Starting phenix.real_space_refine on Sat Jan 20 02:12:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zmw_11302/01_2024/6zmw_11302_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zmw_11302/01_2024/6zmw_11302.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zmw_11302/01_2024/6zmw_11302_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zmw_11302/01_2024/6zmw_11302_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zmw_11302/01_2024/6zmw_11302_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zmw_11302/01_2024/6zmw_11302.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zmw_11302/01_2024/6zmw_11302.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zmw_11302/01_2024/6zmw_11302_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zmw_11302/01_2024/6zmw_11302_updated.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 1820 5.49 5 Mg 89 5.21 5 S 329 5.16 5 C 66884 2.51 5 N 21767 2.21 5 O 27264 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "1 ARG 492": "NH1" <-> "NH2" Residue "1 ARG 501": "NH1" <-> "NH2" Residue "1 ARG 505": "NH1" <-> "NH2" Residue "1 ARG 507": "NH1" <-> "NH2" Residue "1 ASP 531": "OD1" <-> "OD2" Residue "1 ARG 550": "NH1" <-> "NH2" Residue "1 ASP 557": "OD1" <-> "OD2" Residue "6 ARG 317": "NH1" <-> "NH2" Residue "6 ARG 330": "NH1" <-> "NH2" Residue "6 PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u GLU 9": "OE1" <-> "OE2" Residue "u ARG 14": "NH1" <-> "NH2" Residue "u ARG 14": "NH1" <-> "NH2" Residue "u ASP 33": "OD1" <-> "OD2" Residue "u ASP 60": "OD1" <-> "OD2" Residue "u ARG 62": "NH1" <-> "NH2" Residue "u TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ARG 140": "NH1" <-> "NH2" Residue "u ARG 143": "NH1" <-> "NH2" Residue "u ASP 162": "OD1" <-> "OD2" Residue "u ARG 169": "NH1" <-> "NH2" Residue "u PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ARG 195": "NH1" <-> "NH2" Residue "u ARG 298": "NH1" <-> "NH2" Residue "u ARG 304": "NH1" <-> "NH2" Residue "u GLU 305": "OE1" <-> "OE2" Residue "u ARG 307": "NH1" <-> "NH2" Residue "u ARG 317": "NH1" <-> "NH2" Residue "u ARG 321": "NH1" <-> "NH2" Residue "u GLU 334": "OE1" <-> "OE2" Residue "u ASP 343": "OD1" <-> "OD2" Residue "u ARG 376": "NH1" <-> "NH2" Residue "u PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u GLU 386": "OE1" <-> "OE2" Residue "u TYR 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u PHE 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ARG 406": "NH1" <-> "NH2" Residue "u ARG 415": "NH1" <-> "NH2" Residue "u ARG 438": "NH1" <-> "NH2" Residue "u TYR 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u GLU 451": "OE1" <-> "OE2" Residue "u ARG 454": "NH1" <-> "NH2" Residue "u ASP 463": "OD1" <-> "OD2" Residue "u GLU 468": "OE1" <-> "OE2" Residue "u ASP 473": "OD1" <-> "OD2" Residue "u ARG 483": "NH1" <-> "NH2" Residue "u ARG 489": "NH1" <-> "NH2" Residue "u PHE 493": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u TYR 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ARG 502": "NH1" <-> "NH2" Residue "u GLU 517": "OE1" <-> "OE2" Residue "u GLU 548": "OE1" <-> "OE2" Residue "u ARG 572": "NH1" <-> "NH2" Residue "v PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v ASP 230": "OD1" <-> "OD2" Residue "v PHE 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v ASP 266": "OD1" <-> "OD2" Residue "v ASP 276": "OD1" <-> "OD2" Residue "v TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v TYR 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v TYR 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v PHE 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v ASP 381": "OD1" <-> "OD2" Residue "v TYR 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 19": "OD1" <-> "OD2" Residue "S GLU 44": "OE1" <-> "OE2" Residue "S ASP 126": "OD1" <-> "OD2" Residue "S ARG 131": "NH1" <-> "NH2" Residue "S ARG 132": "NH1" <-> "NH2" Residue "S GLU 150": "OE1" <-> "OE2" Residue "S GLU 165": "OE1" <-> "OE2" Residue "S ARG 178": "NH1" <-> "NH2" Residue "S GLU 204": "OE1" <-> "OE2" Residue "S GLU 205": "OE1" <-> "OE2" Residue "S GLU 219": "OE1" <-> "OE2" Residue "y ARG 56": "NH1" <-> "NH2" Residue "y GLU 58": "OE1" <-> "OE2" Residue "y GLU 59": "OE1" <-> "OE2" Residue "y ARG 74": "NH1" <-> "NH2" Residue "y GLU 84": "OE1" <-> "OE2" Residue "y TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y ARG 104": "NH1" <-> "NH2" Residue "y ARG 108": "NH1" <-> "NH2" Residue "y ASP 112": "OD1" <-> "OD2" Residue "y GLU 119": "OE1" <-> "OE2" Residue "y GLU 122": "OE1" <-> "OE2" Residue "y ARG 142": "NH1" <-> "NH2" Residue "y GLU 153": "OE1" <-> "OE2" Residue "y ASP 346": "OD1" <-> "OD2" Residue "y PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y ASP 452": "OD1" <-> "OD2" Residue "y GLU 468": "OE1" <-> "OE2" Residue "y TYR 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y TYR 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y ARG 521": "NH1" <-> "NH2" Residue "y GLU 542": "OE1" <-> "OE2" Residue "y GLU 549": "OE1" <-> "OE2" Residue "y TYR 554": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y ARG 560": "NH1" <-> "NH2" Residue "y ASP 562": "OD1" <-> "OD2" Residue "y ARG 565": "NH1" <-> "NH2" Residue "y ARG 581": "NH1" <-> "NH2" Residue "y ARG 586": "NH1" <-> "NH2" Residue "y ARG 622": "NH1" <-> "NH2" Residue "y ASP 628": "OD1" <-> "OD2" Residue "y ARG 641": "NH1" <-> "NH2" Residue "y ARG 658": "NH1" <-> "NH2" Residue "y GLU 661": "OE1" <-> "OE2" Residue "y GLU 666": "OE1" <-> "OE2" Residue "y ARG 668": "NH1" <-> "NH2" Residue "y ARG 669": "NH1" <-> "NH2" Residue "y ASP 704": "OD1" <-> "OD2" Residue "y ARG 706": "NH1" <-> "NH2" Residue "y ARG 707": "NH1" <-> "NH2" Residue "y ARG 708": "NH1" <-> "NH2" Residue "y ARG 719": "NH1" <-> "NH2" Residue "y ARG 723": "NH1" <-> "NH2" Residue "y ARG 776": "NH1" <-> "NH2" Residue "y ARG 781": "NH1" <-> "NH2" Residue "y GLU 785": "OE1" <-> "OE2" Residue "y GLU 786": "OE1" <-> "OE2" Residue "y ARG 789": "NH1" <-> "NH2" Residue "y TYR 795": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y ASP 809": "OD1" <-> "OD2" Residue "y GLU 848": "OE1" <-> "OE2" Residue "G ASP 17": "OD1" <-> "OD2" Residue "G GLU 18": "OE1" <-> "OE2" Residue "G GLU 29": "OE1" <-> "OE2" Residue "G ASP 35": "OD1" <-> "OD2" Residue "G ARG 57": "NH1" <-> "NH2" Residue "G PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 78": "NH1" <-> "NH2" Residue "G ARG 81": "NH1" <-> "NH2" Residue "G PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 99": "NH1" <-> "NH2" Residue "G ARG 106": "NH1" <-> "NH2" Residue "G ARG 143": "NH1" <-> "NH2" Residue "G ASP 159": "OD1" <-> "OD2" Residue "G PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 6": "OD1" <-> "OD2" Residue "H GLU 15": "OE1" <-> "OE2" Residue "H PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 75": "OE1" <-> "OE2" Residue "K ASP 4": "OD1" <-> "OD2" Residue "K PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 79": "OE1" <-> "OE2" Residue "L GLU 92": "OE1" <-> "OE2" Residue "L ASP 95": "OD1" <-> "OD2" Residue "L PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 105": "OE1" <-> "OE2" Residue "L ARG 117": "NH1" <-> "NH2" Residue "L ARG 123": "NH1" <-> "NH2" Residue "L PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 146": "OE1" <-> "OE2" Residue "L ARG 166": "NH1" <-> "NH2" Residue "L ARG 167": "NH1" <-> "NH2" Residue "L ARG 200": "NH1" <-> "NH2" Residue "L ASP 220": "OD1" <-> "OD2" Residue "L ASP 221": "OD1" <-> "OD2" Residue "L ARG 227": "NH1" <-> "NH2" Residue "L GLU 268": "OE1" <-> "OE2" Residue "O TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 32": "OD1" <-> "OD2" Residue "O PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 68": "OE1" <-> "OE2" Residue "O ASP 73": "OD1" <-> "OD2" Residue "O ASP 77": "OD1" <-> "OD2" Residue "O ARG 82": "NH1" <-> "NH2" Residue "O GLU 89": "OE1" <-> "OE2" Residue "O ASP 108": "OD1" <-> "OD2" Residue "O PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 151": "NH1" <-> "NH2" Residue "O ARG 162": "NH1" <-> "NH2" Residue "O ARG 165": "NH1" <-> "NH2" Residue "O GLU 198": "OE1" <-> "OE2" Residue "O TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 213": "NH1" <-> "NH2" Residue "O PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 13": "OE1" <-> "OE2" Residue "N PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 126": "OD1" <-> "OD2" Residue "N ASP 151": "OD1" <-> "OD2" Residue "N GLU 196": "OE1" <-> "OE2" Residue "Q ARG 10": "NH1" <-> "NH2" Residue "Q GLU 55": "OE1" <-> "OE2" Residue "Q TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 85": "NH1" <-> "NH2" Residue "Q ARG 87": "NH1" <-> "NH2" Residue "Q ARG 89": "NH1" <-> "NH2" Residue "P GLU 23": "OE1" <-> "OE2" Residue "P PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 51": "OE1" <-> "OE2" Residue "P ASP 80": "OD1" <-> "OD2" Residue "P ARG 117": "NH1" <-> "NH2" Residue "P ARG 141": "NH1" <-> "NH2" Residue "P ARG 150": "NH1" <-> "NH2" Residue "I TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 31": "OD1" <-> "OD2" Residue "I TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 104": "NH1" <-> "NH2" Residue "I ARG 114": "NH1" <-> "NH2" Residue "I ARG 121": "NH1" <-> "NH2" Residue "I TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 142": "OE1" <-> "OE2" Residue "x ARG 26": "NH1" <-> "NH2" Residue "x PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x ASP 84": "OD1" <-> "OD2" Residue "x GLU 293": "OE1" <-> "OE2" Residue "x GLU 297": "OE1" <-> "OE2" Residue "x GLU 315": "OE1" <-> "OE2" Residue "x ARG 329": "NH1" <-> "NH2" Residue "x ARG 362": "NH1" <-> "NH2" Residue "x GLU 376": "OE1" <-> "OE2" Residue "x GLU 398": "OE1" <-> "OE2" Residue "x ASP 408": "OD1" <-> "OD2" Residue "x ARG 462": "NH1" <-> "NH2" Residue "x GLU 475": "OE1" <-> "OE2" Residue "9 ARG 2": "NH1" <-> "NH2" Residue "9 ARG 23": "NH1" <-> "NH2" Residue "B GLU 49": "OE1" <-> "OE2" Residue "B GLU 52": "OE1" <-> "OE2" Residue "B ARG 97": "NH1" <-> "NH2" Residue "B ASP 119": "OD1" <-> "OD2" Residue "C ARG 11": "NH1" <-> "NH2" Residue "C ARG 49": "NH1" <-> "NH2" Residue "C ARG 68": "NH1" <-> "NH2" Residue "C ASP 88": "OD1" <-> "OD2" Residue "C GLU 117": "OE1" <-> "OE2" Residue "C PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 151": "OD1" <-> "OD2" Residue "C ASP 158": "OD1" <-> "OD2" Residue "C ARG 191": "NH1" <-> "NH2" Residue "C ARG 198": "NH1" <-> "NH2" Residue "C ARG 221": "NH1" <-> "NH2" Residue "C GLU 251": "OE1" <-> "OE2" Residue "C ARG 252": "NH1" <-> "NH2" Residue "D ARG 17": "NH1" <-> "NH2" Residue "D ARG 18": "NH1" <-> "NH2" Residue "D GLU 21": "OE1" <-> "OE2" Residue "D ASP 26": "OD1" <-> "OD2" Residue "D ARG 54": "NH1" <-> "NH2" Residue "D ARG 69": "NH1" <-> "NH2" Residue "D GLU 73": "OE1" <-> "OE2" Residue "D ASP 104": "OD1" <-> "OD2" Residue "D GLU 107": "OE1" <-> "OE2" Residue "D ASP 158": "OD1" <-> "OD2" Residue "D ARG 169": "NH1" <-> "NH2" Residue "E ARG 5": "NH1" <-> "NH2" Residue "E ARG 8": "NH1" <-> "NH2" Residue "E ARG 17": "NH1" <-> "NH2" Residue "E GLU 58": "OE1" <-> "OE2" Residue "E ARG 67": "NH1" <-> "NH2" Residue "E ASP 98": "OD1" <-> "OD2" Residue "E GLU 99": "OE1" <-> "OE2" Residue "E ARG 107": "NH1" <-> "NH2" Residue "F ARG 105": "NH1" <-> "NH2" Residue "r ARG 7": "NH1" <-> "NH2" Residue "r ARG 25": "NH1" <-> "NH2" Residue "r ARG 57": "NH1" <-> "NH2" Residue "r ARG 75": "NH1" <-> "NH2" Residue "r ASP 77": "OD1" <-> "OD2" Residue "r GLU 79": "OE1" <-> "OE2" Residue "r ARG 88": "NH1" <-> "NH2" Residue "r ARG 89": "NH1" <-> "NH2" Residue "r ARG 113": "NH1" <-> "NH2" Residue "r GLU 128": "OE1" <-> "OE2" Residue "r PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ARG 133": "NH1" <-> "NH2" Residue "r ARG 144": "NH1" <-> "NH2" Residue "r ARG 173": "NH1" <-> "NH2" Residue "r ARG 182": "NH1" <-> "NH2" Residue "r ARG 183": "NH1" <-> "NH2" Residue "r ASP 194": "OD1" <-> "OD2" Residue "r GLU 221": "OE1" <-> "OE2" Residue "r ARG 234": "NH1" <-> "NH2" Residue "r ARG 244": "NH1" <-> "NH2" Residue "r ARG 266": "NH1" <-> "NH2" Residue "J ASP 9": "OD1" <-> "OD2" Residue "J GLU 18": "OE1" <-> "OE2" Residue "J GLU 49": "OE1" <-> "OE2" Residue "J ASP 85": "OD1" <-> "OD2" Residue "J ASP 112": "OD1" <-> "OD2" Residue "R ARG 25": "NH1" <-> "NH2" Residue "R ARG 41": "NH1" <-> "NH2" Residue "R ASP 105": "OD1" <-> "OD2" Residue "R GLU 114": "OE1" <-> "OE2" Residue "R GLU 133": "OE1" <-> "OE2" Residue "R GLU 135": "OE1" <-> "OE2" Residue "R GLU 151": "OE1" <-> "OE2" Residue "R GLU 164": "OE1" <-> "OE2" Residue "R GLU 196": "OE1" <-> "OE2" Residue "T PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 20": "NH1" <-> "NH2" Residue "T ASP 26": "OD1" <-> "OD2" Residue "T ARG 41": "NH1" <-> "NH2" Residue "T ASP 53": "OD1" <-> "OD2" Residue "T ARG 61": "NH1" <-> "NH2" Residue "V ASP 26": "OD1" <-> "OD2" Residue "V ASP 37": "OD1" <-> "OD2" Residue "V ARG 62": "NH1" <-> "NH2" Residue "V ARG 71": "NH1" <-> "NH2" Residue "V ARG 81": "NH1" <-> "NH2" Residue "V ARG 127": "NH1" <-> "NH2" Residue "V ARG 135": "NH1" <-> "NH2" Residue "V GLU 160": "OE1" <-> "OE2" Residue "V ARG 164": "NH1" <-> "NH2" Residue "V GLU 176": "OE1" <-> "OE2" Residue "Y GLU 43": "OE1" <-> "OE2" Residue "Y ARG 45": "NH1" <-> "NH2" Residue "Y ARG 62": "NH1" <-> "NH2" Residue "Y ASP 101": "OD1" <-> "OD2" Residue "Y ARG 125": "NH1" <-> "NH2" Residue "Y ARG 126": "NH1" <-> "NH2" Residue "Y ARG 138": "NH1" <-> "NH2" Residue "Y ARG 140": "NH1" <-> "NH2" Residue "Z ARG 9": "NH1" <-> "NH2" Residue "Z ASP 14": "OD1" <-> "OD2" Residue "Z GLU 20": "OE1" <-> "OE2" Residue "Z GLU 38": "OE1" <-> "OE2" Residue "Z GLU 61": "OE1" <-> "OE2" Residue "Z GLU 81": "OE1" <-> "OE2" Residue "Z GLU 85": "OE1" <-> "OE2" Residue "Z ARG 94": "NH1" <-> "NH2" Residue "Z ARG 143": "NH1" <-> "NH2" Residue "Z ASP 169": "OD1" <-> "OD2" Residue "Z ASP 206": "OD1" <-> "OD2" Residue "Z ASP 215": "OD1" <-> "OD2" Residue "Z GLU 216": "OE1" <-> "OE2" Residue "a ASP 26": "OD1" <-> "OD2" Residue "a ARG 65": "NH1" <-> "NH2" Residue "a PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 74": "OE1" <-> "OE2" Residue "a GLU 88": "OE1" <-> "OE2" Residue "b GLU 31": "OE1" <-> "OE2" Residue "b ARG 61": "NH1" <-> "NH2" Residue "b GLU 71": "OE1" <-> "OE2" Residue "b ASP 82": "OD1" <-> "OD2" Residue "b GLU 110": "OE1" <-> "OE2" Residue "c GLU 3": "OE1" <-> "OE2" Residue "c ARG 47": "NH1" <-> "NH2" Residue "c GLU 49": "OE1" <-> "OE2" Residue "c ARG 57": "NH1" <-> "NH2" Residue "c ARG 100": "NH1" <-> "NH2" Residue "c ASP 126": "OD1" <-> "OD2" Residue "c ASP 144": "OD1" <-> "OD2" Residue "c GLU 149": "OE1" <-> "OE2" Residue "c ASP 213": "OD1" <-> "OD2" Residue "c GLU 223": "OE1" <-> "OE2" Residue "c ASP 231": "OD1" <-> "OD2" Residue "c GLU 262": "OE1" <-> "OE2" Residue "c GLU 269": "OE1" <-> "OE2" Residue "c GLU 273": "OE1" <-> "OE2" Residue "d GLU 13": "OE1" <-> "OE2" Residue "d GLU 44": "OE1" <-> "OE2" Residue "d GLU 50": "OE1" <-> "OE2" Residue "d ARG 62": "NH1" <-> "NH2" Residue "d ARG 102": "NH1" <-> "NH2" Residue "d ARG 121": "NH1" <-> "NH2" Residue "e ASP 56": "OD1" <-> "OD2" Residue "e GLU 75": "OE1" <-> "OE2" Residue "e ARG 80": "NH1" <-> "NH2" Residue "f ARG 14": "NH1" <-> "NH2" Residue "f ARG 39": "NH1" <-> "NH2" Residue "f ARG 55": "NH1" <-> "NH2" Residue "f GLU 61": "OE1" <-> "OE2" Residue "f ASP 81": "OD1" <-> "OD2" Residue "f ARG 86": "NH1" <-> "NH2" Residue "f ARG 108": "NH1" <-> "NH2" Residue "f ARG 141": "NH1" <-> "NH2" Residue "f ARG 142": "NH1" <-> "NH2" Residue "k ARG 118": "NH1" <-> "NH2" Residue "m ASP 29": "OD1" <-> "OD2" Residue "m GLU 66": "OE1" <-> "OE2" Residue "m GLU 71": "OE1" <-> "OE2" Residue "m GLU 97": "OE1" <-> "OE2" Residue "m ASP 122": "OD1" <-> "OD2" Residue "m GLU 125": "OE1" <-> "OE2" Residue "m GLU 126": "OE1" <-> "OE2" Residue "n ARG 13": "NH1" <-> "NH2" Residue "n ARG 40": "NH1" <-> "NH2" Residue "n ARG 44": "NH1" <-> "NH2" Residue "n GLU 52": "OE1" <-> "OE2" Residue "n GLU 60": "OE1" <-> "OE2" Residue "n GLU 62": "OE1" <-> "OE2" Residue "o ASP 249": "OD1" <-> "OD2" Residue "o GLU 252": "OE1" <-> "OE2" Residue "o GLU 257": "OE1" <-> "OE2" Residue "o ARG 295": "NH1" <-> "NH2" Residue "o ASP 306": "OD1" <-> "OD2" Residue "p ARG 38": "NH1" <-> "NH2" Residue "p ASP 52": "OD1" <-> "OD2" Residue "p ASP 53": "OD1" <-> "OD2" Residue "p GLU 81": "OE1" <-> "OE2" Residue "q ARG 24": "NH1" <-> "NH2" Residue "q ASP 31": "OD1" <-> "OD2" Residue "q GLU 34": "OE1" <-> "OE2" Residue "q ASP 83": "OD1" <-> "OD2" Residue "q ASP 90": "OD1" <-> "OD2" Residue "q GLU 108": "OE1" <-> "OE2" Residue "M ARG 3": "NH1" <-> "NH2" Residue "M ARG 5": "NH1" <-> "NH2" Residue "M GLU 18": "OE1" <-> "OE2" Residue "M ARG 78": "NH1" <-> "NH2" Residue "M GLU 79": "OE1" <-> "OE2" Residue "M ARG 81": "NH1" <-> "NH2" Residue "M GLU 94": "OE1" <-> "OE2" Residue "M ASP 101": "OD1" <-> "OD2" Residue "h ARG 21": "NH1" <-> "NH2" Residue "h PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ARG 87": "NH1" <-> "NH2" Residue "h GLU 96": "OE1" <-> "OE2" Residue "h GLU 111": "OE1" <-> "OE2" Residue "h GLU 113": "OE1" <-> "OE2" Residue "s TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ARG 188": "NH1" <-> "NH2" Residue "s ARG 200": "NH1" <-> "NH2" Residue "s ARG 211": "NH1" <-> "NH2" Residue "s PHE 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s GLU 243": "OE1" <-> "OE2" Residue "s ARG 261": "NH1" <-> "NH2" Residue "s PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s GLU 268": "OE1" <-> "OE2" Residue "s GLU 277": "OE1" <-> "OE2" Residue "s ARG 285": "NH1" <-> "NH2" Residue "s ASP 288": "OD1" <-> "OD2" Residue "s ASP 294": "OD1" <-> "OD2" Residue "s ARG 296": "NH1" <-> "NH2" Residue "s PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ARG 308": "NH1" <-> "NH2" Residue "j PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j GLU 53": "OE1" <-> "OE2" Residue "j ASP 71": "OD1" <-> "OD2" Residue "j GLU 111": "OE1" <-> "OE2" Residue "j ARG 141": "NH1" <-> "NH2" Residue "j GLU 143": "OE1" <-> "OE2" Residue "j ARG 190": "NH1" <-> "NH2" Residue "j PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ASP 219": "OD1" <-> "OD2" Residue "j GLU 222": "OE1" <-> "OE2" Residue "j PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j GLU 240": "OE1" <-> "OE2" Residue "j GLU 244": "OE1" <-> "OE2" Residue "j ARG 247": "NH1" <-> "NH2" Residue "j PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ARG 255": "NH1" <-> "NH2" Residue "j GLU 256": "OE1" <-> "OE2" Residue "j ASP 265": "OD1" <-> "OD2" Residue "j PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ARG 295": "NH1" <-> "NH2" Residue "j PHE 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ASP 312": "OD1" <-> "OD2" Residue "j ARG 316": "NH1" <-> "NH2" Residue "j ASP 330": "OD1" <-> "OD2" Residue "j TYR 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ASP 348": "OD1" <-> "OD2" Residue "j ARG 353": "NH1" <-> "NH2" Residue "j ARG 362": "NH1" <-> "NH2" Residue "j ARG 365": "NH1" <-> "NH2" Residue "j ARG 368": "NH1" <-> "NH2" Residue "j ASP 380": "OD1" <-> "OD2" Residue "j ARG 382": "NH1" <-> "NH2" Residue "j GLU 388": "OE1" <-> "OE2" Residue "j PHE 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ARG 763": "NH1" <-> "NH2" Residue "g ARG 765": "NH1" <-> "NH2" Residue "g PHE 776": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 789": "OD1" <-> "OD2" Residue "g GLU 792": "OE1" <-> "OE2" Residue "g ARG 793": "NH1" <-> "NH2" Residue "g ASP 799": "OD1" <-> "OD2" Residue "g PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 808": "OE1" <-> "OE2" Residue "g ARG 820": "NH1" <-> "NH2" Residue "g GLU 831": "OE1" <-> "OE2" Residue "g PHE 839": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ARG 840": "NH1" <-> "NH2" Residue "g ASP 854": "OD1" <-> "OD2" Residue "g GLU 859": "OE1" <-> "OE2" Residue "g GLU 883": "OE1" <-> "OE2" Residue "g GLU 885": "OE1" <-> "OE2" Residue "g GLU 886": "OE1" <-> "OE2" Residue "g ARG 888": "NH1" <-> "NH2" Residue "g ASP 889": "OD1" <-> "OD2" Residue "g ARG 892": "NH1" <-> "NH2" Residue "g GLU 933": "OE1" <-> "OE2" Residue "g ARG 937": "NH1" <-> "NH2" Residue "g PHE 948": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ARG 954": "NH1" <-> "NH2" Residue "g GLU 968": "OE1" <-> "OE2" Residue "g ARG 976": "NH1" <-> "NH2" Residue "g PHE 977": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.19s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 118155 Number of models: 1 Model: "" Number of chains: 62 Chain: "2" Number of atoms: 1493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 1493 Classifications: {'peptide': 304} Incomplete info: {'truncation_to_alanine': 260} Link IDs: {'PTRANS': 10, 'TRANS': 293} Chain breaks: 1 Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 943 Unresolved non-hydrogen angles: 1214 Unresolved non-hydrogen dihedrals: 797 Unresolved non-hydrogen chiralities: 79 Planarities with less than four sites: {'GLN:plan1': 9, 'ASP:plan': 20, 'TYR:plan': 8, 'ASN:plan1': 16, 'TRP:plan': 5, 'HIS:plan': 11, 'PHE:plan': 17, 'GLU:plan': 18, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 544 Chain: "1" Number of atoms: 3258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 588, 3258 Classifications: {'peptide': 588} Incomplete info: {'truncation_to_alanine': 433} Link IDs: {'PTRANS': 26, 'TRANS': 561} Chain breaks: 1 Unresolved chain link angles: 20 Unresolved non-hydrogen bonds: 1710 Unresolved non-hydrogen angles: 2190 Unresolved non-hydrogen dihedrals: 1495 Unresolved non-hydrogen chiralities: 116 Planarities with less than four sites: {'GLN:plan1': 24, 'ASP:plan': 38, 'TYR:plan': 17, 'ASN:plan1': 15, 'TRP:plan': 16, 'HIS:plan': 13, 'PHE:plan': 28, 'GLU:plan': 27, 'ARG:plan': 27} Unresolved non-hydrogen planarities: 994 Chain: "6" Number of atoms: 1917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 1917 Classifications: {'peptide': 350} Incomplete info: {'truncation_to_alanine': 263} Link IDs: {'PTRANS': 6, 'TRANS': 343} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 914 Unresolved non-hydrogen angles: 1159 Unresolved non-hydrogen dihedrals: 747 Unresolved non-hydrogen chiralities: 90 Planarities with less than four sites: {'GLN:plan1': 12, 'HIS:plan': 7, 'TYR:plan': 8, 'ASN:plan1': 11, 'TRP:plan': 2, 'ASP:plan': 20, 'PHE:plan': 10, 'GLU:plan': 27, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 473 Chain: "4" Number of atoms: 1272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 1272 Classifications: {'peptide': 257} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 226} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain breaks: 2 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 767 Unresolved non-hydrogen angles: 993 Unresolved non-hydrogen dihedrals: 618 Unresolved non-hydrogen chiralities: 87 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 8, 'TYR:plan': 11, 'ASN:plan1': 16, 'TRP:plan': 1, 'ASP:plan': 14, 'PHE:plan': 6, 'GLU:plan': 15, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 399 Chain: "u" Number of atoms: 5383 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 706, 5375 Classifications: {'peptide': 706} Incomplete info: {'truncation_to_alanine': 124} Link IDs: {'PTRANS': 25, 'TRANS': 680} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 493 Unresolved non-hydrogen angles: 600 Unresolved non-hydrogen dihedrals: 398 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 11, 'ASP:plan': 6, 'TYR:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 34, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 304 Conformer: "B" Number of residues, atoms: 706, 5375 Classifications: {'peptide': 706} Incomplete info: {'truncation_to_alanine': 124} Link IDs: {'PTRANS': 25, 'TRANS': 680} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 493 Unresolved non-hydrogen angles: 600 Unresolved non-hydrogen dihedrals: 398 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 11, 'ASP:plan': 6, 'TYR:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 34, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 304 bond proxies already assigned to first conformer: 5455 Chain: "v" Number of atoms: 2635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 2635 Classifications: {'peptide': 384} Incomplete info: {'truncation_to_alanine': 145} Link IDs: {'PTRANS': 10, 'TRANS': 373} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 559 Unresolved non-hydrogen angles: 715 Unresolved non-hydrogen dihedrals: 468 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'GLN:plan1': 9, 'ARG:plan': 9, 'TYR:plan': 10, 'ASN:plan1': 8, 'TRP:plan': 2, 'ASP:plan': 15, 'PHE:plan': 7, 'GLU:plan': 13, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 342 Chain: "S" Number of atoms: 1862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1862 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 10, 'TRANS': 219} Chain: "y" Number of atoms: 5470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 697, 5470 Classifications: {'peptide': 697} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PTRANS': 19, 'TRANS': 677} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 236 Unresolved non-hydrogen angles: 279 Unresolved non-hydrogen dihedrals: 206 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASP:plan': 6, 'ASN:plan1': 3, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 12, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 120 Chain: "8" Number of atoms: 1571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 1571 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 285} Link IDs: {'PTRANS': 12, 'TRANS': 304} Chain breaks: 1 Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 1046 Unresolved non-hydrogen angles: 1332 Unresolved non-hydrogen dihedrals: 868 Unresolved non-hydrogen chiralities: 84 Planarities with less than four sites: {'GLN:plan1': 31, 'ASP:plan': 16, 'TYR:plan': 14, 'ASN:plan1': 14, 'TRP:plan': 2, 'HIS:plan': 10, 'ASN%COO:plan1': 1, 'PHE:plan': 10, 'GLU:plan': 24, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 599 Chain: "G" Number of atoms: 1430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1430 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 9, 'TRANS': 167} Chain breaks: 2 Chain: "H" Number of atoms: 631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 631 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 5, 'TRANS': 75} Chain: "K" Number of atoms: 617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 617 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "L" Number of atoms: 1707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1707 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 12, 'TRANS': 207} Chain: "O" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1715 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 5, 'TRANS': 205} Chain: "N" Number of atoms: 1633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1633 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 12, 'TRANS': 194} Chain: "Q" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 792 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 6, 'TRANS': 92} Chain: "P" Number of atoms: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 997 Classifications: {'peptide': 133} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 127} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "I" Number of atoms: 1208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1208 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 141} Chain: "x" Number of atoms: 2831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 2831 Classifications: {'peptide': 421} Incomplete info: {'truncation_to_alanine': 172} Link IDs: {'PTRANS': 16, 'TRANS': 404} Chain breaks: 2 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 633 Unresolved non-hydrogen angles: 806 Unresolved non-hydrogen dihedrals: 531 Unresolved non-hydrogen chiralities: 51 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 7, 'ASN:plan1': 8, 'TRP:plan': 3, 'ASP:plan': 17, 'PHE:plan': 9, 'GLU:plan': 13, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 352 Chain: "3" Number of atoms: 1057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1057 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 189} Link IDs: {'PTRANS': 5, 'TRANS': 207} Chain breaks: 1 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 704 Unresolved non-hydrogen angles: 904 Unresolved non-hydrogen dihedrals: 590 Unresolved non-hydrogen chiralities: 61 Planarities with less than four sites: {'GLN:plan1': 14, 'HIS:plan': 5, 'TYR:plan': 7, 'ASN:plan1': 9, 'TRP:plan': 4, 'ASP:plan': 14, 'PHE:plan': 11, 'GLU:plan': 17, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 404 Chain: "5" Number of atoms: 1581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 1581 Classifications: {'peptide': 319} Incomplete info: {'truncation_to_alanine': 289} Link IDs: {'PTRANS': 5, 'TRANS': 313} Chain breaks: 5 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 1124 Unresolved non-hydrogen angles: 1435 Unresolved non-hydrogen dihedrals: 958 Unresolved non-hydrogen chiralities: 88 Planarities with less than four sites: {'GLN:plan1': 20, 'HIS:plan': 10, 'TYR:plan': 21, 'ASN:plan1': 11, 'TRP:plan': 3, 'ASP:plan': 18, 'PHE:plan': 18, 'GLU:plan': 21, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 653 Chain: "7" Number of atoms: 336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 336 Classifications: {'RNA': 28} Modifications used: {'rna3p_pur': 28} Link IDs: {'rna3p': 27} Unresolved non-hydrogen bonds: 336 Unresolved non-hydrogen angles: 532 Unresolved non-hydrogen dihedrals: 336 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {' A%rna3p_pur:plan2': 28, ' A%rna3p_pur:plan': 28} Unresolved non-hydrogen planarities: 336 Chain: "9" Number of atoms: 230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 230 Classifications: {'peptide': 24} Link IDs: {'TRANS': 23} Chain: "A" Number of atoms: 36670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1719, 36670 Classifications: {'DNA': 2, 'RNA': 1717} Modifications used: {'5*END': 1, 'rna2p': 1, 'rna2p_pur': 153, 'rna2p_pyr': 127, 'rna3p': 20, 'rna3p_pur': 737, 'rna3p_pyr': 670} Link IDs: {'rna2p': 280, 'rna3p': 1438} Chain breaks: 6 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 132 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {' U:plan': 1, ' C:plan': 2, ' C:plan2': 2} Unresolved non-hydrogen planarities: 31 Chain: "B" Number of atoms: 1166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1166 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain breaks: 1 Chain: "C" Number of atoms: 2035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2035 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 14, 'TRANS': 241} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "D" Number of atoms: 1477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1477 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "E" Number of atoms: 1087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1087 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 5, 'TRANS': 134} Chain: "F" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 378 Classifications: {'peptide': 47} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 44} Chain breaks: 1 Chain: "r" Number of atoms: 2215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2215 Classifications: {'peptide': 275} Link IDs: {'PTRANS': 9, 'TRANS': 265} Chain: "J" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1034 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 125} Chain: "R" Number of atoms: 1627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1627 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 6, 'TRANS': 191} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "T" Number of atoms: 1015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1015 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "V" Number of atoms: 1461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1461 Classifications: {'peptide': 184} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 178} Chain breaks: 1 Chain: "Y" Number of atoms: 1124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1124 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 135} Chain: "Z" Number of atoms: 1765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1765 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 11, 'TRANS': 215} Chain: "a" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 834 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 8, 'TRANS': 90} Chain: "b" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 913 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "c" Number of atoms: 2436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2436 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 10, 'TRANS': 302} Chain: "d" Number of atoms: 1105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1105 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 4, 'TRANS': 137} Chain: "e" Number of atoms: 523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 523 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "f" Number of atoms: 1176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1176 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 3, 'TRANS': 138} Chain: "i" Number of atoms: 419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 419 Classifications: {'peptide': 50} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 48} Chain: "k" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 435 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 1, 'TRANS': 51} Chain breaks: 1 Chain: "m" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 950 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 119} Chain: "n" Number of atoms: 498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 498 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "o" Number of atoms: 616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 616 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 1, 'TRANS': 75} Chain: "p" Number of atoms: 691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 691 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "q" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 714 Classifications: {'peptide': 88} Link IDs: {'TRANS': 87} Chain: "z" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 795 Classifications: {'peptide': 160} Incomplete info: {'truncation_to_alanine': 148} Link IDs: {'PTRANS': 2, 'TRANS': 157} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 525 Unresolved non-hydrogen angles: 642 Unresolved non-hydrogen dihedrals: 432 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'GLN:plan1': 9, 'TYR:plan': 3, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 17, 'PHE:plan': 3, 'GLU:plan': 23, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 258 Chain: "M" Number of atoms: 1064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1064 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 6, 'TRANS': 124} Chain: "h" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 817 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "s" Number of atoms: 1123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1123 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 5, 'TRANS': 132} Chain: "w" Number of atoms: 1604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1604 Classifications: {'RNA': 75} Modifications used: {'5*END': 1, 'rna2p_pur': 8, 'rna2p_pyr': 4, 'rna3p_pur': 34, 'rna3p_pyr': 29} Link IDs: {'rna2p': 12, 'rna3p': 62} Chain: "t" Number of atoms: 1750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 356, 1750 Classifications: {'peptide': 356} Incomplete info: {'truncation_to_alanine': 298} Link IDs: {'PTRANS': 15, 'TRANS': 340} Chain breaks: 4 Unresolved chain link angles: 15 Unresolved non-hydrogen bonds: 1009 Unresolved non-hydrogen angles: 1285 Unresolved non-hydrogen dihedrals: 814 Unresolved non-hydrogen chiralities: 125 Planarities with less than four sites: {'GLN:plan1': 13, 'ASP:plan': 9, 'TYR:plan': 6, 'ASN:plan1': 12, 'TRP:plan': 2, 'HIS:plan': 9, 'PHE:plan': 8, 'GLU:plan': 23, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 445 Chain: "j" Number of atoms: 3073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 3073 Classifications: {'peptide': 384} Link IDs: {'PTRANS': 10, 'TRANS': 373} Chain: "g" Number of atoms: 1848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1848 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 5, 'TRANS': 218} Chain breaks: 1 Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 87 Unusual residues: {' MG': 87} Classifications: {'undetermined': 87} Link IDs: {None: 86} Chain: "d" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "f" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "k" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 32793 SG CYS Q 26 172.166 158.017 123.278 1.00 25.98 S ATOM 33176 SG CYS Q 74 167.525 158.392 123.854 1.00 32.58 S ATOM A01RM SG CYS k 121 187.740 238.822 39.026 1.00102.58 S ATOM A01SM SG CYS k 126 183.977 238.502 40.115 1.00107.22 S ATOM A01VW SG CYS k 141 188.294 239.059 42.838 1.00 93.99 S ATOM A01WF SG CYS k 144 188.212 235.855 41.211 1.00 97.63 S Residues with excluded nonbonded symmetry interactions: 22 residue: pdb=" P A 7 10 " occ=0.00 ... (10 atoms not shown) pdb=" C1' A 7 10 " occ=0.00 residue: pdb=" P A 7 11 " occ=0.00 ... (10 atoms not shown) pdb=" C1' A 7 11 " occ=0.00 residue: pdb=" P A 7 12 " occ=0.00 ... (10 atoms not shown) pdb=" C1' A 7 12 " occ=0.00 residue: pdb=" P A 7 13 " occ=0.00 ... (10 atoms not shown) pdb=" C1' A 7 13 " occ=0.00 residue: pdb=" P A 7 14 " occ=0.00 ... (10 atoms not shown) pdb=" C1' A 7 14 " occ=0.00 residue: pdb=" P A 7 15 " occ=0.00 ... (10 atoms not shown) pdb=" C1' A 7 15 " occ=0.00 residue: pdb=" P A 7 16 " occ=0.00 ... (10 atoms not shown) pdb=" C1' A 7 16 " occ=0.00 residue: pdb=" P A 7 17 " occ=0.00 ... (10 atoms not shown) pdb=" C1' A 7 17 " occ=0.00 residue: pdb=" P A 7 18 " occ=0.00 ... (10 atoms not shown) pdb=" C1' A 7 18 " occ=0.00 residue: pdb=" P A 7 19 " occ=0.00 ... (10 atoms not shown) pdb=" C1' A 7 19 " occ=0.00 residue: pdb=" P A 7 20 " occ=0.00 ... (10 atoms not shown) pdb=" C1' A 7 20 " occ=0.00 residue: pdb=" P A 7 21 " occ=0.00 ... (10 atoms not shown) pdb=" C1' A 7 21 " occ=0.00 ... (remaining 10 not shown) Time building chain proxies: 47.93, per 1000 atoms: 0.41 Number of scatterers: 118155 At special positions: 0 Unit cell: (278.166, 313.608, 263.13, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 329 16.00 P 1820 15.00 Mg 89 11.99 O 27264 8.00 N 21767 7.00 C 66884 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: 45.96 Conformation dependent library (CDL) restraints added in 12.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN Q 201 " pdb="ZN ZN Q 201 " - pdb=" SG CYS Q 26 " pdb="ZN ZN Q 201 " - pdb=" SG CYS Q 74 " pdb=" ZN k 201 " pdb="ZN ZN k 201 " - pdb=" SG CYS k 141 " pdb="ZN ZN k 201 " - pdb=" SG CYS k 121 " pdb="ZN ZN k 201 " - pdb=" SG CYS k 144 " pdb="ZN ZN k 201 " - pdb=" SG CYS k 126 " Number of angles added : 6 21898 Ramachandran restraints generated. 