: chain p residue 301 ASN Chi-restraints excluded: chain p residue 322 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 923 random chunks: chunk 581 optimal weight: 0.5980 chunk 780 optimal weight: 0.9980 chunk 224 optimal weight: 4.9990 chunk 675 optimal weight: 10.0000 chunk 108 optimal weight: 0.8980 chunk 203 optimal weight: 0.8980 chunk 733 optimal weight: 5.9990 chunk 306 optimal weight: 0.8980 chunk 753 optimal weight: 8.9990 chunk 92 optimal weight: 2.9990 chunk 135 optimal weight: 10.0000 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 256 ASN ** E 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 379 ASN d 48 HIS d 302 ASN ** g 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.046001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.037266 restraints weight = 555362.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.038273 restraints weight = 272697.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.038910 restraints weight = 164216.683| |-----------------------------------------------------------------------------| r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 69826 Z= 0.186 Angle : 0.629 14.383 94787 Z= 0.313 Chirality : 0.041 0.282 11071 Planarity : 0.004 0.054 12263 Dihedral : 5.153 82.458 10035 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.89 % Favored : 96.08 % Rotamer: Outliers : 2.11 % Allowed : 16.58 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.99 % 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: 9244 helix: 2.34 (0.07), residues: 5453 sheet: -1.02 (0.19), residues: 732 loop : -0.68 (0.12), residues: 3059 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A 567 HIS 0.007 0.001 HIS L 81 PHE 0.027 0.001 PHE e 19 TYR 0.060 0.001 TYR m 144 ARG 0.009 0.000 ARG i 126 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14211.54 seconds wall clock time: 252 minutes 10.03 seconds (15130.03 seconds total)