10949 Oldfield, 0 Emsley, 10949 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 20982 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 376 helices and 104 sheets defined 47.0% alpha, 13.9% beta 482 base pairs and 951 stacking pairs defined. Time for finding SS restraints: 73.97 Creating SS restraints... Processing helix chain '1' and resid 197 through 212 removed outlier: 6.689A pdb=" N GLU 1 201 " --> pdb=" O PRO 1 197 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU 1 203 " --> pdb=" O ARG 1 199 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N ASN 1 205 " --> pdb=" O GLU 1 201 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N VAL 1 206 " --> pdb=" O LYS 1 202 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N HIS 1 208 " --> pdb=" O LYS 1 204 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ILE 1 210 " --> pdb=" O VAL 1 206 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER 1 212 " --> pdb=" O HIS 1 208 " (cutoff:3.500A) Processing helix chain '1' and resid 241 through 250 removed outlier: 4.853A pdb=" N ASP 1 245 " --> pdb=" O ALA 1 241 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL 1 247 " --> pdb=" O ALA 1 243 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N LYS 1 248 " --> pdb=" O VAL 1 244 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASN 1 249 " --> pdb=" O ASP 1 245 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ALA 1 250 " --> pdb=" O ALA 1 246 " (cutoff:3.500A) Processing helix chain '1' and resid 286 through 300 removed outlier: 4.544A pdb=" N LEU 1 293 " --> pdb=" O ASP 1 289 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ARG 1 294 " --> pdb=" O LEU 1 290 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N TYR 1 295 " --> pdb=" O GLY 1 291 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N TRP 1 296 " --> pdb=" O ASN 1 292 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N LEU 1 297 " --> pdb=" O LEU 1 293 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N ALA 1 300 " --> pdb=" O TRP 1 296 " (cutoff:3.500A) Processing helix chain '1' and resid 459 through 464 removed outlier: 4.071A pdb=" N LYS 1 463 " --> pdb=" O LYS 1 459 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE 1 464 " --> pdb=" O LYS 1 460 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 459 through 464' Processing helix chain '1' and resid 713 through 718 Processing helix chain '1' and resid 732 through 745 removed outlier: 4.254A pdb=" N ARG 1 736 " --> pdb=" O GLU 1 732 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N SER 1 738 " --> pdb=" O LYS 1 734 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N GLN 1 739 " --> pdb=" O ASP 1 735 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N SER 1 740 " --> pdb=" O ARG 1 736 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N SER 1 743 " --> pdb=" O GLN 1 739 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LYS 1 744 " --> pdb=" O SER 1 740 " (cutoff:3.500A) Processing helix chain '1' and resid 749 through 763 removed outlier: 4.274A pdb=" N MET 1 753 " --> pdb=" O ARG 1 749 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ASP 1 756 " --> pdb=" O THR 1 752 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N PHE 1 757 " --> pdb=" O MET 1 753 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ARG 1 758 " --> pdb=" O MET 1 754 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ARG 1 761 " --> pdb=" O PHE 1 757 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LYS 1 762 " --> pdb=" O ARG 1 758 " (cutoff:3.500A) Processing helix chain '6' and resid 15 through 27 removed outlier: 5.328A pdb=" N ARG 6 19 " --> pdb=" O ALA 6 15 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ALA 6 20 " --> pdb=" O ALA 6 16 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA 6 27 " --> pdb=" O LYS 6 23 " (cutoff:3.500A) Processing helix chain '6' and resid 29 through 41 removed outlier: 4.986A pdb=" N ASN 6 33 " --> pdb=" O ILE 6 29 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N GLY 6 36 " --> pdb=" O GLU 6 32 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLY 6 37 " --> pdb=" O ASN 6 33 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N LEU 6 38 " --> pdb=" O SER 6 34 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N VAL 6 40 " --> pdb=" O GLY 6 36 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N ASP 6 41 " --> pdb=" O GLY 6 37 " (cutoff:3.500A) Processing helix chain '6' and resid 43 through 54 removed outlier: 3.872A pdb=" N GLU 6 47 " --> pdb=" O ALA 6 43 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ALA 6 48 " --> pdb=" O GLN 6 44 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VAL 6 51 " --> pdb=" O GLU 6 47 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N CYS 6 52 " --> pdb=" O ALA 6 48 " (cutoff:3.500A) Processing helix chain '6' and resid 60 through 78 removed outlier: 4.242A pdb=" N ASN 6 65 " --> pdb=" O GLU 6 61 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N VAL 6 68 " --> pdb=" O MET 6 64 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N SER 6 69 " --> pdb=" O ASN 6 65 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU 6 72 " --> pdb=" O VAL 6 68 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N ILE 6 73 " --> pdb=" O SER 6 69 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N LEU 6 74 " --> pdb=" O LEU 6 70 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLU 6 75 " --> pdb=" O LEU 6 71 " (cutoff:3.500A) Proline residue: 6 76 - end of helix Processing helix chain '6' and resid 79 through 94 removed outlier: 4.767A pdb=" N ILE 6 83 " --> pdb=" O GLN 6 79 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N GLU 6 84 " --> pdb=" O GLU 6 80 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N SER 6 85 " --> pdb=" O ALA 6 81 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N LEU 6 86 " --> pdb=" O LEU 6 82 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N CYS 6 87 " --> pdb=" O ILE 6 83 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N GLU 6 88 " --> pdb=" O GLU 6 84 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N LYS 6 89 " --> pdb=" O SER 6 85 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N LEU 6 90 " --> pdb=" O LEU 6 86 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N VAL 6 91 " --> pdb=" O CYS 6 87 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N PHE 6 93 " --> pdb=" O LYS 6 89 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG 6 94 " --> pdb=" O LEU 6 90 " (cutoff:3.500A) Processing helix chain '6' and resid 97 through 106 removed outlier: 4.358A pdb=" N LEU 6 101 " --> pdb=" O GLU 6 97 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG 6 102 " --> pdb=" O ARG 6 98 " (cutoff:3.500A) Processing helix chain '6' and resid 116 through 131 removed outlier: 4.064A pdb=" N LYS 6 129 " --> pdb=" O CYS 6 125 " (cutoff:3.500A) Processing helix chain '6' and resid 133 through 138 removed outlier: 4.923A pdb=" N ILE 6 137 " --> pdb=" O SER 6 133 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLN 6 138 " --> pdb=" O CYS 6 134 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 133 through 138' Processing helix chain '6' and resid 154 through 172 removed outlier: 4.578A pdb=" N GLU 6 170 " --> pdb=" O ARG 6 166 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA 6 171 " --> pdb=" O LEU 6 167 " (cutoff:3.500A) Processing helix chain '6' and resid 174 through 193 Processing helix chain '6' and resid 198 through 212 removed outlier: 3.774A pdb=" N VAL 6 202 " --> pdb=" O SER 6 198 " (cutoff:3.500A) Processing helix chain '6' and resid 239 through 244 Processing helix chain '6' and resid 262 through 267 removed outlier: 3.570A pdb=" N LEU 6 266 " --> pdb=" O PHE 6 262 " (cutoff:3.500A) Processing helix chain '6' and resid 268 through 287 removed outlier: 4.103A pdb=" N LEU 6 279 " --> pdb=" O ALA 6 275 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N LEU 6 280 " --> pdb=" O LYS 6 276 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N THR 6 281 " --> pdb=" O MET 6 277 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N PHE 6 282 " --> pdb=" O ARG 6 278 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N MET 6 283 " --> pdb=" O LEU 6 279 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N VAL 6 287 " --> pdb=" O MET 6 283 " (cutoff:3.500A) Processing helix chain '6' and resid 295 through 302 removed outlier: 3.951A pdb=" N GLN 6 299 " --> pdb=" O ASP 6 295 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLN 6 302 " --> pdb=" O GLN 6 298 " (cutoff:3.500A) Processing helix chain '6' and resid 306 through 319 removed outlier: 4.591A pdb=" N ALA 6 310 " --> pdb=" O ASP 6 306 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ILE 6 313 " --> pdb=" O GLU 6 309 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR 6 318 " --> pdb=" O ASP 6 314 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N LYS 6 319 " --> pdb=" O ALA 6 315 " (cutoff:3.500A) Processing helix chain '6' and resid 340 through 348 removed outlier: 4.864A pdb=" N LYS 6 344 " --> pdb=" O ARG 6 340 " (cutoff:3.500A) Processing helix chain '6' and resid 349 through 357 removed outlier: 3.762A pdb=" N ALA 6 356 " --> pdb=" O ASP 6 352 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N TRP 6 357 " --> pdb=" O THR 6 353 " (cutoff:3.500A) Processing helix chain '6' and resid 110 through 115 removed outlier: 6.454A pdb=" N LYS 6 115 " --> pdb=" O PHE 6 110 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 110 through 115' Processing helix chain '6' and resid 251 through 257 removed outlier: 3.932A pdb=" N TYR 6 256 " --> pdb=" O SER 6 251 " (cutoff:3.500A) Processing helix chain '4' and resid 95 through 109 removed outlier: 3.576A pdb=" N LEU 4 99 " --> pdb=" O HIS 4 95 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ARG 4 108 " --> pdb=" O ASP 4 104 " (cutoff:3.500A) Processing helix chain '4' and resid 149 through 165 Proline residue: 4 165 - end of helix Processing helix chain '4' and resid 180 through 194 removed outlier: 4.011A pdb=" N GLU 4 193 " --> pdb=" O TYR 4 189 " (cutoff:3.500A) Processing helix chain '4' and resid 244 through 257 removed outlier: 4.830A pdb=" N PHE 4 257 " --> pdb=" O MET 4 253 " (cutoff:3.500A) Processing helix chain '4' and resid 265 through 290 Processing helix chain '4' and resid 294 through 306 removed outlier: 3.904A pdb=" N VAL 4 298 " --> pdb=" O LEU 4 294 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N SER 4 299 " --> pdb=" O SER 4 295 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ALA 4 300 " --> pdb=" O GLY 4 296 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASP 4 301 " --> pdb=" O LYS 4 297 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N ASN 4 302 " --> pdb=" O VAL 4 298 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N THR 4 303 " --> pdb=" O SER 4 299 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N VAL 4 304 " --> pdb=" O ALA 4 300 " (cutoff:3.500A) Processing helix chain '4' and resid 307 through 316 removed outlier: 3.586A pdb=" N VAL 4 315 " --> pdb=" O LEU 4 311 " (cutoff:3.500A) Proline residue: 4 316 - end of helix Processing helix chain '4' and resid 319 through 357 removed outlier: 4.167A pdb=" N LEU 4 354 " --> pdb=" O LEU 4 350 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N VAL 4 355 " --> pdb=" O ASN 4 351 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU 4 357 " --> pdb=" O LYS 4 353 " (cutoff:3.500A) Processing helix chain 'u' and resid 7 through 22 removed outlier: 4.522A pdb=" N ALA u 11 " --> pdb=" O ARG u 7 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LEU u 12 " --> pdb=" O PRO u 8 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS u 13 " --> pdb=" O GLU u 9 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU u 17 " --> pdb=" O LYS u 13 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU u 19 " --> pdb=" O ALA u 15 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU u 20 " --> pdb=" O ASN u 16 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL u 21 " --> pdb=" O GLU u 17 " (cutoff:3.500A) Processing helix chain 'u' and resid 23 through 37 removed outlier: 3.782A pdb=" N LEU u 31 " --> pdb=" O ALA u 27 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N SER u 37 " --> pdb=" O ASP u 33 " (cutoff:3.500A) Processing helix chain 'u' and resid 44 through 62 removed outlier: 4.836A pdb=" N GLU u 48 " --> pdb=" O GLN u 44 " (cutoff:3.500A) Proline residue: u 49 - end of helix removed outlier: 4.901A pdb=" N ARG u 62 " --> pdb=" O CYS u 58 " (cutoff:3.500A) Processing helix chain 'u' and resid 63 through 79 removed outlier: 4.801A pdb=" N ALA u 67 " --> pdb=" O LYS u 63 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLN u 79 " --> pdb=" O LYS u 75 " (cutoff:3.500A) Processing helix chain 'u' and resid 82 through 117 removed outlier: 4.219A pdb=" N LEU u 86 " --> pdb=" O ASN u 82 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ALA u 104 " --> pdb=" O LYS u 100 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLU u 106 " --> pdb=" O GLU u 102 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N GLU u 107 " --> pdb=" O ALA u 103 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ASP u 117 " --> pdb=" O LEU u 113 " (cutoff:3.500A) Processing helix chain 'u' and resid 123 through 133 removed outlier: 4.592A pdb=" N LEU u 128 " --> pdb=" O PRO u 124 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N LEU u 129 " --> pdb=" O GLU u 125 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA u 131 " --> pdb=" O VAL u 127 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL u 132 " --> pdb=" O LEU u 128 " (cutoff:3.500A) Processing helix chain 'u' and resid 136 through 146 removed outlier: 3.836A pdb=" N ARG u 143 " --> pdb=" O ASP u 139 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU u 145 " --> pdb=" O THR u 141 " (cutoff:3.500A) Processing helix chain 'u' and resid 147 through 165 removed outlier: 3.537A pdb=" N LEU u 161 " --> pdb=" O TYR u 157 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LEU u 164 " --> pdb=" O CYS u 160 " (cutoff:3.500A) Processing helix chain 'u' and resid 170 through 189 removed outlier: 3.512A pdb=" N GLN u 187 " --> pdb=" O LYS u 183 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N THR u 189 " --> pdb=" O CYS u 185 " (cutoff:3.500A) Processing helix chain 'u' and resid 190 through 211 removed outlier: 3.997A pdb=" N PHE u 194 " --> pdb=" O ARG u 190 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ARG u 195 " --> pdb=" O LYS u 191 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS u 196 " --> pdb=" O ALA u 192 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU u 205 " --> pdb=" O LEU u 201 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE u 208 " --> pdb=" O HIS u 204 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N GLN u 209 " --> pdb=" O LEU u 205 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ARG u 210 " --> pdb=" O SER u 206 " (cutoff:3.500A) Processing helix chain 'u' and resid 222 through 244 removed outlier: 3.524A pdb=" N GLU u 231 " --> pdb=" O SER u 227 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N THR u 232 " --> pdb=" O MET u 228 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG u 233 " --> pdb=" O HIS u 229 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER u 242 " --> pdb=" O ASP u 238 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N MET u 243 " --> pdb=" O SER u 239 " (cutoff:3.500A) Processing helix chain 'u' and resid 245 through 262 removed outlier: 3.999A pdb=" N PHE u 250 " --> pdb=" O TRP u 246 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N SER u 261 " --> pdb=" O HIS u 257 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LEU u 262 " --> pdb=" O GLY u 258 " (cutoff:3.500A) Processing helix chain 'u' and resid 268 through 287 removed outlier: 3.513A pdb=" N MET u 272 " --> pdb=" O LYS u 268 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N ALA u 273 " --> pdb=" O PRO u 269 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ASN u 274 " --> pdb=" O GLN u 270 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASN u 277 " --> pdb=" O ALA u 273 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N SER u 280 " --> pdb=" O TYR u 276 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N TRP u 284 " --> pdb=" O SER u 280 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LYS u 285 " --> pdb=" O THR u 281 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N GLY u 287 " --> pdb=" O PHE u 283 " (cutoff:3.500A) Processing helix chain 'u' and resid 288 through 307 removed outlier: 4.056A pdb=" N HIS u 292 " --> pdb=" O ASN u 288 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLU u 305 " --> pdb=" O HIS u 301 " (cutoff:3.500A) Processing helix chain 'u' and resid 311 through 329 removed outlier: 3.765A pdb=" N SER u 328 " --> pdb=" O LEU u 324 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ILE u 329 " --> pdb=" O ALA u 325 " (cutoff:3.500A) Processing helix chain 'u' and resid 338 through 345 removed outlier: 5.160A pdb=" N MET u 344 " --> pdb=" O ARG u 340 " (cutoff:3.500A) Processing helix chain 'u' and resid 350 through 360 removed outlier: 4.619A pdb=" N ARG u 354 " --> pdb=" O GLU u 350 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU u 359 " --> pdb=" O LEU u 355 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N GLY u 360 " --> pdb=" O ALA u 356 " (cutoff:3.500A) Processing helix chain 'u' and resid 369 through 377 removed outlier: 4.285A pdb=" N ASP u 373 " --> pdb=" O GLY u 369 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N MET u 374 " --> pdb=" O LEU u 370 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N PHE u 377 " --> pdb=" O ASP u 373 " (cutoff:3.500A) Processing helix chain 'u' and resid 378 through 384 removed outlier: 4.388A pdb=" N TYR u 382 " --> pdb=" O ASN u 378 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N VAL u 384 " --> pdb=" O LEU u 380 " (cutoff:3.500A) Processing helix chain 'u' and resid 389 through 395 removed outlier: 3.505A pdb=" N TRP u 393 " --> pdb=" O ASP u 389 " (cutoff:3.500A) Processing helix chain 'u' and resid 402 through 418 removed outlier: 4.397A pdb=" N VAL u 410 " --> pdb=" O ARG u 406 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLN u 417 " --> pdb=" O TRP u 413 " (cutoff:3.500A) Proline residue: u 418 - end of helix Processing helix chain 'u' and resid 421 through 447 removed outlier: 4.151A pdb=" N GLN u 425 " --> pdb=" O GLU u 421 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLN u 426 " --> pdb=" O PRO u 422 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N TYR u 427 " --> pdb=" O GLU u 423 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N VAL u 428 " --> pdb=" O LEU u 424 " (cutoff:3.500A) Proline residue: u 429 - end of helix removed outlier: 4.400A pdb=" N GLN u 445 " --> pdb=" O GLN u 441 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ILE u 446 " --> pdb=" O GLN u 442 " (cutoff:3.500A) Processing helix chain 'u' and resid 451 through 460 removed outlier: 3.680A pdb=" N LEU u 455 " --> pdb=" O GLU u 451 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N SER u 457 " --> pdb=" O SER u 453 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL u 459 " --> pdb=" O LEU u 455 " (cutoff:3.500A) Proline residue: u 460 - end of helix Processing helix chain 'u' and resid 463 through 478 removed outlier: 4.622A pdb=" N HIS u 477 " --> pdb=" O ASP u 473 " (cutoff:3.500A) Processing helix chain 'u' and resid 516 through 526 removed outlier: 5.923A pdb=" N ARG u 520 " --> pdb=" O SER u 516 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ASN u 521 " --> pdb=" O GLU u 517 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLN u 522 " --> pdb=" O GLN u 518 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ALA u 525 " --> pdb=" O ASN u 521 " (cutoff:3.500A) Processing helix chain 'u' and resid 527 through 540 removed outlier: 4.103A pdb=" N ILE u 537 " --> pdb=" O ALA u 533 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LYS u 538 " --> pdb=" O LEU u 534 " (cutoff:3.500A) Proline residue: u 539 - end of helix Processing helix chain 'u' and resid 541 through 563 removed outlier: 3.669A pdb=" N GLU u 545 " --> pdb=" O HIS u 541 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS u 546 " --> pdb=" O ILE u 542 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N HIS u 550 " --> pdb=" O LYS u 546 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LYS u 563 " --> pdb=" O LYS u 559 " (cutoff:3.500A) Processing helix chain 'u' and resid 569 through 574 removed outlier: 4.195A pdb=" N GLN u 573 " --> pdb=" O LEU u 569 " (cutoff:3.500A) Processing helix chain 'u' and resid 579 through 640 removed outlier: 3.572A pdb=" N GLU u 610 " --> pdb=" O LYS u 606 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ARG u 611 " --> pdb=" O ALA u 607 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N LEU u 640 " --> pdb=" O VAL u 636 " (cutoff:3.500A) Processing helix chain 'u' and resid 652 through 700 removed outlier: 6.051A pdb=" N ILE u 656 " --> pdb=" O ALA u 652 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ASP u 657 " --> pdb=" O PHE u 653 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLU u 659 " --> pdb=" O ASP u 655 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ASP u 660 " --> pdb=" O ILE u 656 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU u 661 " --> pdb=" O ASP u 657 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLU u 662 " --> pdb=" O ILE u 658 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLU u 663 " --> pdb=" O GLU u 659 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LEU u 664 " --> pdb=" O ASP u 660 " (cutoff:3.500A) Proline residue: u 666 - end of helix removed outlier: 3.541A pdb=" N LYS u 682 " --> pdb=" O GLU u 678 " (cutoff:3.500A) Processing helix chain 'v' and resid 48 through 56 removed outlier: 3.611A pdb=" N ASP v 52 " --> pdb=" O THR v 48 " (cutoff:3.500A) Processing helix chain 'v' and resid 61 through 71 removed outlier: 3.832A pdb=" N ASP v 65 " --> pdb=" O LEU v 61 " (cutoff:3.500A) Proline residue: v 67 - end of helix removed outlier: 4.168A pdb=" N ARG v 71 " --> pdb=" O PRO v 67 " (cutoff:3.500A) Processing helix chain 'v' and resid 76 through 85 removed outlier: 3.539A pdb=" N LEU v 84 " --> pdb=" O GLN v 80 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N GLN v 85 " --> pdb=" O LEU v 81 " (cutoff:3.500A) Processing helix chain 'v' and resid 92 through 113 removed outlier: 4.749A pdb=" N GLU v 96 " --> pdb=" O VAL v 92 " (cutoff:3.500A) Proline residue: v 98 - end of helix removed outlier: 4.237A pdb=" N THR v 107 " --> pdb=" O GLN v 103 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N ARG v 108 " --> pdb=" O MET v 104 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N ASP v 109 " --> pdb=" O GLN v 105 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N GLY v 110 " --> pdb=" O SER v 106 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N ARG v 111 " --> pdb=" O THR v 107 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N MET v 112 " --> pdb=" O ARG v 108 " (cutoff:3.500A) Processing helix chain 'v' and resid 127 through 139 removed outlier: 4.901A pdb=" N LEU v 131 " --> pdb=" O TYR v 127 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LYS v 136 " --> pdb=" O TYR v 132 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N PHE v 137 " --> pdb=" O ARG v 133 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR v 139 " --> pdb=" O ALA v 135 " (cutoff:3.500A) Processing helix chain 'v' and resid 146 through 151 Processing helix chain 'v' and resid 164 through 180 removed outlier: 4.441A pdb=" N TRP v 170 " --> pdb=" O LEU v 166 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N SER v 175 " --> pdb=" O GLY v 171 " (cutoff:3.500A) Processing helix chain 'v' and resid 181 through 197 removed outlier: 3.717A pdb=" N ILE v 196 " --> pdb=" O LEU v 192 " (cutoff:3.500A) Processing helix chain 'v' and resid 203 through 219 removed outlier: 4.896A pdb=" N LEU v 219 " --> pdb=" O ILE v 215 " (cutoff:3.500A) Processing helix chain 'v' and resid 224 through 234 removed outlier: 3.741A pdb=" N GLY v 228 " --> pdb=" O ASN v 224 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N ASP v 230 " --> pdb=" O PRO v 226 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N ASN v 231 " --> pdb=" O LYS v 227 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ILE v 232 " --> pdb=" O GLY v 228 " (cutoff:3.500A) Processing helix chain 'v' and resid 237 through 246 removed outlier: 3.711A pdb=" N ILE v 246 " --> pdb=" O TYR v 242 " (cutoff:3.500A) Processing helix chain 'v' and resid 250 through 265 removed outlier: 3.620A pdb=" N ILE v 262 " --> pdb=" O THR v 258 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASN v 264 " --> pdb=" O ALA v 260 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LYS v 265 " --> pdb=" O VAL v 261 " (cutoff:3.500A) Processing helix chain 'v' and resid 272 through 282 removed outlier: 4.659A pdb=" N ASP v 276 " --> pdb=" O GLN v 272 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N VAL v 278 " --> pdb=" O LEU v 274 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LYS v 279 " --> pdb=" O LYS v 275 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ILE v 281 " --> pdb=" O LEU v 277 " (cutoff:3.500A) Processing helix chain 'v' and resid 286 through 291 removed outlier: 3.965A pdb=" N ASP v 290 " --> pdb=" O TYR v 286 " (cutoff:3.500A) Proline residue: v 291 - end of helix No H-bonds generated for 'chain 'v' and resid 286 through 291' Processing helix chain 'v' and resid 292 through 302 removed outlier: 4.544A pdb=" N VAL v 296 " --> pdb=" O ILE v 292 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N LEU v 299 " --> pdb=" O PHE v 295 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N TYR v 300 " --> pdb=" O VAL v 296 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N VAL v 301 " --> pdb=" O GLU v 297 " (cutoff:3.500A) Processing helix chain 'v' and resid 305 through 322 removed outlier: 5.744A pdb=" N GLN v 309 " --> pdb=" O PHE v 305 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N LYS v 310 " --> pdb=" O ASP v 306 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N LYS v 311 " --> pdb=" O GLY v 307 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N LEU v 312 " --> pdb=" O ALA v 308 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N ARG v 313 " --> pdb=" O GLN v 309 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N GLU v 314 " --> pdb=" O LYS v 310 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N SER v 317 " --> pdb=" O ARG v 313 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N VAL v 318 " --> pdb=" O GLU v 314 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN v 321 " --> pdb=" O SER v 317 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ASP v 322 " --> pdb=" O VAL v 318 " (cutoff:3.500A) Processing helix chain 'v' and resid 324 through 348 removed outlier: 5.450A pdb=" N CYS v 328 " --> pdb=" O PHE v 324 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N LEU v 329 " --> pdb=" O LEU v 325 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N GLU v 330 " --> pdb=" O VAL v 326 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N ASP v 331 " --> pdb=" O ALA v 327 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N PHE v 332 " --> pdb=" O CYS v 328 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE v 341 " --> pdb=" O ARG v 337 " (cutoff:3.500A) Processing helix chain 'v' and resid 352 through 358 removed outlier: 3.624A pdb=" N ALA v 357 " --> pdb=" O ILE v 353 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N ASP v 358 " --> pdb=" O ASN v 354 " (cutoff:3.500A) Processing helix chain 'v' and resid 363 through 379 removed outlier: 3.654A pdb=" N GLU v 368 " --> pdb=" O PRO v 364 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ARG v 369 " --> pdb=" O GLU v 365 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N ALA v 378 " --> pdb=" O LEU v 374 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ARG v 379 " --> pdb=" O ILE v 375 " (cutoff:3.500A) Processing helix chain 'v' and resid 402 through 420 removed outlier: 3.936A pdb=" N MET v 420 " --> pdb=" O GLN v 416 " (cutoff:3.500A) Processing helix chain 'v' and resid 37 through 42 removed outlier: 3.905A pdb=" N GLY v 40 " --> pdb=" O LEU v 37 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS v 41 " --> pdb=" O LEU v 38 " (cutoff:3.500A) Processing helix chain 'S' and resid 20 through 28 removed outlier: 5.001A pdb=" N LEU S 24 " --> pdb=" O ASP S 20 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N THR S 26 " --> pdb=" O ARG S 22 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N PHE S 27 " --> pdb=" O LYS S 23 " (cutoff:3.500A) Processing helix chain 'S' and resid 137 through 146 Processing helix chain 'S' and resid 152 through 157 removed outlier: 4.258A pdb=" N TYR S 156 " --> pdb=" O ASP S 152 " (cutoff:3.500A) Processing helix chain 'S' and resid 181 through 229 Processing helix chain 'S' and resid 121 through 126 removed outlier: 3.865A pdb=" N ASP S 126 " --> pdb=" O ILE S 121 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 121 through 126' Processing helix chain 'y' and resid 51 through 74 Processing helix chain 'y' and resid 75 through 98 removed outlier: 4.804A pdb=" N SER y 95 " --> pdb=" O GLY y 91 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N ILE y 96 " --> pdb=" O LYS y 92 " (cutoff:3.500A) Processing helix chain 'y' and resid 103 through 122 removed outlier: 4.770A pdb=" N GLU y 122 " --> pdb=" O ASN y 118 " (cutoff:3.500A) Processing helix chain 'y' and resid 123 through 128 Processing helix chain 'y' and resid 133 through 149 Processing helix chain 'y' and resid 152 through 160 Processing helix chain 'y' and resid 264 through 281 removed outlier: 3.849A pdb=" N LYS y 280 " --> pdb=" O ASP y 276 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N LYS y 281 " --> pdb=" O LYS y 277 " (cutoff:3.500A) Processing helix chain 'y' and resid 287 through 296 removed outlier: 3.881A pdb=" N GLU y 293 " --> pdb=" O LEU y 289 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N GLU y 294 " --> pdb=" O ASP y 290 " (cutoff:3.500A) Processing helix chain 'y' and resid 314 through 319 removed outlier: 5.206A pdb=" N PHE y 318 " --> pdb=" O LYS y 314 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N ALA y 319 " --> pdb=" O PRO y 315 " (cutoff:3.500A) No H-bonds generated for 'chain 'y' and resid 314 through 319' Processing helix chain 'y' and resid 327 through 341 removed outlier: 4.247A pdb=" N LYS y 331 " --> pdb=" O ALA y 327 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ALA y 339 " --> pdb=" O GLU y 335 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ARG y 340 " --> pdb=" O ILE y 336 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N GLY y 341 " --> pdb=" O LEU y 337 " (cutoff:3.500A) Processing helix chain 'y' and resid 346 through 365 removed outlier: 3.690A pdb=" N ILE y 351 " --> pdb=" O ARG y 347 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU y 352 " --> pdb=" O ALA y 348 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ASN y 365 " --> pdb=" O ALA y 361 " (cutoff:3.500A) Processing helix chain 'y' and resid 367 through 386 removed outlier: 4.101A pdb=" N ILE y 371 " --> pdb=" O GLY y 367 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE y 379 " --> pdb=" O LYS y 375 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ASN y 386 " --> pdb=" O LEU y 382 " (cutoff:3.500A) Processing helix chain 'y' and resid 394 through 416 Proline residue: y 416 - end of helix Processing helix chain 'y' and resid 443 through 462 Processing helix chain 'y' and resid 466 through 493 removed outlier: 4.049A pdb=" N VAL y 470 " --> pdb=" O SER y 466 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ASP y 475 " --> pdb=" O GLU y 471 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N GLU y 476 " --> pdb=" O HIS y 472 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N ALA y 477 " --> pdb=" O LEU y 473 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N GLN y 478 " --> pdb=" O LYS y 474 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL y 479 " --> pdb=" O ASP y 475 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU y 491 " --> pdb=" O GLN y 487 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLU y 492 " --> pdb=" O ARG y 488 " (cutoff:3.500A) Processing helix chain 'y' and resid 496 through 511 removed outlier: 3.573A pdb=" N CYS y 500 " --> pdb=" O THR y 496 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N ARG y 501 " --> pdb=" O GLU y 497 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N HIS y 509 " --> pdb=" O LEU y 505 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR y 510 " --> pdb=" O ARG y 506 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TYR y 511 " --> pdb=" O ILE y 507 " (cutoff:3.500A) Processing helix chain 'y' and resid 515 through 522 removed outlier: 4.284A pdb=" N HIS y 519 " --> pdb=" O ASP y 515 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ARG y 521 " --> pdb=" O LYS y 517 " (cutoff:3.500A) Processing helix chain 'y' and resid 543 through 558 removed outlier: 3.531A pdb=" N LEU y 547 " --> pdb=" O ASP y 543 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N MET y 548 " --> pdb=" O SER y 544 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU y 549 " --> pdb=" O ALA y 545 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ILE y 555 " --> pdb=" O LEU y 551 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA y 557 " --> pdb=" O LYS y 553 " (cutoff:3.500A) Processing helix chain 'y' and resid 561 through 580 removed outlier: 4.255A pdb=" N ARG y 565 " --> pdb=" O THR y 561 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N THR y 566 " --> pdb=" O ASP y 562 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N HIS y 579 " --> pdb=" O HIS y 575 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER y 580 " --> pdb=" O HIS y 576 " (cutoff:3.500A) Processing helix chain 'y' and resid 581 through 593 removed outlier: 4.126A pdb=" N ALA y 585 " --> pdb=" O ARG y 581 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ASP y 587 " --> pdb=" O TYR y 583 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LEU y 588 " --> pdb=" O GLN y 584 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N SER y 592 " --> pdb=" O LEU y 588 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N HIS y 593 " --> pdb=" O MET y 589 " (cutoff:3.500A) Processing helix chain 'y' and resid 594 through 602 removed outlier: 5.704A pdb=" N GLN y 599 " --> pdb=" O GLN y 595 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N HIS y 600 " --> pdb=" O ASP y 596 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ALA y 601 " --> pdb=" O ASN y 597 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N ASP y 602 " --> pdb=" O ILE y 598 " (cutoff:3.500A) Processing helix chain 'y' and resid 603 through 624 removed outlier: 4.521A pdb=" N LEU y 608 " --> pdb=" O PRO y 604 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLY y 624 " --> pdb=" O ALA y 620 " (cutoff:3.500A) Processing helix chain 'y' and resid 625 through 640 removed outlier: 4.555A pdb=" N ALA y 629 " --> pdb=" O LEU y 625 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N ASP y 635 " --> pdb=" O ASN y 631 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N ILE y 636 " --> pdb=" O ALA y 632 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER y 639 " --> pdb=" O ASP y 635 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLY y 640 " --> pdb=" O ILE y 636 " (cutoff:3.500A) Processing helix chain 'y' and resid 641 through 647 removed outlier: 4.068A pdb=" N GLY y 647 " --> pdb=" O LYS y 643 " (cutoff:3.500A) Processing helix chain 'y' and resid 650 through 655 removed outlier: 7.210A pdb=" N SER y 654 " --> pdb=" O LEU y 650 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N LEU y 655 " --> pdb=" O LEU y 651 " (cutoff:3.500A) No H-bonds generated for 'chain 'y' and resid 650 through 655' Processing helix chain 'y' and resid 660 through 669 removed outlier: 5.018A pdb=" N ARG y 669 " --> pdb=" O VAL y 665 " (cutoff:3.500A) Processing helix chain 'y' and resid 678 through 700 Proline residue: y 696 - end of helix Processing helix chain 'y' and resid 711 through 724 removed outlier: 4.162A pdb=" N HIS y 715 " --> pdb=" O SER y 711 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLN y 724 " --> pdb=" O VAL y 720 " (cutoff:3.500A) Processing helix chain 'y' and resid 732 through 747 removed outlier: 3.609A pdb=" N LYS y 745 " --> pdb=" O SER y 741 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N MET y 746 " --> pdb=" O LYS y 742 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N GLY y 747 " --> pdb=" O ALA y 743 " (cutoff:3.500A) Processing helix chain 'y' and resid 748 through 758 removed outlier: 5.018A pdb=" N CYS y 752 " --> pdb=" O ASP y 748 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN y 758 " --> pdb=" O SER y 754 " (cutoff:3.500A) Processing helix chain 'y' and resid 759 through 765 Processing helix chain 'y' and resid 771 through 800 removed outlier: 4.480A pdb=" N VAL y 775 " --> pdb=" O GLU y 771 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N SER y 797 " --> pdb=" O PHE y 793 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N VAL y 798 " --> pdb=" O THR y 794 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N ASP y 800 " --> pdb=" O SER y 796 " (cutoff:3.500A) Processing helix chain 'y' and resid 803 through 811 removed outlier: 3.837A pdb=" N LEU y 807 " --> pdb=" O SER y 803 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER y 808 " --> pdb=" O MET y 804 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N ASP y 809 " --> pdb=" O GLU y 805 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N PHE y 811 " --> pdb=" O LEU y 807 " (cutoff:3.500A) Processing helix chain 'y' and resid 814 through 829 removed outlier: 3.617A pdb=" N MET y 825 " --> pdb=" O ILE y 821 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ILE y 826 " --> pdb=" O ILE y 822 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ILE y 827 " --> pdb=" O SER y 823 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ASN y 828 " --> pdb=" O LYS y 824 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N GLU y 829 " --> pdb=" O MET y 825 " (cutoff:3.500A) Processing helix chain 'y' and resid 851 through 862 removed outlier: 3.650A pdb=" N GLU y 861 " --> pdb=" O LEU y 857 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N LYS y 862 " --> pdb=" O GLN y 858 " (cutoff:3.500A) Processing helix chain '8' and resid 42 through 55 removed outlier: 3.614A pdb=" N LYS 8 51 " --> pdb=" O LEU 8 47 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N HIS 8 52 " --> pdb=" O LYS 8 48 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLN 8 54 " --> pdb=" O ILE 8 50 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLU 8 55 " --> pdb=" O LYS 8 51 " (cutoff:3.500A) Processing helix chain '8' and resid 97 through 108 removed outlier: 3.963A pdb=" N MET 8 101 " --> pdb=" O VAL 8 97 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER 8 106 " --> pdb=" O GLU 8 102 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG 8 108 " --> pdb=" O MET 8 104 " (cutoff:3.500A) Processing helix chain '8' and resid 130 through 144 removed outlier: 3.901A pdb=" N LEU 8 134 " --> pdb=" O THR 8 130 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP 8 135 " --> pdb=" O ARG 8 131 " (cutoff:3.500A) Processing helix chain '8' and resid 154 through 159 removed outlier: 5.055A pdb=" N ALA 8 158 " --> pdb=" O PRO 8 154 " (cutoff:3.500A) Processing helix chain '8' and resid 170 through 178 removed outlier: 3.996A pdb=" N LYS 8 178 " --> pdb=" O MET 8 174 " (cutoff:3.500A) Processing helix chain '8' and resid 210 through 225 removed outlier: 4.671A pdb=" N LEU 8 214 " --> pdb=" O LEU 8 210 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL 8 224 " --> pdb=" O LYS 8 220 " (cutoff:3.500A) Processing helix chain '8' and resid 228 through 239 Processing helix chain '8' and resid 247 through 285 removed outlier: 3.865A pdb=" N GLN 8 278 " --> pdb=" O LYS 8 274 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N GLN 8 279 " --> pdb=" O HIS 8 275 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ARG 8 281 " --> pdb=" O TYR 8 277 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N GLN 8 282 " --> pdb=" O GLN 8 278 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N GLN 8 283 " --> pdb=" O GLN 8 279 " (cutoff:3.500A) Processing helix chain '8' and resid 315 through 351 removed outlier: 3.833A pdb=" N ASN 8 351 " --> pdb=" O LEU 8 347 " (cutoff:3.500A) Processing helix chain '8' and resid 186 through 192 removed outlier: 3.559A pdb=" N ILE 8 192 " --> pdb=" O LEU 8 187 " (cutoff:3.500A) Processing helix chain '8' and resid 298 through 303 removed outlier: 3.855A pdb=" N LYS 8 303 " --> pdb=" O GLU 8 298 " (cutoff:3.500A) No H-bonds generated for 'chain '8' and resid 298 through 303' Processing helix chain 'G' and resid 17 through 34 removed outlier: 3.657A pdb=" N ALA G 26 " --> pdb=" O GLY G 22 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU G 29 " --> pdb=" O GLN G 25 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N MET G 32 " --> pdb=" O LEU G 28 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ASN G 33 " --> pdb=" O GLU G 29 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N SER G 34 " --> pdb=" O LEU G 30 " (cutoff:3.500A) Processing helix chain 'G' and resid 65 through 77 removed outlier: 4.356A pdb=" N LYS G 70 " --> pdb=" O VAL G 66 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N SER G 71 " --> pdb=" O PRO G 67 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N LYS G 74 " --> pdb=" O LYS G 70 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N ILE G 75 " --> pdb=" O SER G 71 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLN G 76 " --> pdb=" O PHE G 72 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N VAL G 77 " --> pdb=" O GLN G 73 " (cutoff:3.500A) Processing helix chain 'G' and resid 78 through 88 removed outlier: 3.722A pdb=" N GLU G 82 " --> pdb=" O ARG G 78 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER G 88 " --> pdb=" O GLU G 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 117 through 122 removed outlier: 3.731A pdb=" N THR G 121 " --> pdb=" O PRO G 117 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N LEU G 122 " --> pdb=" O ARG G 118 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 117 through 122' Processing helix chain 'G' and resid 123 through 135 removed outlier: 3.734A pdb=" N LEU G 130 " --> pdb=" O HIS G 126 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASP G 132 " --> pdb=" O ALA G 128 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N VAL G 134 " --> pdb=" O LEU G 130 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N PHE G 135 " --> pdb=" O GLU G 131 " (cutoff:3.500A) Processing helix chain 'G' and resid 162 through 167 removed outlier: 3.987A pdb=" N VAL G 166 " --> pdb=" O GLN G 162 " (cutoff:3.500A) Processing helix chain 'G' and resid 169 through 181 removed outlier: 3.968A pdb=" N SER G 174 " --> pdb=" O VAL G 170 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLY G 175 " --> pdb=" O GLU G 171 " (cutoff:3.500A) Processing helix chain 'H' and resid 11 through 19 removed outlier: 4.279A pdb=" N ARG H 17 " --> pdb=" O GLU H 13 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N LYS H 18 " --> pdb=" O GLU H 14 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N HIS H 19 " --> pdb=" O GLU H 15 " (cutoff:3.500A) Processing helix chain 'K' and resid 56 through 63 Processing helix chain 'K' and resid 64 through 77 removed outlier: 4.566A pdb=" N SER K 68 " --> pdb=" O GLU K 64 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N GLY K 77 " --> pdb=" O ALA K 73 " (cutoff:3.500A) Processing helix chain 'L' and resid 64 through 73 removed outlier: 3.720A pdb=" N LEU L 69 " --> pdb=" O LYS L 65 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N MET L 73 " --> pdb=" O LEU L 69 " (cutoff:3.500A) Processing helix chain 'L' and resid 77 through 85 removed outlier: 4.068A pdb=" N ILE L 81 " --> pdb=" O SER L 77 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N PHE L 84 " --> pdb=" O GLU L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 90 through 98 removed outlier: 4.755A pdb=" N ILE L 94 " --> pdb=" O GLU L 90 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ASP L 95 " --> pdb=" O SER L 91 " (cutoff:3.500A) Processing helix chain 'L' and resid 147 through 162 removed outlier: 3.676A pdb=" N ILE L 151 " --> pdb=" O VAL L 147 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARG L 152 " --> pdb=" O ALA L 148 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N LEU L 160 " --> pdb=" O ILE L 156 " (cutoff:3.500A) Processing helix chain 'L' and resid 208 through 218 removed outlier: 3.587A pdb=" N LYS L 212 " --> pdb=" O PRO L 208 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU L 213 " --> pdb=" O VAL L 209 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N MET L 216 " --> pdb=" O LYS L 212 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA L 217 " --> pdb=" O LEU L 213 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N GLY L 218 " --> pdb=" O LEU L 214 " (cutoff:3.500A) Processing helix chain 'L' and resid 232 through 250 removed outlier: 3.608A pdb=" N ALA L 237 " --> pdb=" O LEU L 233 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N THR L 240 " --> pdb=" O PHE L 236 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE L 244 " --> pdb=" O THR L 240 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR L 247 " --> pdb=" O ALA L 243 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N TYR L 248 " --> pdb=" O ILE L 244 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N SER L 249 " --> pdb=" O SER L 245 " (cutoff:3.500A) Processing helix chain 'L' and resid 252 through 257 removed outlier: 4.144A pdb=" N TRP L 256 " --> pdb=" O THR L 252 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N LYS L 257 " --> pdb=" O PRO L 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 252 through 257' Processing helix chain 'L' and resid 264 through 270 removed outlier: 3.554A pdb=" N PHE L 269 " --> pdb=" O PRO L 265 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N THR L 270 " --> pdb=" O TYR L 266 " (cutoff:3.500A) Processing helix chain 'L' and resid 271 through 276 removed outlier: 4.818A pdb=" N LYS L 275 " --> pdb=" O ASP L 271 " (cutoff:3.500A) Processing helix chain 'O' and resid 24 through 29 removed outlier: 3.525A pdb=" N LYS O 28 " --> pdb=" O PRO O 24 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N ASP O 29 " --> pdb=" O PHE O 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 24 through 29' Processing helix chain 'O' and resid 57 through 64 removed outlier: 4.690A pdb=" N GLY O 61 " --> pdb=" O ILE O 57 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LEU O 62 " --> pdb=" O ALA O 58 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N GLY O 64 " --> pdb=" O ASP O 60 " (cutoff:3.500A) Processing helix chain 'O' and resid 70 through 76 removed outlier: 3.733A pdb=" N LEU O 74 " --> pdb=" O SER O 70 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASN O 76 " --> pdb=" O ALA O 72 " (cutoff:3.500A) Processing helix chain 'O' and resid 106 through 115 removed outlier: 3.855A pdb=" N SER O 112 " --> pdb=" O ASP O 108 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N VAL O 114 " --> pdb=" O MET O 110 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N LYS O 115 " --> pdb=" O CYS O 111 " (cutoff:3.500A) Processing helix chain 'O' and resid 157 through 179 removed outlier: 3.912A pdb=" N ARG O 162 " --> pdb=" O HIS O 158 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LYS O 166 " --> pdb=" O ARG O 162 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N THR O 173 " --> pdb=" O MET O 169 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N VAL O 176 " --> pdb=" O MET O 172 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N THR O 178 " --> pdb=" O ARG O 174 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ASN O 179 " --> pdb=" O GLU O 175 " (cutoff:3.500A) Processing helix chain 'O' and resid 180 through 191 Proline residue: O 190 - end of helix Processing helix chain 'O' and resid 192 through 203 removed outlier: 3.573A pdb=" N LYS O 199 " --> pdb=" O LYS O 195 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN O 202 " --> pdb=" O GLU O 198 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N SER O 203 " --> pdb=" O LYS O 199 " (cutoff:3.500A) Processing helix chain 'O' and resid 224 through 233 removed outlier: 3.701A pdb=" N LEU O 228 " --> pdb=" O GLU O 224 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N MET O 229 " --> pdb=" O LEU O 225 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLY O 233 " --> pdb=" O MET O 229 " (cutoff:3.500A) Processing helix chain 'N' and resid 11 through 22 removed outlier: 3.699A pdb=" N ALA N 20 " --> pdb=" O LEU N 16 " (cutoff:3.500A) Processing helix chain 'N' and resid 34 through 39 removed outlier: 5.361A pdb=" N ILE N 38 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N TYR N 39 " --> pdb=" O GLU N 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 34 through 39' Processing helix chain 'N' and resid 50 through 68 removed outlier: 3.548A pdb=" N TRP N 55 " --> pdb=" O LEU N 51 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU N 58 " --> pdb=" O THR N 54 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU N 60 " --> pdb=" O GLU N 56 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ILE N 68 " --> pdb=" O ALA N 64 " (cutoff:3.500A) Processing helix chain 'N' and resid 80 through 94 removed outlier: 4.366A pdb=" N GLN N 84 " --> pdb=" O ARG N 80 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N ARG N 85 " --> pdb=" O ASN N 81 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N ALA N 86 " --> pdb=" O THR N 82 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU N 88 " --> pdb=" O GLN N 84 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA N 91 " --> pdb=" O VAL N 87 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA N 93 " --> pdb=" O LYS N 89 " (cutoff:3.500A) Processing helix chain 'N' and resid 126 through 131 removed outlier: 3.764A pdb=" N HIS N 131 " --> pdb=" O PRO N 127 " (cutoff:3.500A) Processing helix chain 'N' and resid 132 through 141 removed outlier: 4.093A pdb=" N TYR N 139 " --> pdb=" O THR N 135 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL N 140 " --> pdb=" O GLU N 136 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ASN N 141 " --> pdb=" O ALA N 137 " (cutoff:3.500A) Processing helix chain 'N' and resid 167 through 187 removed outlier: 3.753A pdb=" N VAL N 171 " --> pdb=" O GLY N 167 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLY N 172 " --> pdb=" O ALA N 168 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N MET N 174 " --> pdb=" O SER N 170 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU N 183 " --> pdb=" O ALA N 179 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N MET N 185 " --> pdb=" O GLU N 181 " (cutoff:3.500A) Processing helix chain 'N' and resid 198 through 204 removed outlier: 4.451A pdb=" N TYR N 202 " --> pdb=" O MET N 198 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N PHE N 203 " --> pdb=" O PRO N 199 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N TYR N 204 " --> pdb=" O ASP N 200 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 198 through 204' Processing helix chain 'N' and resid 70 through 75 removed outlier: 3.834A pdb=" N VAL N 74 " --> pdb=" O PRO N 71 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N SER N 75 " --> pdb=" O ALA N 72 " (cutoff:3.500A) Processing helix chain 'Q' and resid 49 through 57 removed outlier: 3.826A pdb=" N ILE Q 53 " --> pdb=" O ALA Q 49 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA Q 56 " --> pdb=" O ASP Q 52 " (cutoff:3.500A) Processing helix chain 'Q' and resid 74 through 82 removed outlier: 4.559A pdb=" N ILE Q 79 " --> pdb=" O VAL Q 75 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N HIS Q 80 " --> pdb=" O SER Q 76 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LYS Q 82 " --> pdb=" O ALA Q 78 " (cutoff:3.500A) Processing helix chain 'Q' and resid 89 through 94 removed outlier: 3.682A pdb=" N ARG Q 92 " --> pdb=" O ARG Q 89 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LYS Q 93 " --> pdb=" O GLU Q 90 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ASP Q 94 " --> pdb=" O ALA Q 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 89 through 94' Processing helix chain 'P' and resid 57 through 63 removed outlier: 4.414A pdb=" N LYS P 61 " --> pdb=" O THR P 57 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N VAL P 62 " --> pdb=" O GLY P 58 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N LYS P 63 " --> pdb=" O GLY P 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 57 through 63' Processing helix chain 'P' and resid 64 through 69 removed outlier: 5.816A pdb=" N GLU P 68 " --> pdb=" O ALA P 64 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N SER P 69 " --> pdb=" O ASP P 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 64 through 69' Processing helix chain 'P' and resid 70 through 89 removed outlier: 4.277A pdb=" N ASP P 80 " --> pdb=" O LEU P 76 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL P 81 " --> pdb=" O ALA P 77 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLN P 83 " --> pdb=" O GLN P 79 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ARG P 84 " --> pdb=" O ASP P 80 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLU P 87 " --> pdb=" O GLN P 83 " (cutoff:3.500A) Processing helix chain 'P' and resid 109 through 123 removed outlier: 4.773A pdb=" N GLN P 113 " --> pdb=" O GLY P 109 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N SER P 114 " --> pdb=" O PRO P 110 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LEU P 116 " --> pdb=" O ALA P 112 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ARG P 117 " --> pdb=" O GLN P 113 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N GLY P 123 " --> pdb=" O LEU P 119 " (cutoff:3.500A) Processing helix chain 'I' and resid 29 through 44 removed outlier: 4.042A pdb=" N LYS I 34 " --> pdb=" O SER I 30 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LYS I 42 " --> pdb=" O TYR I 38 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LYS I 43 " --> pdb=" O LYS I 39 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N GLY I 44 " --> pdb=" O LEU I 40 " (cutoff:3.500A) Processing helix chain 'I' and resid 46 through 57 removed outlier: 4.125A pdb=" N GLY I 51 " --> pdb=" O PRO I 47 " (cutoff:3.500A) Processing helix chain 'I' and resid 62 through 67 removed outlier: 3.591A pdb=" N VAL I 66 " --> pdb=" O GLN I 62 " (cutoff:3.500A) Processing helix chain 'I' and resid 70 through 79 removed outlier: 4.229A pdb=" N SER I 77 " --> pdb=" O ARG I 73 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS I 78 " --> pdb=" O ILE I 74 " (cutoff:3.500A) Processing helix chain 'I' and resid 85 through 106 removed outlier: 4.637A pdb=" N LEU I 91 " --> pdb=" O ASP I 87 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N VAL I 96 " --> pdb=" O ILE I 92 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL I 98 " --> pdb=" O LYS I 94 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG I 99 " --> pdb=" O ALA I 95 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU I 103 " --> pdb=" O ARG I 99 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ARG I 104 " --> pdb=" O LYS I 100 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ARG I 106 " --> pdb=" O LEU I 102 " (cutoff:3.500A) Processing helix chain 'I' and resid 108 through 133 removed outlier: 4.406A pdb=" N PHE I 113 " --> pdb=" O LYS I 109 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ILE I 116 " --> pdb=" O LYS I 112 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ARG I 121 " --> pdb=" O LEU I 117 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N HIS I 123 " --> pdb=" O GLU I 119 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG I 124 " --> pdb=" O SER I 120 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR I 131 " --> pdb=" O ARG I 127 " (cutoff:3.500A) Processing helix chain 'I' and resid 145 through 151 removed outlier: 4.274A pdb=" N LEU I 149 " --> pdb=" O THR I 145 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL I 150 " --> pdb=" O ALA I 146 " (cutoff:3.500A) Processing helix chain 'x' and resid 175 through 182 removed outlier: 3.771A pdb=" N LYS x 181 " --> pdb=" O PRO x 177 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N MET x 182 " --> pdb=" O GLN x 178 " (cutoff:3.500A) Processing helix chain 'x' and resid 203 through 209 Processing helix chain 'x' and resid 228 through 233 Proline residue: x 233 - end of helix Processing helix chain 'x' and resid 234 through 242 removed outlier: 3.639A pdb=" N LEU x 238 " --> pdb=" O VAL x 234 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N LYS x 240 " --> pdb=" O ARG x 236 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N THR x 241 " --> pdb=" O LYS x 237 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLN x 242 " --> pdb=" O LEU x 238 " (cutoff:3.500A) Processing helix chain 'x' and resid 250 through 257 removed outlier: 5.393A pdb=" N THR x 254 " --> pdb=" O ALA x 250 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N LEU x 255 " --> pdb=" O ILE x 251 " (cutoff:3.500A) Processing helix chain 'x' and resid 308 through 327 removed outlier: 4.160A pdb=" N SER x 324 " --> pdb=" O ASN x 320 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLN x 325 " --> pdb=" O HIS x 321 " (cutoff:3.500A) Processing helix chain 'x' and resid 416 through 428 removed outlier: 3.578A pdb=" N VAL x 420 " --> pdb=" O GLN x 416 " (cutoff:3.500A) Processing helix chain 'x' and resid 429 through 443 removed outlier: 3.961A pdb=" N CYS x 438 " --> pdb=" O ARG x 434 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLY x 443 " --> pdb=" O ALA x 439 " (cutoff:3.500A) Processing helix chain 'x' and resid 472 through 481 removed outlier: 4.314A pdb=" N ASN x 481 " --> pdb=" O ALA x 477 " (cutoff:3.500A) Processing helix chain 'x' and resid 483 through 501 removed outlier: 3.991A pdb=" N LYS x 500 " --> pdb=" O ASP x 496 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N LEU x 501 " --> pdb=" O ILE x 497 " (cutoff:3.500A) Processing helix chain '3' and resid 2 through 18 removed outlier: 3.537A pdb=" N ALA 3 9 " --> pdb=" O GLU 3 5 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ASN 3 10 " --> pdb=" O GLN 3 6 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLY 3 17 " --> pdb=" O LYS 3 13 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N ILE 3 18 " --> pdb=" O LEU 3 14 " (cutoff:3.500A) Processing helix chain '3' and resid 22 through 39 removed outlier: 4.410A pdb=" N LEU 3 26 " --> pdb=" O ASN 3 22 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N ALA 3 27 " --> pdb=" O PRO 3 23 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N THR 3 28 " --> pdb=" O GLU 3 24 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU 3 29 " --> pdb=" O ASN 3 25 " (cutoff:3.500A) Processing helix chain '3' and resid 43 through 57 removed outlier: 4.040A pdb=" N ASN 3 47 " --> pdb=" O ASP 3 43 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU 3 48 " --> pdb=" O LEU 3 44 " (cutoff:3.500A) Processing helix chain '3' and resid 62 through 76 removed outlier: 3.706A pdb=" N THR 3 66 " --> pdb=" O GLN 3 62 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE 3 69 " --> pdb=" O VAL 3 65 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS 3 72 " --> pdb=" O GLN 3 68 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N THR 3 75 " --> pdb=" O LEU 3 71 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N ASN 3 76 " --> pdb=" O LYS 3 72 " (cutoff:3.500A) Processing helix chain '3' and resid 80 through 90 removed outlier: 5.382A pdb=" N ASP 3 90 " --> pdb=" O LYS 3 86 " (cutoff:3.500A) Processing helix chain '3' and resid 91 through 96 removed outlier: 4.118A pdb=" N GLU 3 95 " --> pdb=" O GLN 3 91 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N GLU 3 96 " --> pdb=" O ALA 3 92 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 91 through 96' Processing helix chain '3' and resid 97 through 112 removed outlier: 3.843A pdb=" N LEU 3 105 " --> pdb=" O GLN 3 101 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLY 3 106 " --> pdb=" O ILE 3 102 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU 3 108 " --> pdb=" O TYR 3 104 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU 3 109 " --> pdb=" O LEU 3 105 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N CYS 3 112 " --> pdb=" O LEU 3 108 " (cutoff:3.500A) Processing helix chain '3' and resid 113 through 121 removed outlier: 3.583A pdb=" N GLN 3 119 " --> pdb=" O GLN 3 115 " (cutoff:3.500A) Processing helix chain '3' and resid 125 through 132 removed outlier: 3.837A pdb=" N GLY 3 130 " --> pdb=" O ASP 3 126 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ILE 3 131 " --> pdb=" O LEU 3 127 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N THR 3 132 " --> pdb=" O LEU 3 128 " (cutoff:3.500A) Processing helix chain '3' and resid 133 through 149 removed outlier: 4.014A pdb=" N VAL 3 138 " --> pdb=" O PHE 3 134 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N ARG 3 139 " --> pdb=" O GLU 3 135 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N LYS 3 140 " --> pdb=" O ASP 3 136 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N HIS 3 144 " --> pdb=" O LYS 3 140 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLY 3 147 " --> pdb=" O CYS 3 143 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ILE 3 148 " --> pdb=" O HIS 3 144 " (cutoff:3.500A) Processing helix chain '3' and resid 154 through 163 Processing helix chain '3' and resid 166 through 178 removed outlier: 3.510A pdb=" N LYS 3 176 " --> pdb=" O VAL 3 172 " (cutoff:3.500A) Processing helix chain '3' and resid 191 through 196 removed outlier: 4.053A pdb=" N ILE 3 196 " --> pdb=" O GLN 3 192 " (cutoff:3.500A) Processing helix chain '3' and resid 206 through 216 Processing helix chain '5' and resid 183 through 206 removed outlier: 3.791A pdb=" N ILE 5 187 " --> pdb=" O LEU 5 183 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N CYS 5 202 " --> pdb=" O SER 5 198 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N LYS 5 203 " --> pdb=" O GLN 5 199 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR 5 204 " --> pdb=" O TYR 5 200 " (cutoff:3.500A) Processing helix chain '5' and resid 208 through 217 removed outlier: 3.515A pdb=" N ILE 5 212 " --> pdb=" O SER 5 208 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU 5 215 " --> pdb=" O GLU 5 211 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG 5 216 " --> pdb=" O ILE 5 212 " (cutoff:3.500A) Processing helix chain '5' and resid 222 through 248 removed outlier: 3.933A pdb=" N SER 5 226 " --> pdb=" O TRP 5 222 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS 5 237 " --> pdb=" O SER 5 233 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG 5 242 " --> pdb=" O SER 5 238 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL 5 246 " --> pdb=" O ARG 5 242 " (cutoff:3.500A) Processing helix chain '5' and resid 253 through 268 removed outlier: 3.615A pdb=" N ARG 5 262 " --> pdb=" O GLY 5 258 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N HIS 5 263 " --> pdb=" O GLU 5 259 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N MET 5 268 " --> pdb=" O SER 5 264 " (cutoff:3.500A) Processing helix chain '5' and resid 274 through 291 removed outlier: 3.548A pdb=" N LEU 5 278 " --> pdb=" O LEU 5 274 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG 5 279 " --> pdb=" O VAL 5 275 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU 5 283 " --> pdb=" O ARG 5 279 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU 5 284 " --> pdb=" O LEU 5 280 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ILE 5 291 " --> pdb=" O TYR 5 287 " (cutoff:3.500A) Processing helix chain '5' and resid 297 through 304 removed outlier: 5.127A pdb=" N MET 5 304 " --> pdb=" O ASN 5 300 " (cutoff:3.500A) Processing helix chain '5' and resid 311 through 327 removed outlier: 3.529A pdb=" N VAL 5 319 " --> pdb=" O THR 5 315 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY 5 320 " --> pdb=" O TYR 5 316 " (cutoff:3.500A) Processing helix chain '5' and resid 328 through 342 removed outlier: 3.783A pdb=" N ILE 5 333 " --> pdb=" O TYR 5 329 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ARG 5 334 " --> pdb=" O GLN 5 330 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N PHE 5 336 " --> pdb=" O ALA 5 332 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N ALA 5 337 " --> pdb=" O ILE 5 333 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N ASN 5 338 " --> pdb=" O ARG 5 334 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ILE 5 339 " --> pdb=" O VAL 5 335 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU 5 340 " --> pdb=" O PHE 5 336 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TYR 5 342 " --> pdb=" O ASN 5 338 " (cutoff:3.500A) Processing helix chain '5' and resid 357 through 375 removed outlier: 3.632A pdb=" N ASN 5 361 " --> pdb=" O TYR 5 357 " (cutoff:3.500A) Processing helix chain '5' and resid 388 through 403 removed outlier: 4.110A pdb=" N LYS 5 393 " --> pdb=" O GLN 5 389 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N LYS 5 403 " --> pdb=" O LEU 5 399 " (cutoff:3.500A) Processing helix chain '5' and resid 405 through 417 removed outlier: 4.110A pdb=" N TYR 5 409 " --> pdb=" O ASP 5 405 " (cutoff:3.500A) Processing helix chain '5' and resid 438 through 463 removed outlier: 3.554A pdb=" N GLU 5 450 " --> pdb=" O VAL 5 446 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE 5 460 " --> pdb=" O GLN 5 456 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N PHE 5 463 " --> pdb=" O THR 5 459 " (cutoff:3.500A) Processing helix chain '5' and resid 471 through 481 Processing helix chain '5' and resid 490 through 499 removed outlier: 3.514A pdb=" N LYS 5 498 " --> pdb=" O LYS 5 494 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ASN 5 499 " --> pdb=" O HIS 5 495 " (cutoff:3.500A) Processing helix chain '5' and resid 526 through 549 removed outlier: 3.676A pdb=" N ALA 5 531 " --> pdb=" O MET 5 527 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE 5 547 " --> pdb=" O PHE 5 543 " (cutoff:3.500A) Processing helix chain '9' and resid 2 through 24 removed outlier: 3.702A pdb=" N LYS 9 19 " --> pdb=" O ARG 9 15 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG 9 23 " --> pdb=" O LYS 9 19 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N SER 9 24 " --> pdb=" O MET 9 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 53 Processing helix chain 'C' and resid 43 through 50 Processing helix chain 'C' and resid 57 through 68 removed outlier: 4.077A pdb=" N LYS C 62 " --> pdb=" O GLY C 58 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLN C 67 " --> pdb=" O LYS C 63 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ARG C 68 " --> pdb=" O ILE C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 120 removed outlier: 4.163A pdb=" N LYS C 120 " --> pdb=" O PRO C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 257 removed outlier: 4.618A pdb=" N ALA C 257 " --> pdb=" O ASP C 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 36 Processing helix chain 'D' and resid 39 through 64 removed outlier: 3.994A pdb=" N VAL D 43 " --> pdb=" O ASN D 39 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N VAL D 46 " --> pdb=" O GLU D 42 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU D 63 " --> pdb=" O GLU D 59 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N ASP D 64 " --> pdb=" O LEU D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 85 Processing helix chain 'D' and resid 93 through 100 removed outlier: 3.776A pdb=" N ILE D 97 " --> pdb=" O LYS D 93 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU D 98 " --> pdb=" O LEU D 94 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLY D 99 " --> pdb=" O ASP D 95 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LEU D 100 " --> pdb=" O TYR D 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 93 through 100' Processing helix chain 'D' and resid 101 through 109 removed outlier: 4.247A pdb=" N PHE D 105 " --> pdb=" O LYS D 101 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU D 106 " --> pdb=" O ILE D 102 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU D 107 " --> pdb=" O GLU D 103 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ARG D 108 " --> pdb=" O ASP D 104 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ARG D 109 " --> pdb=" O PHE D 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 101 through 109' Processing helix chain 'D' and resid 110 through 118 removed outlier: 3.560A pdb=" N LEU D 117 " --> pdb=" O GLN D 113 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLY D 118 " --> pdb=" O VAL D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 133 removed outlier: 3.715A pdb=" N ARG D 127 " --> pdb=" O ILE D 123 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG D 133 " --> pdb=" O LEU D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 155 removed outlier: 4.439A pdb=" N LYS D 155 " --> pdb=" O LEU D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 178 removed outlier: 3.699A pdb=" N ASN D 177 " --> pdb=" O VAL D 173 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA D 178 " --> pdb=" O LYS D 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 24 removed outlier: 4.273A pdb=" N TRP E 22 " --> pdb=" O ARG E 18 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N HIS E 23 " --> pdb=" O ASP E 19 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ASP E 24 " --> pdb=" O GLN E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 25 through 32 Processing helix chain 'E' and resid 33 through 39 removed outlier: 4.152A pdb=" N LYS E 37 " --> pdb=" O GLY E 33 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA E 38 " --> pdb=" O THR E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 95 removed outlier: 4.394A pdb=" N PHE E 93 " --> pdb=" O GLY E 89 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ILE E 94 " --> pdb=" O CYS E 90 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N GLU E 95 " --> pdb=" O LEU E 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 89 through 95' Processing helix chain 'E' and resid 129 through 136 Processing helix chain 'F' and resid 84 through 90 Processing helix chain 'F' and resid 104 through 116 removed outlier: 3.902A pdb=" N ARG F 108 " --> pdb=" O GLY F 104 " (cutoff:3.500A) Processing helix chain 'r' and resid 58 through 63 removed outlier: 3.662A pdb=" N LEU r 62 " --> pdb=" O SER r 58 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE r 63 " --> pdb=" O ILE r 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 58 through 63' Processing helix chain 'r' and resid 91 through 120 removed outlier: 3.516A pdb=" N ALA r 95 " --> pdb=" O SER r 91 " (cutoff:3.500A) Processing helix chain 'r' and resid 123 through 143 removed outlier: 3.530A pdb=" N GLU r 128 " --> pdb=" O ASP r 124 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR r 134 " --> pdb=" O LEU r 130 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N TRP r 136 " --> pdb=" O GLN r 132 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N VAL r 137 " --> pdb=" O ARG r 133 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE r 138 " --> pdb=" O THR r 134 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TYR r 142 " --> pdb=" O PHE r 138 " (cutoff:3.500A) Processing helix chain 'r' and resid 146 through 159 removed outlier: 4.372A pdb=" N SER r 158 " --> pdb=" O LYS r 154 " (cutoff:3.500A) Processing helix chain 'r' and resid 160 through 166 removed outlier: 3.686A pdb=" N SER r 165 " --> pdb=" O SER r 161 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N LEU r 166 " --> pdb=" O ILE r 162 " (cutoff:3.500A) Processing helix chain 'r' and resid 169 through 185 removed outlier: 3.906A pdb=" N ARG r 173 " --> pdb=" O ASN r 169 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLU r 174 " --> pdb=" O GLU r 170 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL r 175 " --> pdb=" O ASP r 171 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASN r 181 " --> pdb=" O ILE r 177 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N ARG r 182 " --> pdb=" O ASN r 178 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N ARG r 183 " --> pdb=" O ASN r 179 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N LEU r 184 " --> pdb=" O ILE r 180 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR r 185 " --> pdb=" O ASN r 181 " (cutoff:3.500A) Processing helix chain 'r' and resid 203 through 219 removed outlier: 5.217A pdb=" N SER r 219 " --> pdb=" O GLY r 215 " (cutoff:3.500A) Processing helix chain 'r' and resid 243 through 265 removed outlier: 3.641A pdb=" N GLY r 247 " --> pdb=" O GLU r 243 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N SER r 249 " --> pdb=" O THR r 245 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLU r 264 " --> pdb=" O GLU r 260 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N LYS r 265 " --> pdb=" O LYS r 261 " (cutoff:3.500A) Processing helix chain 'J' and resid 5 through 21 removed outlier: 3.515A pdb=" N ASP J 9 " --> pdb=" O ASN J 5 " (cutoff:3.500A) Processing helix chain 'J' and resid 31 through 45 removed outlier: 3.842A pdb=" N HIS J 44 " --> pdb=" O VAL J 40 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY J 45 " --> pdb=" O MET J 41 " (cutoff:3.500A) Processing helix chain 'J' and resid 82 through 93 removed outlier: 4.784A pdb=" N GLU J 87 " --> pdb=" O LEU J 83 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N LYS J 88 " --> pdb=" O LYS J 84 " (cutoff:3.500A) Processing helix chain 'J' and resid 112 through 120 removed outlier: 4.101A pdb=" N ARG J 117 " --> pdb=" O HIS J 113 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N HIS J 120 " --> pdb=" O ALA J 116 " (cutoff:3.500A) Processing helix chain 'R' and resid 87 through 94 removed outlier: 4.201A pdb=" N VAL R 91 " --> pdb=" O ASN R 87 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ARG R 92 " --> pdb=" O ASN R 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 106 through 117 Processing helix chain 'R' and resid 145 through 156 removed outlier: 3.594A pdb=" N ARG R 152 " --> pdb=" O LYS R 148 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ASN R 155 " --> pdb=" O GLU R 151 " (cutoff:3.500A) Processing helix chain 'R' and resid 159 through 169 Processing helix chain 'R' and resid 192 through 207 removed outlier: 4.737A pdb=" N GLY R 207 " --> pdb=" O LYS R 203 " (cutoff:3.500A) Processing helix chain 'T' and resid 36 through 49 Processing helix chain 'T' and resid 51 through 56 removed outlier: 4.298A pdb=" N ILE T 55 " --> pdb=" O THR T 51 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N PHE T 56 " --> pdb=" O PRO T 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 51 through 56' Processing helix chain 'T' and resid 78 through 86 Processing helix chain 'T' and resid 87 through 95 removed outlier: 3.757A pdb=" N HIS T 94 " --> pdb=" O ARG T 90 " (cutoff:3.500A) Processing helix chain 'T' and resid 103 through 118 removed outlier: 4.442A pdb=" N LYS T 116 " --> pdb=" O ASN T 112 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N VAL T 117 " --> pdb=" O ARG T 113 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N ARG T 118 " --> pdb=" O MET T 114 " (cutoff:3.500A) Processing helix chain 'T' and resid 119 through 128 removed outlier: 4.836A pdb=" N ALA T 123 " --> pdb=" O GLY T 119 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ASN T 124 " --> pdb=" O THR T 120 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY T 126 " --> pdb=" O LYS T 122 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLY T 128 " --> pdb=" O ASN T 124 " (cutoff:3.500A) Processing helix chain 'V' and resid 35 through 40 removed outlier: 5.570A pdb=" N ALA V 40 " --> pdb=" O GLN V 36 " (cutoff:3.500A) Processing helix chain 'V' and resid 61 through 66 removed outlier: 4.319A pdb=" N GLN V 65 " --> pdb=" O PHE V 61 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N CYS V 66 " --> pdb=" O ARG V 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 61 through 66' Processing helix chain 'V' and resid 67 through 77 removed outlier: 3.523A pdb=" N MET V 76 " --> pdb=" O LEU V 72 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N MET V 77 " --> pdb=" O THR V 73 " (cutoff:3.500A) Processing helix chain 'V' and resid 85 through 104 removed outlier: 3.769A pdb=" N THR V 89 " --> pdb=" O LYS V 85 " (cutoff:3.500A) Processing helix chain 'V' and resid 107 through 120 Processing helix chain 'V' and resid 142 through 163 removed outlier: 4.023A pdb=" N PHE V 163 " --> pdb=" O ARG V 159 " (cutoff:3.500A) Processing helix chain 'V' and resid 168 through 183 Processing helix chain 'V' and resid 187 through 204 removed outlier: 3.858A pdb=" N LYS V 191 " --> pdb=" O SER V 187 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ARG V 204 " --> pdb=" O ALA V 200 " (cutoff:3.500A) Processing helix chain 'Y' and resid 47 through 59 removed outlier: 3.669A pdb=" N LEU Y 51 " --> pdb=" O LEU Y 47 " (cutoff:3.500A) Proline residue: Y 54 - end of helix Processing helix chain 'Y' and resid 76 through 99 removed outlier: 3.506A pdb=" N ILE Y 81 " --> pdb=" O HIS Y 77 " (cutoff:3.500A) Processing helix chain 'Y' and resid 101 through 114 Processing helix chain 'Z' and resid 6 through 29 Processing helix chain 'Z' and resid 54 through 60 Processing helix chain 'Z' and resid 63 through 78 Processing helix chain 'Z' and resid 93 through 98 removed outlier: 4.651A pdb=" N CYS Z 97 " --> pdb=" O THR Z 93 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N ALA Z 98 " --> pdb=" O ARG Z 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 93 through 98' Processing helix chain 'Z' and resid 99 through 112 removed outlier: 4.645A pdb=" N GLY Z 112 " --> pdb=" O LYS Z 108 " (cutoff:3.500A) Processing helix chain 'Z' and resid 114 through 130 removed outlier: 3.869A pdb=" N GLY Z 130 " --> pdb=" O ILE Z 126 " (cutoff:3.500A) Processing helix chain 'Z' and resid 161 through 167 removed outlier: 5.109A pdb=" N ASN Z 165 " --> pdb=" O GLY Z 161 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N TYR Z 166 " --> pdb=" O ASP Z 162 " (cutoff:3.500A) Processing helix chain 'a' and resid 4 through 19 Processing helix chain 'a' and resid 41 through 56 removed outlier: 3.925A pdb=" N ARG a 55 " --> pdb=" O SER a 51 " (cutoff:3.500A) Processing helix chain 'a' and resid 72 through 84 removed outlier: 3.509A pdb=" N GLN a 77 " --> pdb=" O ASN a 73 " (cutoff:3.500A) Processing helix chain 'b' and resid 21 through 29 removed outlier: 5.986A pdb=" N SER b 29 " --> pdb=" O LEU b 25 " (cutoff:3.500A) Processing helix chain 'b' and resid 30 through 38 removed outlier: 4.005A pdb=" N GLN b 35 " --> pdb=" O GLU b 31 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N LEU b 36 " --> pdb=" O GLN b 32 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N TYR b 37 " --> pdb=" O LEU b 33 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N SER b 38 " --> pdb=" O MET b 34 " (cutoff:3.500A) Processing helix chain 'b' and resid 39 through 48 removed outlier: 4.913A pdb=" N GLY b 48 " --> pdb=" O ARG b 44 " (cutoff:3.500A) Processing helix chain 'b' and resid 50 through 67 removed outlier: 3.704A pdb=" N ALA b 67 " --> pdb=" O ALA b 63 " (cutoff:3.500A) Processing helix chain 'b' and resid 115 through 121 removed outlier: 4.941A pdb=" N PHE b 119 " --> pdb=" O TYR b 115 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N SER b 120 " --> pdb=" O LEU b 116 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N ILE b 121 " --> pdb=" O GLY b 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 115 through 121' Processing helix chain 'd' and resid 10 through 26 removed outlier: 3.639A pdb=" N ARG d 16 " --> pdb=" O GLN d 12 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N GLY d 26 " --> pdb=" O LEU d 22 " (cutoff:3.500A) Processing helix chain 'd' and resid 51 through 67 removed outlier: 4.812A pdb=" N ARG d 67 " --> pdb=" O HIS d 63 " (cutoff:3.500A) Processing helix chain 'd' and resid 71 through 80 Processing helix chain 'd' and resid 96 through 111 removed outlier: 4.090A pdb=" N ALA d 100 " --> pdb=" O SER d 96 " (cutoff:3.500A) Processing helix chain 'd' and resid 124 through 144 removed outlier: 3.542A pdb=" N LYS d 143 " --> pdb=" O ALA d 139 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N LYS d 144 " --> pdb=" O ALA d 140 " (cutoff:3.500A) Processing helix chain 'e' and resid 51 through 61 Processing helix chain 'e' and resid 69 through 78 removed outlier: 3.557A pdb=" N VAL e 73 " --> pdb=" O THR e 69 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N SER e 74 " --> pdb=" O PRO e 70 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLU e 75 " --> pdb=" O ALA e 71 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N LYS e 78 " --> pdb=" O SER e 74 " (cutoff:3.500A) Processing helix chain 'e' and resid 80 through 95 Processing helix chain 'f' and resid 26 through 33 removed outlier: 3.650A pdb=" N ILE f 30 " --> pdb=" O ILE f 26 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N THR f 31 " --> pdb=" O ALA f 27 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ALA f 32 " --> pdb=" O PHE f 28 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N ILE f 33 " --> pdb=" O ALA f 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 26 through 33' Processing helix chain 'f' and resid 37 through 49 removed outlier: 4.698A pdb=" N ASP f 49 " --> pdb=" O LEU f 45 " (cutoff:3.500A) Processing helix chain 'f' and resid 60 through 74 Proline residue: f 74 - end of helix Processing helix chain 'f' and resid 99 through 118 removed outlier: 4.485A pdb=" N ASP f 104 " --> pdb=" O ALA f 100 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ARG f 118 " --> pdb=" O LEU f 114 " (cutoff:3.500A) Processing helix chain 'f' and resid 119 through 128 Processing helix chain 'f' and resid 140 through 145 removed outlier: 3.953A pdb=" N ARG f 144 " --> pdb=" O GLY f 140 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N THR f 145 " --> pdb=" O ARG f 141 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 140 through 145' Processing helix chain 'i' and resid 15 through 20 removed outlier: 5.043A pdb=" N SER i 20 " --> pdb=" O GLN i 16 " (cutoff:3.500A) Processing helix chain 'i' and resid 39 through 51 removed outlier: 5.923A pdb=" N LYS i 48 " --> pdb=" O ARG i 44 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N ASP i 49 " --> pdb=" O GLN i 45 " (cutoff:3.500A) Processing helix chain 'm' and resid 13 through 29 Processing helix chain 'm' and resid 34 through 45 removed outlier: 4.179A pdb=" N ALA m 38 " --> pdb=" O GLY m 34 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG m 45 " --> pdb=" O ALA m 41 " (cutoff:3.500A) Processing helix chain 'm' and resid 58 through 73 removed outlier: 3.974A pdb=" N VAL m 62 " --> pdb=" O GLU m 58 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N HIS m 72 " --> pdb=" O LEU m 68 " (cutoff:3.500A) Processing helix chain 'm' and resid 81 through 90 Processing helix chain 'm' and resid 119 through 132 removed outlier: 4.928A pdb=" N VAL m 123 " --> pdb=" O GLN m 119 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ILE m 124 " --> pdb=" O ALA m 120 " (cutoff:3.500A) Processing helix chain 'o' and resid 251 through 261 removed outlier: 3.640A pdb=" N LEU o 255 " --> pdb=" O ARG o 251 " (cutoff:3.500A) Proline residue: o 261 - end of helix Processing helix chain 'o' and resid 289 through 300 removed outlier: 3.730A pdb=" N ALA o 294 " --> pdb=" O ARG o 290 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ALA o 298 " --> pdb=" O ALA o 294 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY o 299 " --> pdb=" O ARG o 295 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL o 300 " --> pdb=" O ALA o 296 " (cutoff:3.500A) Processing helix chain 'p' and resid 55 through 67 removed outlier: 4.101A pdb=" N LEU p 59 " --> pdb=" O ASP p 55 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LYS p 61 " --> pdb=" O LYS p 57 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA p 62 " --> pdb=" O LYS p 58 " (cutoff:3.500A) Processing helix chain 'p' and resid 89 through 101 removed outlier: 3.865A pdb=" N CYS p 94 " --> pdb=" O ARG p 90 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN p 95 " --> pdb=" O LYS p 91 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N GLU p 99 " --> pdb=" O GLN p 95 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ILE p 100 " --> pdb=" O PHE p 96 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY p 101 " --> pdb=" O LEU p 97 " (cutoff:3.500A) Processing helix chain 'p' and resid 104 through 109 removed outlier: 6.328A pdb=" N LYS p 109 " --> pdb=" O ASP p 105 " (cutoff:3.500A) Processing helix chain 'q' and resid 97 through 107 removed outlier: 3.679A pdb=" N SER q 102 " --> pdb=" O ASP q 98 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ALA q 105 " --> pdb=" O ARG q 101 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N TYR q 106 " --> pdb=" O SER q 102 " (cutoff:3.500A) Processing helix chain 'z' and resid 53 through 66 removed outlier: 4.854A pdb=" N ASP z 57 " --> pdb=" O ASP z 53 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N LYS z 66 " --> pdb=" O GLU z 62 " (cutoff:3.500A) Processing helix chain 'z' and resid 72 through 94 removed outlier: 4.380A pdb=" N LYS z 76 " --> pdb=" O SER z 72 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N ALA z 78 " --> pdb=" O LYS z 74 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N GLN z 87 " --> pdb=" O GLU z 83 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N GLN z 88 " --> pdb=" O LYS z 84 " (cutoff:3.500A) Processing helix chain 'z' and resid 114 through 135 removed outlier: 3.652A pdb=" N LYS z 133 " --> pdb=" O LEU z 129 " (cutoff:3.500A) Processing helix chain 'z' and resid 153 through 171 removed outlier: 3.701A pdb=" N THR z 157 " --> pdb=" O ARG z 153 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU z 158 " --> pdb=" O ASP z 154 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N TYR z 170 " --> pdb=" O LYS z 166 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N GLU z 171 " --> pdb=" O ILE z 167 " (cutoff:3.500A) Processing helix chain 'z' and resid 172 through 192 removed outlier: 3.672A pdb=" N TYR z 176 " --> pdb=" O LYS z 172 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ALA z 177 " --> pdb=" O SER z 173 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE z 179 " --> pdb=" O TYR z 175 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N LEU z 180 " --> pdb=" O TYR z 176 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N SER z 190 " --> pdb=" O ASP z 186 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU z 192 " --> pdb=" O CYS z 188 " (cutoff:3.500A) Processing helix chain 'z' and resid 197 through 214 removed outlier: 3.616A pdb=" N SER z 202 " --> pdb=" O LYS z 198 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU z 214 " --> pdb=" O LYS z 210 " (cutoff:3.500A) Processing helix chain 'M' and resid 6 through 20 Processing helix chain 'M' and resid 27 through 39 Processing helix chain 'M' and resid 43 through 64 removed outlier: 3.755A pdb=" N ARG M 47 " --> pdb=" O SER M 43 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG M 60 " --> pdb=" O HIS M 56 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLN M 62 " --> pdb=" O MET M 58 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N ARG M 63 " --> pdb=" O LYS M 59 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLY M 64 " --> pdb=" O ARG M 60 " (cutoff:3.500A) Processing helix chain 'M' and resid 71 through 81 removed outlier: 4.164A pdb=" N GLU M 75 " --> pdb=" O ILE M 71 " (cutoff:3.500A) Processing helix chain 'M' and resid 99 through 110 removed outlier: 4.522A pdb=" N MET M 105 " --> pdb=" O ASP M 101 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU M 106 " --> pdb=" O THR M 102 " (cutoff:3.500A) Processing helix chain 'h' and resid 28 through 47 removed outlier: 3.703A pdb=" N LEU h 32 " --> pdb=" O ASN h 28 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS h 46 " --> pdb=" O GLY h 42 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASN h 47 " --> pdb=" O ALA h 43 " (cutoff:3.500A) Processing helix chain 'h' and resid 94 through 103 removed outlier: 3.671A pdb=" N VAL h 98 " --> pdb=" O PRO h 94 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLN h 100 " --> pdb=" O GLU h 96 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N SER h 103 " --> pdb=" O LYS h 99 " (cutoff:3.500A) Processing helix chain 's' and resid 176 through 186 removed outlier: 3.585A pdb=" N ASN s 181 " --> pdb=" O GLU s 177 " (cutoff:3.500A) Processing helix chain 's' and resid 221 through 228 removed outlier: 3.732A pdb=" N ILE s 225 " --> pdb=" O ASN s 221 " (cutoff:3.500A) Processing helix chain 's' and resid 232 through 245 removed outlier: 4.021A pdb=" N LEU s 236 " --> pdb=" O GLN s 232 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LEU s 237 " --> pdb=" O PRO s 233 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ALA s 238 " --> pdb=" O LYS s 234 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N PHE s 239 " --> pdb=" O HIS s 235 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N LEU s 244 " --> pdb=" O LEU s 240 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLY s 245 " --> pdb=" O LEU s 241 " (cutoff:3.500A) Processing helix chain 's' and resid 263 through 278 removed outlier: 3.873A pdb=" N ILE s 267 " --> pdb=" O GLN s 263 " (cutoff:3.500A) Processing helix chain 't' and resid 53 through 63 Processing helix chain 't' and resid 69 through 76 Processing helix chain 't' and resid 141 through 152 removed outlier: 3.726A pdb=" N MET t 145 " --> pdb=" O LEU t 141 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASN t 147 " --> pdb=" O ALA t 143 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ALA t 150 " --> pdb=" O LEU t 146 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N VAL t 151 " --> pdb=" O ASN t 147 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N MET t 152 " --> pdb=" O GLY t 148 " (cutoff:3.500A) Processing helix chain 't' and resid 168 through 181 Processing helix chain 't' and resid 191 through 196 removed outlier: 3.506A pdb=" N VAL t 195 " --> pdb=" O LYS t 191 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N LYS t 196 " --> pdb=" O ILE t 192 " (cutoff:3.500A) No H-bonds generated for 'chain 't' and resid 191 through 196' Processing helix chain 't' and resid 197 through 211 removed outlier: 3.524A pdb=" N GLU t 205 " --> pdb=" O LYS t 201 " (cutoff:3.500A) Processing helix chain 't' and resid 215 through 220 removed outlier: 4.714A pdb=" N ALA t 219 " --> pdb=" O VAL t 215 " (cutoff:3.500A) Proline residue: t 220 - end of helix No H-bonds generated for 'chain 't' and resid 215 through 220' Processing helix chain 't' and resid 231 through 243 Processing helix chain 't' and resid 344 through 349 removed outlier: 3.501A pdb=" N CYS t 348 " --> pdb=" O ASP t 344 " (cutoff:3.500A) Processing helix chain 'j' and resid 33 through 38 removed outlier: 4.122A pdb=" N MET j 37 " --> pdb=" O SER j 33 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N ASN j 38 " --> pdb=" O PHE j 34 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 33 through 38' Processing helix chain 'j' and resid 40 through 51 removed outlier: 3.644A pdb=" N GLY j 51 " --> pdb=" O ILE j 47 " (cutoff:3.500A) Processing helix chain 'j' and resid 56 through 69 removed outlier: 3.597A pdb=" N ILE j 63 " --> pdb=" O GLN j 59 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N LEU j 64 " --> pdb=" O GLN j 60 " (cutoff:3.500A) Proline residue: j 65 - end of helix Processing helix chain 'j' and resid 81 through 94 removed outlier: 3.580A pdb=" N SER j 89 " --> pdb=" O THR j 85 " (cutoff:3.500A) Processing helix chain 'j' and resid 109 through 125 Processing helix chain 'j' and resid 139 through 149 removed outlier: 4.087A pdb=" N GLU j 143 " --> pdb=" O ASN j 139 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N GLN j 145 " --> pdb=" O ARG j 141 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N LYS j 146 " --> pdb=" O ALA j 142 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N LEU j 147 " --> pdb=" O GLU j 143 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N GLN j 148 " --> pdb=" O VAL j 144 " (cutoff:3.500A) Processing helix chain 'j' and resid 158 through 169 Processing helix chain 'j' and resid 183 through 191 removed outlier: 3.600A pdb=" N GLY j 191 " --> pdb=" O MET j 187 " (cutoff:3.500A) Processing helix chain 'j' and resid 192 through 204 removed outlier: 3.572A pdb=" N GLN j 201 " --> pdb=" O TYR j 197 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N ASN j 204 " --> pdb=" O PHE j 200 " (cutoff:3.500A) Processing helix chain 'j' and resid 217 through 227 Processing helix chain 'j' and resid 255 through 270 removed outlier: 3.857A pdb=" N LYS j 259 " --> pdb=" O ARG j 255 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N LEU j 260 " --> pdb=" O GLU j 256 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N ASP j 261 " --> pdb=" O GLU j 257 " (cutoff:3.500A) Processing helix chain 'j' and resid 281 through 296 Processing helix chain 'j' and resid 307 through 321 Processing helix chain 'j' and resid 329 through 337 removed outlier: 4.005A pdb=" N ALA j 333 " --> pdb=" O THR j 329 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N ARG j 334 " --> pdb=" O ASP j 330 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N GLY j 335 " --> pdb=" O LEU j 331 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE j 336 " --> pdb=" O LEU j 332 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ASP j 337 " --> pdb=" O ALA j 333 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 329 through 337' Processing helix chain 'j' and resid 354 through 361 removed outlier: 4.575A pdb=" N HIS j 358 " --> pdb=" O GLU j 354 " (cutoff:3.500A) Processing helix chain 'j' and resid 378 through 392 removed outlier: 4.772A pdb=" N ARG j 382 " --> pdb=" O GLU j 378 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N THR j 383 " --> pdb=" O GLU j 379 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASN j 392 " --> pdb=" O GLU j 388 " (cutoff:3.500A) Processing helix chain 'g' and resid 756 through 771 Processing helix chain 'g' and resid 775 through 790 removed outlier: 4.250A pdb=" N THR g 790 " --> pdb=" O LEU g 786 " (cutoff:3.500A) Processing helix chain 'g' and resid 791 through 809 removed outlier: 4.407A pdb=" N LYS g 795 " --> pdb=" O GLU g 791 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N GLY g 796 " --> pdb=" O GLU g 792 " (cutoff:3.500A) Proline residue: g 809 - end of helix Processing helix chain 'g' and resid 810 through 826 removed outlier: 5.647A pdb=" N ALA g 814 " --> pdb=" O ASN g 810 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LYS g 826 " --> pdb=" O LEU g 822 " (cutoff:3.500A) Processing helix chain 'g' and resid 838 through 863 removed outlier: 4.700A pdb=" N LEU g 842 " --> pdb=" O ASN g 838 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ASP g 854 " --> pdb=" O GLU g 850 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N LYS g 855 " --> pdb=" O PHE g 851 " (cutoff:3.500A) removed outlier: 8.565A pdb=" N ASP g 856 " --> pdb=" O GLU g 852 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N ASP g 857 " --> pdb=" O LYS g 853 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ASP g 858 " --> pdb=" O ASP g 854 " (cutoff:3.500A) Processing helix chain 'g' and resid 883 through 909 removed outlier: 5.470A pdb=" N ALA g 887 " --> pdb=" O GLU g 883 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ARG g 888 " --> pdb=" O LEU g 884 " (cutoff:3.500A) Processing helix chain 'g' and resid 912 through 927 removed outlier: 4.516A pdb=" N HIS g 927 " --> pdb=" O LEU g 923 " (cutoff:3.500A) Processing helix chain 'g' and resid 928 through 942 Processing helix chain 'g' and resid 949 through 968 Proline residue: g 953 - end of helix Processing helix chain 'g' and resid 972 through 989 Processing sheet with id= 1, first strand: chain '2' and resid 3 through 7 removed outlier: 6.051A pdb=" N GLU 2 305 " --> pdb=" O ASP 2 306 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N TYR 2 308 " --> pdb=" O GLY 2 303 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N GLY 2 303 " --> pdb=" O TYR 2 308 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ARG 2 310 " --> pdb=" O SER 2 301 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N SER 2 301 " --> pdb=" O ARG 2 310 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N HIS 2 312 " --> pdb=" O SER 2 299 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N SER 2 299 " --> pdb=" O HIS 2 312 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N SER 2 299 " --> pdb=" O HIS 2 294 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA 2 292 " --> pdb=" O SER 2 301 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N SER 2 290 " --> pdb=" O GLY 2 303 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain '2' and resid 24 through 28 removed outlier: 3.829A pdb=" N GLY 2 46 " --> pdb=" O VAL 2 36 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain '2' and resid 106 through 112 removed outlier: 5.031A pdb=" N ASN 2 106 " --> pdb=" O LEU 2 127 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N PHE 2 121 " --> pdb=" O THR 2 112 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain '2' and resid 151 through 155 removed outlier: 5.420A pdb=" N CYS 2 160 " --> pdb=" O GLY 2 155 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain '2' and resid 168 through 175 removed outlier: 7.850A pdb=" N GLY 2 168 " --> pdb=" O LYS 2 185 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N LYS 2 185 " --> pdb=" O GLY 2 168 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LEU 2 170 " --> pdb=" O ASN 2 183 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ASN 2 183 " --> pdb=" O LEU 2 170 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N GLN 2 172 " --> pdb=" O LEU 2 181 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain '2' and resid 243 through 249 removed outlier: 3.888A pdb=" N VAL 2 244 " --> pdb=" O PHE 2 270 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU 2 246 " --> pdb=" O ARG 2 268 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG 2 268 " --> pdb=" O LEU 2 246 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N GLY 2 248 " --> pdb=" O GLU 2 266 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLU 2 266 " --> pdb=" O GLY 2 248 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain '1' and resid 232 through 236 removed outlier: 3.779A pdb=" N VAL 1 189 " --> pdb=" O ILE 1 233 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N ASP 1 190 " --> pdb=" O ARG 1 262 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N ARG 1 262 " --> pdb=" O ASP 1 190 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain '1' and resid 315 through 319 Processing sheet with id= 9, first strand: chain '1' and resid 340 through 343 removed outlier: 5.511A pdb=" N TYR 1 348 " --> pdb=" O SER 1 343 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain '1' and resid 377 through 382 removed outlier: 5.641A pdb=" N TYR 1 387 " --> pdb=" O SER 1 382 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N ARG 1 386 " --> pdb=" O ILE 1 409 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ILE 1 406 " --> pdb=" O LYS 1 415 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N HIS 1 413 " --> pdb=" O ASP 1 408 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain '1' and resid 429 through 432 removed outlier: 5.999A pdb=" N PHE 1 437 " --> pdb=" O SER 1 432 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LYS 1 436 " --> pdb=" O THR 1 451 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N ILE 1 448 " --> pdb=" O LEU 1 457 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY 1 455 " --> pdb=" O GLU 1 450 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain '1' and resid 469 through 473 removed outlier: 5.009A pdb=" N ILE 1 478 " --> pdb=" O SER 1 473 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N ARG 1 505 " --> pdb=" O LEU 1 495 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain '1' and resid 513 through 520 removed outlier: 4.221A pdb=" N ASP 1 514 " --> pdb=" O ASP 1 531 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS 1 516 " --> pdb=" O LYS 1 529 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N TYR 1 525 " --> pdb=" O GLN 1 520 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU 1 526 " --> pdb=" O PHE 1 547 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N VAL 1 541 " --> pdb=" O ARG 1 532 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR 1 542 " --> pdb=" O MET 1 561 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain '1' and resid 566 through 571 removed outlier: 5.548A pdb=" N LYS 1 576 " --> pdb=" O GLU 1 571 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N SER 1 575 " --> pdb=" O VAL 1 594 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N PHE 1 591 " --> pdb=" O ILE 1 603 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain '1' and resid 614 through 617 removed outlier: 3.627A pdb=" N PHE 1 615 " --> pdb=" O VAL 1 624 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N PHE 1 622 " --> pdb=" O SER 1 617 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N GLN 1 621 " --> pdb=" O THR 1 640 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ALA 1 636 " --> pdb=" O LEU 1 625 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU 1 635 " --> pdb=" O ALA 1 649 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ASN 1 647 " --> pdb=" O PHE 1 637 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain '1' and resid 655 through 660 removed outlier: 5.541A pdb=" N TYR 1 665 " --> pdb=" O ASP 1 660 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N TRP 1 684 " --> pdb=" O VAL 1 666 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ALA 1 680 " --> pdb=" O VAL 1 670 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N ASN 1 679 " --> pdb=" O LYS 1 696 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLN 1 692 " --> pdb=" O LEU 1 683 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain '1' and resid 588 through 591 Processing sheet with id= 18, first strand: chain '4' and resid 91 through 94 removed outlier: 3.715A pdb=" N VAL 4 129 " --> pdb=" O VAL 4 91 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain '4' and resid 133 through 136 removed outlier: 4.155A pdb=" N VAL 4 116 " --> pdb=" O THR 4 175 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR 4 175 " --> pdb=" O VAL 4 116 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ILE 4 198 " --> pdb=" O LEU 4 170 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU 4 200 " --> pdb=" O TRP 4 172 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL 4 202 " --> pdb=" O ALA 4 174 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N SER 4 212 " --> pdb=" O ASP 4 203 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'u' and resid 482 through 486 Processing sheet with id= 21, first strand: chain 'S' and resid 11 through 17 removed outlier: 6.126A pdb=" N ASN S 110 " --> pdb=" O SER S 53 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N VAL S 49 " --> pdb=" O VAL S 114 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N THR S 34 " --> pdb=" O ILE S 52 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'S' and resid 159 through 163 removed outlier: 4.297A pdb=" N ARG S 170 " --> pdb=" O LEU S 162 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'y' and resid 831 through 836 removed outlier: 5.386A pdb=" N LEU y 831 " --> pdb=" O MET y 844 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain '8' and resid 38 through 41 removed outlier: 3.831A pdb=" N ILE 8 78 " --> pdb=" O GLN 8 40 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain '8' and resid 65 through 68 removed outlier: 3.787A pdb=" N GLY 8 65 " --> pdb=" O TYR 8 120 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain '8' and resid 148 through 153 removed outlier: 4.987A pdb=" N VAL 8 149 " --> pdb=" O TYR 8 167 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ASP 8 153 " --> pdb=" O SER 8 163 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N SER 8 163 " --> pdb=" O ASP 8 153 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'G' and resid 47 through 52 removed outlier: 4.289A pdb=" N ALA G 47 " --> pdb=" O PHE G 63 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE G 61 " --> pdb=" O LYS G 49 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE G 51 " --> pdb=" O ALA G 59 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'G' and resid 141 through 146 removed outlier: 4.617A pdb=" N GLY G 141 " --> pdb=" O HIS G 157 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG G 145 " --> pdb=" O LEU G 153 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'H' and resid 43 through 47 removed outlier: 7.056A pdb=" N PHE H 32 " --> pdb=" O LYS H 82 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'K' and resid 32 through 38 removed outlier: 4.024A pdb=" N ILE K 55 " --> pdb=" O ILE K 32 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N GLN K 49 " --> pdb=" O GLU K 38 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'L' and resid 102 through 107 removed outlier: 3.516A pdb=" N GLY L 131 " --> pdb=" O LYS L 103 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N PHE L 127 " --> pdb=" O LEU L 107 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'L' and resid 183 through 187 removed outlier: 3.781A pdb=" N VAL L 184 " --> pdb=" O LEU L 195 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER L 225 " --> pdb=" O ARG L 194 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ALA L 198 " --> pdb=" O ASP L 221 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ASP L 221 " --> pdb=" O ALA L 198 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'L' and resid 123 through 127 Processing sheet with id= 34, first strand: chain 'O' and resid 45 through 48 removed outlier: 3.909A pdb=" N GLY O 45 " --> pdb=" O VAL O 33 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N THR O 98 " --> pdb=" O LYS O 34 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR O 88 " --> pdb=" O ARG O 65 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N ARG O 65 " --> pdb=" O THR O 88 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'O' and resid 119 through 128 removed outlier: 5.392A pdb=" N THR O 119 " --> pdb=" O THR O 143 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR O 143 " --> pdb=" O THR O 119 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N LEU O 134 " --> pdb=" O LEU O 218 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N LYS O 214 " --> pdb=" O PHE O 138 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'O' and resid 101 through 105 removed outlier: 8.217A pdb=" N HIS O 101 " --> pdb=" O MET O 217 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N MET O 217 " --> pdb=" O HIS O 101 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL O 215 " --> pdb=" O MET O 103 " (cutoff:3.500A) removed outlier: 8.661A pdb=" N ARG O 213 " --> pdb=" O LEU O 105 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'N' and resid 121 through 125 Processing sheet with id= 38, first strand: chain 'Q' and resid 20 through 24 removed outlier: 4.416A pdb=" N ARG Q 28 " --> pdb=" O CYS Q 23 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'Q' and resid 36 through 43 Processing sheet with id= 40, first strand: chain 'P' and resid 40 through 46 removed outlier: 3.657A pdb=" N HIS P 43 " --> pdb=" O HIS P 32 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA P 92 " --> pdb=" O VAL P 27 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N ILE P 95 " --> pdb=" O GLY P 127 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'x' and resid 190 through 193 removed outlier: 6.476A pdb=" N TYR x 360 " --> pdb=" O ILE x 193 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'x' and resid 379 through 383 removed outlier: 3.910A pdb=" N SER x 389 " --> pdb=" O MET x 381 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY x 383 " --> pdb=" O GLU x 387 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N GLU x 387 " --> pdb=" O GLY x 383 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR x 446 " --> pdb=" O PHE x 390 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N VAL x 452 " --> pdb=" O LEU x 396 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG x 454 " --> pdb=" O GLU x 398 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N TYR x 451 " --> pdb=" O LEU x 466 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'x' and resid 516 through 522 removed outlier: 3.801A pdb=" N VAL x 516 " --> pdb=" O ASP x 511 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG x 518 " --> pdb=" O LEU x 509 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N LYS x 505 " --> pdb=" O LEU x 522 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN x 270 " --> pdb=" O PHE x 277 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N PHE x 277 " --> pdb=" O GLN x 270 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N THR x 248 " --> pdb=" O PHE x 278 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N LYS x 280 " --> pdb=" O THR x 248 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'x' and resid 355 through 363 No H-bonds generated for sheet with id= 44 Processing sheet with id= 45, first strand: chain 'x' and resid 447 through 451 Processing sheet with id= 46, first strand: chain '5' and resid 504 through 507 removed outlier: 3.848A pdb=" N SER 5 507 " --> pdb=" O GLU 5 512 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N GLU 5 512 " --> pdb=" O SER 5 507 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'B' and resid 71 through 76 removed outlier: 5.657A pdb=" N ARG B 71 " --> pdb=" O GLU B 130 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N THR B 127 " --> pdb=" O LEU B 143 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'B' and resid 85 through 97 No H-bonds generated for sheet with id= 48 Processing sheet with id= 49, first strand: chain 'B' and resid 124 through 127 Processing sheet with id= 50, first strand: chain 'C' and resid 88 through 93 removed outlier: 4.682A pdb=" N ASP C 88 " --> pdb=" O LEU C 101 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ASN C 98 " --> pdb=" O ILE C 114 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N HIS C 112 " --> pdb=" O ARG C 100 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ILE C 102 " --> pdb=" O ALA C 110 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'C' and resid 121 through 126 removed outlier: 4.324A pdb=" N ASP C 158 " --> pdb=" O VAL C 126 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'C' and resid 128 through 132 removed outlier: 4.495A pdb=" N ARG C 145 " --> pdb=" O THR C 141 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'C' and resid 180 through 183 removed outlier: 6.437A pdb=" N LEU C 180 " --> pdb=" O ILE C 228 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'C' and resid 197 through 200 Processing sheet with id= 55, first strand: chain 'E' and resid 46 through 49 removed outlier: 6.566A pdb=" N LEU E 101 " --> pdb=" O VAL E 123 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'E' and resid 53 through 59 removed outlier: 3.551A pdb=" N GLU E 53 " --> pdb=" O ARG E 71 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N ALA E 65 " --> pdb=" O ALA E 59 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N LYS E 79 " --> pdb=" O LEU E 74 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'r' and resid 19 through 23 Processing sheet with id= 58, first strand: chain 'r' and resid 31 through 37 Processing sheet with id= 59, first strand: chain 'r' and resid 74 through 78 No H-bonds generated for sheet with id= 59 Processing sheet with id= 60, first strand: chain 'r' and resid 223 through 229 removed outlier: 4.279A pdb=" N THR r 240 " --> pdb=" O PRO r 224 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASN r 228 " --> pdb=" O VAL r 236 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N VAL r 268 " --> pdb=" O ALA r 198 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'J' and resid 23 through 28 removed outlier: 6.075A pdb=" N ARG J 23 " --> pdb=" O LEU J 65 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU J 65 " --> pdb=" O ARG J 23 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN J 64 " --> pdb=" O GLU J 49 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N GLU J 49 " --> pdb=" O ASN J 64 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'R' and resid 42 through 47 removed outlier: 6.473A pdb=" N ARG R 42 " --> pdb=" O LEU R 58 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS R 54 " --> pdb=" O VAL R 46 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'R' and resid 71 through 76 removed outlier: 3.683A pdb=" N ASN R 64 " --> pdb=" O ALA R 185 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N GLY R 68 " --> pdb=" O VAL R 189 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ASP R 186 " --> pdb=" O ALA R 176 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N LEU R 172 " --> pdb=" O LEU R 190 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE R 175 " --> pdb=" O CYS R 100 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N CYS R 100 " --> pdb=" O ILE R 175 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ILE R 101 " --> pdb=" O VAL R 82 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ASP R 80 " --> pdb=" O LEU R 103 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'T' and resid 5 through 10 removed outlier: 4.370A pdb=" N VAL T 24 " --> pdb=" O LYS T 11 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N LYS T 11 " --> pdb=" O VAL T 24 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'T' and resid 59 through 63 removed outlier: 5.313A pdb=" N GLY T 59 " --> pdb=" O PHE T 72 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N PHE T 72 " --> pdb=" O GLY T 59 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N LYS T 68 " --> pdb=" O HIS T 63 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'T' and resid 20 through 29 removed outlier: 4.058A pdb=" N GLY T 67 " --> pdb=" O HIS T 29 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'V' and resid 122 through 127 No H-bonds generated for sheet with id= 67 Processing sheet with id= 68, first strand: chain 'Y' and resid 8 through 15 removed outlier: 7.042A pdb=" N GLN Y 8 " --> pdb=" O ARG Y 27 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'Y' and resid 30 through 34 Processing sheet with id= 70, first strand: chain 'Z' and resid 36 through 42 removed outlier: 3.804A pdb=" N GLY Z 36 " --> pdb=" O LEU Z 51 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG Z 45 " --> pdb=" O THR Z 42 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'Z' and resid 148 through 155 removed outlier: 3.552A pdb=" N GLY Z 180 " --> pdb=" O LEU Z 177 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'a' and resid 20 through 24 Processing sheet with id= 73, first strand: chain 'b' and resid 75 through 78 Processing sheet with id= 74, first strand: chain 'c' and resid 3 through 8 removed outlier: 4.501A pdb=" N GLN c 4 " --> pdb=" O THR c 313 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N VAL c 309 " --> pdb=" O ARG c 8 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL c 307 " --> pdb=" O LEU c 11 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY c 9 " --> pdb=" O VAL c 309 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'c' and resid 19 through 23 removed outlier: 3.509A pdb=" N GLN c 20 " --> pdb=" O ALA c 34 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N ASP c 29 " --> pdb=" O LEU c 45 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ILE c 31 " --> pdb=" O TRP c 43 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N MET c 42 " --> pdb=" O GLN c 56 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N TYR c 52 " --> pdb=" O THR c 46 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'c' and resid 68 through 72 removed outlier: 6.052A pdb=" N PHE c 77 " --> pdb=" O SER c 72 " (cutoff:3.500A) removed outlier: 8.361A pdb=" N GLN c 76 " --> pdb=" O LEU c 92 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LEU c 89 " --> pdb=" O THR c 98 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N THR c 96 " --> pdb=" O ASP c 91 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 'c' and resid 110 through 114 removed outlier: 6.793A pdb=" N GLN c 119 " --> pdb=" O SER c 114 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ILE c 129 " --> pdb=" O VAL c 142 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N TYR c 140 " --> pdb=" O LEU c 131 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 'c' and resid 153 through 157 removed outlier: 5.017A pdb=" N ILE c 164 " --> pdb=" O SER c 157 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N VAL c 176 " --> pdb=" O LYS c 185 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain 'c' and resid 197 through 201 removed outlier: 5.489A pdb=" N LEU c 206 " --> pdb=" O SER c 201 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N SER c 205 " --> pdb=" O LEU c 221 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N LEU c 218 " --> pdb=" O LEU c 227 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS c 225 " --> pdb=" O ASP c 220 " (cutoff:3.500A) Processing sheet with id= 80, first strand: chain 'c' and resid 238 through 242 removed outlier: 3.651A pdb=" N ALA c 238 " --> pdb=" O ALA c 251 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N TRP c 247 " --> pdb=" O SER c 242 " (cutoff:3.500A) Processing sheet with id= 81, first strand: chain 'c' and resid 288 through 292 removed outlier: 4.267A pdb=" N SER c 288 " --> pdb=" O GLY c 301 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N THR c 297 " --> pdb=" O SER c 292 " (cutoff:3.500A) Processing sheet with id= 82, first strand: chain 'c' and resid 39 through 42 No H-bonds generated for sheet with id= 82 Processing sheet with id= 83, first strand: chain 'c' and resid 86 through 89 Processing sheet with id= 84, first strand: chain 'c' and resid 173 through 176 Processing sheet with id= 85, first strand: chain 'c' and resid 214 through 218 removed outlier: 5.626A pdb=" N GLY c 214 " --> pdb=" O GLY c 232 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N TYR c 228 " --> pdb=" O LEU c 218 " (cutoff:3.500A) Processing sheet with id= 86, first strand: chain 'c' and resid 296 through 302 removed outlier: 6.720A pdb=" N GLN c 296 " --> pdb=" O VAL c 312 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N LEU c 306 " --> pdb=" O TYR c 302 " (cutoff:3.500A) Processing sheet with id= 87, first strand: chain 'd' and resid 81 through 84 Processing sheet with id= 88, first strand: chain 'd' and resid 113 through 116 removed outlier: 4.688A pdb=" N GLY d 120 " --> pdb=" O ASP d 116 " (cutoff:3.500A) Processing sheet with id= 89, first strand: chain 'k' and resid 138 through 141 removed outlier: 3.870A pdb=" N LEU k 146 " --> pdb=" O CYS k 141 " (cutoff:3.500A) Processing sheet with id= 90, first strand: chain 'm' and resid 30 through 33 removed outlier: 7.113A pdb=" N GLY m 30 " --> pdb=" O LYS m 112 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA m 32 " --> pdb=" O VAL m 110 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL m 110 " --> pdb=" O ALA m 32 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N ASN m 75 " --> pdb=" O HIS m 48 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU m 52 " --> pdb=" O ILE m 77 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N VAL m 79 " --> pdb=" O LEU m 52 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N SER m 54 " --> pdb=" O VAL m 79 " (cutoff:3.500A) Processing sheet with id= 91, first strand: chain 'n' and resid 9 through 13 Processing sheet with id= 92, first strand: chain 'n' and resid 18 through 22 removed outlier: 3.524A pdb=" N CYS n 27 " --> pdb=" O THR n 21 " (cutoff:3.500A) Processing sheet with id= 93, first strand: chain 'o' and resid 267 through 271 removed outlier: 5.176A pdb=" N PHE o 282 " --> pdb=" O ALA o 271 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N ALA o 239 " --> pdb=" O PHE o 287 " (cutoff:3.500A) Processing sheet with id= 94, first strand: chain 'p' and resid 32 through 38 removed outlier: 6.619A pdb=" N HIS p 32 " --> pdb=" O GLN p 48 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N LYS p 42 " --> pdb=" O ARG p 38 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N ASN p 70 " --> pdb=" O GLN p 86 " (cutoff:3.500A) Processing sheet with id= 95, first strand: chain 'q' and resid 46 through 51 removed outlier: 4.976A pdb=" N VAL q 55 " --> pdb=" O CYS q 51 " (cutoff:3.500A) Processing sheet with id= 96, first strand: chain 'M' and resid 95 through 98 Processing sheet with id= 97, first strand: chain 'h' and resid 53 through 56 removed outlier: 4.846A pdb=" N LYS h 86 " --> pdb=" O MET h 56 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N SER h 93 " --> pdb=" O HIS h 18 " (cutoff:3.500A) Processing sheet with id= 98, first strand: chain 'h' and resid 58 through 66 Processing sheet with id= 99, first strand: chain 't' and resid 81 through 87 removed outlier: 3.686A pdb=" N ILE t 42 " --> pdb=" O HIS t 129 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N GLY t 48 " --> pdb=" O CYS t 135 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N HIS t 184 " --> pdb=" O ASP t 153 " (cutoff:3.500A) Processing sheet with id=100, first strand: chain 't' and resid 292 through 297 removed outlier: 4.434A pdb=" N GLN t 292 " --> pdb=" O ILE t 318 " (cutoff:3.500A) Processing sheet with id=101, first strand: chain 't' and resid 319 through 322 removed outlier: 4.464A pdb=" N SER t 320 " --> pdb=" O GLY t 340 " (cutoff:3.500A) Processing sheet with id=102, first strand: chain 't' and resid 404 through 407 removed outlier: 3.569A pdb=" N GLU t 439 " --> pdb=" O ILE t 459 " (cutoff:3.500A) Processing sheet with id=103, first strand: chain 'j' and resid 131 through 134 removed outlier: 3.820A pdb=" N ALA j 76 " --> pdb=" O SER j 213 " (cutoff:3.500A) Processing sheet with id=104, first strand: chain 'j' and resid 245 through 253 removed outlier: 4.081A pdb=" N GLY j 370 " --> pdb=" O GLY j 245 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG j 247 " --> pdb=" O GLY j 370 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N SER j 342 " --> pdb=" O LYS j 369 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU j 343 " --> pdb=" O GLN j 274 " (cutoff:3.500A) 3622 hydrogen bonds defined for protein. 10760 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1174 hydrogen bonds 1780 hydrogen bond angles 0 basepair planarities 482 basepair parallelities 951 stacking parallelities Total time for adding SS restraints: 85.71 Time building geometry restraints manager: 49.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 19528 1.32 - 1.45: 40944 1.45 - 1.58: 59056 1.58 - 1.70: 3623 1.70 - 1.83: 514 Bond restraints: 123665 Sorted by residual: bond pdb=" C4 5MU A 814 " pdb=" C5 5MU A 814 " ideal model delta sigma weight residual 1.802 1.443 0.359 2.00e-02 2.50e+03 3.23e+02 bond pdb=" N1 5MU A 814 " pdb=" C6 5MU A 814 " ideal model delta sigma weight residual 1.635 1.384 0.251 2.00e-02 2.50e+03 1.57e+02 bond pdb=" C2' A2M A 668 " pdb=" C1' A2M A 668 " ideal model delta sigma weight residual 1.305 1.530 -0.225 2.00e-02 2.50e+03 1.27e+02 bond pdb=" C2' A2M A1678 " pdb=" C1' A2M A1678 " ideal model delta sigma weight residual 1.305 1.528 -0.223 2.00e-02 2.50e+03 1.25e+02 bond pdb=" C2' A2M A 484 " pdb=" C1' A2M A 484 " ideal model delta sigma weight residual 1.305 1.527 -0.222 2.00e-02 2.50e+03 1.23e+02 ... (remaining 123660 not shown) Histogram of bond angle deviations from ideal: 94.16 - 102.82: 3950 102.82 - 111.48: 61744 111.48 - 120.14: 60961 120.14 - 128.80: 47087 128.80 - 137.46: 2461 Bond angle restraints: 176203 Sorted by residual: angle pdb=" C1' A2M A 27 " pdb=" N9 A2M A 27 " pdb=" C8 A2M A 27 " ideal model delta sigma weight residual 88.50 127.55 -39.05 3.00e+00 1.11e-01 1.69e+02 angle pdb=" C1' A2M A 166 " pdb=" N9 A2M A 166 " pdb=" C8 A2M A 166 " ideal model delta sigma weight residual 88.50 127.34 -38.84 3.00e+00 1.11e-01 1.68e+02 angle pdb=" C1' A2M A 668 " pdb=" N9 A2M A 668 " pdb=" C8 A2M A 668 " ideal model delta sigma weight residual 88.50 127.22 -38.72 3.00e+00 1.11e-01 1.67e+02 angle pdb=" C1' A2M A1031 " pdb=" N9 A2M A1031 " pdb=" C8 A2M A1031 " ideal model delta sigma weight residual 88.50 126.74 -38.24 3.00e+00 1.11e-01 1.63e+02 angle pdb=" C1' A2M A1678 " pdb=" N9 A2M A1678 " pdb=" C8 A2M A1678 " ideal model delta sigma weight residual 88.50 126.57 -38.07 3.00e+00 1.11e-01 1.61e+02 ... (remaining 176198 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.87: 70863 35.87 - 71.75: 4469 71.75 - 107.62: 609 107.62 - 143.49: 19 143.49 - 179.37: 16 Dihedral angle restraints: 75976 sinusoidal: 43723 harmonic: 32253 Sorted by residual: dihedral pdb=" CD BARG u 14 " pdb=" NE BARG u 14 " pdb=" CZ BARG u 14 " pdb=" NH1BARG u 14 " ideal model delta sinusoidal sigma weight residual 0.00 -179.27 179.27 1 1.00e+01 1.00e-02 1.92e+02 dihedral pdb=" O4' C A1139 " pdb=" C1' C A1139 " pdb=" N1 C A1139 " pdb=" C2 C A1139 " ideal model delta sinusoidal sigma weight residual -160.00 19.10 -179.10 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' C A1752 " pdb=" C1' C A1752 " pdb=" N1 C A1752 " pdb=" C2 C A1752 " ideal model delta sinusoidal sigma weight residual -160.00 15.41 -175.41 1 1.50e+01 4.44e-03 8.52e+01 ... (remaining 75973 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 19285 0.093 - 0.185: 2196 0.185 - 0.278: 193 0.278 - 0.371: 43 0.371 - 0.463: 13 Chirality restraints: 21730 Sorted by residual: chirality pdb=" C4' U A1242 " pdb=" C5' U A1242 " pdb=" O4' U A1242 " pdb=" C3' U A1242 " both_signs ideal model delta sigma weight residual False -2.50 -2.04 -0.46 2.00e-01 2.50e+01 5.37e+00 chirality pdb=" CB VAL N 140 " pdb=" CA VAL N 140 " pdb=" CG1 VAL N 140 " pdb=" CG2 VAL N 140 " both_signs ideal model delta sigma weight residual False -2.63 -2.21 -0.42 2.00e-01 2.50e+01 4.37e+00 chirality pdb=" CB VAL c 142 " pdb=" CA VAL c 142 " pdb=" CG1 VAL c 142 " pdb=" CG2 VAL c 142 " both_signs ideal model delta sigma weight residual False -2.63 -2.21 -0.42 2.00e-01 2.50e+01 4.35e+00 ... (remaining 21727 not shown) Planarity restraints: 16084 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' OMG A 509 " -0.062 2.00e-02 2.50e+03 6.22e-01 8.71e+03 pdb=" C4' OMG A 509 " -0.431 2.00e-02 2.50e+03 pdb=" O4' OMG A 509 " -0.689 2.00e-02 2.50e+03 pdb=" C3' OMG A 509 " 0.613 2.00e-02 2.50e+03 pdb=" O3' OMG A 509 " 0.662 2.00e-02 2.50e+03 pdb=" C2' OMG A 509 " 0.171 2.00e-02 2.50e+03 pdb=" O2' OMG A 509 " -1.014 2.00e-02 2.50e+03 pdb=" C1' OMG A 509 " -0.202 2.00e-02 2.50e+03 pdb=" N9 OMG A 509 " 0.952 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMG A 683 " -0.100 2.00e-02 2.50e+03 6.05e-01 8.22e+03 pdb=" C4' OMG A 683 " -0.415 2.00e-02 2.50e+03 pdb=" O4' OMG A 683 " -0.586 2.00e-02 2.50e+03 pdb=" C3' OMG A 683 " 0.610 2.00e-02 2.50e+03 pdb=" O3' OMG A 683 " 0.671 2.00e-02 2.50e+03 pdb=" C2' OMG A 683 " 0.162 2.00e-02 2.50e+03 pdb=" O2' OMG A 683 " -1.031 2.00e-02 2.50e+03 pdb=" C1' OMG A 683 " -0.210 2.00e-02 2.50e+03 pdb=" N9 OMG A 683 " 0.899 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 5MU A 814 " 0.073 2.00e-02 2.50e+03 6.01e-01 8.13e+03 pdb=" C4' 5MU A 814 " 0.434 2.00e-02 2.50e+03 pdb=" O4' 5MU A 814 " 0.596 2.00e-02 2.50e+03 pdb=" C3' 5MU A 814 " -0.607 2.00e-02 2.50e+03 pdb=" O3' 5MU A 814 " -0.671 2.00e-02 2.50e+03 pdb=" C2' 5MU A 814 " -0.169 2.00e-02 2.50e+03 pdb=" O2' 5MU A 814 " 1.012 2.00e-02 2.50e+03 pdb=" C1' 5MU A 814 " 0.218 2.00e-02 2.50e+03 pdb=" N1 5MU A 814 " -0.886 2.00e-02 2.50e+03 ... (remaining 16081 not shown) Histogram of nonbonded interaction distances: 1.29 - 2.01: 1 2.01 - 2.73: 12705 2.73 - 3.46: 162701 3.46 - 4.18: 327480 4.18 - 4.90: 497359 Nonbonded interactions: 1000246 Sorted by model distance: nonbonded pdb="MG MG A1916 " pdb="MG MG A1929 " model vdw 1.291 1.300 nonbonded pdb=" O6 G A1335 " pdb="MG MG A1915 " model vdw 2.033 2.170 nonbonded pdb=" O6 G A1491 " pdb="MG MG A1915 " model vdw 2.034 2.170 nonbonded pdb=" OP2 OMG A 509 " pdb="MG MG A1952 " model vdw 2.037 2.170 nonbonded pdb=" OP2 U A 100 " pdb="MG MG A1978 " model vdw 2.044 2.170 ... (remaining 1000241 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.450 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: 27.680 Check model and map are aligned: 1.300 Set scattering table: 0.800 Process input model: 367.780 Find NCS groups from input model: 3.420 Set up NCS constraints: 0.350 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 409.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6533 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.359 123665 Z= 0.498 Angle : 1.250 39.052 176203 Z= 0.688 Chirality : 0.061 0.463 21730 Planarity : 0.015 0.622 16084 Dihedral : 20.519 179.367 54994 Min Nonbonded Distance : 1.291 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.45 % Favored : 93.30 % Rotamer: Outliers : 2.46 % Allowed : 12.22 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.63 (0.07), residues: 10949 helix: -1.18 (0.07), residues: 4063 sheet: -1.35 (0.13), residues: 1464 loop : -2.30 (0.07), residues: 5422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.004 TRP g 990 HIS 0.033 0.003 HIS p 32 PHE 0.055 0.003 PHE f 28 TYR 0.069 0.003 TYR j 48 ARG 0.056 0.002 ARG g 893 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21898 Ramachandran restraints generated. 10949 Oldfield, 0 Emsley, 10949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21898 Ramachandran restraints generated. 10949 Oldfield, 0 Emsley, 10949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2537 residues out of total 9800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 2367 time to evaluate : 8.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASN P 26 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 477 ASN cc_start: 0.4015 (m-40) cc_final: 0.3425 (t0) REVERT: 1 488 ASP cc_start: 0.7363 (m-30) cc_final: 0.6899 (t0) REVERT: 1 501 ARG cc_start: 0.5535 (tmm160) cc_final: 0.5322 (tmt-80) REVERT: 1 508 ASN cc_start: 0.6097 (m-40) cc_final: 0.5805 (m-40) REVERT: 1 518 HIS cc_start: 0.1372 (m-70) cc_final: 0.0846 (m170) REVERT: 1 524 ASP cc_start: -0.0233 (m-30) cc_final: -0.0686 (m-30) REVERT: 1 526 LEU cc_start: 0.7534 (tp) cc_final: 0.7326 (tt) REVERT: 1 549 MET cc_start: 0.3292 (mtp) cc_final: 0.2918 (mtp) REVERT: 6 8 ASP cc_start: 0.3264 (t0) cc_final: 0.2842 (p0) REVERT: 6 320 MET cc_start: 0.1761 (tpt) cc_final: 0.1238 (mmt) REVERT: 6 353 THR cc_start: 0.6129 (p) cc_final: 0.5814 (p) REVERT: u 331 ILE cc_start: 0.4048 (OUTLIER) cc_final: 0.3734 (mt) REVERT: u 398 PHE cc_start: 0.1494 (p90) cc_final: 0.1165 (p90) REVERT: v 233 ILE cc_start: 0.6359 (tt) cc_final: 0.6153 (tp) REVERT: v 243 LEU cc_start: 0.6739 (OUTLIER) cc_final: 0.6474 (mt) REVERT: v 281 ILE cc_start: 0.7450 (tp) cc_final: 0.7189 (tp) REVERT: v 341 PHE cc_start: 0.5726 (m-10) cc_final: 0.5363 (m-10) REVERT: v 391 VAL cc_start: 0.3972 (t) cc_final: 0.3729 (t) REVERT: S 2 LYS cc_start: 0.7917 (mttt) cc_final: 0.7130 (mtpt) REVERT: S 6 SER cc_start: 0.8865 (m) cc_final: 0.8649 (p) REVERT: S 13 GLN cc_start: 0.6643 (mt0) cc_final: 0.6354 (mt0) REVERT: S 39 ASP cc_start: 0.7451 (m-30) cc_final: 0.6886 (p0) REVERT: S 45 TRP cc_start: 0.8596 (m100) cc_final: 0.7837 (m-10) REVERT: S 51 ARG cc_start: 0.7843 (ttp80) cc_final: 0.7554 (ptm160) REVERT: S 139 SER cc_start: 0.8415 (m) cc_final: 0.8095 (t) REVERT: y 54 ASP cc_start: 0.7186 (m-30) cc_final: 0.6903 (m-30) REVERT: y 86 LEU cc_start: 0.7350 (mt) cc_final: 0.7137 (tp) REVERT: y 116 TYR cc_start: 0.4592 (OUTLIER) cc_final: 0.3762 (t80) REVERT: y 134 ASN cc_start: 0.7637 (m-40) cc_final: 0.7336 (m110) REVERT: y 418 ILE cc_start: 0.8487 (mt) cc_final: 0.8081 (tt) REVERT: y 454 GLU cc_start: 0.6930 (mm-30) cc_final: 0.6389 (mm-30) REVERT: y 473 LEU cc_start: 0.8398 (tp) cc_final: 0.7761 (tp) REVERT: y 571 CYS cc_start: 0.7908 (m) cc_final: 0.7456 (m) REVERT: H 6 ASP cc_start: 0.8463 (t0) cc_final: 0.8000 (m-30) REVERT: H 8 LEU cc_start: 0.9140 (mm) cc_final: 0.8926 (mt) REVERT: L 73 MET cc_start: 0.7204 (mmp) cc_final: 0.6802 (mmt) REVERT: L 106 VAL cc_start: 0.8670 (t) cc_final: 0.8439 (m) REVERT: L 108 LYS cc_start: 0.7743 (tppt) cc_final: 0.7493 (tttp) REVERT: L 132 ASP cc_start: 0.8922 (p0) cc_final: 0.8519 (p0) REVERT: L 134 ASN cc_start: 0.8779 (t0) cc_final: 0.8270 (t0) REVERT: L 215 MET cc_start: 0.7903 (ptp) cc_final: 0.7529 (mtp) REVERT: O 191 ASP cc_start: 0.6365 (p0) cc_final: 0.5418 (p0) REVERT: N 56 GLU cc_start: 0.8010 (mm-30) cc_final: 0.7665 (mm-30) REVERT: N 57 LYS cc_start: 0.8574 (mmmm) cc_final: 0.8357 (tptp) REVERT: N 70 ASN cc_start: 0.8681 (t0) cc_final: 0.8329 (t0) REVERT: N 73 ASP cc_start: 0.7756 (m-30) cc_final: 0.7534 (m-30) REVERT: N 177 MET cc_start: 0.8004 (tpp) cc_final: 0.7793 (mmm) REVERT: x 25 PHE cc_start: 0.6731 (p90) cc_final: 0.5971 (p90) REVERT: x 26 ARG cc_start: 0.4692 (mmp80) cc_final: 0.3193 (ptm160) REVERT: x 330 MET cc_start: 0.0038 (ttp) cc_final: -0.0831 (ttp) REVERT: 9 14 LYS cc_start: 0.8692 (ttpt) cc_final: 0.8040 (tttp) REVERT: B 54 THR cc_start: 0.9162 (p) cc_final: 0.8950 (t) REVERT: B 104 LYS cc_start: 0.8690 (tptp) cc_final: 0.8364 (tptt) REVERT: B 130 GLU cc_start: 0.8525 (tt0) cc_final: 0.8116 (tm-30) REVERT: C 121 TYR cc_start: 0.8879 (p90) cc_final: 0.8638 (p90) REVERT: C 131 VAL cc_start: 0.9344 (t) cc_final: 0.9067 (m) REVERT: C 164 LEU cc_start: 0.9236 (mt) cc_final: 0.8977 (mt) REVERT: C 216 ASN cc_start: 0.8446 (m110) cc_final: 0.8017 (m-40) REVERT: D 47 LYS cc_start: 0.8719 (ttmt) cc_final: 0.8451 (ttpt) REVERT: D 52 LYS cc_start: 0.9002 (mtmt) cc_final: 0.8605 (mtmm) REVERT: D 93 LYS cc_start: 0.8428 (mttm) cc_final: 0.8227 (mtpp) REVERT: D 101 LYS cc_start: 0.9125 (mmtt) cc_final: 0.8913 (mmtm) REVERT: D 102 ILE cc_start: 0.9314 (tt) cc_final: 0.9084 (tt) REVERT: D 150 ARG cc_start: 0.8643 (mtm-85) cc_final: 0.7392 (mtm110) REVERT: D 154 GLN cc_start: 0.8565 (OUTLIER) cc_final: 0.8240 (tt0) REVERT: E 18 ARG cc_start: 0.8613 (ttp-170) cc_final: 0.8318 (ttm170) REVERT: E 53 GLU cc_start: 0.8301 (pt0) cc_final: 0.7977 (pm20) REVERT: r 45 MET cc_start: 0.1920 (ptm) cc_final: 0.1290 (tmm) REVERT: r 48 LEU cc_start: 0.4148 (OUTLIER) cc_final: 0.3183 (tp) REVERT: r 196 GLU cc_start: 0.1595 (mp0) cc_final: 0.0732 (tm-30) REVERT: r 223 MET cc_start: 0.5168 (ptp) cc_final: 0.4300 (ptm) REVERT: J 114 GLU cc_start: 0.8527 (mt-10) cc_final: 0.8035 (mt-10) REVERT: J 115 GLU cc_start: 0.8371 (tt0) cc_final: 0.7798 (tt0) REVERT: J 118 ARG cc_start: 0.8611 (mtm-85) cc_final: 0.7795 (mtm-85) REVERT: R 111 GLN cc_start: 0.8650 (mt0) cc_final: 0.8314 (mt0) REVERT: T 19 GLN cc_start: 0.8900 (mp10) cc_final: 0.8565 (mp10) REVERT: T 25 ILE cc_start: 0.8992 (mt) cc_final: 0.8780 (mt) REVERT: T 26 ASP cc_start: 0.8193 (m-30) cc_final: 0.7966 (m-30) REVERT: T 86 GLU cc_start: 0.8657 (tp30) cc_final: 0.7878 (tp30) REVERT: T 100 LYS cc_start: 0.8267 (OUTLIER) cc_final: 0.7839 (pttm) REVERT: V 127 ARG cc_start: 0.4324 (tmt170) cc_final: 0.3941 (mmm-85) REVERT: V 173 LEU cc_start: 0.6820 (tp) cc_final: 0.6606 (tp) REVERT: V 177 LEU cc_start: 0.5531 (pp) cc_final: 0.5249 (tt) REVERT: Z 49 ILE cc_start: 0.5940 (mm) cc_final: 0.5428 (mt) REVERT: Z 57 ASN cc_start: 0.6945 (m-40) cc_final: 0.6306 (t0) REVERT: Z 169 ASP cc_start: 0.8020 (p0) cc_final: 0.7739 (p0) REVERT: Z 227 LYS cc_start: 0.3524 (ptpp) cc_final: 0.3165 (mmtt) REVERT: c 113 PHE cc_start: 0.5113 (OUTLIER) cc_final: 0.4598 (t80) REVERT: c 126 ASP cc_start: 0.6110 (p0) cc_final: 0.5815 (p0) REVERT: c 134 THR cc_start: 0.5168 (OUTLIER) cc_final: 0.4748 (m) REVERT: f 83 PHE cc_start: 0.1703 (OUTLIER) cc_final: 0.0478 (m-80) REVERT: i 36 LEU cc_start: 0.6513 (mt) cc_final: 0.6223 (mp) REVERT: i 46 TYR cc_start: 0.6301 (m-80) cc_final: 0.5901 (m-80) REVERT: k 144 CYS cc_start: 0.4794 (OUTLIER) cc_final: 0.4159 (p) REVERT: n 35 MET cc_start: 0.4369 (mmm) cc_final: 0.3798 (tpp) REVERT: p 58 LYS cc_start: 0.8795 (mmmt) cc_final: 0.8107 (mmtp) REVERT: p 61 LYS cc_start: 0.7823 (mtpp) cc_final: 0.7514 (ttpp) REVERT: p 69 CYS cc_start: 0.8628 (p) cc_final: 0.8290 (p) REVERT: p 89 GLN cc_start: 0.8314 (mm-40) cc_final: 0.7934 (mp10) REVERT: q 88 LYS cc_start: 0.5109 (mmtt) cc_final: 0.4887 (ttpt) REVERT: M 58 MET cc_start: 0.7628 (mmm) cc_final: 0.6966 (mmm) REVERT: M 104 GLU cc_start: 0.8151 (mm-30) cc_final: 0.7913 (mm-30) REVERT: h 29 VAL cc_start: 0.7870 (t) cc_final: 0.7612 (p) REVERT: j 290 GLU cc_start: 0.4578 (mt-10) cc_final: 0.4090 (pt0) outliers start: 170 outliers final: 44 residues processed: 2491 average time/residue: 1.1903 time to fit residues: 5028.5961 Evaluate side-chains 1476 residues out of total 9800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 1422 time to evaluate : 7.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain u residue 109 GLN Chi-restraints excluded: chain u residue 331 ILE Chi-restraints excluded: chain u residue 340 ARG Chi-restraints excluded: chain v residue 243 LEU Chi-restraints excluded: chain S residue 158 VAL Chi-restraints excluded: chain y residue 77 THR Chi-restraints excluded: chain y residue 102 VAL Chi-restraints excluded: chain y residue 116 TYR Chi-restraints excluded: chain y residue 140 THR Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain L residue 227 ARG Chi-restraints excluded: chain Q residue 86 ASN Chi-restraints excluded: chain Q residue 87 ARG Chi-restraints excluded: chain x residue 470 GLN Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 154 GLN Chi-restraints excluded: chain E residue 105 PHE Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain r residue 48 LEU Chi-restraints excluded: chain r residue 56 ILE Chi-restraints excluded: chain r residue 88 ARG Chi-restraints excluded: chain r residue 195 ILE Chi-restraints excluded: chain r residue 240 THR Chi-restraints excluded: chain r residue 271 VAL Chi-restraints excluded: chain r residue 278 VAL Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 30 CYS Chi-restraints excluded: chain J residue 80 ASP Chi-restraints excluded: chain T residue 27 VAL Chi-restraints excluded: chain T residue 80 ASP Chi-restraints excluded: chain T residue 100 LYS Chi-restraints excluded: chain Z residue 42 THR Chi-restraints excluded: chain c residue 113 PHE Chi-restraints excluded: chain c residue 134 THR Chi-restraints excluded: chain d residue 34 VAL Chi-restraints excluded: chain d residue 96 SER Chi-restraints excluded: chain e residue 51 ASP Chi-restraints excluded: chain f residue 83 PHE Chi-restraints excluded: chain k residue 144 CYS Chi-restraints excluded: chain m residue 91 LEU Chi-restraints excluded: chain m residue 94 ILE Chi-restraints excluded: chain m residue 123 VAL Chi-restraints excluded: chain n residue 46 VAL Chi-restraints excluded: chain q residue 39 ILE Chi-restraints excluded: chain q residue 47 LEU Chi-restraints excluded: chain q residue 51 CYS Chi-restraints excluded: chain q residue 55 VAL Chi-restraints excluded: chain q residue 81 LEU Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain s residue 279 VAL Chi-restraints excluded: chain j residue 299 VAL Chi-restraints excluded: chain j residue 357 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1269 random chunks: chunk 1071 optimal weight: 1.9990 chunk 961 optimal weight: 9.9990 chunk 533 optimal weight: 20.0000 chunk 328 optimal weight: 0.9990 chunk 648 optimal weight: 2.9990 chunk 513 optimal weight: 6.9990 chunk 994 optimal weight: 20.0000 chunk 384 optimal weight: 0.3980 chunk 604 optimal weight: 30.0000 chunk 740 optimal weight: 10.0000 chunk 1152 optimal weight: 0.0980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 518 HIS 1 543 ASN u 44 GLN ** u 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 229 HIS ** u 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 301 HIS u 316 GLN u 392 ASN ** u 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 477 HIS ** u 486 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 510 HIS ** v 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 478 GLN ** y 579 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 637 GLN ** G 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 126 HIS K 21 ASN ** L 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 272 HIS O 147 ASN O 179 ASN ** N 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 62 GLN ** x 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 470 GLN ** x 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 GLN ** B 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 ASN F 130 ASN ** r 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 90 GLN R 146 GLN T 63 HIS ** V 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 82 ASN V 110 GLN ** V 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 165 ASN ** V 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 76 GLN ** c 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 135 HIS i 45 GLN o 256 GLN ** p 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 84 GLN ** h 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 253 ASN ** s 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 208 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6606 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 123665 Z= 0.234 Angle : 0.753 17.204 176203 Z= 0.394 Chirality : 0.042 0.455 21730 Planarity : 0.006 0.131 16084 Dihedral : 20.806 179.621 38767 Min Nonbonded Distance : 1.136 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.57 % Favored : 95.35 % Rotamer: Outliers : 3.85 % Allowed : 20.24 % Favored : 75.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.07), residues: 10949 helix: -0.52 (0.08), residues: 4278 sheet: -0.96 (0.13), residues: 1481 loop : -2.00 (0.08), residues: 5190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP c 177 HIS 0.018 0.001 HIS a 66 PHE 0.027 0.002 PHE j 86 TYR 0.030 0.002 TYR v 242 ARG 0.010 0.001 ARG V 159 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21898 Ramachandran restraints generated. 10949 Oldfield, 0 Emsley, 10949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21898 Ramachandran restraints generated. 10949 Oldfield, 0 Emsley, 10949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1816 residues out of total 9800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 266 poor density : 1550 time to evaluate : 7.855 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 TARDY: cannot create tardy model for: "ASN P 26 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 488 ASP cc_start: 0.7248 (m-30) cc_final: 0.6959 (t0) REVERT: 1 511 ASN cc_start: 0.2392 (m-40) cc_final: 0.2132 (t0) REVERT: 1 558 VAL cc_start: 0.5741 (OUTLIER) cc_final: 0.5473 (m) REVERT: 6 313 ILE cc_start: 0.5055 (mt) cc_final: 0.4777 (mt) REVERT: 6 317 ARG cc_start: 0.5983 (mmm160) cc_final: 0.5673 (tpp80) REVERT: u 563 LYS cc_start: 0.4833 (OUTLIER) cc_final: 0.3496 (ttmm) REVERT: v 203 SER cc_start: 0.6405 (OUTLIER) cc_final: 0.6196 (p) REVERT: v 341 PHE cc_start: 0.5952 (m-10) cc_final: 0.5732 (m-10) REVERT: v 346 ARG cc_start: 0.7551 (tpp-160) cc_final: 0.7110 (tpp80) REVERT: S 13 GLN cc_start: 0.6366 (mt0) cc_final: 0.5972 (mt0) REVERT: S 139 SER cc_start: 0.8288 (OUTLIER) cc_final: 0.8034 (t) REVERT: S 163 ASN cc_start: 0.7675 (t0) cc_final: 0.7046 (p0) REVERT: y 116 TYR cc_start: 0.4513 (OUTLIER) cc_final: 0.3581 (t80) REVERT: y 134 ASN cc_start: 0.7053 (m-40) cc_final: 0.6400 (m110) REVERT: y 453 GLU cc_start: 0.6787 (tm-30) cc_final: 0.6483 (tm-30) REVERT: y 591 MET cc_start: 0.6308 (ptp) cc_final: 0.5859 (ptt) REVERT: H 6 ASP cc_start: 0.8406 (t70) cc_final: 0.7938 (m-30) REVERT: H 20 LYS cc_start: 0.8952 (OUTLIER) cc_final: 0.8735 (ptpp) REVERT: H 33 MET cc_start: 0.8810 (ptp) cc_final: 0.8600 (mtp) REVERT: L 73 MET cc_start: 0.7389 (mmp) cc_final: 0.6877 (mmt) REVERT: L 134 ASN cc_start: 0.8923 (t0) cc_final: 0.8293 (t0) REVERT: L 161 SER cc_start: 0.8878 (m) cc_final: 0.8613 (t) REVERT: L 202 THR cc_start: 0.9159 (t) cc_final: 0.8741 (p) REVERT: L 215 MET cc_start: 0.8065 (ptp) cc_final: 0.7836 (mtp) REVERT: L 227 ARG cc_start: 0.8576 (OUTLIER) cc_final: 0.8265 (tmm-80) REVERT: N 44 ASP cc_start: 0.7748 (p0) cc_final: 0.7253 (p0) REVERT: N 70 ASN cc_start: 0.8834 (t0) cc_final: 0.8622 (t0) REVERT: N 73 ASP cc_start: 0.7863 (m-30) cc_final: 0.7625 (m-30) REVERT: Q 87 ARG cc_start: 0.9061 (OUTLIER) cc_final: 0.8351 (mtm180) REVERT: P 124 MET cc_start: 0.8384 (mmm) cc_final: 0.7983 (mmm) REVERT: x 26 ARG cc_start: 0.5145 (mmp80) cc_final: 0.3385 (ptm160) REVERT: x 302 GLU cc_start: 0.4402 (tm-30) cc_final: 0.3064 (mt-10) REVERT: x 330 MET cc_start: -0.0631 (ttp) cc_final: -0.1481 (ttp) REVERT: 9 14 LYS cc_start: 0.8333 (ttpt) cc_final: 0.7752 (ttpp) REVERT: B 39 ASN cc_start: 0.8368 (t0) cc_final: 0.8150 (t0) REVERT: B 122 ILE cc_start: 0.9501 (mp) cc_final: 0.9240 (mt) REVERT: C 121 TYR cc_start: 0.9050 (p90) cc_final: 0.8784 (p90) REVERT: C 131 VAL cc_start: 0.9294 (t) cc_final: 0.9007 (m) REVERT: C 164 LEU cc_start: 0.9153 (mt) cc_final: 0.8879 (mt) REVERT: C 216 ASN cc_start: 0.8575 (m110) cc_final: 0.8129 (m-40) REVERT: C 250 GLU cc_start: 0.7998 (mt-10) cc_final: 0.7752 (mt-10) REVERT: D 47 LYS cc_start: 0.8670 (ttmt) cc_final: 0.8365 (ttpt) REVERT: D 107 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7947 (tm-30) REVERT: E 14 ARG cc_start: 0.8651 (ttp-170) cc_final: 0.8356 (ttp80) REVERT: E 37 LYS cc_start: 0.8795 (tppt) cc_final: 0.8076 (mmtp) REVERT: E 87 ASN cc_start: 0.8356 (OUTLIER) cc_final: 0.8132 (m-40) REVERT: r 48 LEU cc_start: 0.4625 (OUTLIER) cc_final: 0.3616 (tp) REVERT: r 223 MET cc_start: 0.4882 (ptp) cc_final: 0.4447 (ptp) REVERT: r 237 MET cc_start: 0.3858 (ptp) cc_final: 0.3408 (ptm) REVERT: r 255 MET cc_start: 0.1446 (mmt) cc_final: 0.0588 (ptm) REVERT: J 51 GLU cc_start: 0.8196 (tt0) cc_final: 0.7843 (tt0) REVERT: R 6 ASP cc_start: 0.8100 (p0) cc_final: 0.7889 (p0) REVERT: R 111 GLN cc_start: 0.8806 (mt0) cc_final: 0.8397 (mt0) REVERT: T 18 LEU cc_start: 0.9275 (mt) cc_final: 0.9008 (mm) REVERT: T 19 GLN cc_start: 0.9004 (mp10) cc_final: 0.8583 (mp10) REVERT: T 61 ARG cc_start: 0.7579 (tpp-160) cc_final: 0.7205 (mtt-85) REVERT: V 55 ARG cc_start: 0.6937 (mtp180) cc_final: 0.6728 (ttp-170) REVERT: V 127 ARG cc_start: 0.4160 (tmt170) cc_final: 0.3834 (mmm-85) REVERT: V 144 LEU cc_start: 0.7812 (OUTLIER) cc_final: 0.7529 (tt) REVERT: V 202 SER cc_start: 0.6461 (OUTLIER) cc_final: 0.5527 (t) REVERT: Y 7 LEU cc_start: 0.6327 (mt) cc_final: 0.6042 (pt) REVERT: Z 57 ASN cc_start: 0.6944 (m-40) cc_final: 0.6390 (t0) REVERT: c 126 ASP cc_start: 0.6334 (p0) cc_final: 0.5755 (p0) REVERT: c 149 GLU cc_start: 0.6300 (tp30) cc_final: 0.6097 (tp30) REVERT: f 77 TYR cc_start: 0.3827 (m-80) cc_final: 0.3028 (m-80) REVERT: i 44 ARG cc_start: 0.8542 (mmm160) cc_final: 0.8196 (tpp80) REVERT: n 35 MET cc_start: 0.4948 (mmm) cc_final: 0.4249 (tpp) REVERT: p 69 CYS cc_start: 0.8715 (p) cc_final: 0.8289 (p) REVERT: p 89 GLN cc_start: 0.8468 (mm-40) cc_final: 0.8068 (mp10) REVERT: p 107 GLN cc_start: 0.6037 (tp-100) cc_final: 0.5798 (tp40) REVERT: q 38 VAL cc_start: 0.5072 (OUTLIER) cc_final: 0.4674 (m) REVERT: q 50 MET cc_start: 0.3290 (tmm) cc_final: 0.2426 (tpp) REVERT: M 58 MET cc_start: 0.7738 (mmm) cc_final: 0.7512 (mmm) REVERT: M 92 ASP cc_start: 0.8405 (t0) cc_final: 0.8122 (t0) REVERT: j 165 MET cc_start: 0.0355 (mtt) cc_final: 0.0133 (mtt) REVERT: j 227 PHE cc_start: 0.2606 (m-80) cc_final: 0.1878 (m-10) REVERT: j 290 GLU cc_start: 0.4058 (mt-10) cc_final: 0.3678 (pt0) REVERT: j 292 MET cc_start: 0.1174 (mtm) cc_final: 0.0673 (mmt) REVERT: j 299 VAL cc_start: 0.0383 (OUTLIER) cc_final: 0.0116 (m) REVERT: j 302 MET cc_start: 0.0280 (mtt) cc_final: -0.0010 (mmt) REVERT: g 916 MET cc_start: -0.0740 (tpt) cc_final: -0.0982 (tpt) REVERT: g 985 LEU cc_start: 0.2677 (OUTLIER) cc_final: 0.2452 (mt) outliers start: 266 outliers final: 133 residues processed: 1716 average time/residue: 1.0236 time to fit residues: 3045.7132 Evaluate side-chains 1446 residues out of total 9800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 1297 time to evaluate : 7.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 513 VAL Chi-restraints excluded: chain 1 residue 543 ASN Chi-restraints excluded: chain 1 residue 558 VAL Chi-restraints excluded: chain 1 residue 566 ILE Chi-restraints excluded: chain 6 residue 312 VAL Chi-restraints excluded: chain 6 residue 316 VAL Chi-restraints excluded: chain 6 residue 318 THR Chi-restraints excluded: chain u residue 109 GLN Chi-restraints excluded: chain u residue 242 SER Chi-restraints excluded: chain u residue 316 GLN Chi-restraints excluded: chain u residue 342 LEU Chi-restraints excluded: chain u residue 357 THR Chi-restraints excluded: chain u residue 563 LYS Chi-restraints excluded: chain v residue 203 SER Chi-restraints excluded: chain v residue 278 VAL Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 114 VAL Chi-restraints excluded: chain S residue 139 SER Chi-restraints excluded: chain S residue 158 VAL Chi-restraints excluded: chain S residue 219 GLU Chi-restraints excluded: chain y residue 102 VAL Chi-restraints excluded: chain y residue 116 TYR Chi-restraints excluded: chain y residue 157 THR Chi-restraints excluded: chain y residue 495 THR Chi-restraints excluded: chain y residue 510 THR Chi-restraints excluded: chain y residue 562 ASP Chi-restraints excluded: chain y residue 608 LEU Chi-restraints excluded: chain y residue 798 VAL Chi-restraints excluded: chain G residue 44 ASN Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 119 SER Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 164 ASN Chi-restraints excluded: chain G residue 174 SER Chi-restraints excluded: chain H residue 20 LYS Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 36 LYS Chi-restraints excluded: chain H residue 37 CYS Chi-restraints excluded: chain H residue 40 CYS Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 80 SER Chi-restraints excluded: chain L residue 59 GLU Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 172 ASN Chi-restraints excluded: chain L residue 205 VAL Chi-restraints excluded: chain L residue 225 SER Chi-restraints excluded: chain L residue 227 ARG Chi-restraints excluded: chain L residue 248 TYR Chi-restraints excluded: chain O residue 55 THR Chi-restraints excluded: chain O residue 91 VAL Chi-restraints excluded: chain O residue 131 ASP Chi-restraints excluded: chain O residue 153 THR Chi-restraints excluded: chain O residue 227 LYS Chi-restraints excluded: chain N residue 49 ILE Chi-restraints excluded: chain N residue 97 THR Chi-restraints excluded: chain Q residue 43 ASN Chi-restraints excluded: chain Q residue 44 ILE Chi-restraints excluded: chain Q residue 87 ARG Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain I residue 69 ASN Chi-restraints excluded: chain x residue 69 TYR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 87 ASN Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 127 ASN Chi-restraints excluded: chain r residue 30 MET Chi-restraints excluded: chain r residue 48 LEU Chi-restraints excluded: chain r residue 76 VAL Chi-restraints excluded: chain r residue 88 ARG Chi-restraints excluded: chain r residue 106 LYS Chi-restraints excluded: chain r residue 227 ILE Chi-restraints excluded: chain r residue 240 THR Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain J residue 94 LEU Chi-restraints excluded: chain J residue 98 GLN Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 89 GLU Chi-restraints excluded: chain T residue 80 ASP Chi-restraints excluded: chain T residue 125 VAL Chi-restraints excluded: chain V residue 72 LEU Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain V residue 78 MET Chi-restraints excluded: chain V residue 144 LEU Chi-restraints excluded: chain V residue 165 ASN Chi-restraints excluded: chain V residue 176 GLU Chi-restraints excluded: chain V residue 202 SER Chi-restraints excluded: chain Y residue 34 VAL Chi-restraints excluded: chain Y residue 68 ILE Chi-restraints excluded: chain Y residue 81 ILE Chi-restraints excluded: chain Y residue 104 SER Chi-restraints excluded: chain Z residue 42 THR Chi-restraints excluded: chain Z residue 84 VAL Chi-restraints excluded: chain Z residue 86 LEU Chi-restraints excluded: chain Z residue 182 LEU Chi-restraints excluded: chain a residue 70 TYR Chi-restraints excluded: chain c residue 11 LEU Chi-restraints excluded: chain c residue 132 TRP Chi-restraints excluded: chain c residue 137 VAL Chi-restraints excluded: chain c residue 265 ILE Chi-restraints excluded: chain c residue 297 THR Chi-restraints excluded: chain e residue 51 ASP Chi-restraints excluded: chain e residue 74 SER Chi-restraints excluded: chain f residue 39 ARG Chi-restraints excluded: chain f residue 73 ASN Chi-restraints excluded: chain f residue 83 PHE Chi-restraints excluded: chain i residue 9 SER Chi-restraints excluded: chain m residue 91 LEU Chi-restraints excluded: chain m residue 123 VAL Chi-restraints excluded: chain m residue 124 ILE Chi-restraints excluded: chain n residue 46 VAL Chi-restraints excluded: chain o residue 254 ASP Chi-restraints excluded: chain p residue 30 TYR Chi-restraints excluded: chain p residue 43 THR Chi-restraints excluded: chain p residue 73 VAL Chi-restraints excluded: chain p residue 93 ILE Chi-restraints excluded: chain q residue 38 VAL Chi-restraints excluded: chain q residue 47 LEU Chi-restraints excluded: chain q residue 81 LEU Chi-restraints excluded: chain M residue 6 THR Chi-restraints excluded: chain M residue 8 THR Chi-restraints excluded: chain M residue 22 THR Chi-restraints excluded: chain M residue 54 VAL Chi-restraints excluded: chain M residue 61 ILE Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain M residue 116 ASN Chi-restraints excluded: chain h residue 20 ILE Chi-restraints excluded: chain h residue 60 THR Chi-restraints excluded: chain h residue 65 THR Chi-restraints excluded: chain h residue 89 ILE Chi-restraints excluded: chain h residue 93 SER Chi-restraints excluded: chain h residue 106 ILE Chi-restraints excluded: chain h residue 114 VAL Chi-restraints excluded: chain s residue 187 MET Chi-restraints excluded: chain s residue 220 VAL Chi-restraints excluded: chain s residue 279 VAL Chi-restraints excluded: chain s residue 290 ILE Chi-restraints excluded: chain j residue 268 GLU Chi-restraints excluded: chain j residue 299 VAL Chi-restraints excluded: chain j residue 357 ILE Chi-restraints excluded: chain g residue 795 LYS Chi-restraints excluded: chain g residue 985 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1269 random chunks: chunk 640 optimal weight: 4.9990 chunk 357 optimal weight: 50.0000 chunk 959 optimal weight: 7.9990 chunk 784 optimal weight: 0.6980 chunk 317 optimal weight: 10.0000 chunk 1154 optimal weight: 2.9990 chunk 1247 optimal weight: 7.9990 chunk 1028 optimal weight: 10.0000 chunk 1144 optimal weight: 9.9990 chunk 393 optimal weight: 4.9990 chunk 926 optimal weight: 7.9990 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 543 ASN ** 1 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 339 HIS u 175 HIS u 187 GLN u 236 GLN ** u 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 361 ASN ** v 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 364 ASN ** y 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 519 HIS ** y 579 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 762 ASN G 114 GLN G 168 HIS H 49 HIS K 2 GLN K 29 HIS ** L 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 232 HIS ** N 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 132 GLN Q 72 HIS P 38 ASN I 62 GLN x 311 ASN x 427 ASN ** x 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 216 ASN E 61 GLN F 89 GLN F 130 ASN ** r 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 168 GLN R 181 GLN T 112 ASN ** V 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 110 GLN V 165 ASN ** V 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 50 GLN ** a 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 147 HIS ** c 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 29 GLN ** o 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 84 GLN ** s 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 308 GLN ** j 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 355 ASN g 817 ASN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6790 moved from start: 0.3831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.113 123665 Z= 0.501 Angle : 0.898 17.895 176203 Z= 0.460 Chirality : 0.049 0.476 21730 Planarity : 0.007 0.144 16084 Dihedral : 20.866 178.515 38718 Min Nonbonded Distance : 0.996 Molprobity Statistics. All-atom Clashscore : 18.56 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.47 % Favored : 93.48 % Rotamer: Outliers : 6.69 % Allowed : 21.55 % Favored : 71.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.95 (0.08), residues: 10949 helix: -0.46 (0.08), residues: 4268 sheet: -1.04 (0.13), residues: 1432 loop : -2.08 (0.08), residues: 5249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP c 177 HIS 0.015 0.002 HIS a 66 PHE 0.039 0.003 PHE G 135 TYR 0.049 0.003 TYR i 34 ARG 0.025 0.001 ARG d 133 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21898 Ramachandran restraints generated. 10949 Oldfield, 0 Emsley, 10949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21898 Ramachandran restraints generated. 10949 Oldfield, 0 Emsley, 10949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1815 residues out of total 9800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 462 poor density : 1353 time to evaluate : 7.927 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 TARDY: cannot create tardy model for: "ASN P 26 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 488 ASP cc_start: 0.7393 (m-30) cc_final: 0.7064 (t0) REVERT: 1 507 ARG cc_start: 0.5720 (tpm170) cc_final: 0.5419 (tpp-160) REVERT: 1 527 CYS cc_start: 0.5173 (m) cc_final: 0.4464 (m) REVERT: 1 552 LYS cc_start: 0.6505 (tptp) cc_final: 0.6101 (pptt) REVERT: 6 320 MET cc_start: -0.0861 (OUTLIER) cc_final: -0.1064 (mmt) REVERT: 6 342 PHE cc_start: 0.4627 (m-80) cc_final: 0.4380 (m-80) REVERT: u 306 MET cc_start: 0.6759 (ppp) cc_final: 0.6046 (ptm) REVERT: u 398 PHE cc_start: 0.2773 (OUTLIER) cc_final: 0.1881 (p90) REVERT: v 267 VAL cc_start: 0.7004 (OUTLIER) cc_final: 0.6737 (p) REVERT: v 346 ARG cc_start: 0.7905 (tpp-160) cc_final: 0.7515 (tpp80) REVERT: S 2 LYS cc_start: 0.8211 (mttt) cc_final: 0.7105 (mtpp) REVERT: S 45 TRP cc_start: 0.8825 (m100) cc_final: 0.8475 (m-10) REVERT: S 163 ASN cc_start: 0.7859 (t0) cc_final: 0.7107 (p0) REVERT: y 116 TYR cc_start: 0.4534 (OUTLIER) cc_final: 0.3668 (t80) REVERT: y 134 ASN cc_start: 0.7402 (m-40) cc_final: 0.6867 (m110) REVERT: y 422 GLU cc_start: 0.3949 (mp0) cc_final: 0.3556 (mp0) REVERT: y 519 HIS cc_start: 0.7038 (m90) cc_final: 0.6607 (p-80) REVERT: G 98 ARG cc_start: 0.7833 (OUTLIER) cc_final: 0.7600 (mtt-85) REVERT: L 110 MET cc_start: 0.8729 (ptp) cc_final: 0.8463 (ptm) REVERT: L 120 GLN cc_start: 0.7448 (mt0) cc_final: 0.7038 (mt0) REVERT: L 176 LYS cc_start: 0.8484 (tptp) cc_final: 0.8091 (ttpt) REVERT: L 227 ARG cc_start: 0.8713 (OUTLIER) cc_final: 0.8288 (tmm-80) REVERT: N 44 ASP cc_start: 0.8111 (p0) cc_final: 0.7911 (p0) REVERT: N 57 LYS cc_start: 0.8549 (mmtm) cc_final: 0.8325 (tptt) REVERT: N 73 ASP cc_start: 0.8061 (m-30) cc_final: 0.7793 (m-30) REVERT: N 78 SER cc_start: 0.9132 (t) cc_final: 0.8817 (t) REVERT: N 118 GLU cc_start: 0.7021 (tm-30) cc_final: 0.6799 (tm-30) REVERT: Q 89 ARG cc_start: 0.8498 (tmm-80) cc_final: 0.8288 (ttm170) REVERT: P 70 SER cc_start: 0.8959 (t) cc_final: 0.8644 (m) REVERT: P 128 ARG cc_start: 0.8138 (OUTLIER) cc_final: 0.7727 (mmt90) REVERT: x 50 TYR cc_start: 0.6526 (OUTLIER) cc_final: 0.6204 (m-10) REVERT: x 302 GLU cc_start: 0.4549 (tm-30) cc_final: 0.3225 (mt-10) REVERT: 9 14 LYS cc_start: 0.8319 (ttpt) cc_final: 0.7806 (ttpp) REVERT: B 104 LYS cc_start: 0.8805 (tptp) cc_final: 0.8484 (tptp) REVERT: B 124 ASP cc_start: 0.8597 (m-30) cc_final: 0.8346 (m-30) REVERT: C 244 ILE cc_start: 0.9355 (mt) cc_final: 0.9113 (tp) REVERT: C 248 ILE cc_start: 0.9013 (OUTLIER) cc_final: 0.8733 (mt) REVERT: D 21 GLU cc_start: 0.7836 (mt-10) cc_final: 0.7584 (mt-10) REVERT: D 107 GLU cc_start: 0.8580 (mm-30) cc_final: 0.8275 (tm-30) REVERT: E 114 ASP cc_start: 0.8999 (p0) cc_final: 0.8736 (p0) REVERT: E 129 SER cc_start: 0.9296 (t) cc_final: 0.9059 (p) REVERT: r 4 LEU cc_start: 0.4897 (OUTLIER) cc_final: 0.4462 (tt) REVERT: r 37 LEU cc_start: 0.1023 (OUTLIER) cc_final: 0.0550 (tp) REVERT: r 48 LEU cc_start: 0.4915 (OUTLIER) cc_final: 0.4195 (tp) REVERT: r 117 GLU cc_start: 0.5014 (OUTLIER) cc_final: 0.4272 (tm-30) REVERT: r 223 MET cc_start: 0.4820 (OUTLIER) cc_final: 0.4599 (ptp) REVERT: r 237 MET cc_start: 0.5054 (ptp) cc_final: 0.4405 (ptm) REVERT: r 255 MET cc_start: 0.1946 (mmt) cc_final: 0.1018 (ptt) REVERT: r 263 GLU cc_start: 0.2862 (OUTLIER) cc_final: 0.1912 (tt0) REVERT: R 111 GLN cc_start: 0.8908 (mt0) cc_final: 0.8481 (mt0) REVERT: R 137 LEU cc_start: 0.5451 (OUTLIER) cc_final: 0.4997 (mm) REVERT: V 127 ARG cc_start: 0.4809 (tmt170) cc_final: 0.4073 (mmm-85) REVERT: Z 57 ASN cc_start: 0.7490 (OUTLIER) cc_final: 0.6480 (t0) REVERT: Z 127 MET cc_start: 0.8313 (mmm) cc_final: 0.8087 (mmm) REVERT: b 30 TYR cc_start: 0.2405 (OUTLIER) cc_final: 0.0328 (m-80) REVERT: c 126 ASP cc_start: 0.6819 (p0) cc_final: 0.6091 (p0) REVERT: c 222 ASN cc_start: 0.5283 (OUTLIER) cc_final: 0.3323 (t0) REVERT: d 15 VAL cc_start: 0.6077 (m) cc_final: 0.5858 (p) REVERT: f 117 ILE cc_start: 0.5788 (OUTLIER) cc_final: 0.5501 (mt) REVERT: i 41 GLN cc_start: 0.8269 (mp10) cc_final: 0.7867 (mp10) REVERT: m 33 ARG cc_start: 0.2155 (OUTLIER) cc_final: -0.0201 (mtm180) REVERT: n 35 MET cc_start: 0.4990 (mmm) cc_final: 0.4145 (tpp) REVERT: n 42 ILE cc_start: 0.6371 (OUTLIER) cc_final: 0.6071 (mm) REVERT: p 32 HIS cc_start: 0.5992 (OUTLIER) cc_final: 0.5309 (m90) REVERT: p 69 CYS cc_start: 0.8613 (p) cc_final: 0.8149 (p) REVERT: p 70 ASN cc_start: 0.8725 (t0) cc_final: 0.8171 (t0) REVERT: p 89 GLN cc_start: 0.8504 (mm-40) cc_final: 0.7774 (mp10) REVERT: p 107 GLN cc_start: 0.6348 (tp-100) cc_final: 0.4848 (tp-100) REVERT: q 83 ASP cc_start: 0.8504 (t0) cc_final: 0.8225 (t0) REVERT: M 58 MET cc_start: 0.7486 (mmm) cc_final: 0.7053 (mmm) REVERT: M 92 ASP cc_start: 0.8234 (t0) cc_final: 0.7760 (t0) REVERT: h 113 GLU cc_start: 0.6853 (tm-30) cc_final: 0.6198 (tm-30) REVERT: j 54 LYS cc_start: 0.3968 (ptpp) cc_final: 0.3110 (tmmt) REVERT: j 165 MET cc_start: 0.0252 (mtt) cc_final: -0.0276 (mtt) REVERT: j 283 ARG cc_start: 0.4182 (OUTLIER) cc_final: 0.3618 (mtt180) REVERT: j 290 GLU cc_start: 0.3944 (mt-10) cc_final: 0.3433 (pt0) REVERT: j 292 MET cc_start: 0.1469 (mtm) cc_final: 0.0753 (mmt) REVERT: j 302 MET cc_start: 0.0905 (mtt) cc_final: 0.0444 (mmt) REVERT: j 306 MET cc_start: 0.2732 (mtp) cc_final: 0.1577 (mpp) REVERT: g 962 MET cc_start: 0.3171 (ppp) cc_final: 0.1170 (mmp) REVERT: g 985 LEU cc_start: 0.2759 (OUTLIER) cc_final: 0.2548 (mt) outliers start: 462 outliers final: 272 residues processed: 1656 average time/residue: 0.9849 time to fit residues: 2845.7919 Evaluate side-chains 1494 residues out of total 9800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 297 poor density : 1197 time to evaluate : 7.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 477 ASN Chi-restraints excluded: chain 1 residue 481 PHE Chi-restraints excluded: chain 1 residue 494 THR Chi-restraints excluded: chain 1 residue 513 VAL Chi-restraints excluded: chain 1 residue 515 CYS Chi-restraints excluded: chain 1 residue 522 ASN Chi-restraints excluded: chain 1 residue 556 VAL Chi-restraints excluded: chain 1 residue 566 ILE Chi-restraints excluded: chain 6 residue 312 VAL Chi-restraints excluded: chain 6 residue 316 VAL Chi-restraints excluded: chain 6 residue 318 THR Chi-restraints excluded: chain 6 residue 320 MET Chi-restraints excluded: chain 6 residue 338 THR Chi-restraints excluded: chain 6 residue 339 HIS Chi-restraints excluded: chain u residue 60 ASP Chi-restraints excluded: chain u residue 109 GLN Chi-restraints excluded: chain u residue 133 SER Chi-restraints excluded: chain u residue 173 LEU Chi-restraints excluded: chain u residue 230 LEU Chi-restraints excluded: chain u residue 242 SER Chi-restraints excluded: chain u residue 256 ILE Chi-restraints excluded: chain u residue 342 LEU Chi-restraints excluded: chain u residue 344 MET Chi-restraints excluded: chain u residue 361 LEU Chi-restraints excluded: chain u residue 394 LEU Chi-restraints excluded: chain u residue 398 PHE Chi-restraints excluded: chain v residue 267 VAL Chi-restraints excluded: chain v residue 278 VAL Chi-restraints excluded: chain v residue 296 VAL Chi-restraints excluded: chain v residue 304 ASP Chi-restraints excluded: chain v residue 315 CYS Chi-restraints excluded: chain S residue 49 VAL Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 114 VAL Chi-restraints excluded: chain S residue 153 VAL Chi-restraints excluded: chain S residue 158 VAL Chi-restraints excluded: chain S residue 181 THR Chi-restraints excluded: chain S residue 208 GLU Chi-restraints excluded: chain S residue 219 GLU Chi-restraints excluded: chain y residue 102 VAL Chi-restraints excluded: chain y residue 116 TYR Chi-restraints excluded: chain y residue 157 THR Chi-restraints excluded: chain y residue 330 ILE Chi-restraints excluded: chain y residue 393 MET Chi-restraints excluded: chain y residue 412 LEU Chi-restraints excluded: chain y residue 445 LEU Chi-restraints excluded: chain y residue 475 ASP Chi-restraints excluded: chain y residue 495 THR Chi-restraints excluded: chain y residue 510 THR Chi-restraints excluded: chain y residue 608 LEU Chi-restraints excluded: chain y residue 628 ASP Chi-restraints excluded: chain y residue 677 ILE Chi-restraints excluded: chain y residue 718 LEU Chi-restraints excluded: chain y residue 748 ASP Chi-restraints excluded: chain y residue 773 ASP Chi-restraints excluded: chain y residue 792 LEU Chi-restraints excluded: chain y residue 798 VAL Chi-restraints excluded: chain y residue 846 ARG Chi-restraints excluded: chain y residue 854 ASN Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 24 SER Chi-restraints excluded: chain G residue 27 LEU Chi-restraints excluded: chain G residue 44 ASN Chi-restraints excluded: chain G residue 98 ARG Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain G residue 119 SER Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 164 ASN Chi-restraints excluded: chain G residue 174 SER Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 37 CYS Chi-restraints excluded: chain H residue 40 CYS Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 67 THR Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 77 CYS Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 23 ILE Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 80 SER Chi-restraints excluded: chain K residue 81 LYS Chi-restraints excluded: chain L residue 59 GLU Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain L residue 162 ILE Chi-restraints excluded: chain L residue 172 ASN Chi-restraints excluded: chain L residue 202 THR Chi-restraints excluded: chain L residue 205 VAL Chi-restraints excluded: chain L residue 225 SER Chi-restraints excluded: chain L residue 227 ARG Chi-restraints excluded: chain L residue 248 TYR Chi-restraints excluded: chain L residue 252 THR Chi-restraints excluded: chain L residue 268 GLU Chi-restraints excluded: chain O residue 55 THR Chi-restraints excluded: chain O residue 91 VAL Chi-restraints excluded: chain O residue 127 VAL Chi-restraints excluded: chain O residue 153 THR Chi-restraints excluded: chain O residue 170 GLU Chi-restraints excluded: chain O residue 201 CYS Chi-restraints excluded: chain O residue 210 VAL Chi-restraints excluded: chain N residue 15 VAL Chi-restraints excluded: chain N residue 38 ILE Chi-restraints excluded: chain N residue 54 THR Chi-restraints excluded: chain N residue 97 THR Chi-restraints excluded: chain N residue 144 THR Chi-restraints excluded: chain N residue 163 CYS Chi-restraints excluded: chain N residue 170 SER Chi-restraints excluded: chain Q residue 2 THR Chi-restraints excluded: chain Q residue 24 THR Chi-restraints excluded: chain Q residue 45 VAL Chi-restraints excluded: chain Q residue 52 ASP Chi-restraints excluded: chain Q residue 58 VAL Chi-restraints excluded: chain Q residue 88 SER Chi-restraints excluded: chain P residue 47 LEU Chi-restraints excluded: chain P residue 67 ASP Chi-restraints excluded: chain P residue 100 THR Chi-restraints excluded: chain P residue 128 ARG Chi-restraints excluded: chain P residue 139 SER Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain I residue 31 ASP Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 69 ASN Chi-restraints excluded: chain I residue 93 LYS Chi-restraints excluded: chain I residue 102 LEU Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain x residue 27 ASP Chi-restraints excluded: chain x residue 50 TYR Chi-restraints excluded: chain x residue 69 TYR Chi-restraints excluded: chain x residue 76 ASP Chi-restraints excluded: chain x residue 367 ASP Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 142 HIS Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 232 ASN Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 122 SER Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 127 ASN Chi-restraints excluded: chain F residue 98 LYS Chi-restraints excluded: chain r residue 4 LEU Chi-restraints excluded: chain r residue 37 LEU Chi-restraints excluded: chain r residue 48 LEU Chi-restraints excluded: chain r residue 76 VAL Chi-restraints excluded: chain r residue 88 ARG Chi-restraints excluded: chain r residue 117 GLU Chi-restraints excluded: chain r residue 185 THR Chi-restraints excluded: chain r residue 223 MET Chi-restraints excluded: chain r residue 227 ILE Chi-restraints excluded: chain r residue 240 THR Chi-restraints excluded: chain r residue 263 GLU Chi-restraints excluded: chain J residue 13 SER Chi-restraints excluded: chain J residue 30 CYS Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain J residue 80 ASP Chi-restraints excluded: chain J residue 84 LYS Chi-restraints excluded: chain J residue 94 LEU Chi-restraints excluded: chain J residue 98 GLN Chi-restraints excluded: chain J residue 121 THR Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 89 GLU Chi-restraints excluded: chain R residue 137 LEU Chi-restraints excluded: chain R residue 182 CYS Chi-restraints excluded: chain T residue 27 VAL Chi-restraints excluded: chain T residue 28 LEU Chi-restraints excluded: chain T residue 80 ASP Chi-restraints excluded: chain T residue 102 THR Chi-restraints excluded: chain V residue 41 VAL Chi-restraints excluded: chain V residue 72 LEU Chi-restraints excluded: chain V residue 78 MET Chi-restraints excluded: chain V residue 92 ILE Chi-restraints excluded: chain V residue 176 GLU Chi-restraints excluded: chain V residue 197 GLU Chi-restraints excluded: chain V residue 202 SER Chi-restraints excluded: chain Y residue 32 ILE Chi-restraints excluded: chain Y residue 34 VAL Chi-restraints excluded: chain Y residue 47 LEU Chi-restraints excluded: chain Y residue 78 VAL Chi-restraints excluded: chain Y residue 81 ILE Chi-restraints excluded: chain Z residue 42 THR Chi-restraints excluded: chain Z residue 57 ASN Chi-restraints excluded: chain Z residue 84 VAL Chi-restraints excluded: chain Z residue 135 GLU Chi-restraints excluded: chain Z residue 139 SER Chi-restraints excluded: chain Z residue 182 LEU Chi-restraints excluded: chain a residue 20 VAL Chi-restraints excluded: chain a residue 70 TYR Chi-restraints excluded: chain a residue 73 ASN Chi-restraints excluded: chain b residue 20 VAL Chi-restraints excluded: chain b residue 30 TYR Chi-restraints excluded: chain b residue 96 VAL Chi-restraints excluded: chain c residue 101 PHE Chi-restraints excluded: chain c residue 102 VAL Chi-restraints excluded: chain c residue 132 TRP Chi-restraints excluded: chain c residue 137 VAL Chi-restraints excluded: chain c residue 171 ASP Chi-restraints excluded: chain c residue 183 LYS Chi-restraints excluded: chain c residue 197 THR Chi-restraints excluded: chain c residue 222 ASN Chi-restraints excluded: chain c residue 265 ILE Chi-restraints excluded: chain c residue 274 VAL Chi-restraints excluded: chain c residue 297 THR Chi-restraints excluded: chain d residue 66 LEU Chi-restraints excluded: chain d residue 96 SER Chi-restraints excluded: chain d residue 107 LEU Chi-restraints excluded: chain e residue 48 VAL Chi-restraints excluded: chain e residue 51 ASP Chi-restraints excluded: chain e residue 73 VAL Chi-restraints excluded: chain f residue 39 ARG Chi-restraints excluded: chain f residue 83 PHE Chi-restraints excluded: chain f residue 117 ILE Chi-restraints excluded: chain i residue 9 SER Chi-restraints excluded: chain i residue 34 TYR Chi-restraints excluded: chain i residue 42 CYS Chi-restraints excluded: chain i residue 49 ASP Chi-restraints excluded: chain k residue 117 LEU Chi-restraints excluded: chain m residue 33 ARG Chi-restraints excluded: chain m residue 51 VAL Chi-restraints excluded: chain m residue 80 ASP Chi-restraints excluded: chain m residue 85 LEU Chi-restraints excluded: chain m residue 91 LEU Chi-restraints excluded: chain m residue 94 ILE Chi-restraints excluded: chain m residue 124 ILE Chi-restraints excluded: chain n residue 42 ILE Chi-restraints excluded: chain n residue 45 ASN Chi-restraints excluded: chain n residue 46 VAL Chi-restraints excluded: chain n residue 55 VAL Chi-restraints excluded: chain o residue 254 ASP Chi-restraints excluded: chain o residue 297 ILE Chi-restraints excluded: chain p residue 30 TYR Chi-restraints excluded: chain p residue 32 HIS Chi-restraints excluded: chain p residue 43 THR Chi-restraints excluded: chain p residue 45 THR Chi-restraints excluded: chain p residue 50 ILE Chi-restraints excluded: chain p residue 58 LYS Chi-restraints excluded: chain p residue 73 VAL Chi-restraints excluded: chain p residue 94 CYS Chi-restraints excluded: chain q residue 27 VAL Chi-restraints excluded: chain q residue 47 LEU Chi-restraints excluded: chain q residue 51 CYS Chi-restraints excluded: chain q residue 53 ASP Chi-restraints excluded: chain q residue 81 LEU Chi-restraints excluded: chain M residue 6 THR Chi-restraints excluded: chain M residue 22 THR Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain M residue 54 VAL Chi-restraints excluded: chain M residue 55 THR Chi-restraints excluded: chain M residue 71 ILE Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain M residue 106 LEU Chi-restraints excluded: chain M residue 116 ASN Chi-restraints excluded: chain M residue 119 VAL Chi-restraints excluded: chain M residue 124 VAL Chi-restraints excluded: chain M residue 130 THR Chi-restraints excluded: chain h residue 20 ILE Chi-restraints excluded: chain h residue 29 VAL Chi-restraints excluded: chain h residue 31 SER Chi-restraints excluded: chain h residue 35 VAL Chi-restraints excluded: chain h residue 54 VAL Chi-restraints excluded: chain h residue 60 THR Chi-restraints excluded: chain h residue 65 THR Chi-restraints excluded: chain h residue 68 THR Chi-restraints excluded: chain h residue 74 SER Chi-restraints excluded: chain h residue 76 THR Chi-restraints excluded: chain h residue 81 GLN Chi-restraints excluded: chain h residue 93 SER Chi-restraints excluded: chain h residue 106 ILE Chi-restraints excluded: chain h residue 110 VAL Chi-restraints excluded: chain s residue 187 MET Chi-restraints excluded: chain s residue 194 MET Chi-restraints excluded: chain s residue 220 VAL Chi-restraints excluded: chain s residue 279 VAL Chi-restraints excluded: chain s residue 290 ILE Chi-restraints excluded: chain j residue 179 PHE Chi-restraints excluded: chain j residue 263 LEU Chi-restraints excluded: chain j residue 268 GLU Chi-restraints excluded: chain j residue 283 ARG Chi-restraints excluded: chain j residue 299 VAL Chi-restraints excluded: chain j residue 336 ILE Chi-restraints excluded: chain j residue 338 VAL Chi-restraints excluded: chain j residue 357 ILE Chi-restraints excluded: chain g residue 856 ASP Chi-restraints excluded: chain g residue 921 VAL Chi-restraints excluded: chain g residue 985 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1269 random chunks: chunk 1140 optimal weight: 0.0770 chunk 867 optimal weight: 0.4980 chunk 599 optimal weight: 50.0000 chunk 127 optimal weight: 50.0000 chunk 550 optimal weight: 9.9990 chunk 775 optimal weight: 6.9990 chunk 1158 optimal weight: 6.9990 chunk 1226 optimal weight: 8.9990 chunk 605 optimal weight: 30.0000 chunk 1098 optimal weight: 0.4980 chunk 330 optimal weight: 4.9990 overall best weight: 2.6142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 543 ASN ** 1 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 339 HIS u 187 GLN u 316 GLN u 430 GLN ** u 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 522 GLN ** v 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 105 ASN ** y 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 579 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 762 ASN y 858 GLN ** G 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 2 GLN L 113 GLN O 147 ASN N 113 GLN ** P 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 132 GLN F 130 ASN ** r 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 9 HIS T 106 GLN ** V 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 50 GLN ** a 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 238 ASN ** o 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 84 GLN M 118 GLN s 301 GLN s 306 HIS ** j 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6746 moved from start: 0.4101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 123665 Z= 0.311 Angle : 0.730 17.048 176203 Z= 0.380 Chirality : 0.043 0.419 21730 Planarity : 0.005 0.130 16084 Dihedral : 20.773 179.896 38709 Min Nonbonded Distance : 1.030 Molprobity Statistics. All-atom Clashscore : 15.85 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.52 % Favored : 94.43 % Rotamer: Outliers : 5.39 % Allowed : 23.99 % Favored : 70.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.62 (0.08), residues: 10949 helix: -0.11 (0.08), residues: 4284 sheet: -0.95 (0.13), residues: 1442 loop : -1.95 (0.08), residues: 5223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP u 149 HIS 0.012 0.001 HIS 6 339 PHE 0.035 0.002 PHE c 65 TYR 0.032 0.002 TYR i 34 ARG 0.028 0.001 ARG I 19 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21898 Ramachandran restraints generated. 10949 Oldfield, 0 Emsley, 10949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21898 Ramachandran restraints generated. 10949 Oldfield, 0 Emsley, 10949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1634 residues out of total 9800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 372 poor density : 1262 time to evaluate : 7.899 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 TARDY: cannot create tardy model for: "ASN P 26 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 552 LYS cc_start: 0.6510 (tptp) cc_final: 0.6110 (pptt) REVERT: 6 319 LYS cc_start: 0.3247 (tptt) cc_final: 0.2888 (tptp) REVERT: 6 320 MET cc_start: -0.1399 (mmt) cc_final: -0.1773 (mmt) REVERT: 6 353 THR cc_start: 0.6082 (p) cc_final: 0.5379 (p) REVERT: u 338 ILE cc_start: 0.6398 (tp) cc_final: 0.6156 (mp) REVERT: u 344 MET cc_start: 0.5546 (OUTLIER) cc_final: 0.5012 (mmm) REVERT: u 398 PHE cc_start: 0.2713 (OUTLIER) cc_final: 0.1600 (p90) REVERT: u 443 VAL cc_start: 0.7171 (OUTLIER) cc_final: 0.6943 (p) REVERT: u 521 ASN cc_start: 0.6048 (t0) cc_final: 0.5707 (m110) REVERT: v 267 VAL cc_start: 0.6820 (OUTLIER) cc_final: 0.6509 (p) REVERT: S 46 LYS cc_start: 0.9025 (OUTLIER) cc_final: 0.8752 (tppt) REVERT: S 163 ASN cc_start: 0.7939 (t0) cc_final: 0.7227 (p0) REVERT: y 116 TYR cc_start: 0.4570 (OUTLIER) cc_final: 0.3757 (t80) REVERT: y 134 ASN cc_start: 0.7494 (m-40) cc_final: 0.7008 (m110) REVERT: y 519 HIS cc_start: 0.6921 (m90) cc_final: 0.6569 (p90) REVERT: H 15 GLU cc_start: 0.7544 (mm-30) cc_final: 0.7296 (mm-30) REVERT: K 67 ASP cc_start: 0.8254 (OUTLIER) cc_final: 0.8051 (t0) REVERT: L 110 MET cc_start: 0.8689 (ptp) cc_final: 0.8474 (ptm) REVERT: L 176 LYS cc_start: 0.8524 (tptp) cc_final: 0.8211 (ttpt) REVERT: L 227 ARG cc_start: 0.8614 (OUTLIER) cc_final: 0.8152 (tmm-80) REVERT: O 38 MET cc_start: 0.7649 (mpp) cc_final: 0.7320 (mtt) REVERT: O 135 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8722 (mt) REVERT: O 227 LYS cc_start: 0.7887 (OUTLIER) cc_final: 0.7683 (tptt) REVERT: N 73 ASP cc_start: 0.8054 (m-30) cc_final: 0.7803 (m-30) REVERT: N 78 SER cc_start: 0.9076 (t) cc_final: 0.8746 (t) REVERT: Q 89 ARG cc_start: 0.8517 (tmm-80) cc_final: 0.8266 (ttm170) REVERT: P 70 SER cc_start: 0.8941 (t) cc_final: 0.8534 (m) REVERT: x 50 TYR cc_start: 0.6457 (OUTLIER) cc_final: 0.6163 (m-10) REVERT: x 302 GLU cc_start: 0.4577 (tm-30) cc_final: 0.3279 (mt-10) REVERT: x 397 ASN cc_start: 0.2052 (p0) cc_final: 0.1601 (t0) REVERT: x 401 SER cc_start: 0.3742 (OUTLIER) cc_final: 0.3495 (p) REVERT: 9 14 LYS cc_start: 0.8254 (ttpt) cc_final: 0.7715 (ttpp) REVERT: B 124 ASP cc_start: 0.8588 (m-30) cc_final: 0.8324 (m-30) REVERT: C 23 LEU cc_start: 0.9506 (OUTLIER) cc_final: 0.9278 (mp) REVERT: C 244 ILE cc_start: 0.9305 (mt) cc_final: 0.9082 (tp) REVERT: D 18 ARG cc_start: 0.8972 (ttm-80) cc_final: 0.8745 (ttm170) REVERT: D 21 GLU cc_start: 0.7702 (mt-10) cc_final: 0.7438 (mt-10) REVERT: D 27 GLN cc_start: 0.8453 (tp40) cc_final: 0.8208 (tp40) REVERT: D 107 GLU cc_start: 0.8647 (mm-30) cc_final: 0.8322 (tm-30) REVERT: r 4 LEU cc_start: 0.4925 (OUTLIER) cc_final: 0.4425 (tt) REVERT: r 48 LEU cc_start: 0.5098 (OUTLIER) cc_final: 0.4247 (tp) REVERT: r 183 ARG cc_start: 0.5488 (mmm-85) cc_final: 0.4774 (mmm-85) REVERT: r 208 VAL cc_start: 0.4059 (m) cc_final: 0.3823 (t) REVERT: r 223 MET cc_start: 0.4857 (OUTLIER) cc_final: 0.4617 (ptp) REVERT: r 237 MET cc_start: 0.5031 (ptp) cc_final: 0.4404 (ptp) REVERT: r 255 MET cc_start: 0.1860 (mmt) cc_final: 0.0594 (ptt) REVERT: R 111 GLN cc_start: 0.8913 (mt0) cc_final: 0.8469 (mt0) REVERT: R 137 LEU cc_start: 0.5445 (OUTLIER) cc_final: 0.4986 (mm) REVERT: T 19 GLN cc_start: 0.9134 (mp10) cc_final: 0.8786 (mp10) REVERT: V 127 ARG cc_start: 0.4793 (tmt170) cc_final: 0.4096 (mmm-85) REVERT: Y 38 PRO cc_start: 0.7796 (Cg_exo) cc_final: 0.7551 (Cg_endo) REVERT: Z 57 ASN cc_start: 0.7473 (m-40) cc_final: 0.6658 (t0) REVERT: Z 127 MET cc_start: 0.8287 (mmm) cc_final: 0.8076 (mmm) REVERT: b 30 TYR cc_start: 0.2475 (OUTLIER) cc_final: 0.0387 (m-80) REVERT: c 126 ASP cc_start: 0.6643 (p0) cc_final: 0.5910 (p0) REVERT: c 130 LYS cc_start: 0.5244 (mttm) cc_final: 0.5025 (mttm) REVERT: e 51 ASP cc_start: 0.0993 (OUTLIER) cc_final: 0.0375 (t0) REVERT: m 12 MET cc_start: 0.2094 (pmm) cc_final: 0.1449 (tpp) REVERT: m 33 ARG cc_start: 0.1802 (OUTLIER) cc_final: -0.0189 (mtm180) REVERT: n 35 MET cc_start: 0.5024 (mmm) cc_final: 0.4113 (tpp) REVERT: n 42 ILE cc_start: 0.6135 (OUTLIER) cc_final: 0.5915 (mm) REVERT: p 69 CYS cc_start: 0.8564 (p) cc_final: 0.8223 (p) REVERT: p 89 GLN cc_start: 0.8448 (mm-40) cc_final: 0.7784 (mp10) REVERT: p 102 LEU cc_start: 0.6232 (OUTLIER) cc_final: 0.5769 (mm) REVERT: q 83 ASP cc_start: 0.8597 (t0) cc_final: 0.8230 (t0) REVERT: M 3 ARG cc_start: 0.8494 (mmt90) cc_final: 0.7759 (mmm-85) REVERT: M 122 PRO cc_start: 0.8670 (Cg_endo) cc_final: 0.8430 (Cg_exo) REVERT: h 113 GLU cc_start: 0.6905 (tm-30) cc_final: 0.6212 (tm-30) REVERT: s 291 LEU cc_start: -0.0192 (OUTLIER) cc_final: -0.0458 (mp) REVERT: s 306 HIS cc_start: 0.2643 (OUTLIER) cc_final: 0.2039 (t-90) REVERT: j 165 MET cc_start: 0.0445 (mtt) cc_final: -0.0097 (mtt) REVERT: j 290 GLU cc_start: 0.3984 (mt-10) cc_final: 0.3636 (pt0) REVERT: j 292 MET cc_start: 0.1219 (mtm) cc_final: 0.0732 (mmt) REVERT: j 302 MET cc_start: 0.0967 (mtt) cc_final: 0.0643 (mmt) REVERT: j 356 TYR cc_start: 0.2005 (t80) cc_final: 0.1648 (t80) REVERT: g 910 MET cc_start: 0.1033 (ptp) cc_final: 0.0573 (ptp) REVERT: g 962 MET cc_start: 0.3114 (ppp) cc_final: 0.1143 (mmp) REVERT: g 985 LEU cc_start: 0.2419 (OUTLIER) cc_final: 0.2118 (mt) outliers start: 372 outliers final: 248 residues processed: 1509 average time/residue: 0.9717 time to fit residues: 2561.4658 Evaluate side-chains 1454 residues out of total 9800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 273 poor density : 1181 time to evaluate : 7.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 494 THR Chi-restraints excluded: chain 1 residue 513 VAL Chi-restraints excluded: chain 1 residue 515 CYS Chi-restraints excluded: chain 1 residue 543 ASN Chi-restraints excluded: chain 6 residue 312 VAL Chi-restraints excluded: chain 6 residue 316 VAL Chi-restraints excluded: chain 6 residue 318 THR Chi-restraints excluded: chain 6 residue 339 HIS Chi-restraints excluded: chain u residue 60 ASP Chi-restraints excluded: chain u residue 109 GLN Chi-restraints excluded: chain u residue 133 SER Chi-restraints excluded: chain u residue 242 SER Chi-restraints excluded: chain u residue 299 LEU Chi-restraints excluded: chain u residue 344 MET Chi-restraints excluded: chain u residue 394 LEU Chi-restraints excluded: chain u residue 398 PHE Chi-restraints excluded: chain u residue 443 VAL Chi-restraints excluded: chain v residue 267 VAL Chi-restraints excluded: chain v residue 278 VAL Chi-restraints excluded: chain v residue 296 VAL Chi-restraints excluded: chain v residue 304 ASP Chi-restraints excluded: chain v residue 315 CYS Chi-restraints excluded: chain v residue 408 THR Chi-restraints excluded: chain S residue 46 LYS Chi-restraints excluded: chain S residue 49 VAL Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 67 VAL Chi-restraints excluded: chain S residue 114 VAL Chi-restraints excluded: chain S residue 139 SER Chi-restraints excluded: chain S residue 158 VAL Chi-restraints excluded: chain S residue 192 ILE Chi-restraints excluded: chain S residue 208 GLU Chi-restraints excluded: chain S residue 219 GLU Chi-restraints excluded: chain y residue 63 LEU Chi-restraints excluded: chain y residue 102 VAL Chi-restraints excluded: chain y residue 116 TYR Chi-restraints excluded: chain y residue 157 THR Chi-restraints excluded: chain y residue 330 ILE Chi-restraints excluded: chain y residue 412 LEU Chi-restraints excluded: chain y residue 475 ASP Chi-restraints excluded: chain y residue 495 THR Chi-restraints excluded: chain y residue 510 THR Chi-restraints excluded: chain y residue 578 LEU Chi-restraints excluded: chain y residue 608 LEU Chi-restraints excluded: chain y residue 628 ASP Chi-restraints excluded: chain y residue 671 VAL Chi-restraints excluded: chain y residue 677 ILE Chi-restraints excluded: chain y residue 718 LEU Chi-restraints excluded: chain y residue 748 ASP Chi-restraints excluded: chain y residue 752 CYS Chi-restraints excluded: chain y residue 773 ASP Chi-restraints excluded: chain y residue 798 VAL Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 24 SER Chi-restraints excluded: chain G residue 27 LEU Chi-restraints excluded: chain G residue 44 ASN Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain G residue 119 SER Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 137 SER Chi-restraints excluded: chain G residue 164 ASN Chi-restraints excluded: chain G residue 174 SER Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 37 CYS Chi-restraints excluded: chain H residue 40 CYS Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 21 ASN Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 67 ASP Chi-restraints excluded: chain K residue 76 ASP Chi-restraints excluded: chain K residue 80 SER Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain L residue 116 THR Chi-restraints excluded: chain L residue 172 ASN Chi-restraints excluded: chain L residue 205 VAL Chi-restraints excluded: chain L residue 225 SER Chi-restraints excluded: chain L residue 227 ARG Chi-restraints excluded: chain L residue 252 THR Chi-restraints excluded: chain L residue 268 GLU Chi-restraints excluded: chain O residue 55 THR Chi-restraints excluded: chain O residue 91 VAL Chi-restraints excluded: chain O residue 105 LEU Chi-restraints excluded: chain O residue 126 ASP Chi-restraints excluded: chain O residue 135 LEU Chi-restraints excluded: chain O residue 153 THR Chi-restraints excluded: chain O residue 154 SER Chi-restraints excluded: chain O residue 170 GLU Chi-restraints excluded: chain O residue 192 SER Chi-restraints excluded: chain O residue 210 VAL Chi-restraints excluded: chain O residue 227 LYS Chi-restraints excluded: chain N residue 15 VAL Chi-restraints excluded: chain N residue 35 GLU Chi-restraints excluded: chain N residue 54 THR Chi-restraints excluded: chain N residue 69 GLU Chi-restraints excluded: chain N residue 163 CYS Chi-restraints excluded: chain Q residue 24 THR Chi-restraints excluded: chain Q residue 45 VAL Chi-restraints excluded: chain Q residue 52 ASP Chi-restraints excluded: chain Q residue 58 VAL Chi-restraints excluded: chain Q residue 64 LEU Chi-restraints excluded: chain Q residue 88 SER Chi-restraints excluded: chain P residue 100 THR Chi-restraints excluded: chain P residue 139 SER Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain I residue 31 ASP Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 69 ASN Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain x residue 27 ASP Chi-restraints excluded: chain x residue 50 TYR Chi-restraints excluded: chain x residue 69 TYR Chi-restraints excluded: chain x residue 76 ASP Chi-restraints excluded: chain x residue 369 ILE Chi-restraints excluded: chain x residue 401 SER Chi-restraints excluded: chain 9 residue 9 ARG Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 116 CYS Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain F residue 98 LYS Chi-restraints excluded: chain r residue 4 LEU Chi-restraints excluded: chain r residue 48 LEU Chi-restraints excluded: chain r residue 76 VAL Chi-restraints excluded: chain r residue 88 ARG Chi-restraints excluded: chain r residue 106 LYS Chi-restraints excluded: chain r residue 223 MET Chi-restraints excluded: chain r residue 227 ILE Chi-restraints excluded: chain r residue 240 THR Chi-restraints excluded: chain J residue 30 CYS Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain J residue 51 GLU Chi-restraints excluded: chain J residue 84 LYS Chi-restraints excluded: chain J residue 94 LEU Chi-restraints excluded: chain J residue 98 GLN Chi-restraints excluded: chain J residue 121 THR Chi-restraints excluded: chain R residue 89 GLU Chi-restraints excluded: chain R residue 90 LEU Chi-restraints excluded: chain R residue 137 LEU Chi-restraints excluded: chain T residue 27 VAL Chi-restraints excluded: chain T residue 80 ASP Chi-restraints excluded: chain T residue 102 THR Chi-restraints excluded: chain T residue 125 VAL Chi-restraints excluded: chain V residue 41 VAL Chi-restraints excluded: chain V residue 72 LEU Chi-restraints excluded: chain V residue 78 MET Chi-restraints excluded: chain V residue 82 ASN Chi-restraints excluded: chain V residue 92 ILE Chi-restraints excluded: chain V residue 165 ASN Chi-restraints excluded: chain V residue 197 GLU Chi-restraints excluded: chain Y residue 34 VAL Chi-restraints excluded: chain Y residue 47 LEU Chi-restraints excluded: chain Y residue 51 LEU Chi-restraints excluded: chain Y residue 78 VAL Chi-restraints excluded: chain Z residue 5 ILE Chi-restraints excluded: chain Z residue 26 THR Chi-restraints excluded: chain Z residue 41 VAL Chi-restraints excluded: chain Z residue 42 THR Chi-restraints excluded: chain Z residue 84 VAL Chi-restraints excluded: chain Z residue 86 LEU Chi-restraints excluded: chain Z residue 139 SER Chi-restraints excluded: chain Z residue 182 LEU Chi-restraints excluded: chain Z residue 221 THR Chi-restraints excluded: chain a residue 13 GLU Chi-restraints excluded: chain a residue 50 GLN Chi-restraints excluded: chain a residue 70 TYR Chi-restraints excluded: chain b residue 20 VAL Chi-restraints excluded: chain b residue 30 TYR Chi-restraints excluded: chain c residue 101 PHE Chi-restraints excluded: chain c residue 109 LEU Chi-restraints excluded: chain c residue 137 VAL Chi-restraints excluded: chain c residue 171 ASP Chi-restraints excluded: chain c residue 197 THR Chi-restraints excluded: chain c residue 246 TYR Chi-restraints excluded: chain c residue 265 ILE Chi-restraints excluded: chain c residue 297 THR Chi-restraints excluded: chain d residue 66 LEU Chi-restraints excluded: chain e residue 48 VAL Chi-restraints excluded: chain e residue 51 ASP Chi-restraints excluded: chain e residue 73 VAL Chi-restraints excluded: chain e residue 77 LEU Chi-restraints excluded: chain f residue 17 ASN Chi-restraints excluded: chain f residue 34 LYS Chi-restraints excluded: chain f residue 39 ARG Chi-restraints excluded: chain f residue 43 VAL Chi-restraints excluded: chain f residue 83 PHE Chi-restraints excluded: chain f residue 90 VAL Chi-restraints excluded: chain f residue 99 LEU Chi-restraints excluded: chain i residue 9 SER Chi-restraints excluded: chain i residue 16 GLN Chi-restraints excluded: chain i residue 49 ASP Chi-restraints excluded: chain m residue 11 VAL Chi-restraints excluded: chain m residue 33 ARG Chi-restraints excluded: chain m residue 51 VAL Chi-restraints excluded: chain m residue 80 ASP Chi-restraints excluded: chain m residue 91 LEU Chi-restraints excluded: chain m residue 94 ILE Chi-restraints excluded: chain m residue 124 ILE Chi-restraints excluded: chain n residue 42 ILE Chi-restraints excluded: chain n residue 45 ASN Chi-restraints excluded: chain n residue 55 VAL Chi-restraints excluded: chain o residue 238 ASN Chi-restraints excluded: chain o residue 254 ASP Chi-restraints excluded: chain o residue 297 ILE Chi-restraints excluded: chain p residue 30 TYR Chi-restraints excluded: chain p residue 43 THR Chi-restraints excluded: chain p residue 45 THR Chi-restraints excluded: chain p residue 58 LYS Chi-restraints excluded: chain p residue 73 VAL Chi-restraints excluded: chain p residue 90 ARG Chi-restraints excluded: chain p residue 94 CYS Chi-restraints excluded: chain p residue 102 LEU Chi-restraints excluded: chain q residue 27 VAL Chi-restraints excluded: chain q residue 47 LEU Chi-restraints excluded: chain q residue 53 ASP Chi-restraints excluded: chain q residue 55 VAL Chi-restraints excluded: chain q residue 64 LYS Chi-restraints excluded: chain q residue 81 LEU Chi-restraints excluded: chain q residue 86 ASP Chi-restraints excluded: chain M residue 6 THR Chi-restraints excluded: chain M residue 22 THR Chi-restraints excluded: chain M residue 54 VAL Chi-restraints excluded: chain M residue 55 THR Chi-restraints excluded: chain M residue 71 ILE Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain M residue 106 LEU Chi-restraints excluded: chain M residue 110 ASP Chi-restraints excluded: chain M residue 116 ASN Chi-restraints excluded: chain M residue 119 VAL Chi-restraints excluded: chain M residue 130 THR Chi-restraints excluded: chain h residue 20 ILE Chi-restraints excluded: chain h residue 29 VAL Chi-restraints excluded: chain h residue 31 SER Chi-restraints excluded: chain h residue 58 THR Chi-restraints excluded: chain h residue 65 THR Chi-restraints excluded: chain h residue 90 ASP Chi-restraints excluded: chain h residue 93 SER Chi-restraints excluded: chain h residue 106 ILE Chi-restraints excluded: chain h residue 114 VAL Chi-restraints excluded: chain s residue 184 PHE Chi-restraints excluded: chain s residue 187 MET Chi-restraints excluded: chain s residue 194 MET Chi-restraints excluded: chain s residue 220 VAL Chi-restraints excluded: chain s residue 232 GLN Chi-restraints excluded: chain s residue 279 VAL Chi-restraints excluded: chain s residue 282 HIS Chi-restraints excluded: chain s residue 290 ILE Chi-restraints excluded: chain s residue 291 LEU Chi-restraints excluded: chain s residue 306 HIS Chi-restraints excluded: chain j residue 268 GLU Chi-restraints excluded: chain j residue 299 VAL Chi-restraints excluded: chain j residue 357 ILE Chi-restraints excluded: chain j residue 371 VAL Chi-restraints excluded: chain g residue 978 MET Chi-restraints excluded: chain g residue 985 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1269 random chunks: chunk 1021 optimal weight: 20.0000 chunk 696 optimal weight: 4.9990 chunk 17 optimal weight: 20.0000 chunk 913 optimal weight: 3.9990 chunk 506 optimal weight: 0.6980 chunk 1046 optimal weight: 1.9990 chunk 847 optimal weight: 0.0970 chunk 1 optimal weight: 40.0000 chunk 626 optimal weight: 5.9990 chunk 1100 optimal weight: 10.0000 chunk 309 optimal weight: 1.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 339 HIS ** u 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 402 GLN S 65 GLN ** y 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 579 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 2 GLN L 113 GLN N 113 GLN ** Q 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 83 GLN ** x 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 GLN ** B 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 ASN ** J 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 112 ASN ** V 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 137 GLN ** V 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 101 GLN ** a 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 73 ASN n 29 GLN o 238 ASN o 256 GLN ** p 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 86 GLN ** s 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 248 GLN j 339 GLN ** j 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6718 moved from start: 0.4336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 123665 Z= 0.232 Angle : 0.682 17.080 176203 Z= 0.356 Chirality : 0.041 0.420 21730 Planarity : 0.005 0.130 16084 Dihedral : 20.690 179.791 38708 Min Nonbonded Distance : 1.071 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.79 % Favored : 94.18 % Rotamer: Outliers : 5.33 % Allowed : 24.80 % Favored : 69.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.36 (0.08), residues: 10949 helix: 0.19 (0.08), residues: 4306 sheet: -0.87 (0.13), residues: 1451 loop : -1.87 (0.08), residues: 5192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.002 TRP u 149 HIS 0.025 0.001 HIS s 306 PHE 0.027 0.002 PHE d 14 TYR 0.032 0.002 TYR i 34 ARG 0.008 0.000 ARG u 195 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21898 Ramachandran restraints generated. 10949 Oldfield, 0 Emsley, 10949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21898 Ramachandran restraints generated. 10949 Oldfield, 0 Emsley, 10949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1659 residues out of total 9800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 368 poor density : 1291 time to evaluate : 9.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASN P 26 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 552 LYS cc_start: 0.6735 (tptp) cc_final: 0.6302 (pptt) REVERT: 6 320 MET cc_start: -0.1297 (mmt) cc_final: -0.1758 (mmt) REVERT: u 246 TRP cc_start: 0.7246 (m100) cc_final: 0.6699 (m100) REVERT: u 344 MET cc_start: 0.5754 (OUTLIER) cc_final: 0.5045 (mmm) REVERT: u 398 PHE cc_start: 0.2678 (OUTLIER) cc_final: 0.1646 (p90) REVERT: u 443 VAL cc_start: 0.7165 (OUTLIER) cc_final: 0.6937 (p) REVERT: u 521 ASN cc_start: 0.6028 (t0) cc_final: 0.5689 (m110) REVERT: v 267 VAL cc_start: 0.6734 (OUTLIER) cc_final: 0.6452 (p) REVERT: S 45 TRP cc_start: 0.8742 (m100) cc_final: 0.8429 (m100) REVERT: S 46 LYS cc_start: 0.9009 (OUTLIER) cc_final: 0.8737 (tppt) REVERT: S 163 ASN cc_start: 0.7988 (t0) cc_final: 0.7267 (p0) REVERT: S 165 GLU cc_start: 0.7794 (mp0) cc_final: 0.7333 (pt0) REVERT: y 116 TYR cc_start: 0.4632 (OUTLIER) cc_final: 0.3813 (t80) REVERT: y 134 ASN cc_start: 0.7517 (m-40) cc_final: 0.7054 (m-40) REVERT: y 412 LEU cc_start: 0.8120 (mm) cc_final: 0.7810 (tp) REVERT: y 422 GLU cc_start: 0.4480 (mp0) cc_final: 0.3699 (mp0) REVERT: y 519 HIS cc_start: 0.6910 (m90) cc_final: 0.6571 (p90) REVERT: H 15 GLU cc_start: 0.7536 (mm-30) cc_final: 0.7305 (mm-30) REVERT: K 64 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7876 (mm-30) REVERT: K 67 ASP cc_start: 0.8311 (OUTLIER) cc_final: 0.8078 (t0) REVERT: L 110 MET cc_start: 0.8724 (ptp) cc_final: 0.8499 (ptm) REVERT: L 121 ARG cc_start: 0.8283 (ttp80) cc_final: 0.8076 (ttp80) REVERT: L 176 LYS cc_start: 0.8488 (tptp) cc_final: 0.8197 (ttpt) REVERT: L 227 ARG cc_start: 0.8592 (OUTLIER) cc_final: 0.8299 (tmm-80) REVERT: O 38 MET cc_start: 0.7616 (mpp) cc_final: 0.7255 (mtm) REVERT: N 56 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7072 (mp0) REVERT: N 73 ASP cc_start: 0.8022 (m-30) cc_final: 0.7730 (m-30) REVERT: N 78 SER cc_start: 0.9037 (t) cc_final: 0.8733 (t) REVERT: Q 89 ARG cc_start: 0.8440 (tmm-80) cc_final: 0.8069 (ttm170) REVERT: P 70 SER cc_start: 0.8925 (t) cc_final: 0.8499 (m) REVERT: P 128 ARG cc_start: 0.8002 (OUTLIER) cc_final: 0.7665 (mmt90) REVERT: I 92 ILE cc_start: 0.9310 (mt) cc_final: 0.9059 (mt) REVERT: x 50 TYR cc_start: 0.6401 (OUTLIER) cc_final: 0.6030 (m-10) REVERT: x 302 GLU cc_start: 0.4524 (tm-30) cc_final: 0.3319 (mt-10) REVERT: x 401 SER cc_start: 0.3873 (OUTLIER) cc_final: 0.3626 (p) REVERT: 9 14 LYS cc_start: 0.8225 (ttpt) cc_final: 0.7690 (ttpp) REVERT: 9 17 ARG cc_start: 0.8094 (mtt180) cc_final: 0.7823 (ttm170) REVERT: B 103 GLU cc_start: 0.8491 (pt0) cc_final: 0.8246 (pt0) REVERT: C 23 LEU cc_start: 0.9486 (OUTLIER) cc_final: 0.9267 (mp) REVERT: D 18 ARG cc_start: 0.8982 (ttm-80) cc_final: 0.8744 (ttm170) REVERT: D 21 GLU cc_start: 0.7668 (mt-10) cc_final: 0.7369 (mt-10) REVERT: D 107 GLU cc_start: 0.8650 (mm-30) cc_final: 0.8295 (tm-30) REVERT: E 110 HIS cc_start: 0.8188 (t-90) cc_final: 0.7904 (t-90) REVERT: r 4 LEU cc_start: 0.4965 (OUTLIER) cc_final: 0.4442 (tt) REVERT: r 48 LEU cc_start: 0.5045 (OUTLIER) cc_final: 0.4252 (tp) REVERT: r 223 MET cc_start: 0.4908 (OUTLIER) cc_final: 0.4526 (ptp) REVERT: r 237 MET cc_start: 0.4984 (ptp) cc_final: 0.4519 (ptm) REVERT: r 255 MET cc_start: 0.1802 (mmt) cc_final: 0.0606 (ptt) REVERT: R 6 ASP cc_start: 0.8064 (p0) cc_final: 0.7798 (p0) REVERT: R 111 GLN cc_start: 0.8854 (mt0) cc_final: 0.8436 (mt0) REVERT: R 137 LEU cc_start: 0.5484 (OUTLIER) cc_final: 0.5011 (mm) REVERT: T 19 GLN cc_start: 0.9143 (mp10) cc_final: 0.8872 (mp10) REVERT: T 25 ILE cc_start: 0.8752 (mt) cc_final: 0.8542 (mt) REVERT: V 127 ARG cc_start: 0.4946 (tmt170) cc_final: 0.4222 (mmm-85) REVERT: Y 10 VAL cc_start: 0.7242 (OUTLIER) cc_final: 0.6936 (p) REVERT: Y 84 ILE cc_start: 0.8391 (mt) cc_final: 0.8115 (mt) REVERT: Z 22 ASN cc_start: 0.6880 (m-40) cc_final: 0.6593 (m-40) REVERT: Z 57 ASN cc_start: 0.7394 (OUTLIER) cc_final: 0.6650 (t0) REVERT: a 3 MET cc_start: -0.0070 (tmm) cc_final: -0.2607 (ppp) REVERT: b 30 TYR cc_start: 0.2492 (OUTLIER) cc_final: 0.0402 (m-80) REVERT: c 126 ASP cc_start: 0.6723 (p0) cc_final: 0.6112 (p0) REVERT: c 259 TRP cc_start: 0.4793 (m-90) cc_final: 0.4356 (m-90) REVERT: f 77 TYR cc_start: 0.3525 (m-80) cc_final: 0.2595 (m-80) REVERT: n 35 MET cc_start: 0.5160 (mmm) cc_final: 0.4299 (tpp) REVERT: n 42 ILE cc_start: 0.6138 (OUTLIER) cc_final: 0.5894 (mm) REVERT: p 69 CYS cc_start: 0.8464 (p) cc_final: 0.8093 (p) REVERT: p 84 GLN cc_start: 0.8114 (mt0) cc_final: 0.7841 (mt0) REVERT: p 89 GLN cc_start: 0.8485 (mm-40) cc_final: 0.7759 (mp10) REVERT: p 102 LEU cc_start: 0.6239 (OUTLIER) cc_final: 0.5836 (mm) REVERT: q 38 VAL cc_start: 0.4642 (OUTLIER) cc_final: 0.4320 (m) REVERT: M 3 ARG cc_start: 0.8460 (mmt90) cc_final: 0.7789 (mmm-85) REVERT: M 105 MET cc_start: 0.8522 (ttp) cc_final: 0.8298 (tmm) REVERT: h 113 GLU cc_start: 0.6745 (OUTLIER) cc_final: 0.6091 (tm-30) REVERT: s 291 LEU cc_start: -0.0305 (OUTLIER) cc_final: -0.0560 (mp) REVERT: j 54 LYS cc_start: 0.4058 (OUTLIER) cc_final: 0.3181 (tmmt) REVERT: j 165 MET cc_start: 0.0221 (mtt) cc_final: -0.0233 (mtt) REVERT: j 228 MET cc_start: -0.1229 (mtt) cc_final: -0.1661 (mmt) REVERT: j 268 GLU cc_start: 0.6218 (OUTLIER) cc_final: 0.6002 (mp0) REVERT: j 283 ARG cc_start: 0.3874 (OUTLIER) cc_final: 0.3300 (mtt180) REVERT: j 292 MET cc_start: 0.1374 (mtm) cc_final: 0.0861 (mmt) REVERT: j 302 MET cc_start: 0.0999 (mtt) cc_final: 0.0611 (mmt) REVERT: g 910 MET cc_start: 0.1212 (ptp) cc_final: 0.0889 (ptp) REVERT: g 962 MET cc_start: 0.2800 (OUTLIER) cc_final: 0.0635 (mmp) REVERT: g 985 LEU cc_start: 0.2230 (OUTLIER) cc_final: 0.1912 (mt) outliers start: 368 outliers final: 253 residues processed: 1538 average time/residue: 0.9973 time to fit residues: 2689.1713 Evaluate side-chains 1496 residues out of total 9800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 284 poor density : 1212 time to evaluate : 7.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 513 VAL Chi-restraints excluded: chain 1 residue 542 THR Chi-restraints excluded: chain 1 residue 543 ASN Chi-restraints excluded: chain 6 residue 312 VAL Chi-restraints excluded: chain 6 residue 316 VAL Chi-restraints excluded: chain 6 residue 318 THR Chi-restraints excluded: chain 6 residue 328 THR Chi-restraints excluded: chain u residue 60 ASP Chi-restraints excluded: chain u residue 109 GLN Chi-restraints excluded: chain u residue 121 ILE Chi-restraints excluded: chain u residue 133 SER Chi-restraints excluded: chain u residue 173 LEU Chi-restraints excluded: chain u residue 230 LEU Chi-restraints excluded: chain u residue 237 LEU Chi-restraints excluded: chain u residue 242 SER Chi-restraints excluded: chain u residue 344 MET Chi-restraints excluded: chain u residue 357 THR Chi-restraints excluded: chain u residue 394 LEU Chi-restraints excluded: chain u residue 398 PHE Chi-restraints excluded: chain u residue 443 VAL Chi-restraints excluded: chain u residue 534 LEU Chi-restraints excluded: chain v residue 267 VAL Chi-restraints excluded: chain v residue 278 VAL Chi-restraints excluded: chain v residue 296 VAL Chi-restraints excluded: chain v residue 304 ASP Chi-restraints excluded: chain v residue 315 CYS Chi-restraints excluded: chain v residue 362 MET Chi-restraints excluded: chain v residue 396 ASN Chi-restraints excluded: chain v residue 408 THR Chi-restraints excluded: chain v residue 422 ILE Chi-restraints excluded: chain S residue 46 LYS Chi-restraints excluded: chain S residue 49 VAL Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 114 VAL Chi-restraints excluded: chain S residue 139 SER Chi-restraints excluded: chain S residue 158 VAL Chi-restraints excluded: chain S residue 219 GLU Chi-restraints excluded: chain y residue 63 LEU Chi-restraints excluded: chain y residue 102 VAL Chi-restraints excluded: chain y residue 116 TYR Chi-restraints excluded: chain y residue 157 THR Chi-restraints excluded: chain y residue 330 ILE Chi-restraints excluded: chain y residue 475 ASP Chi-restraints excluded: chain y residue 495 THR Chi-restraints excluded: chain y residue 499 VAL Chi-restraints excluded: chain y residue 578 LEU Chi-restraints excluded: chain y residue 608 LEU Chi-restraints excluded: chain y residue 628 ASP Chi-restraints excluded: chain y residue 677 ILE Chi-restraints excluded: chain y residue 718 LEU Chi-restraints excluded: chain y residue 748 ASP Chi-restraints excluded: chain y residue 773 ASP Chi-restraints excluded: chain y residue 798 VAL Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 24 SER Chi-restraints excluded: chain G residue 27 LEU Chi-restraints excluded: chain G residue 44 ASN Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain G residue 107 LYS Chi-restraints excluded: chain G residue 119 SER Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 137 SER Chi-restraints excluded: chain G residue 164 ASN Chi-restraints excluded: chain G residue 174 SER Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 37 CYS Chi-restraints excluded: chain H residue 40 CYS Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 21 ASN Chi-restraints excluded: chain K residue 64 GLU Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 67 ASP Chi-restraints excluded: chain K residue 80 SER Chi-restraints excluded: chain L residue 59 GLU Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain L residue 113 GLN Chi-restraints excluded: chain L residue 116 THR Chi-restraints excluded: chain L residue 157 LEU Chi-restraints excluded: chain L residue 162 ILE Chi-restraints excluded: chain L residue 172 ASN Chi-restraints excluded: chain L residue 180 VAL Chi-restraints excluded: chain L residue 205 VAL Chi-restraints excluded: chain L residue 225 SER Chi-restraints excluded: chain L residue 227 ARG Chi-restraints excluded: chain L residue 252 THR Chi-restraints excluded: chain O residue 55 THR Chi-restraints excluded: chain O residue 91 VAL Chi-restraints excluded: chain O residue 105 LEU Chi-restraints excluded: chain O residue 126 ASP Chi-restraints excluded: chain O residue 153 THR Chi-restraints excluded: chain O residue 154 SER Chi-restraints excluded: chain O residue 170 GLU Chi-restraints excluded: chain N residue 15 VAL Chi-restraints excluded: chain N residue 35 GLU Chi-restraints excluded: chain N residue 54 THR Chi-restraints excluded: chain N residue 56 GLU Chi-restraints excluded: chain N residue 69 GLU Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 147 LEU Chi-restraints excluded: chain N residue 163 CYS Chi-restraints excluded: chain N residue 170 SER Chi-restraints excluded: chain Q residue 24 THR Chi-restraints excluded: chain Q residue 45 VAL Chi-restraints excluded: chain Q residue 58 VAL Chi-restraints excluded: chain Q residue 64 LEU Chi-restraints excluded: chain Q residue 67 LEU Chi-restraints excluded: chain Q residue 88 SER Chi-restraints excluded: chain P residue 47 LEU Chi-restraints excluded: chain P residue 62 VAL Chi-restraints excluded: chain P residue 67 ASP Chi-restraints excluded: chain P residue 100 THR Chi-restraints excluded: chain P residue 128 ARG Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain I residue 31 ASP Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 69 ASN Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain x residue 21 VAL Chi-restraints excluded: chain x residue 27 ASP Chi-restraints excluded: chain x residue 50 TYR Chi-restraints excluded: chain x residue 69 TYR Chi-restraints excluded: chain x residue 369 ILE Chi-restraints excluded: chain x residue 401 SER Chi-restraints excluded: chain 9 residue 9 ARG Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 232 ASN Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 39 ASN Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain F residue 98 LYS Chi-restraints excluded: chain r residue 4 LEU Chi-restraints excluded: chain r residue 37 LEU Chi-restraints excluded: chain r residue 48 LEU Chi-restraints excluded: chain r residue 88 ARG Chi-restraints excluded: chain r residue 106 LYS Chi-restraints excluded: chain r residue 223 MET Chi-restraints excluded: chain r residue 227 ILE Chi-restraints excluded: chain r residue 240 THR Chi-restraints excluded: chain J residue 13 SER Chi-restraints excluded: chain J residue 30 CYS Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain J residue 51 GLU Chi-restraints excluded: chain J residue 94 LEU Chi-restraints excluded: chain J residue 98 GLN Chi-restraints excluded: chain J residue 121 THR Chi-restraints excluded: chain R residue 72 CYS Chi-restraints excluded: chain R residue 89 GLU Chi-restraints excluded: chain R residue 90 LEU Chi-restraints excluded: chain R residue 137 LEU Chi-restraints excluded: chain T residue 27 VAL Chi-restraints excluded: chain T residue 80 ASP Chi-restraints excluded: chain T residue 102 THR Chi-restraints excluded: chain T residue 125 VAL Chi-restraints excluded: chain V residue 72 LEU Chi-restraints excluded: chain V residue 78 MET Chi-restraints excluded: chain V residue 82 ASN Chi-restraints excluded: chain V residue 92 ILE Chi-restraints excluded: chain V residue 165 ASN Chi-restraints excluded: chain V residue 197 GLU Chi-restraints excluded: chain Y residue 10 VAL Chi-restraints excluded: chain Y residue 34 VAL Chi-restraints excluded: chain Y residue 51 LEU Chi-restraints excluded: chain Y residue 78 VAL Chi-restraints excluded: chain Z residue 5 ILE Chi-restraints excluded: chain Z residue 6 SER Chi-restraints excluded: chain Z residue 26 THR Chi-restraints excluded: chain Z residue 41 VAL Chi-restraints excluded: chain Z residue 42 THR Chi-restraints excluded: chain Z residue 57 ASN Chi-restraints excluded: chain Z residue 84 VAL Chi-restraints excluded: chain Z residue 103 GLU Chi-restraints excluded: chain Z residue 139 SER Chi-restraints excluded: chain Z residue 182 LEU Chi-restraints excluded: chain Z residue 221 THR Chi-restraints excluded: chain a residue 64 TRP Chi-restraints excluded: chain a residue 70 TYR Chi-restraints excluded: chain b residue 20 VAL Chi-restraints excluded: chain b residue 30 TYR Chi-restraints excluded: chain c residue 102 VAL Chi-restraints excluded: chain c residue 109 LEU Chi-restraints excluded: chain c residue 137 VAL Chi-restraints excluded: chain c residue 171 ASP Chi-restraints excluded: chain c residue 188 HIS Chi-restraints excluded: chain c residue 197 THR Chi-restraints excluded: chain c residue 246 TYR Chi-restraints excluded: chain c residue 265 ILE Chi-restraints excluded: chain c residue 297 THR Chi-restraints excluded: chain d residue 96 SER Chi-restraints excluded: chain e residue 48 VAL Chi-restraints excluded: chain e residue 51 ASP Chi-restraints excluded: chain e residue 77 LEU Chi-restraints excluded: chain f residue 17 ASN Chi-restraints excluded: chain f residue 34 LYS Chi-restraints excluded: chain f residue 39 ARG Chi-restraints excluded: chain f residue 43 VAL Chi-restraints excluded: chain f residue 83 PHE Chi-restraints excluded: chain f residue 90 VAL Chi-restraints excluded: chain i residue 16 GLN Chi-restraints excluded: chain i residue 34 TYR Chi-restraints excluded: chain k residue 98 VAL Chi-restraints excluded: chain m residue 11 VAL Chi-restraints excluded: chain m residue 51 VAL Chi-restraints excluded: chain m residue 80 ASP Chi-restraints excluded: chain m residue 91 LEU Chi-restraints excluded: chain m residue 94 ILE Chi-restraints excluded: chain m residue 124 ILE Chi-restraints excluded: chain n residue 42 ILE Chi-restraints excluded: chain n residue 45 ASN Chi-restraints excluded: chain n residue 55 VAL Chi-restraints excluded: chain o residue 254 ASP Chi-restraints excluded: chain o residue 275 THR Chi-restraints excluded: chain o residue 312 VAL Chi-restraints excluded: chain p residue 30 TYR Chi-restraints excluded: chain p residue 43 THR Chi-restraints excluded: chain p residue 58 LYS Chi-restraints excluded: chain p residue 90 ARG Chi-restraints excluded: chain p residue 94 CYS Chi-restraints excluded: chain p residue 102 LEU Chi-restraints excluded: chain q residue 27 VAL Chi-restraints excluded: chain q residue 38 VAL Chi-restraints excluded: chain q residue 47 LEU Chi-restraints excluded: chain q residue 53 ASP Chi-restraints excluded: chain q residue 64 LYS Chi-restraints excluded: chain q residue 81 LEU Chi-restraints excluded: chain q residue 86 ASP Chi-restraints excluded: chain M residue 6 THR Chi-restraints excluded: chain M residue 22 THR Chi-restraints excluded: chain M residue 54 VAL Chi-restraints excluded: chain M residue 55 THR Chi-restraints excluded: chain M residue 71 ILE Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain M residue 106 LEU Chi-restraints excluded: chain M residue 110 ASP Chi-restraints excluded: chain M residue 116 ASN Chi-restraints excluded: chain M residue 119 VAL Chi-restraints excluded: chain M residue 123 THR Chi-restraints excluded: chain M residue 130 THR Chi-restraints excluded: chain h residue 20 ILE Chi-restraints excluded: chain h residue 29 VAL Chi-restraints excluded: chain h residue 60 THR Chi-restraints excluded: chain h residue 65 THR Chi-restraints excluded: chain h residue 68 THR Chi-restraints excluded: chain h residue 74 SER Chi-restraints excluded: chain h residue 90 ASP Chi-restraints excluded: chain h residue 93 SER Chi-restraints excluded: chain h residue 106 ILE Chi-restraints excluded: chain h residue 113 GLU Chi-restraints excluded: chain h residue 114 VAL Chi-restraints excluded: chain s residue 184 PHE Chi-restraints excluded: chain s residue 187 MET Chi-restraints excluded: chain s residue 194 MET Chi-restraints excluded: chain s residue 220 VAL Chi-restraints excluded: chain s residue 232 GLN Chi-restraints excluded: chain s residue 279 VAL Chi-restraints excluded: chain s residue 282 HIS Chi-restraints excluded: chain s residue 291 LEU Chi-restraints excluded: chain j residue 54 LYS Chi-restraints excluded: chain j residue 268 GLU Chi-restraints excluded: chain j residue 283 ARG Chi-restraints excluded: chain j residue 299 VAL Chi-restraints excluded: chain j residue 357 ILE Chi-restraints excluded: chain j residue 371 VAL Chi-restraints excluded: chain g residue 921 VAL Chi-restraints excluded: chain g residue 962 MET Chi-restraints excluded: chain g residue 978 MET Chi-restraints excluded: chain g residue 985 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1269 random chunks: chunk 412 optimal weight: 4.9990 chunk 1104 optimal weight: 10.0000 chunk 242 optimal weight: 9.9990 chunk 720 optimal weight: 10.0000 chunk 302 optimal weight: 2.9990 chunk 1227 optimal weight: 8.9990 chunk 1019 optimal weight: 10.0000 chunk 568 optimal weight: 50.0000 chunk 102 optimal weight: 40.0000 chunk 406 optimal weight: 4.9990 chunk 644 optimal weight: 3.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 543 ASN ** 1 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 339 HIS ** u 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 579 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 659 ASN G 73 GLN ** G 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 113 GLN ** L 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 113 GLN ** Q 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 5 GLN B 94 HIS ** B 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 31 HIS F 130 ASN ** J 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 112 ASN V 74 ASN ** V 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 86 GLN ** Y 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 238 ASN o 256 GLN ** p 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 118 GLN ** s 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6850 moved from start: 0.4944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.110 123665 Z= 0.562 Angle : 0.901 17.101 176203 Z= 0.459 Chirality : 0.049 0.440 21730 Planarity : 0.007 0.144 16084 Dihedral : 20.915 179.584 38708 Min Nonbonded Distance : 1.006 Molprobity Statistics. All-atom Clashscore : 20.02 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.98 % Favored : 91.98 % Rotamer: Outliers : 7.18 % Allowed : 24.33 % Favored : 68.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.08), residues: 10949 helix: -0.31 (0.08), residues: 4287 sheet: -1.07 (0.13), residues: 1396 loop : -2.13 (0.08), residues: 5266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP c 132 HIS 0.020 0.002 HIS a 28 PHE 0.029 0.003 PHE c 241 TYR 0.028 0.003 TYR c 140 ARG 0.011 0.001 ARG u 195 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21898 Ramachandran restraints generated. 10949 Oldfield, 0 Emsley, 10949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21898 Ramachandran restraints generated. 10949 Oldfield, 0 Emsley, 10949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1691 residues out of total 9800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 496 poor density : 1195 time to evaluate : 7.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASN P 26 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 477 ASN cc_start: 0.5614 (OUTLIER) cc_final: 0.5224 (t0) REVERT: 1 552 LYS cc_start: 0.6724 (tptp) cc_final: 0.6265 (pptt) REVERT: 6 318 THR cc_start: 0.3744 (OUTLIER) cc_final: 0.3322 (p) REVERT: 6 319 LYS cc_start: 0.3846 (tptt) cc_final: 0.3475 (tptp) REVERT: 6 320 MET cc_start: -0.0361 (mmt) cc_final: -0.0750 (mmt) REVERT: 6 353 THR cc_start: 0.6122 (p) cc_final: 0.5906 (p) REVERT: u 246 TRP cc_start: 0.7565 (m100) cc_final: 0.6621 (m100) REVERT: u 318 MET cc_start: 0.4647 (ptt) cc_final: 0.4158 (ptm) REVERT: u 398 PHE cc_start: 0.2815 (OUTLIER) cc_final: 0.2183 (p90) REVERT: v 267 VAL cc_start: 0.6759 (OUTLIER) cc_final: 0.6363 (p) REVERT: S 46 LYS cc_start: 0.9029 (OUTLIER) cc_final: 0.8737 (tppt) REVERT: S 163 ASN cc_start: 0.8115 (t0) cc_final: 0.7261 (p0) REVERT: y 116 TYR cc_start: 0.4437 (OUTLIER) cc_final: 0.3788 (t80) REVERT: y 134 ASN cc_start: 0.7650 (m-40) cc_final: 0.7200 (m110) REVERT: y 422 GLU cc_start: 0.4927 (mp0) cc_final: 0.4080 (mp0) REVERT: H 15 GLU cc_start: 0.7633 (mm-30) cc_final: 0.7408 (mm-30) REVERT: K 64 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.8046 (mm-30) REVERT: L 113 GLN cc_start: 0.9140 (pt0) cc_final: 0.8933 (pt0) REVERT: L 121 ARG cc_start: 0.8328 (ttp80) cc_final: 0.8074 (ttp80) REVERT: L 176 LYS cc_start: 0.8651 (tptp) cc_final: 0.8420 (ttmt) REVERT: O 134 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8778 (tp) REVERT: O 135 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8712 (mt) REVERT: N 73 ASP cc_start: 0.8149 (m-30) cc_final: 0.7874 (m-30) REVERT: N 78 SER cc_start: 0.9136 (t) cc_final: 0.8817 (t) REVERT: Q 89 ARG cc_start: 0.8620 (tmm-80) cc_final: 0.8226 (ttm170) REVERT: Q 96 THR cc_start: 0.8734 (m) cc_final: 0.8310 (p) REVERT: P 70 SER cc_start: 0.8965 (t) cc_final: 0.8682 (m) REVERT: P 128 ARG cc_start: 0.8100 (OUTLIER) cc_final: 0.7746 (mmt90) REVERT: I 107 LYS cc_start: 0.8389 (OUTLIER) cc_final: 0.8104 (ttmm) REVERT: x 50 TYR cc_start: 0.6846 (OUTLIER) cc_final: 0.6463 (m-10) REVERT: x 426 LYS cc_start: 0.1739 (tptp) cc_final: 0.1417 (tptp) REVERT: 9 14 LYS cc_start: 0.8308 (ttpt) cc_final: 0.7795 (ttpp) REVERT: B 39 ASN cc_start: 0.8439 (t0) cc_final: 0.7789 (p0) REVERT: B 124 ASP cc_start: 0.8582 (m-30) cc_final: 0.8333 (m-30) REVERT: C 23 LEU cc_start: 0.9588 (OUTLIER) cc_final: 0.9320 (mp) REVERT: D 107 GLU cc_start: 0.8784 (mm-30) cc_final: 0.8298 (tm-30) REVERT: D 150 ARG cc_start: 0.8805 (OUTLIER) cc_final: 0.7942 (mtm110) REVERT: E 21 LYS cc_start: 0.9140 (OUTLIER) cc_final: 0.8929 (mtmt) REVERT: F 82 ARG cc_start: 0.8353 (OUTLIER) cc_final: 0.7926 (ptt-90) REVERT: F 98 LYS cc_start: 0.8481 (OUTLIER) cc_final: 0.7959 (mttt) REVERT: r 4 LEU cc_start: 0.4650 (OUTLIER) cc_final: 0.4046 (tt) REVERT: r 48 LEU cc_start: 0.5472 (OUTLIER) cc_final: 0.4596 (tp) REVERT: r 86 SER cc_start: 0.4054 (OUTLIER) cc_final: 0.3615 (t) REVERT: r 117 GLU cc_start: 0.5323 (OUTLIER) cc_final: 0.4774 (tm-30) REVERT: J 49 GLU cc_start: 0.7879 (mt-10) cc_final: 0.7284 (mt-10) REVERT: R 105 ASP cc_start: 0.8373 (t0) cc_final: 0.8133 (t0) REVERT: R 111 GLN cc_start: 0.8932 (mt0) cc_final: 0.8521 (mt0) REVERT: R 137 LEU cc_start: 0.5962 (OUTLIER) cc_final: 0.5538 (mm) REVERT: V 127 ARG cc_start: 0.5090 (tmt170) cc_final: 0.4480 (mmm-85) REVERT: V 186 ASN cc_start: 0.6456 (m110) cc_final: 0.6192 (t0) REVERT: Y 10 VAL cc_start: 0.6962 (OUTLIER) cc_final: 0.6750 (p) REVERT: Z 57 ASN cc_start: 0.7584 (OUTLIER) cc_final: 0.6794 (t0) REVERT: a 3 MET cc_start: 0.0478 (tmm) cc_final: -0.2106 (ppp) REVERT: b 30 TYR cc_start: 0.2549 (OUTLIER) cc_final: 0.0158 (m-80) REVERT: c 126 ASP cc_start: 0.6987 (p0) cc_final: 0.6337 (p0) REVERT: c 220 ASP cc_start: 0.6688 (OUTLIER) cc_final: 0.6222 (m-30) REVERT: f 77 TYR cc_start: 0.3322 (m-80) cc_final: 0.2859 (m-80) REVERT: i 41 GLN cc_start: 0.8457 (mp10) cc_final: 0.8123 (mp10) REVERT: m 33 ARG cc_start: 0.1958 (OUTLIER) cc_final: -0.0159 (mtm180) REVERT: n 15 THR cc_start: 0.6180 (OUTLIER) cc_final: 0.5671 (p) REVERT: n 35 MET cc_start: 0.5236 (mmm) cc_final: 0.4264 (tpp) REVERT: n 42 ILE cc_start: 0.6352 (OUTLIER) cc_final: 0.6138 (mm) REVERT: p 69 CYS cc_start: 0.8465 (p) cc_final: 0.8066 (p) REVERT: p 89 GLN cc_start: 0.8418 (mm-40) cc_final: 0.7648 (mp10) REVERT: p 102 LEU cc_start: 0.6498 (OUTLIER) cc_final: 0.6064 (mm) REVERT: q 75 ASP cc_start: 0.5403 (p0) cc_final: 0.4929 (m-30) REVERT: q 99 GLU cc_start: 0.4080 (OUTLIER) cc_final: 0.2464 (pp20) REVERT: h 113 GLU cc_start: 0.6823 (OUTLIER) cc_final: 0.6473 (tt0) REVERT: s 291 LEU cc_start: 0.0040 (OUTLIER) cc_final: -0.0197 (mp) REVERT: j 165 MET cc_start: 0.0123 (mtt) cc_final: -0.0421 (mtm) REVERT: j 178 MET cc_start: 0.1833 (mpp) cc_final: 0.1547 (mpp) REVERT: j 267 TYR cc_start: 0.4125 (OUTLIER) cc_final: 0.2108 (t80) REVERT: j 292 MET cc_start: 0.1580 (mtm) cc_final: 0.0991 (mmt) REVERT: j 302 MET cc_start: 0.1341 (mtt) cc_final: 0.0799 (mmt) REVERT: g 962 MET cc_start: 0.3291 (OUTLIER) cc_final: 0.0904 (mmp) REVERT: g 985 LEU cc_start: 0.2287 (OUTLIER) cc_final: 0.2050 (mt) outliers start: 496 outliers final: 336 residues processed: 1542 average time/residue: 0.9886 time to fit residues: 2658.7423 Evaluate side-chains 1499 residues out of total 9800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 372 poor density : 1127 time to evaluate : 9.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 477 ASN Chi-restraints excluded: chain 1 residue 493 VAL Chi-restraints excluded: chain 1 residue 494 THR Chi-restraints excluded: chain 1 residue 513 VAL Chi-restraints excluded: chain 1 residue 515 CYS Chi-restraints excluded: chain 6 residue 312 VAL Chi-restraints excluded: chain 6 residue 316 VAL Chi-restraints excluded: chain 6 residue 318 THR Chi-restraints excluded: chain 6 residue 328 THR Chi-restraints excluded: chain 6 residue 338 THR Chi-restraints excluded: chain 6 residue 341 THR Chi-restraints excluded: chain u residue 17 GLU Chi-restraints excluded: chain u residue 60 ASP Chi-restraints excluded: chain u residue 109 GLN Chi-restraints excluded: chain u residue 121 ILE Chi-restraints excluded: chain u residue 133 SER Chi-restraints excluded: chain u residue 187 GLN Chi-restraints excluded: chain u residue 230 LEU Chi-restraints excluded: chain u residue 237 LEU Chi-restraints excluded: chain u residue 242 SER Chi-restraints excluded: chain u residue 355 LEU Chi-restraints excluded: chain u residue 358 LEU Chi-restraints excluded: chain u residue 361 LEU Chi-restraints excluded: chain u residue 394 LEU Chi-restraints excluded: chain u residue 398 PHE Chi-restraints excluded: chain u residue 534 LEU Chi-restraints excluded: chain v residue 267 VAL Chi-restraints excluded: chain v residue 278 VAL Chi-restraints excluded: chain v residue 296 VAL Chi-restraints excluded: chain v residue 304 ASP Chi-restraints excluded: chain v residue 315 CYS Chi-restraints excluded: chain v residue 362 MET Chi-restraints excluded: chain v residue 396 ASN Chi-restraints excluded: chain v residue 408 THR Chi-restraints excluded: chain v residue 422 ILE Chi-restraints excluded: chain S residue 46 LYS Chi-restraints excluded: chain S residue 49 VAL Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 67 VAL Chi-restraints excluded: chain S residue 114 VAL Chi-restraints excluded: chain S residue 139 SER Chi-restraints excluded: chain S residue 158 VAL Chi-restraints excluded: chain S residue 181 THR Chi-restraints excluded: chain S residue 192 ILE Chi-restraints excluded: chain S residue 208 GLU Chi-restraints excluded: chain S residue 219 GLU Chi-restraints excluded: chain y residue 63 LEU Chi-restraints excluded: chain y residue 66 THR Chi-restraints excluded: chain y residue 102 VAL Chi-restraints excluded: chain y residue 116 TYR Chi-restraints excluded: chain y residue 157 THR Chi-restraints excluded: chain y residue 393 MET Chi-restraints excluded: chain y residue 412 LEU Chi-restraints excluded: chain y residue 495 THR Chi-restraints excluded: chain y residue 499 VAL Chi-restraints excluded: chain y residue 510 THR Chi-restraints excluded: chain y residue 543 ASP Chi-restraints excluded: chain y residue 578 LEU Chi-restraints excluded: chain y residue 608 LEU Chi-restraints excluded: chain y residue 628 ASP Chi-restraints excluded: chain y residue 671 VAL Chi-restraints excluded: chain y residue 677 ILE Chi-restraints excluded: chain y residue 701 HIS Chi-restraints excluded: chain y residue 718 LEU Chi-restraints excluded: chain y residue 748 ASP Chi-restraints excluded: chain y residue 752 CYS Chi-restraints excluded: chain y residue 773 ASP Chi-restraints excluded: chain y residue 798 VAL Chi-restraints excluded: chain y residue 847 THR Chi-restraints excluded: chain y residue 854 ASN Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 24 SER Chi-restraints excluded: chain G residue 27 LEU Chi-restraints excluded: chain G residue 33 ASN Chi-restraints excluded: chain G residue 44 ASN Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain G residue 119 SER Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 125 VAL Chi-restraints excluded: chain G residue 137 SER Chi-restraints excluded: chain G residue 164 ASN Chi-restraints excluded: chain G residue 174 SER Chi-restraints excluded: chain H residue 17 ARG Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 37 CYS Chi-restraints excluded: chain H residue 40 CYS Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain K residue 2 GLN Chi-restraints excluded: chain K residue 9 VAL Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 21 ASN Chi-restraints excluded: chain K residue 23 ILE Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain K residue 64 GLU Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 76 ASP Chi-restraints excluded: chain K residue 80 SER Chi-restraints excluded: chain K residue 81 LYS Chi-restraints excluded: chain L residue 59 GLU Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain L residue 116 THR Chi-restraints excluded: chain L residue 143 CYS Chi-restraints excluded: chain L residue 162 ILE Chi-restraints excluded: chain L residue 172 ASN Chi-restraints excluded: chain L residue 180 VAL Chi-restraints excluded: chain L residue 202 THR Chi-restraints excluded: chain L residue 205 VAL Chi-restraints excluded: chain L residue 206 SER Chi-restraints excluded: chain L residue 225 SER Chi-restraints excluded: chain L residue 227 ARG Chi-restraints excluded: chain L residue 252 THR Chi-restraints excluded: chain O residue 55 THR Chi-restraints excluded: chain O residue 91 VAL Chi-restraints excluded: chain O residue 126 ASP Chi-restraints excluded: chain O residue 127 VAL Chi-restraints excluded: chain O residue 134 LEU Chi-restraints excluded: chain O residue 135 LEU Chi-restraints excluded: chain O residue 153 THR Chi-restraints excluded: chain O residue 154 SER Chi-restraints excluded: chain O residue 170 GLU Chi-restraints excluded: chain O residue 178 THR Chi-restraints excluded: chain O residue 192 SER Chi-restraints excluded: chain O residue 228 LEU Chi-restraints excluded: chain N residue 15 VAL Chi-restraints excluded: chain N residue 38 ILE Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain N residue 54 THR Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 69 GLU Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 147 LEU Chi-restraints excluded: chain N residue 163 CYS Chi-restraints excluded: chain N residue 170 SER Chi-restraints excluded: chain Q residue 12 LYS Chi-restraints excluded: chain Q residue 24 THR Chi-restraints excluded: chain Q residue 45 VAL Chi-restraints excluded: chain Q residue 52 ASP Chi-restraints excluded: chain Q residue 57 SER Chi-restraints excluded: chain Q residue 64 LEU Chi-restraints excluded: chain Q residue 67 LEU Chi-restraints excluded: chain Q residue 88 SER Chi-restraints excluded: chain Q residue 90 GLU Chi-restraints excluded: chain P residue 47 LEU Chi-restraints excluded: chain P residue 62 VAL Chi-restraints excluded: chain P residue 67 ASP Chi-restraints excluded: chain P residue 93 LEU Chi-restraints excluded: chain P residue 100 THR Chi-restraints excluded: chain P residue 128 ARG Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 27 LYS Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain I residue 31 ASP Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 69 ASN Chi-restraints excluded: chain I residue 102 LEU Chi-restraints excluded: chain I residue 107 LYS Chi-restraints excluded: chain I residue 122 ILE Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain x residue 27 ASP Chi-restraints excluded: chain x residue 50 TYR Chi-restraints excluded: chain x residue 56 THR Chi-restraints excluded: chain x residue 69 TYR Chi-restraints excluded: chain x residue 76 ASP Chi-restraints excluded: chain x residue 369 ILE Chi-restraints excluded: chain 9 residue 9 ARG Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 116 CYS Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 224 ASN Chi-restraints excluded: chain C residue 232 ASN Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 39 ASN Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 122 SER Chi-restraints excluded: chain D residue 150 ARG Chi-restraints excluded: chain E residue 21 LYS Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 61 GLN Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 127 ASN Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain F residue 82 ARG Chi-restraints excluded: chain F residue 98 LYS Chi-restraints excluded: chain r residue 4 LEU Chi-restraints excluded: chain r residue 47 LEU Chi-restraints excluded: chain r residue 48 LEU Chi-restraints excluded: chain r residue 58 SER Chi-restraints excluded: chain r residue 76 VAL Chi-restraints excluded: chain r residue 86 SER Chi-restraints excluded: chain r residue 106 LYS Chi-restraints excluded: chain r residue 117 GLU Chi-restraints excluded: chain r residue 185 THR Chi-restraints excluded: chain r residue 189 VAL Chi-restraints excluded: chain r residue 208 VAL Chi-restraints excluded: chain r residue 216 LEU Chi-restraints excluded: chain r residue 227 ILE Chi-restraints excluded: chain r residue 240 THR Chi-restraints excluded: chain J residue 30 CYS Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain J residue 51 GLU Chi-restraints excluded: chain J residue 80 ASP Chi-restraints excluded: chain J residue 94 LEU Chi-restraints excluded: chain J residue 98 GLN Chi-restraints excluded: chain J residue 121 THR Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain R residue 66 SER Chi-restraints excluded: chain R residue 72 CYS Chi-restraints excluded: chain R residue 89 GLU Chi-restraints excluded: chain R residue 90 LEU Chi-restraints excluded: chain R residue 95 THR Chi-restraints excluded: chain R residue 137 LEU Chi-restraints excluded: chain R residue 182 CYS Chi-restraints excluded: chain T residue 27 VAL Chi-restraints excluded: chain T residue 28 LEU Chi-restraints excluded: chain T residue 34 THR Chi-restraints excluded: chain T residue 77 ASP Chi-restraints excluded: chain T residue 80 ASP Chi-restraints excluded: chain T residue 102 THR Chi-restraints excluded: chain T residue 112 ASN Chi-restraints excluded: chain T residue 125 VAL Chi-restraints excluded: chain V residue 41 VAL Chi-restraints excluded: chain V residue 82 ASN Chi-restraints excluded: chain V residue 92 ILE Chi-restraints excluded: chain V residue 165 ASN Chi-restraints excluded: chain V residue 168 THR Chi-restraints excluded: chain V residue 197 GLU Chi-restraints excluded: chain Y residue 10 VAL Chi-restraints excluded: chain Y residue 18 THR Chi-restraints excluded: chain Y residue 34 VAL Chi-restraints excluded: chain Y residue 47 LEU Chi-restraints excluded: chain Y residue 51 LEU Chi-restraints excluded: chain Y residue 78 VAL Chi-restraints excluded: chain Y residue 81 ILE Chi-restraints excluded: chain Z residue 26 THR Chi-restraints excluded: chain Z residue 41 VAL Chi-restraints excluded: chain Z residue 42 THR Chi-restraints excluded: chain Z residue 57 ASN Chi-restraints excluded: chain Z residue 84 VAL Chi-restraints excluded: chain Z residue 86 LEU Chi-restraints excluded: chain Z residue 139 SER Chi-restraints excluded: chain Z residue 182 LEU Chi-restraints excluded: chain Z residue 208 VAL Chi-restraints excluded: chain Z residue 221 THR Chi-restraints excluded: chain a residue 20 VAL Chi-restraints excluded: chain a residue 52 LEU Chi-restraints excluded: chain a residue 60 GLU Chi-restraints excluded: chain a residue 64 TRP Chi-restraints excluded: chain a residue 70 TYR Chi-restraints excluded: chain a residue 83 LEU Chi-restraints excluded: chain b residue 20 VAL Chi-restraints excluded: chain b residue 28 MET Chi-restraints excluded: chain b residue 30 TYR Chi-restraints excluded: chain c residue 102 VAL Chi-restraints excluded: chain c residue 109 LEU Chi-restraints excluded: chain c residue 171 ASP Chi-restraints excluded: chain c residue 197 THR Chi-restraints excluded: chain c residue 217 MET Chi-restraints excluded: chain c residue 220 ASP Chi-restraints excluded: chain c residue 265 ILE Chi-restraints excluded: chain c residue 297 THR Chi-restraints excluded: chain d residue 34 VAL Chi-restraints excluded: chain d residue 66 LEU Chi-restraints excluded: chain d residue 96 SER Chi-restraints excluded: chain d residue 103 VAL Chi-restraints excluded: chain d residue 107 LEU Chi-restraints excluded: chain e residue 48 VAL Chi-restraints excluded: chain e residue 73 VAL Chi-restraints excluded: chain e residue 77 LEU Chi-restraints excluded: chain f residue 17 ASN Chi-restraints excluded: chain f residue 34 LYS Chi-restraints excluded: chain f residue 39 ARG Chi-restraints excluded: chain f residue 43 VAL Chi-restraints excluded: chain f residue 90 VAL Chi-restraints excluded: chain f residue 112 GLU Chi-restraints excluded: chain i residue 16 GLN Chi-restraints excluded: chain i residue 49 ASP Chi-restraints excluded: chain k residue 98 VAL Chi-restraints excluded: chain m residue 11 VAL Chi-restraints excluded: chain m residue 33 ARG Chi-restraints excluded: chain m residue 51 VAL Chi-restraints excluded: chain m residue 60 MET Chi-restraints excluded: chain m residue 80 ASP Chi-restraints excluded: chain m residue 91 LEU Chi-restraints excluded: chain m residue 94 ILE Chi-restraints excluded: chain m residue 124 ILE Chi-restraints excluded: chain n residue 15 THR Chi-restraints excluded: chain n residue 26 GLN Chi-restraints excluded: chain n residue 42 ILE Chi-restraints excluded: chain n residue 45 ASN Chi-restraints excluded: chain n residue 55 VAL Chi-restraints excluded: chain o residue 238 ASN Chi-restraints excluded: chain o residue 254 ASP Chi-restraints excluded: chain o residue 275 THR Chi-restraints excluded: chain p residue 43 THR Chi-restraints excluded: chain p residue 45 THR Chi-restraints excluded: chain p residue 50 ILE Chi-restraints excluded: chain p residue 58 LYS Chi-restraints excluded: chain p residue 73 VAL Chi-restraints excluded: chain p residue 90 ARG Chi-restraints excluded: chain p residue 94 CYS Chi-restraints excluded: chain p residue 100 ILE Chi-restraints excluded: chain p residue 102 LEU Chi-restraints excluded: chain q residue 27 VAL Chi-restraints excluded: chain q residue 47 LEU Chi-restraints excluded: chain q residue 51 CYS Chi-restraints excluded: chain q residue 53 ASP Chi-restraints excluded: chain q residue 64 LYS Chi-restraints excluded: chain q residue 81 LEU Chi-restraints excluded: chain q residue 86 ASP Chi-restraints excluded: chain q residue 99 GLU Chi-restraints excluded: chain M residue 6 THR Chi-restraints excluded: chain M residue 17 ILE Chi-restraints excluded: chain M residue 22 THR Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain M residue 54 VAL Chi-restraints excluded: chain M residue 55 THR Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain M residue 106 LEU Chi-restraints excluded: chain M residue 110 ASP Chi-restraints excluded: chain M residue 116 ASN Chi-restraints excluded: chain M residue 119 VAL Chi-restraints excluded: chain M residue 123 THR Chi-restraints excluded: chain M residue 130 THR Chi-restraints excluded: chain h residue 17 ILE Chi-restraints excluded: chain h residue 20 ILE Chi-restraints excluded: chain h residue 29 VAL Chi-restraints excluded: chain h residue 58 THR Chi-restraints excluded: chain h residue 65 THR Chi-restraints excluded: chain h residue 68 THR Chi-restraints excluded: chain h residue 74 SER Chi-restraints excluded: chain h residue 76 THR Chi-restraints excluded: chain h residue 93 SER Chi-restraints excluded: chain h residue 106 ILE Chi-restraints excluded: chain h residue 112 VAL Chi-restraints excluded: chain h residue 113 GLU Chi-restraints excluded: chain h residue 114 VAL Chi-restraints excluded: chain s residue 184 PHE Chi-restraints excluded: chain s residue 194 MET Chi-restraints excluded: chain s residue 220 VAL Chi-restraints excluded: chain s residue 258 ILE Chi-restraints excluded: chain s residue 279 VAL Chi-restraints excluded: chain s residue 282 HIS Chi-restraints excluded: chain s residue 291 LEU Chi-restraints excluded: chain j residue 179 PHE Chi-restraints excluded: chain j residue 267 TYR Chi-restraints excluded: chain j residue 299 VAL Chi-restraints excluded: chain j residue 338 VAL Chi-restraints excluded: chain j residue 357 ILE Chi-restraints excluded: chain g residue 856 ASP Chi-restraints excluded: chain g residue 921 VAL Chi-restraints excluded: chain g residue 962 MET Chi-restraints excluded: chain g residue 978 MET Chi-restraints excluded: chain g residue 985 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1269 random chunks: chunk 1183 optimal weight: 40.0000 chunk 138 optimal weight: 20.0000 chunk 699 optimal weight: 0.5980 chunk 896 optimal weight: 0.9990 chunk 694 optimal weight: 1.9990 chunk 1033 optimal weight: 4.9990 chunk 685 optimal weight: 10.0000 chunk 1223 optimal weight: 1.9990 chunk 765 optimal weight: 0.9990 chunk 745 optimal weight: 10.0000 chunk 564 optimal weight: 20.0000 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 200 ASN ** u 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 423 ASN ** y 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 579 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 51 GLN ** L 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 113 GLN ** Q 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 113 GLN I 62 GLN ** x 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 61 GLN F 130 ASN ** J 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 165 GLN ** V 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 105 GLN ** e 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 139 HIS o 238 ASN o 256 GLN ** p 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 306 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6731 moved from start: 0.4982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 123665 Z= 0.205 Angle : 0.692 17.204 176203 Z= 0.361 Chirality : 0.041 0.428 21730 Planarity : 0.005 0.127 16084 Dihedral : 20.767 179.528 38699 Min Nonbonded Distance : 1.100 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.53 % Favored : 94.45 % Rotamer: Outliers : 4.56 % Allowed : 27.19 % Favored : 68.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.08), residues: 10949 helix: 0.16 (0.08), residues: 4307 sheet: -0.96 (0.13), residues: 1431 loop : -1.93 (0.08), residues: 5211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP m 88 HIS 0.013 0.001 HIS a 66 PHE 0.044 0.002 PHE c 241 TYR 0.041 0.002 TYR i 34 ARG 0.016 0.001 ARG r 88 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21898 Ramachandran restraints generated. 10949 Oldfield, 0 Emsley, 10949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21898 Ramachandran restraints generated. 10949 Oldfield, 0 Emsley, 10949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1582 residues out of total 9800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 315 poor density : 1267 time to evaluate : 8.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASN P 26 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 477 ASN cc_start: 0.5697 (OUTLIER) cc_final: 0.5230 (t0) REVERT: 1 552 LYS cc_start: 0.6726 (tptp) cc_final: 0.6256 (pptt) REVERT: 6 318 THR cc_start: 0.3740 (OUTLIER) cc_final: 0.3369 (p) REVERT: 6 320 MET cc_start: -0.0645 (mmt) cc_final: -0.0987 (mmt) REVERT: 6 347 TRP cc_start: 0.6947 (m-10) cc_final: 0.6366 (m-90) REVERT: 6 353 THR cc_start: 0.6079 (p) cc_final: 0.5851 (p) REVERT: u 246 TRP cc_start: 0.7412 (m100) cc_final: 0.6547 (m100) REVERT: u 306 MET cc_start: 0.7088 (ppp) cc_final: 0.6634 (ppp) REVERT: u 318 MET cc_start: 0.4485 (ptt) cc_final: 0.4200 (ptm) REVERT: v 267 VAL cc_start: 0.6629 (OUTLIER) cc_final: 0.6243 (p) REVERT: S 46 LYS cc_start: 0.8982 (OUTLIER) cc_final: 0.8732 (tppt) REVERT: S 163 ASN cc_start: 0.8098 (t0) cc_final: 0.7302 (p0) REVERT: S 165 GLU cc_start: 0.7794 (mp0) cc_final: 0.7273 (pt0) REVERT: y 116 TYR cc_start: 0.4540 (OUTLIER) cc_final: 0.3842 (t80) REVERT: y 134 ASN cc_start: 0.7638 (m-40) cc_final: 0.7166 (m110) REVERT: G 35 ASP cc_start: 0.6346 (t70) cc_final: 0.5752 (t0) REVERT: H 11 SER cc_start: 0.8955 (p) cc_final: 0.8688 (t) REVERT: H 20 LYS cc_start: 0.8924 (OUTLIER) cc_final: 0.8702 (ptpp) REVERT: L 176 LYS cc_start: 0.8514 (tptp) cc_final: 0.8251 (ttmt) REVERT: L 227 ARG cc_start: 0.8554 (OUTLIER) cc_final: 0.8221 (tmm-80) REVERT: O 38 MET cc_start: 0.7660 (mpp) cc_final: 0.7349 (mtm) REVERT: N 78 SER cc_start: 0.8944 (t) cc_final: 0.8658 (t) REVERT: N 111 GLN cc_start: 0.9369 (pm20) cc_final: 0.9014 (pm20) REVERT: Q 85 ARG cc_start: 0.7681 (mtp85) cc_final: 0.7288 (mtp85) REVERT: Q 96 THR cc_start: 0.8742 (m) cc_final: 0.8370 (p) REVERT: P 45 THR cc_start: 0.8840 (p) cc_final: 0.8509 (t) REVERT: P 70 SER cc_start: 0.8948 (t) cc_final: 0.8486 (m) REVERT: P 124 MET cc_start: 0.8571 (mmm) cc_final: 0.8187 (mtp) REVERT: P 128 ARG cc_start: 0.7908 (OUTLIER) cc_final: 0.7630 (mmt90) REVERT: x 50 TYR cc_start: 0.6650 (OUTLIER) cc_final: 0.6269 (m-10) REVERT: 9 14 LYS cc_start: 0.8255 (ttpt) cc_final: 0.7722 (ttpp) REVERT: B 39 ASN cc_start: 0.8452 (t0) cc_final: 0.7764 (p0) REVERT: B 124 ASP cc_start: 0.8556 (m-30) cc_final: 0.8261 (m-30) REVERT: B 130 GLU cc_start: 0.8413 (tt0) cc_final: 0.8118 (tt0) REVERT: C 23 LEU cc_start: 0.9485 (OUTLIER) cc_final: 0.9258 (mp) REVERT: D 21 GLU cc_start: 0.7614 (mt-10) cc_final: 0.7370 (mt-10) REVERT: D 107 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.8219 (tm-30) REVERT: F 98 LYS cc_start: 0.8506 (OUTLIER) cc_final: 0.8022 (mttt) REVERT: r 4 LEU cc_start: 0.4717 (OUTLIER) cc_final: 0.4079 (tt) REVERT: r 48 LEU cc_start: 0.5354 (OUTLIER) cc_final: 0.4424 (tp) REVERT: r 117 GLU cc_start: 0.4741 (OUTLIER) cc_final: 0.4537 (tm-30) REVERT: J 49 GLU cc_start: 0.7802 (mt-10) cc_final: 0.7303 (mt-10) REVERT: R 105 ASP cc_start: 0.8262 (t0) cc_final: 0.8057 (t0) REVERT: R 111 GLN cc_start: 0.8880 (mt0) cc_final: 0.8477 (mt0) REVERT: R 137 LEU cc_start: 0.5859 (OUTLIER) cc_final: 0.5486 (mm) REVERT: V 72 LEU cc_start: 0.7683 (OUTLIER) cc_final: 0.7370 (tp) REVERT: V 127 ARG cc_start: 0.4627 (tmt170) cc_final: 0.4016 (mmm-85) REVERT: Y 84 ILE cc_start: 0.8450 (mt) cc_final: 0.7697 (tt) REVERT: Z 57 ASN cc_start: 0.7385 (m-40) cc_final: 0.6636 (t0) REVERT: a 3 MET cc_start: 0.0366 (tmm) cc_final: -0.2170 (ppp) REVERT: b 30 TYR cc_start: 0.2541 (OUTLIER) cc_final: 0.0171 (m-80) REVERT: c 102 VAL cc_start: 0.6264 (OUTLIER) cc_final: 0.6047 (m) REVERT: c 126 ASP cc_start: 0.6782 (p0) cc_final: 0.6105 (p0) REVERT: c 220 ASP cc_start: 0.6633 (OUTLIER) cc_final: 0.6271 (m-30) REVERT: f 77 TYR cc_start: 0.3354 (m-80) cc_final: 0.2720 (m-80) REVERT: f 79 ILE cc_start: 0.4631 (mp) cc_final: 0.4418 (tp) REVERT: m 33 ARG cc_start: 0.1338 (OUTLIER) cc_final: -0.0214 (mtm180) REVERT: n 35 MET cc_start: 0.4893 (mmm) cc_final: 0.4138 (tpp) REVERT: p 69 CYS cc_start: 0.8390 (p) cc_final: 0.8059 (p) REVERT: p 84 GLN cc_start: 0.8065 (mt0) cc_final: 0.7767 (mt0) REVERT: p 89 GLN cc_start: 0.8430 (mm-40) cc_final: 0.7725 (mp10) REVERT: M 3 ARG cc_start: 0.8419 (mmt90) cc_final: 0.7671 (mmm-85) REVERT: M 65 PRO cc_start: 0.8058 (Cg_endo) cc_final: 0.7833 (Cg_exo) REVERT: M 70 SER cc_start: 0.7042 (t) cc_final: 0.6770 (m) REVERT: M 77 GLU cc_start: 0.6852 (tm-30) cc_final: 0.6606 (mt-10) REVERT: h 113 GLU cc_start: 0.6672 (OUTLIER) cc_final: 0.6359 (tt0) REVERT: s 306 HIS cc_start: 0.2656 (OUTLIER) cc_final: 0.2174 (t-90) REVERT: j 267 TYR cc_start: 0.4444 (OUTLIER) cc_final: 0.2751 (t80) REVERT: j 292 MET cc_start: 0.1229 (mtm) cc_final: 0.0884 (mmt) REVERT: j 297 PHE cc_start: -0.0349 (m-80) cc_final: -0.1140 (m-80) REVERT: j 302 MET cc_start: 0.1204 (mtt) cc_final: 0.0924 (mmt) REVERT: g 910 MET cc_start: 0.1002 (ptp) cc_final: 0.0721 (ptp) REVERT: g 916 MET cc_start: 0.1326 (ttp) cc_final: 0.1120 (ttt) REVERT: g 962 MET cc_start: 0.3129 (OUTLIER) cc_final: 0.0548 (mmp) REVERT: g 985 LEU cc_start: 0.2225 (OUTLIER) cc_final: 0.1925 (mt) outliers start: 315 outliers final: 218 residues processed: 1476 average time/residue: 1.0222 time to fit residues: 2642.3428 Evaluate side-chains 1427 residues out of total 9800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 244 poor density : 1183 time to evaluate : 7.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 471 SER Chi-restraints excluded: chain 1 residue 477 ASN Chi-restraints excluded: chain 1 residue 494 THR Chi-restraints excluded: chain 6 residue 312 VAL Chi-restraints excluded: chain 6 residue 316 VAL Chi-restraints excluded: chain 6 residue 318 THR Chi-restraints excluded: chain 6 residue 328 THR Chi-restraints excluded: chain 6 residue 338 THR Chi-restraints excluded: chain 6 residue 339 HIS Chi-restraints excluded: chain u residue 17 GLU Chi-restraints excluded: chain u residue 60 ASP Chi-restraints excluded: chain u residue 109 GLN Chi-restraints excluded: chain u residue 121 ILE Chi-restraints excluded: chain u residue 133 SER Chi-restraints excluded: chain u residue 230 LEU Chi-restraints excluded: chain u residue 237 LEU Chi-restraints excluded: chain u residue 242 SER Chi-restraints excluded: chain u residue 394 LEU Chi-restraints excluded: chain u residue 534 LEU Chi-restraints excluded: chain v residue 267 VAL Chi-restraints excluded: chain v residue 278 VAL Chi-restraints excluded: chain v residue 296 VAL Chi-restraints excluded: chain v residue 304 ASP Chi-restraints excluded: chain v residue 315 CYS Chi-restraints excluded: chain v residue 396 ASN Chi-restraints excluded: chain v residue 408 THR Chi-restraints excluded: chain v residue 422 ILE Chi-restraints excluded: chain S residue 46 LYS Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 67 VAL Chi-restraints excluded: chain S residue 114 VAL Chi-restraints excluded: chain S residue 139 SER Chi-restraints excluded: chain S residue 158 VAL Chi-restraints excluded: chain S residue 219 GLU Chi-restraints excluded: chain y residue 63 LEU Chi-restraints excluded: chain y residue 102 VAL Chi-restraints excluded: chain y residue 116 TYR Chi-restraints excluded: chain y residue 157 THR Chi-restraints excluded: chain y residue 475 ASP Chi-restraints excluded: chain y residue 495 THR Chi-restraints excluded: chain y residue 608 LEU Chi-restraints excluded: chain y residue 628 ASP Chi-restraints excluded: chain y residue 677 ILE Chi-restraints excluded: chain y residue 701 HIS Chi-restraints excluded: chain y residue 718 LEU Chi-restraints excluded: chain y residue 748 ASP Chi-restraints excluded: chain y residue 752 CYS Chi-restraints excluded: chain y residue 773 ASP Chi-restraints excluded: chain y residue 798 VAL Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 24 SER Chi-restraints excluded: chain G residue 44 ASN Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain G residue 119 SER Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 164 ASN Chi-restraints excluded: chain H residue 20 LYS Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain K residue 2 GLN Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 21 ASN Chi-restraints excluded: chain K residue 23 ILE Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 80 SER Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 116 THR Chi-restraints excluded: chain L residue 143 CYS Chi-restraints excluded: chain L residue 157 LEU Chi-restraints excluded: chain L residue 172 ASN Chi-restraints excluded: chain L residue 180 VAL Chi-restraints excluded: chain L residue 205 VAL Chi-restraints excluded: chain L residue 206 SER Chi-restraints excluded: chain L residue 225 SER Chi-restraints excluded: chain L residue 227 ARG Chi-restraints excluded: chain L residue 252 THR Chi-restraints excluded: chain O residue 55 THR Chi-restraints excluded: chain O residue 91 VAL Chi-restraints excluded: chain O residue 126 ASP Chi-restraints excluded: chain O residue 127 VAL Chi-restraints excluded: chain O residue 154 SER Chi-restraints excluded: chain O residue 170 GLU Chi-restraints excluded: chain O residue 192 SER Chi-restraints excluded: chain N residue 15 VAL Chi-restraints excluded: chain N residue 35 GLU Chi-restraints excluded: chain N residue 54 THR Chi-restraints excluded: chain N residue 69 GLU Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain N residue 163 CYS Chi-restraints excluded: chain N residue 170 SER Chi-restraints excluded: chain Q residue 12 LYS Chi-restraints excluded: chain Q residue 24 THR Chi-restraints excluded: chain Q residue 44 ILE Chi-restraints excluded: chain Q residue 57 SER Chi-restraints excluded: chain Q residue 64 LEU Chi-restraints excluded: chain Q residue 88 SER Chi-restraints excluded: chain P residue 38 ASN Chi-restraints excluded: chain P residue 47 LEU Chi-restraints excluded: chain P residue 62 VAL Chi-restraints excluded: chain P residue 91 THR Chi-restraints excluded: chain P residue 100 THR Chi-restraints excluded: chain P residue 128 ARG Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain I residue 31 ASP Chi-restraints excluded: chain I residue 69 ASN Chi-restraints excluded: chain x residue 21 VAL Chi-restraints excluded: chain x residue 26 ARG Chi-restraints excluded: chain x residue 27 ASP Chi-restraints excluded: chain x residue 50 TYR Chi-restraints excluded: chain x residue 69 TYR Chi-restraints excluded: chain x residue 369 ILE Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 224 ASN Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain F residue 98 LYS Chi-restraints excluded: chain r residue 4 LEU Chi-restraints excluded: chain r residue 48 LEU Chi-restraints excluded: chain r residue 58 SER Chi-restraints excluded: chain r residue 76 VAL Chi-restraints excluded: chain r residue 106 LYS Chi-restraints excluded: chain r residue 117 GLU Chi-restraints excluded: chain r residue 189 VAL Chi-restraints excluded: chain r residue 227 ILE Chi-restraints excluded: chain r residue 240 THR Chi-restraints excluded: chain r residue 271 VAL Chi-restraints excluded: chain J residue 30 CYS Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain J residue 51 GLU Chi-restraints excluded: chain J residue 84 LYS Chi-restraints excluded: chain J residue 94 LEU Chi-restraints excluded: chain J residue 98 GLN Chi-restraints excluded: chain J residue 121 THR Chi-restraints excluded: chain R residue 89 GLU Chi-restraints excluded: chain R residue 90 LEU Chi-restraints excluded: chain R residue 95 THR Chi-restraints excluded: chain R residue 107 THR Chi-restraints excluded: chain R residue 137 LEU Chi-restraints excluded: chain R residue 182 CYS Chi-restraints excluded: chain T residue 80 ASP Chi-restraints excluded: chain T residue 102 THR Chi-restraints excluded: chain V residue 72 LEU Chi-restraints excluded: chain V residue 82 ASN Chi-restraints excluded: chain V residue 165 ASN Chi-restraints excluded: chain V residue 197 GLU Chi-restraints excluded: chain Y residue 34 VAL Chi-restraints excluded: chain Y residue 47 LEU Chi-restraints excluded: chain Y residue 51 LEU Chi-restraints excluded: chain Z residue 42 THR Chi-restraints excluded: chain Z residue 84 VAL Chi-restraints excluded: chain Z residue 86 LEU Chi-restraints excluded: chain Z residue 103 GLU Chi-restraints excluded: chain Z residue 135 GLU Chi-restraints excluded: chain Z residue 139 SER Chi-restraints excluded: chain Z residue 208 VAL Chi-restraints excluded: chain Z residue 221 THR Chi-restraints excluded: chain a residue 22 VAL Chi-restraints excluded: chain a residue 52 LEU Chi-restraints excluded: chain a residue 64 TRP Chi-restraints excluded: chain a residue 70 TYR Chi-restraints excluded: chain a residue 83 LEU Chi-restraints excluded: chain b residue 20 VAL Chi-restraints excluded: chain b residue 30 TYR Chi-restraints excluded: chain c residue 102 VAL Chi-restraints excluded: chain c residue 109 LEU Chi-restraints excluded: chain c residue 171 ASP Chi-restraints excluded: chain c residue 188 HIS Chi-restraints excluded: chain c residue 197 THR Chi-restraints excluded: chain c residue 220 ASP Chi-restraints excluded: chain c residue 265 ILE Chi-restraints excluded: chain c residue 297 THR Chi-restraints excluded: chain d residue 66 LEU Chi-restraints excluded: chain d residue 96 SER Chi-restraints excluded: chain d residue 107 LEU Chi-restraints excluded: chain e residue 48 VAL Chi-restraints excluded: chain e residue 77 LEU Chi-restraints excluded: chain f residue 17 ASN Chi-restraints excluded: chain f residue 34 LYS Chi-restraints excluded: chain f residue 43 VAL Chi-restraints excluded: chain f residue 112 GLU Chi-restraints excluded: chain i residue 16 GLN Chi-restraints excluded: chain i residue 34 TYR Chi-restraints excluded: chain k residue 98 VAL Chi-restraints excluded: chain k residue 131 PHE Chi-restraints excluded: chain m residue 11 VAL Chi-restraints excluded: chain m residue 33 ARG Chi-restraints excluded: chain m residue 51 VAL Chi-restraints excluded: chain m residue 80 ASP Chi-restraints excluded: chain m residue 91 LEU Chi-restraints excluded: chain m residue 94 ILE Chi-restraints excluded: chain m residue 124 ILE Chi-restraints excluded: chain n residue 45 ASN Chi-restraints excluded: chain n residue 55 VAL Chi-restraints excluded: chain o residue 238 ASN Chi-restraints excluded: chain o residue 254 ASP Chi-restraints excluded: chain o residue 269 TYR Chi-restraints excluded: chain o residue 275 THR Chi-restraints excluded: chain o residue 297 ILE Chi-restraints excluded: chain p residue 43 THR Chi-restraints excluded: chain p residue 58 LYS Chi-restraints excluded: chain p residue 90 ARG Chi-restraints excluded: chain p residue 94 CYS Chi-restraints excluded: chain q residue 47 LEU Chi-restraints excluded: chain q residue 53 ASP Chi-restraints excluded: chain q residue 81 LEU Chi-restraints excluded: chain q residue 86 ASP Chi-restraints excluded: chain M residue 22 THR Chi-restraints excluded: chain M residue 54 VAL Chi-restraints excluded: chain M residue 55 THR Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain M residue 106 LEU Chi-restraints excluded: chain M residue 110 ASP Chi-restraints excluded: chain h residue 68 THR Chi-restraints excluded: chain h residue 88 LEU Chi-restraints excluded: chain h residue 93 SER Chi-restraints excluded: chain h residue 106 ILE Chi-restraints excluded: chain h residue 113 GLU Chi-restraints excluded: chain h residue 114 VAL Chi-restraints excluded: chain s residue 184 PHE Chi-restraints excluded: chain s residue 187 MET Chi-restraints excluded: chain s residue 194 MET Chi-restraints excluded: chain s residue 232 GLN Chi-restraints excluded: chain s residue 279 VAL Chi-restraints excluded: chain s residue 282 HIS Chi-restraints excluded: chain s residue 306 HIS Chi-restraints excluded: chain j residue 238 LYS Chi-restraints excluded: chain j residue 246 ILE Chi-restraints excluded: chain j residue 267 TYR Chi-restraints excluded: chain j residue 299 VAL Chi-restraints excluded: chain j residue 338 VAL Chi-restraints excluded: chain j residue 357 ILE Chi-restraints excluded: chain j residue 371 VAL Chi-restraints excluded: chain g residue 962 MET Chi-restraints excluded: chain g residue 985 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1269 random chunks: chunk 756 optimal weight: 20.0000 chunk 488 optimal weight: 0.6980 chunk 730 optimal weight: 5.9990 chunk 368 optimal weight: 30.0000 chunk 240 optimal weight: 0.2980 chunk 236 optimal weight: 0.8980 chunk 777 optimal weight: 8.9990 chunk 833 optimal weight: 3.9990 chunk 604 optimal weight: 30.0000 chunk 113 optimal weight: 30.0000 chunk 961 optimal weight: 0.9980 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 448 GLN ** v 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 241 GLN ** v 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 579 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 136 HIS O 186 ASN N 113 GLN ** x 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 61 GLN ** J 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 106 GLN V 82 ASN V 179 ASN V 186 ASN ** V 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 159 HIS ** a 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 238 ASN ** p 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 306 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6723 moved from start: 0.5143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 123665 Z= 0.208 Angle : 0.675 16.966 176203 Z= 0.352 Chirality : 0.040 0.383 21730 Planarity : 0.005 0.130 16084 Dihedral : 20.629 179.832 38699 Min Nonbonded Distance : 1.066 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.07 % Favored : 93.91 % Rotamer: Outliers : 4.15 % Allowed : 28.01 % Favored : 67.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.20 (0.08), residues: 10949 helix: 0.41 (0.08), residues: 4307 sheet: -0.92 (0.13), residues: 1442 loop : -1.82 (0.08), residues: 5200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.077 0.002 TRP u 149 HIS 0.048 0.001 HIS s 306 PHE 0.027 0.002 PHE c 241 TYR 0.045 0.002 TYR f 40 ARG 0.012 0.000 ARG s 308 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21898 Ramachandran restraints generated. 10949 Oldfield, 0 Emsley, 10949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21898 Ramachandran restraints generated. 10949 Oldfield, 0 Emsley, 10949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1521 residues out of total 9800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 287 poor density : 1234 time to evaluate : 7.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASN P 26 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 477 ASN cc_start: 0.5667 (m-40) cc_final: 0.5241 (t0) REVERT: 1 552 LYS cc_start: 0.6729 (tptp) cc_final: 0.6235 (pptt) REVERT: 6 318 THR cc_start: 0.3776 (OUTLIER) cc_final: 0.3424 (p) REVERT: 6 319 LYS cc_start: 0.3769 (tptt) cc_final: 0.3171 (tptp) REVERT: 6 320 MET cc_start: -0.0406 (mmt) cc_final: -0.0761 (mmt) REVERT: 6 347 TRP cc_start: 0.6790 (m-10) cc_final: 0.6296 (m-90) REVERT: 6 353 THR cc_start: 0.6012 (p) cc_final: 0.5801 (p) REVERT: u 246 TRP cc_start: 0.7405 (m100) cc_final: 0.6485 (m100) REVERT: u 306 MET cc_start: 0.7037 (ppp) cc_final: 0.6501 (ppp) REVERT: v 267 VAL cc_start: 0.6565 (OUTLIER) cc_final: 0.6149 (p) REVERT: S 163 ASN cc_start: 0.8025 (t0) cc_final: 0.7272 (p0) REVERT: S 165 GLU cc_start: 0.7952 (mp0) cc_final: 0.7373 (pt0) REVERT: y 116 TYR cc_start: 0.4564 (OUTLIER) cc_final: 0.3818 (t80) REVERT: y 134 ASN cc_start: 0.7674 (m-40) cc_final: 0.7187 (m110) REVERT: y 384 ASP cc_start: 0.7319 (t0) cc_final: 0.7004 (t0) REVERT: y 412 LEU cc_start: 0.8138 (mm) cc_final: 0.7870 (tp) REVERT: y 559 ASP cc_start: 0.5537 (t0) cc_final: 0.4980 (p0) REVERT: y 571 CYS cc_start: 0.8058 (m) cc_final: 0.7656 (m) REVERT: G 35 ASP cc_start: 0.6237 (t70) cc_final: 0.5636 (t0) REVERT: H 11 SER cc_start: 0.8918 (p) cc_final: 0.8672 (t) REVERT: H 20 LYS cc_start: 0.8872 (OUTLIER) cc_final: 0.8575 (ptpp) REVERT: H 34 ASP cc_start: 0.7503 (m-30) cc_final: 0.7284 (m-30) REVERT: L 133 TYR cc_start: 0.9195 (m-80) cc_final: 0.8964 (m-80) REVERT: L 176 LYS cc_start: 0.8310 (tptp) cc_final: 0.8047 (ttmt) REVERT: L 227 ARG cc_start: 0.8556 (OUTLIER) cc_final: 0.8336 (tmm-80) REVERT: O 38 MET cc_start: 0.7628 (mpp) cc_final: 0.7350 (mtm) REVERT: N 73 ASP cc_start: 0.8016 (m-30) cc_final: 0.7803 (m-30) REVERT: N 78 SER cc_start: 0.8994 (t) cc_final: 0.8587 (t) REVERT: N 111 GLN cc_start: 0.9379 (pm20) cc_final: 0.9048 (pm20) REVERT: Q 85 ARG cc_start: 0.7644 (mtp85) cc_final: 0.7383 (mtp85) REVERT: Q 96 THR cc_start: 0.8764 (m) cc_final: 0.8397 (p) REVERT: P 45 THR cc_start: 0.8739 (p) cc_final: 0.8494 (t) REVERT: P 128 ARG cc_start: 0.7962 (OUTLIER) cc_final: 0.7656 (mmt90) REVERT: x 28 MET cc_start: 0.6197 (tpp) cc_final: 0.5946 (tpp) REVERT: x 50 TYR cc_start: 0.6654 (OUTLIER) cc_final: 0.6158 (m-10) REVERT: x 302 GLU cc_start: 0.4568 (tm-30) cc_final: 0.3366 (mt-10) REVERT: B 39 ASN cc_start: 0.8448 (t0) cc_final: 0.7842 (p0) REVERT: B 124 ASP cc_start: 0.8554 (m-30) cc_final: 0.8259 (m-30) REVERT: B 130 GLU cc_start: 0.8437 (tt0) cc_final: 0.8106 (tt0) REVERT: C 23 LEU cc_start: 0.9483 (OUTLIER) cc_final: 0.9234 (mp) REVERT: D 107 GLU cc_start: 0.8717 (mm-30) cc_final: 0.8269 (tm-30) REVERT: r 4 LEU cc_start: 0.4559 (OUTLIER) cc_final: 0.3871 (tt) REVERT: r 48 LEU cc_start: 0.4788 (OUTLIER) cc_final: 0.4170 (tp) REVERT: r 117 GLU cc_start: 0.4803 (OUTLIER) cc_final: 0.4554 (tm-30) REVERT: R 105 ASP cc_start: 0.8250 (t0) cc_final: 0.8047 (t0) REVERT: R 111 GLN cc_start: 0.8867 (mt0) cc_final: 0.8451 (mt0) REVERT: R 137 LEU cc_start: 0.5798 (OUTLIER) cc_final: 0.5389 (mm) REVERT: Y 84 ILE cc_start: 0.8448 (mt) cc_final: 0.7662 (tt) REVERT: Z 57 ASN cc_start: 0.7418 (OUTLIER) cc_final: 0.6717 (t0) REVERT: Z 202 LYS cc_start: 0.8767 (OUTLIER) cc_final: 0.8552 (ptpp) REVERT: a 2 LEU cc_start: 0.3554 (pt) cc_final: 0.2494 (mt) REVERT: a 3 MET cc_start: 0.0379 (tmm) cc_final: -0.2107 (ppp) REVERT: b 30 TYR cc_start: 0.2507 (OUTLIER) cc_final: 0.0186 (m-80) REVERT: c 102 VAL cc_start: 0.6053 (OUTLIER) cc_final: 0.5842 (m) REVERT: c 126 ASP cc_start: 0.6632 (p0) cc_final: 0.5933 (p0) REVERT: c 220 ASP cc_start: 0.6480 (OUTLIER) cc_final: 0.6069 (m-30) REVERT: f 71 MET cc_start: 0.7322 (tmm) cc_final: 0.7057 (tmm) REVERT: f 77 TYR cc_start: 0.3089 (m-80) cc_final: 0.2563 (m-80) REVERT: f 79 ILE cc_start: 0.5001 (mp) cc_final: 0.4589 (tp) REVERT: i 27 ARG cc_start: 0.7132 (mtt-85) cc_final: 0.5809 (mtt90) REVERT: i 44 ARG cc_start: 0.8499 (mmm160) cc_final: 0.8132 (tpt-90) REVERT: k 140 TYR cc_start: -0.2106 (OUTLIER) cc_final: -0.2433 (t80) REVERT: m 33 ARG cc_start: 0.1155 (OUTLIER) cc_final: -0.0300 (mtm180) REVERT: n 35 MET cc_start: 0.4892 (mmm) cc_final: 0.4073 (tpp) REVERT: p 69 CYS cc_start: 0.8302 (p) cc_final: 0.7966 (p) REVERT: p 89 GLN cc_start: 0.8413 (mm-40) cc_final: 0.7710 (mp10) REVERT: M 3 ARG cc_start: 0.8432 (mmt90) cc_final: 0.7678 (mmm-85) REVERT: M 65 PRO cc_start: 0.8083 (Cg_endo) cc_final: 0.7816 (Cg_exo) REVERT: M 70 SER cc_start: 0.7073 (t) cc_final: 0.6837 (p) REVERT: M 105 MET cc_start: 0.8600 (ttp) cc_final: 0.8312 (tmm) REVERT: h 113 GLU cc_start: 0.6676 (OUTLIER) cc_final: 0.5987 (tm-30) REVERT: s 204 MET cc_start: 0.3769 (ptt) cc_final: 0.3112 (mtm) REVERT: s 232 GLN cc_start: 0.4816 (OUTLIER) cc_final: 0.4390 (tt0) REVERT: j 267 TYR cc_start: 0.4450 (OUTLIER) cc_final: 0.2869 (t80) REVERT: j 292 MET cc_start: 0.1163 (mtm) cc_final: 0.0799 (mmt) REVERT: j 302 MET cc_start: 0.1148 (mtt) cc_final: 0.0776 (mmt) REVERT: g 910 MET cc_start: 0.1006 (ptp) cc_final: 0.0709 (ptp) REVERT: g 962 MET cc_start: 0.3091 (OUTLIER) cc_final: 0.0452 (mmp) REVERT: g 985 LEU cc_start: 0.2083 (OUTLIER) cc_final: 0.1795 (mt) outliers start: 287 outliers final: 221 residues processed: 1427 average time/residue: 0.9731 time to fit residues: 2434.4917 Evaluate side-chains 1432 residues out of total 9800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 245 poor density : 1187 time to evaluate : 7.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 471 SER Chi-restraints excluded: chain 1 residue 494 THR Chi-restraints excluded: chain 1 residue 543 ASN Chi-restraints excluded: chain 6 residue 312 VAL Chi-restraints excluded: chain 6 residue 316 VAL Chi-restraints excluded: chain 6 residue 318 THR Chi-restraints excluded: chain 6 residue 328 THR Chi-restraints excluded: chain 6 residue 338 THR Chi-restraints excluded: chain 6 residue 339 HIS Chi-restraints excluded: chain u residue 60 ASP Chi-restraints excluded: chain u residue 109 GLN Chi-restraints excluded: chain u residue 121 ILE Chi-restraints excluded: chain u residue 133 SER Chi-restraints excluded: chain u residue 230 LEU Chi-restraints excluded: chain u residue 237 LEU Chi-restraints excluded: chain u residue 242 SER Chi-restraints excluded: chain u residue 394 LEU Chi-restraints excluded: chain u residue 534 LEU Chi-restraints excluded: chain v residue 223 PHE Chi-restraints excluded: chain v residue 267 VAL Chi-restraints excluded: chain v residue 278 VAL Chi-restraints excluded: chain v residue 296 VAL Chi-restraints excluded: chain v residue 304 ASP Chi-restraints excluded: chain v residue 315 CYS Chi-restraints excluded: chain v residue 396 ASN Chi-restraints excluded: chain v residue 408 THR Chi-restraints excluded: chain v residue 422 ILE Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 67 VAL Chi-restraints excluded: chain S residue 114 VAL Chi-restraints excluded: chain S residue 158 VAL Chi-restraints excluded: chain S residue 219 GLU Chi-restraints excluded: chain y residue 63 LEU Chi-restraints excluded: chain y residue 102 VAL Chi-restraints excluded: chain y residue 116 TYR Chi-restraints excluded: chain y residue 157 THR Chi-restraints excluded: chain y residue 330 ILE Chi-restraints excluded: chain y residue 495 THR Chi-restraints excluded: chain y residue 499 VAL Chi-restraints excluded: chain y residue 543 ASP Chi-restraints excluded: chain y residue 608 LEU Chi-restraints excluded: chain y residue 628 ASP Chi-restraints excluded: chain y residue 677 ILE Chi-restraints excluded: chain y residue 701 HIS Chi-restraints excluded: chain y residue 718 LEU Chi-restraints excluded: chain y residue 748 ASP Chi-restraints excluded: chain y residue 752 CYS Chi-restraints excluded: chain y residue 773 ASP Chi-restraints excluded: chain y residue 798 VAL Chi-restraints excluded: chain y residue 847 THR Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 27 LEU Chi-restraints excluded: chain G residue 44 ASN Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain G residue 119 SER Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 164 ASN Chi-restraints excluded: chain G residue 180 LEU Chi-restraints excluded: chain H residue 20 LYS Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain K residue 2 GLN Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 21 ASN Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 80 SER Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain L residue 116 THR Chi-restraints excluded: chain L residue 141 VAL Chi-restraints excluded: chain L residue 143 CYS Chi-restraints excluded: chain L residue 157 LEU Chi-restraints excluded: chain L residue 172 ASN Chi-restraints excluded: chain L residue 180 VAL Chi-restraints excluded: chain L residue 205 VAL Chi-restraints excluded: chain L residue 206 SER Chi-restraints excluded: chain L residue 225 SER Chi-restraints excluded: chain L residue 227 ARG Chi-restraints excluded: chain L residue 260 VAL Chi-restraints excluded: chain O residue 55 THR Chi-restraints excluded: chain O residue 91 VAL Chi-restraints excluded: chain O residue 126 ASP Chi-restraints excluded: chain O residue 127 VAL Chi-restraints excluded: chain O residue 131 ASP Chi-restraints excluded: chain O residue 153 THR Chi-restraints excluded: chain O residue 154 SER Chi-restraints excluded: chain O residue 170 GLU Chi-restraints excluded: chain N residue 54 THR Chi-restraints excluded: chain N residue 69 GLU Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain N residue 147 LEU Chi-restraints excluded: chain N residue 170 SER Chi-restraints excluded: chain Q residue 2 THR Chi-restraints excluded: chain Q residue 12 LYS Chi-restraints excluded: chain Q residue 24 THR Chi-restraints excluded: chain Q residue 64 LEU Chi-restraints excluded: chain Q residue 88 SER Chi-restraints excluded: chain P residue 38 ASN Chi-restraints excluded: chain P residue 62 VAL Chi-restraints excluded: chain P residue 100 THR Chi-restraints excluded: chain P residue 128 ARG Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain I residue 31 ASP Chi-restraints excluded: chain I residue 69 ASN Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain x residue 21 VAL Chi-restraints excluded: chain x residue 26 ARG Chi-restraints excluded: chain x residue 50 TYR Chi-restraints excluded: chain x residue 69 TYR Chi-restraints excluded: chain x residue 369 ILE Chi-restraints excluded: chain 9 residue 9 ARG Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 142 HIS Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 224 ASN Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 152 ASP Chi-restraints excluded: chain E residue 26 GLN Chi-restraints excluded: chain E residue 105 PHE Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain r residue 4 LEU Chi-restraints excluded: chain r residue 13 PHE Chi-restraints excluded: chain r residue 48 LEU Chi-restraints excluded: chain r residue 58 SER Chi-restraints excluded: chain r residue 76 VAL Chi-restraints excluded: chain r residue 106 LYS Chi-restraints excluded: chain r residue 117 GLU Chi-restraints excluded: chain r residue 189 VAL Chi-restraints excluded: chain r residue 227 ILE Chi-restraints excluded: chain r residue 240 THR Chi-restraints excluded: chain r residue 271 VAL Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain J residue 84 LYS Chi-restraints excluded: chain J residue 94 LEU Chi-restraints excluded: chain J residue 98 GLN Chi-restraints excluded: chain J residue 121 THR Chi-restraints excluded: chain R residue 29 LEU Chi-restraints excluded: chain R residue 89 GLU Chi-restraints excluded: chain R residue 90 LEU Chi-restraints excluded: chain R residue 95 THR Chi-restraints excluded: chain R residue 137 LEU Chi-restraints excluded: chain R residue 182 CYS Chi-restraints excluded: chain R residue 184 ARG Chi-restraints excluded: chain T residue 27 VAL Chi-restraints excluded: chain T residue 80 ASP Chi-restraints excluded: chain T residue 102 THR Chi-restraints excluded: chain V residue 165 ASN Chi-restraints excluded: chain V residue 197 GLU Chi-restraints excluded: chain Y residue 12 VAL Chi-restraints excluded: chain Y residue 32 ILE Chi-restraints excluded: chain Y residue 34 VAL Chi-restraints excluded: chain Y residue 51 LEU Chi-restraints excluded: chain Z residue 41 VAL Chi-restraints excluded: chain Z residue 42 THR Chi-restraints excluded: chain Z residue 57 ASN Chi-restraints excluded: chain Z residue 84 VAL Chi-restraints excluded: chain Z residue 86 LEU Chi-restraints excluded: chain Z residue 103 GLU Chi-restraints excluded: chain Z residue 139 SER Chi-restraints excluded: chain Z residue 202 LYS Chi-restraints excluded: chain Z residue 208 VAL Chi-restraints excluded: chain Z residue 221 THR Chi-restraints excluded: chain a residue 13 GLU Chi-restraints excluded: chain a residue 52 LEU Chi-restraints excluded: chain a residue 64 TRP Chi-restraints excluded: chain a residue 70 TYR Chi-restraints excluded: chain a residue 89 ILE Chi-restraints excluded: chain b residue 20 VAL Chi-restraints excluded: chain b residue 30 TYR Chi-restraints excluded: chain c residue 102 VAL Chi-restraints excluded: chain c residue 109 LEU Chi-restraints excluded: chain c residue 171 ASP Chi-restraints excluded: chain c residue 188 HIS Chi-restraints excluded: chain c residue 220 ASP Chi-restraints excluded: chain c residue 265 ILE Chi-restraints excluded: chain c residue 297 THR Chi-restraints excluded: chain d residue 107 LEU Chi-restraints excluded: chain e residue 48 VAL Chi-restraints excluded: chain e residue 51 ASP Chi-restraints excluded: chain e residue 77 LEU Chi-restraints excluded: chain f residue 17 ASN Chi-restraints excluded: chain f residue 43 VAL Chi-restraints excluded: chain f residue 90 VAL Chi-restraints excluded: chain f residue 112 GLU Chi-restraints excluded: chain i residue 16 GLN Chi-restraints excluded: chain i residue 49 ASP Chi-restraints excluded: chain k residue 98 VAL Chi-restraints excluded: chain k residue 140 TYR Chi-restraints excluded: chain m residue 11 VAL Chi-restraints excluded: chain m residue 33 ARG Chi-restraints excluded: chain m residue 51 VAL Chi-restraints excluded: chain m residue 80 ASP Chi-restraints excluded: chain m residue 91 LEU Chi-restraints excluded: chain m residue 94 ILE Chi-restraints excluded: chain m residue 124 ILE Chi-restraints excluded: chain n residue 45 ASN Chi-restraints excluded: chain n residue 55 VAL Chi-restraints excluded: chain o residue 238 ASN Chi-restraints excluded: chain o residue 254 ASP Chi-restraints excluded: chain o residue 269 TYR Chi-restraints excluded: chain o residue 275 THR Chi-restraints excluded: chain o residue 297 ILE Chi-restraints excluded: chain p residue 43 THR Chi-restraints excluded: chain p residue 58 LYS Chi-restraints excluded: chain p residue 90 ARG Chi-restraints excluded: chain p residue 94 CYS Chi-restraints excluded: chain q residue 27 VAL Chi-restraints excluded: chain q residue 47 LEU Chi-restraints excluded: chain q residue 53 ASP Chi-restraints excluded: chain q residue 55 VAL Chi-restraints excluded: chain q residue 64 LYS Chi-restraints excluded: chain q residue 81 LEU Chi-restraints excluded: chain q residue 86 ASP Chi-restraints excluded: chain M residue 17 ILE Chi-restraints excluded: chain M residue 22 THR Chi-restraints excluded: chain M residue 54 VAL Chi-restraints excluded: chain M residue 55 THR Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain M residue 106 LEU Chi-restraints excluded: chain M residue 110 ASP Chi-restraints excluded: chain h residue 68 THR Chi-restraints excluded: chain h residue 93 SER Chi-restraints excluded: chain h residue 106 ILE Chi-restraints excluded: chain h residue 113 GLU Chi-restraints excluded: chain h residue 114 VAL Chi-restraints excluded: chain s residue 184 PHE Chi-restraints excluded: chain s residue 187 MET Chi-restraints excluded: chain s residue 194 MET Chi-restraints excluded: chain s residue 232 GLN Chi-restraints excluded: chain s residue 282 HIS Chi-restraints excluded: chain j residue 246 ILE Chi-restraints excluded: chain j residue 267 TYR Chi-restraints excluded: chain j residue 357 ILE Chi-restraints excluded: chain g residue 962 MET Chi-restraints excluded: chain g residue 985 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1269 random chunks: chunk 1112 optimal weight: 0.2980 chunk 1171 optimal weight: 20.0000 chunk 1069 optimal weight: 0.9980 chunk 1139 optimal weight: 0.5980 chunk 686 optimal weight: 10.0000 chunk 496 optimal weight: 1.9990 chunk 895 optimal weight: 0.0670 chunk 349 optimal weight: 40.0000 chunk 1029 optimal weight: 4.9990 chunk 1077 optimal weight: 9.9990 chunk 1135 optimal weight: 0.9990 overall best weight: 0.5920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 579 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 GLN ** G 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 235 ASN ** L 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 113 GLN P 113 GLN ** x 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 ASN E 110 HIS ** J 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 101 HIS V 186 ASN ** a 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 305 ASN ** e 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 89 GLN ** f 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 29 GLN o 238 ASN ** p 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 76 HIS p 84 GLN M 93 GLN ** s 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 293 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6658 moved from start: 0.5285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 123665 Z= 0.157 Angle : 0.656 17.098 176203 Z= 0.342 Chirality : 0.039 0.420 21730 Planarity : 0.005 0.125 16084 Dihedral : 20.533 179.110 38697 Min Nonbonded Distance : 1.172 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.86 % Favored : 95.11 % Rotamer: Outliers : 3.03 % Allowed : 29.27 % Favored : 67.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.08), residues: 10949 helix: 0.60 (0.08), residues: 4347 sheet: -0.77 (0.13), residues: 1421 loop : -1.71 (0.08), residues: 5181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.002 TRP u 149 HIS 0.011 0.001 HIS j 293 PHE 0.044 0.001 PHE c 65 TYR 0.039 0.001 TYR i 34 ARG 0.014 0.000 ARG b 18 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21898 Ramachandran restraints generated. 10949 Oldfield, 0 Emsley, 10949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21898 Ramachandran restraints generated. 10949 Oldfield, 0 Emsley, 10949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1491 residues out of total 9800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 209 poor density : 1282 time to evaluate : 7.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASN P 26 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 477 ASN cc_start: 0.5707 (m-40) cc_final: 0.5293 (t0) REVERT: 1 552 LYS cc_start: 0.6658 (tptp) cc_final: 0.6131 (pptt) REVERT: 6 318 THR cc_start: 0.3682 (OUTLIER) cc_final: 0.3326 (p) REVERT: 6 320 MET cc_start: -0.0415 (mmt) cc_final: -0.0800 (mmt) REVERT: 6 347 TRP cc_start: 0.6764 (m-10) cc_final: 0.6367 (m-90) REVERT: 6 353 THR cc_start: 0.6043 (p) cc_final: 0.5829 (p) REVERT: u 246 TRP cc_start: 0.7212 (m100) cc_final: 0.6525 (m100) REVERT: u 268 LYS cc_start: 0.6803 (tmtt) cc_final: 0.6175 (mttt) REVERT: u 306 MET cc_start: 0.7044 (ppp) cc_final: 0.6601 (ppp) REVERT: v 267 VAL cc_start: 0.6461 (OUTLIER) cc_final: 0.6107 (p) REVERT: v 362 MET cc_start: 0.4876 (tmm) cc_final: 0.4628 (tmm) REVERT: S 163 ASN cc_start: 0.7982 (t0) cc_final: 0.7243 (p0) REVERT: S 165 GLU cc_start: 0.7867 (mp0) cc_final: 0.7296 (pt0) REVERT: y 116 TYR cc_start: 0.4617 (OUTLIER) cc_final: 0.3742 (t80) REVERT: y 134 ASN cc_start: 0.7650 (m-40) cc_final: 0.7183 (m110) REVERT: y 384 ASP cc_start: 0.7307 (t0) cc_final: 0.7034 (t0) REVERT: y 519 HIS cc_start: 0.6853 (m90) cc_final: 0.5836 (t70) REVERT: y 571 CYS cc_start: 0.7976 (m) cc_final: 0.7555 (m) REVERT: G 35 ASP cc_start: 0.6144 (t70) cc_final: 0.5546 (t0) REVERT: H 11 SER cc_start: 0.8939 (p) cc_final: 0.8686 (t) REVERT: H 20 LYS cc_start: 0.8723 (OUTLIER) cc_final: 0.8463 (ptpp) REVERT: L 105 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7829 (tt0) REVERT: L 176 LYS cc_start: 0.8232 (tptp) cc_final: 0.8006 (ttpt) REVERT: L 205 VAL cc_start: 0.9033 (OUTLIER) cc_final: 0.8736 (m) REVERT: L 215 MET cc_start: 0.8357 (ptp) cc_final: 0.8138 (mtp) REVERT: O 38 MET cc_start: 0.7656 (mpp) cc_final: 0.7313 (mtm) REVERT: O 95 ASN cc_start: 0.7488 (t0) cc_final: 0.7208 (t0) REVERT: O 146 ARG cc_start: 0.8584 (mtp85) cc_final: 0.8128 (mmp80) REVERT: N 40 LYS cc_start: 0.8286 (ttmt) cc_final: 0.7971 (ttmm) REVERT: N 58 LEU cc_start: 0.9402 (tp) cc_final: 0.9082 (tt) REVERT: N 73 ASP cc_start: 0.7888 (m-30) cc_final: 0.7649 (m-30) REVERT: N 78 SER cc_start: 0.9003 (t) cc_final: 0.8731 (t) REVERT: N 111 GLN cc_start: 0.9313 (pm20) cc_final: 0.9016 (pm20) REVERT: Q 85 ARG cc_start: 0.7554 (mtp85) cc_final: 0.7216 (mtp85) REVERT: Q 89 ARG cc_start: 0.8438 (tmm-80) cc_final: 0.8032 (ttm170) REVERT: Q 96 THR cc_start: 0.8807 (m) cc_final: 0.8453 (p) REVERT: P 45 THR cc_start: 0.8818 (p) cc_final: 0.8543 (t) REVERT: P 132 VAL cc_start: 0.8856 (p) cc_final: 0.8605 (t) REVERT: x 26 ARG cc_start: 0.5565 (OUTLIER) cc_final: 0.3043 (ptt-90) REVERT: x 50 TYR cc_start: 0.6781 (OUTLIER) cc_final: 0.6179 (m-10) REVERT: x 302 GLU cc_start: 0.4523 (tm-30) cc_final: 0.3340 (mt-10) REVERT: B 39 ASN cc_start: 0.8377 (t0) cc_final: 0.7708 (p0) REVERT: B 124 ASP cc_start: 0.8533 (m-30) cc_final: 0.8204 (m-30) REVERT: B 130 GLU cc_start: 0.8464 (tt0) cc_final: 0.8121 (tt0) REVERT: C 23 LEU cc_start: 0.9425 (OUTLIER) cc_final: 0.9200 (mp) REVERT: C 251 GLU cc_start: 0.8378 (tm-30) cc_final: 0.8087 (tm-30) REVERT: D 21 GLU cc_start: 0.7525 (mt-10) cc_final: 0.7237 (mt-10) REVERT: D 89 GLU cc_start: 0.8452 (mp0) cc_final: 0.8129 (mp0) REVERT: D 107 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.8234 (tm-30) REVERT: E 25 LYS cc_start: 0.8948 (tttt) cc_final: 0.8640 (tppt) REVERT: E 110 HIS cc_start: 0.8123 (t-90) cc_final: 0.7810 (t-90) REVERT: r 4 LEU cc_start: 0.4413 (OUTLIER) cc_final: 0.3790 (tt) REVERT: r 48 LEU cc_start: 0.4843 (OUTLIER) cc_final: 0.4109 (tp) REVERT: R 7 ASN cc_start: 0.8320 (p0) cc_final: 0.8098 (p0) REVERT: R 111 GLN cc_start: 0.8887 (mt0) cc_final: 0.8465 (mt0) REVERT: V 97 PHE cc_start: 0.2548 (t80) cc_final: 0.2179 (t80) REVERT: Z 22 ASN cc_start: 0.7052 (m-40) cc_final: 0.6665 (t0) REVERT: Z 57 ASN cc_start: 0.7269 (m-40) cc_final: 0.6659 (t0) REVERT: a 2 LEU cc_start: 0.3764 (pt) cc_final: 0.2865 (mt) REVERT: a 3 MET cc_start: 0.0048 (tmm) cc_final: -0.2370 (ppp) REVERT: b 30 TYR cc_start: 0.2188 (OUTLIER) cc_final: 0.0061 (m-80) REVERT: c 107 ASP cc_start: 0.5834 (m-30) cc_final: 0.5509 (m-30) REVERT: c 126 ASP cc_start: 0.6456 (p0) cc_final: 0.5738 (p0) REVERT: c 220 ASP cc_start: 0.6562 (OUTLIER) cc_final: 0.6194 (m-30) REVERT: f 114 LEU cc_start: 0.6403 (mm) cc_final: 0.6201 (mm) REVERT: i 44 ARG cc_start: 0.8396 (mmm160) cc_final: 0.7834 (tpt-90) REVERT: k 140 TYR cc_start: -0.2038 (OUTLIER) cc_final: -0.2514 (t80) REVERT: m 33 ARG cc_start: 0.0845 (OUTLIER) cc_final: -0.0374 (mtm180) REVERT: n 35 MET cc_start: 0.4995 (mmm) cc_final: 0.4162 (tpp) REVERT: o 256 GLN cc_start: 0.4257 (OUTLIER) cc_final: 0.4034 (tm-30) REVERT: p 69 CYS cc_start: 0.8207 (p) cc_final: 0.7829 (p) REVERT: p 89 GLN cc_start: 0.8448 (mm-40) cc_final: 0.7784 (mp10) REVERT: p 96 PHE cc_start: 0.8819 (t80) cc_final: 0.8529 (t80) REVERT: p 108 LEU cc_start: 0.7759 (pt) cc_final: 0.7484 (pt) REVERT: M 65 PRO cc_start: 0.7996 (Cg_endo) cc_final: 0.7738 (Cg_exo) REVERT: h 66 ARG cc_start: 0.6776 (mmm-85) cc_final: 0.6501 (mmm-85) REVERT: h 113 GLU cc_start: 0.6650 (OUTLIER) cc_final: 0.5864 (tm-30) REVERT: s 204 MET cc_start: 0.3664 (ptt) cc_final: 0.3029 (mtm) REVERT: s 232 GLN cc_start: 0.4829 (OUTLIER) cc_final: 0.4278 (tt0) REVERT: j 201 GLN cc_start: 0.1889 (mm-40) cc_final: 0.0262 (tp-100) REVERT: j 267 TYR cc_start: 0.4033 (OUTLIER) cc_final: 0.2442 (t80) REVERT: g 962 MET cc_start: 0.3062 (OUTLIER) cc_final: 0.0360 (mmp) REVERT: g 985 LEU cc_start: 0.1830 (OUTLIER) cc_final: 0.1577 (mt) outliers start: 209 outliers final: 151 residues processed: 1416 average time/residue: 0.9802 time to fit residues: 2423.3159 Evaluate side-chains 1368 residues out of total 9800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 1195 time to evaluate : 7.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 471 SER Chi-restraints excluded: chain 1 residue 515 CYS Chi-restraints excluded: chain 1 residue 543 ASN Chi-restraints excluded: chain 6 residue 312 VAL Chi-restraints excluded: chain 6 residue 316 VAL Chi-restraints excluded: chain 6 residue 318 THR Chi-restraints excluded: chain 6 residue 328 THR Chi-restraints excluded: chain 6 residue 339 HIS Chi-restraints excluded: chain u residue 60 ASP Chi-restraints excluded: chain u residue 109 GLN Chi-restraints excluded: chain u residue 121 ILE Chi-restraints excluded: chain u residue 133 SER Chi-restraints excluded: chain u residue 230 LEU Chi-restraints excluded: chain u residue 237 LEU Chi-restraints excluded: chain u residue 242 SER Chi-restraints excluded: chain u residue 394 LEU Chi-restraints excluded: chain v residue 267 VAL Chi-restraints excluded: chain v residue 278 VAL Chi-restraints excluded: chain v residue 296 VAL Chi-restraints excluded: chain v residue 396 ASN Chi-restraints excluded: chain v residue 408 THR Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 158 VAL Chi-restraints excluded: chain S residue 180 VAL Chi-restraints excluded: chain S residue 219 GLU Chi-restraints excluded: chain y residue 63 LEU Chi-restraints excluded: chain y residue 76 VAL Chi-restraints excluded: chain y residue 102 VAL Chi-restraints excluded: chain y residue 116 TYR Chi-restraints excluded: chain y residue 495 THR Chi-restraints excluded: chain y residue 499 VAL Chi-restraints excluded: chain y residue 543 ASP Chi-restraints excluded: chain y residue 628 ASP Chi-restraints excluded: chain y residue 677 ILE Chi-restraints excluded: chain y residue 701 HIS Chi-restraints excluded: chain y residue 718 LEU Chi-restraints excluded: chain y residue 748 ASP Chi-restraints excluded: chain y residue 752 CYS Chi-restraints excluded: chain y residue 773 ASP Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 44 ASN Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 164 ASN Chi-restraints excluded: chain H residue 20 LYS Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain K residue 2 GLN Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 21 ASN Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain L residue 116 THR Chi-restraints excluded: chain L residue 143 CYS Chi-restraints excluded: chain L residue 157 LEU Chi-restraints excluded: chain L residue 172 ASN Chi-restraints excluded: chain L residue 180 VAL Chi-restraints excluded: chain L residue 205 VAL Chi-restraints excluded: chain L residue 206 SER Chi-restraints excluded: chain L residue 225 SER Chi-restraints excluded: chain L residue 260 VAL Chi-restraints excluded: chain O residue 55 THR Chi-restraints excluded: chain O residue 91 VAL Chi-restraints excluded: chain O residue 105 LEU Chi-restraints excluded: chain O residue 126 ASP Chi-restraints excluded: chain O residue 127 VAL Chi-restraints excluded: chain O residue 131 ASP Chi-restraints excluded: chain O residue 170 GLU Chi-restraints excluded: chain N residue 69 GLU Chi-restraints excluded: chain N residue 170 SER Chi-restraints excluded: chain Q residue 2 THR Chi-restraints excluded: chain Q residue 12 LYS Chi-restraints excluded: chain Q residue 58 VAL Chi-restraints excluded: chain P residue 38 ASN Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 69 ASN Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain x residue 21 VAL Chi-restraints excluded: chain x residue 26 ARG Chi-restraints excluded: chain x residue 50 TYR Chi-restraints excluded: chain x residue 69 TYR Chi-restraints excluded: chain x residue 369 ILE Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 232 ASN Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 39 ASN Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain E residue 26 GLN Chi-restraints excluded: chain E residue 105 PHE Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain r residue 4 LEU Chi-restraints excluded: chain r residue 13 PHE Chi-restraints excluded: chain r residue 47 LEU Chi-restraints excluded: chain r residue 48 LEU Chi-restraints excluded: chain r residue 58 SER Chi-restraints excluded: chain r residue 76 VAL Chi-restraints excluded: chain r residue 106 LYS Chi-restraints excluded: chain r residue 227 ILE Chi-restraints excluded: chain r residue 240 THR Chi-restraints excluded: chain J residue 84 LYS Chi-restraints excluded: chain J residue 94 LEU Chi-restraints excluded: chain J residue 96 SER Chi-restraints excluded: chain J residue 98 GLN Chi-restraints excluded: chain R residue 29 LEU Chi-restraints excluded: chain R residue 89 GLU Chi-restraints excluded: chain R residue 90 LEU Chi-restraints excluded: chain R residue 95 THR Chi-restraints excluded: chain R residue 184 ARG Chi-restraints excluded: chain T residue 27 VAL Chi-restraints excluded: chain T residue 80 ASP Chi-restraints excluded: chain V residue 165 ASN Chi-restraints excluded: chain Y residue 34 VAL Chi-restraints excluded: chain Y residue 51 LEU Chi-restraints excluded: chain Z residue 84 VAL Chi-restraints excluded: chain Z residue 86 LEU Chi-restraints excluded: chain Z residue 103 GLU Chi-restraints excluded: chain Z residue 221 THR Chi-restraints excluded: chain a residue 13 GLU Chi-restraints excluded: chain a residue 52 LEU Chi-restraints excluded: chain a residue 64 TRP Chi-restraints excluded: chain a residue 70 TYR Chi-restraints excluded: chain b residue 20 VAL Chi-restraints excluded: chain b residue 30 TYR Chi-restraints excluded: chain c residue 109 LEU Chi-restraints excluded: chain c residue 188 HIS Chi-restraints excluded: chain c residue 197 THR Chi-restraints excluded: chain c residue 220 ASP Chi-restraints excluded: chain c residue 297 THR Chi-restraints excluded: chain d residue 107 LEU Chi-restraints excluded: chain e residue 51 ASP Chi-restraints excluded: chain f residue 43 VAL Chi-restraints excluded: chain f residue 112 GLU Chi-restraints excluded: chain k residue 98 VAL Chi-restraints excluded: chain k residue 140 TYR Chi-restraints excluded: chain m residue 11 VAL Chi-restraints excluded: chain m residue 33 ARG Chi-restraints excluded: chain m residue 51 VAL Chi-restraints excluded: chain m residue 80 ASP Chi-restraints excluded: chain m residue 91 LEU Chi-restraints excluded: chain m residue 94 ILE Chi-restraints excluded: chain n residue 45 ASN Chi-restraints excluded: chain n residue 55 VAL Chi-restraints excluded: chain o residue 238 ASN Chi-restraints excluded: chain o residue 254 ASP Chi-restraints excluded: chain o residue 256 GLN Chi-restraints excluded: chain o residue 269 TYR Chi-restraints excluded: chain o residue 275 THR Chi-restraints excluded: chain o residue 297 ILE Chi-restraints excluded: chain p residue 90 ARG Chi-restraints excluded: chain q residue 47 LEU Chi-restraints excluded: chain q residue 53 ASP Chi-restraints excluded: chain q residue 86 ASP Chi-restraints excluded: chain M residue 22 THR Chi-restraints excluded: chain M residue 106 LEU Chi-restraints excluded: chain M residue 110 ASP Chi-restraints excluded: chain h residue 65 THR Chi-restraints excluded: chain h residue 68 THR Chi-restraints excluded: chain h residue 93 SER Chi-restraints excluded: chain h residue 106 ILE Chi-restraints excluded: chain h residue 113 GLU Chi-restraints excluded: chain s residue 232 GLN Chi-restraints excluded: chain s residue 282 HIS Chi-restraints excluded: chain j residue 238 LYS Chi-restraints excluded: chain j residue 267 TYR Chi-restraints excluded: chain j residue 357 ILE Chi-restraints excluded: chain g residue 962 MET Chi-restraints excluded: chain g residue 985 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1269 random chunks: chunk 748 optimal weight: 10.0000 chunk 1205 optimal weight: 10.0000 chunk 735 optimal weight: 10.0000 chunk 571 optimal weight: 40.0000 chunk 837 optimal weight: 2.9990 chunk 1264 optimal weight: 7.9990 chunk 1163 optimal weight: 1.9990 chunk 1006 optimal weight: 5.9990 chunk 104 optimal weight: 30.0000 chunk 777 optimal weight: 8.9990 chunk 617 optimal weight: 8.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** u 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 221 ASN ** u 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 518 GLN ** v 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 155 GLN ** y 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 157 HIS ** H 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 113 GLN P 32 HIS ** x 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 ASN F 130 ASN ** J 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 165 GLN V 74 ASN V 101 HIS ** V 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 105 GLN ** e 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 105 ASN o 238 ASN ** p 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 93 GLN ** s 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 28 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6862 moved from start: 0.5664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.127 123665 Z= 0.602 Angle : 0.939 18.347 176203 Z= 0.474 Chirality : 0.051 0.449 21730 Planarity : 0.007 0.146 16084 Dihedral : 20.828 178.414 38690 Min Nonbonded Distance : 1.038 Molprobity Statistics. All-atom Clashscore : 20.80 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.33 % Favored : 91.60 % Rotamer: Outliers : 3.76 % Allowed : 28.79 % Favored : 67.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.74 (0.08), residues: 10949 helix: -0.12 (0.08), residues: 4325 sheet: -1.08 (0.13), residues: 1418 loop : -2.10 (0.08), residues: 5206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP u 149 HIS 0.016 0.002 HIS a 66 PHE 0.053 0.003 PHE x 33 TYR 0.039 0.003 TYR f 40 ARG 0.039 0.001 ARG D 38 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21898 Ramachandran restraints generated. 10949 Oldfield, 0 Emsley, 10949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21898 Ramachandran restraints generated. 10949 Oldfield, 0 Emsley, 10949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1381 residues out of total 9800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 260 poor density : 1121 time to evaluate : 7.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASN P 26 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 477 ASN cc_start: 0.5590 (OUTLIER) cc_final: 0.5216 (t0) REVERT: 1 552 LYS cc_start: 0.6716 (tptp) cc_final: 0.6234 (pptt) REVERT: 6 318 THR cc_start: 0.3746 (OUTLIER) cc_final: 0.3402 (p) REVERT: 6 319 LYS cc_start: 0.4123 (tptt) cc_final: 0.3564 (tptp) REVERT: 6 347 TRP cc_start: 0.6952 (m-10) cc_final: 0.6423 (m-90) REVERT: 6 353 THR cc_start: 0.6231 (p) cc_final: 0.6016 (p) REVERT: u 246 TRP cc_start: 0.7411 (m100) cc_final: 0.6430 (m100) REVERT: u 318 MET cc_start: 0.4616 (ptt) cc_final: 0.4320 (ptt) REVERT: v 267 VAL cc_start: 0.6635 (OUTLIER) cc_final: 0.6187 (p) REVERT: S 163 ASN cc_start: 0.8114 (t0) cc_final: 0.7336 (p0) REVERT: S 227 GLN cc_start: 0.6221 (mm-40) cc_final: 0.6000 (tm-30) REVERT: y 116 TYR cc_start: 0.4435 (OUTLIER) cc_final: 0.3755 (t80) REVERT: y 134 ASN cc_start: 0.7713 (m-40) cc_final: 0.7363 (m-40) REVERT: y 384 ASP cc_start: 0.7301 (t0) cc_final: 0.6980 (t0) REVERT: L 176 LYS cc_start: 0.8561 (tptp) cc_final: 0.8303 (ttmt) REVERT: L 248 TYR cc_start: 0.9223 (OUTLIER) cc_final: 0.8946 (m-10) REVERT: O 68 GLU cc_start: 0.7010 (tm-30) cc_final: 0.6701 (tm-30) REVERT: O 95 ASN cc_start: 0.7563 (t0) cc_final: 0.7313 (t0) REVERT: N 73 ASP cc_start: 0.8189 (m-30) cc_final: 0.7873 (m-30) REVERT: N 78 SER cc_start: 0.9101 (t) cc_final: 0.8783 (t) REVERT: N 111 GLN cc_start: 0.9447 (pm20) cc_final: 0.8792 (pm20) REVERT: N 181 GLU cc_start: 0.8068 (mm-30) cc_final: 0.7858 (mm-30) REVERT: Q 85 ARG cc_start: 0.7844 (mtp85) cc_final: 0.7535 (mtp85) REVERT: Q 89 ARG cc_start: 0.8565 (tmm-80) cc_final: 0.8156 (ttm170) REVERT: Q 96 THR cc_start: 0.8819 (m) cc_final: 0.8486 (p) REVERT: P 45 THR cc_start: 0.8790 (p) cc_final: 0.8498 (t) REVERT: P 70 SER cc_start: 0.8991 (t) cc_final: 0.8555 (m) REVERT: P 96 LYS cc_start: 0.9131 (mtpp) cc_final: 0.8720 (mtpp) REVERT: P 128 ARG cc_start: 0.7990 (OUTLIER) cc_final: 0.7746 (mmt90) REVERT: I 56 ASP cc_start: 0.8835 (m-30) cc_final: 0.8634 (m-30) REVERT: x 50 TYR cc_start: 0.6934 (OUTLIER) cc_final: 0.6460 (m-10) REVERT: x 302 GLU cc_start: 0.4648 (tm-30) cc_final: 0.3337 (mt-10) REVERT: 9 14 LYS cc_start: 0.8206 (ttmt) cc_final: 0.7792 (ttpp) REVERT: B 39 ASN cc_start: 0.8417 (t0) cc_final: 0.7785 (p0) REVERT: B 130 GLU cc_start: 0.8425 (tt0) cc_final: 0.8067 (tt0) REVERT: C 23 LEU cc_start: 0.9606 (OUTLIER) cc_final: 0.9260 (mt) REVERT: D 89 GLU cc_start: 0.8540 (mp0) cc_final: 0.8207 (mp0) REVERT: D 107 GLU cc_start: 0.8796 (OUTLIER) cc_final: 0.8316 (tm-30) REVERT: r 48 LEU cc_start: 0.5265 (OUTLIER) cc_final: 0.4694 (tp) REVERT: r 117 GLU cc_start: 0.4666 (OUTLIER) cc_final: 0.4234 (tm-30) REVERT: r 208 VAL cc_start: 0.3905 (t) cc_final: 0.3471 (t) REVERT: r 255 MET cc_start: 0.0569 (mmt) cc_final: -0.0377 (ptt) REVERT: J 49 GLU cc_start: 0.7672 (mt-10) cc_final: 0.7353 (mt-10) REVERT: R 80 ASP cc_start: 0.8253 (t0) cc_final: 0.7909 (t0) REVERT: R 111 GLN cc_start: 0.8969 (mt0) cc_final: 0.8502 (mt0) REVERT: R 137 LEU cc_start: 0.5997 (OUTLIER) cc_final: 0.5668 (mm) REVERT: R 195 LEU cc_start: 0.8874 (tt) cc_final: 0.8666 (tt) REVERT: T 106 GLN cc_start: 0.8249 (mt0) cc_final: 0.7941 (mt0) REVERT: V 97 PHE cc_start: 0.3495 (t80) cc_final: 0.3044 (t80) REVERT: Z 57 ASN cc_start: 0.7555 (OUTLIER) cc_final: 0.6912 (t0) REVERT: a 3 MET cc_start: 0.0933 (tmm) cc_final: -0.1673 (ppp) REVERT: b 30 TYR cc_start: 0.3050 (OUTLIER) cc_final: 0.0340 (m-80) REVERT: b 111 MET cc_start: 0.3982 (mtt) cc_final: 0.3420 (mtt) REVERT: c 126 ASP cc_start: 0.6971 (p0) cc_final: 0.6251 (p0) REVERT: f 71 MET cc_start: 0.7547 (tmm) cc_final: 0.7014 (tmm) REVERT: f 77 TYR cc_start: 0.2673 (m-80) cc_final: 0.2131 (m-80) REVERT: f 79 ILE cc_start: 0.5203 (mp) cc_final: 0.4905 (tp) REVERT: k 140 TYR cc_start: -0.2072 (OUTLIER) cc_final: -0.2442 (t80) REVERT: m 33 ARG cc_start: 0.1851 (OUTLIER) cc_final: 0.0119 (mtm180) REVERT: n 35 MET cc_start: 0.5193 (mmm) cc_final: 0.4187 (tpp) REVERT: p 69 CYS cc_start: 0.8369 (p) cc_final: 0.7963 (p) REVERT: p 89 GLN cc_start: 0.8431 (mm-40) cc_final: 0.7935 (mp10) REVERT: q 46 ARG cc_start: 0.5420 (ttt180) cc_final: 0.4984 (ptt180) REVERT: q 99 GLU cc_start: 0.4681 (OUTLIER) cc_final: 0.2987 (pp20) REVERT: h 113 GLU cc_start: 0.6767 (OUTLIER) cc_final: 0.6210 (tm-30) REVERT: s 204 MET cc_start: 0.3688 (ptt) cc_final: 0.3089 (mtm) REVERT: j 267 TYR cc_start: 0.4357 (OUTLIER) cc_final: 0.2396 (t80) REVERT: g 962 MET cc_start: 0.3613 (OUTLIER) cc_final: 0.0947 (mmp) outliers start: 260 outliers final: 186 residues processed: 1303 average time/residue: 0.9564 time to fit residues: 2190.4374 Evaluate side-chains 1271 residues out of total 9800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 206 poor density : 1065 time to evaluate : 6.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 477 ASN Chi-restraints excluded: chain 1 residue 515 CYS Chi-restraints excluded: chain 1 residue 543 ASN Chi-restraints excluded: chain 6 residue 312 VAL Chi-restraints excluded: chain 6 residue 316 VAL Chi-restraints excluded: chain 6 residue 318 THR Chi-restraints excluded: chain 6 residue 328 THR Chi-restraints excluded: chain 6 residue 338 THR Chi-restraints excluded: chain u residue 60 ASP Chi-restraints excluded: chain u residue 109 GLN Chi-restraints excluded: chain u residue 121 ILE Chi-restraints excluded: chain u residue 133 SER Chi-restraints excluded: chain u residue 230 LEU Chi-restraints excluded: chain u residue 237 LEU Chi-restraints excluded: chain u residue 242 SER Chi-restraints excluded: chain u residue 394 LEU Chi-restraints excluded: chain u residue 534 LEU Chi-restraints excluded: chain v residue 267 VAL Chi-restraints excluded: chain v residue 278 VAL Chi-restraints excluded: chain v residue 296 VAL Chi-restraints excluded: chain v residue 396 ASN Chi-restraints excluded: chain v residue 408 THR Chi-restraints excluded: chain v residue 422 ILE Chi-restraints excluded: chain S residue 6 SER Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 67 VAL Chi-restraints excluded: chain S residue 139 SER Chi-restraints excluded: chain S residue 158 VAL Chi-restraints excluded: chain S residue 180 VAL Chi-restraints excluded: chain S residue 192 ILE Chi-restraints excluded: chain S residue 219 GLU Chi-restraints excluded: chain y residue 63 LEU Chi-restraints excluded: chain y residue 102 VAL Chi-restraints excluded: chain y residue 116 TYR Chi-restraints excluded: chain y residue 495 THR Chi-restraints excluded: chain y residue 499 VAL Chi-restraints excluded: chain y residue 543 ASP Chi-restraints excluded: chain y residue 628 ASP Chi-restraints excluded: chain y residue 671 VAL Chi-restraints excluded: chain y residue 677 ILE Chi-restraints excluded: chain y residue 701 HIS Chi-restraints excluded: chain y residue 718 LEU Chi-restraints excluded: chain y residue 748 ASP Chi-restraints excluded: chain y residue 752 CYS Chi-restraints excluded: chain y residue 773 ASP Chi-restraints excluded: chain y residue 798 VAL Chi-restraints excluded: chain y residue 847 THR Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 27 LEU Chi-restraints excluded: chain G residue 33 ASN Chi-restraints excluded: chain G residue 44 ASN Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain H residue 17 ARG Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain K residue 2 GLN Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 21 ASN Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain L residue 116 THR Chi-restraints excluded: chain L residue 143 CYS Chi-restraints excluded: chain L residue 172 ASN Chi-restraints excluded: chain L residue 180 VAL Chi-restraints excluded: chain L residue 205 VAL Chi-restraints excluded: chain L residue 206 SER Chi-restraints excluded: chain L residue 225 SER Chi-restraints excluded: chain L residue 248 TYR Chi-restraints excluded: chain O residue 55 THR Chi-restraints excluded: chain O residue 91 VAL Chi-restraints excluded: chain O residue 126 ASP Chi-restraints excluded: chain O residue 127 VAL Chi-restraints excluded: chain O residue 154 SER Chi-restraints excluded: chain O residue 170 GLU Chi-restraints excluded: chain O residue 192 SER Chi-restraints excluded: chain N residue 54 THR Chi-restraints excluded: chain N residue 69 GLU Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain N residue 170 SER Chi-restraints excluded: chain Q residue 2 THR Chi-restraints excluded: chain Q residue 12 LYS Chi-restraints excluded: chain Q residue 57 SER Chi-restraints excluded: chain Q residue 67 LEU Chi-restraints excluded: chain Q residue 88 SER Chi-restraints excluded: chain P residue 62 VAL Chi-restraints excluded: chain P residue 128 ARG Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 69 ASN Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain x residue 26 ARG Chi-restraints excluded: chain x residue 50 TYR Chi-restraints excluded: chain x residue 69 TYR Chi-restraints excluded: chain x residue 369 ILE Chi-restraints excluded: chain 9 residue 9 ARG Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 142 HIS Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 224 ASN Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain r residue 4 LEU Chi-restraints excluded: chain r residue 13 PHE Chi-restraints excluded: chain r residue 48 LEU Chi-restraints excluded: chain r residue 58 SER Chi-restraints excluded: chain r residue 76 VAL Chi-restraints excluded: chain r residue 106 LYS Chi-restraints excluded: chain r residue 117 GLU Chi-restraints excluded: chain r residue 227 ILE Chi-restraints excluded: chain r residue 240 THR Chi-restraints excluded: chain r residue 271 VAL Chi-restraints excluded: chain J residue 30 CYS Chi-restraints excluded: chain J residue 94 LEU Chi-restraints excluded: chain J residue 96 SER Chi-restraints excluded: chain J residue 98 GLN Chi-restraints excluded: chain J residue 121 THR Chi-restraints excluded: chain R residue 66 SER Chi-restraints excluded: chain R residue 72 CYS Chi-restraints excluded: chain R residue 89 GLU Chi-restraints excluded: chain R residue 90 LEU Chi-restraints excluded: chain R residue 95 THR Chi-restraints excluded: chain R residue 104 ILE Chi-restraints excluded: chain R residue 107 THR Chi-restraints excluded: chain R residue 137 LEU Chi-restraints excluded: chain R residue 182 CYS Chi-restraints excluded: chain T residue 27 VAL Chi-restraints excluded: chain T residue 40 ILE Chi-restraints excluded: chain T residue 80 ASP Chi-restraints excluded: chain T residue 125 VAL Chi-restraints excluded: chain V residue 28 VAL Chi-restraints excluded: chain V residue 82 ASN Chi-restraints excluded: chain V residue 165 ASN Chi-restraints excluded: chain Y residue 51 LEU Chi-restraints excluded: chain Z residue 57 ASN Chi-restraints excluded: chain Z residue 84 VAL Chi-restraints excluded: chain Z residue 86 LEU Chi-restraints excluded: chain Z residue 221 THR Chi-restraints excluded: chain a residue 13 GLU Chi-restraints excluded: chain a residue 52 LEU Chi-restraints excluded: chain a residue 64 TRP Chi-restraints excluded: chain a residue 70 TYR Chi-restraints excluded: chain a residue 89 ILE Chi-restraints excluded: chain b residue 20 VAL Chi-restraints excluded: chain b residue 30 TYR Chi-restraints excluded: chain c residue 109 LEU Chi-restraints excluded: chain c residue 171 ASP Chi-restraints excluded: chain c residue 197 THR Chi-restraints excluded: chain c residue 265 ILE Chi-restraints excluded: chain c residue 297 THR Chi-restraints excluded: chain d residue 107 LEU Chi-restraints excluded: chain e residue 51 ASP Chi-restraints excluded: chain e residue 77 LEU Chi-restraints excluded: chain f residue 90 VAL Chi-restraints excluded: chain f residue 101 ASN Chi-restraints excluded: chain i residue 16 GLN Chi-restraints excluded: chain k residue 98 VAL Chi-restraints excluded: chain k residue 140 TYR Chi-restraints excluded: chain m residue 11 VAL Chi-restraints excluded: chain m residue 33 ARG Chi-restraints excluded: chain m residue 51 VAL Chi-restraints excluded: chain m residue 80 ASP Chi-restraints excluded: chain m residue 91 LEU Chi-restraints excluded: chain m residue 124 ILE Chi-restraints excluded: chain n residue 45 ASN Chi-restraints excluded: chain n residue 55 VAL Chi-restraints excluded: chain o residue 238 ASN Chi-restraints excluded: chain o residue 254 ASP Chi-restraints excluded: chain o residue 256 GLN Chi-restraints excluded: chain o residue 269 TYR Chi-restraints excluded: chain o residue 275 THR Chi-restraints excluded: chain o residue 297 ILE Chi-restraints excluded: chain p residue 30 TYR Chi-restraints excluded: chain p residue 43 THR Chi-restraints excluded: chain p residue 90 ARG Chi-restraints excluded: chain q residue 27 VAL Chi-restraints excluded: chain q residue 47 LEU Chi-restraints excluded: chain q residue 53 ASP Chi-restraints excluded: chain q residue 55 VAL Chi-restraints excluded: chain q residue 86 ASP Chi-restraints excluded: chain q residue 99 GLU Chi-restraints excluded: chain M residue 22 THR Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain M residue 106 LEU Chi-restraints excluded: chain M residue 110 ASP Chi-restraints excluded: chain h residue 61 LEU Chi-restraints excluded: chain h residue 65 THR Chi-restraints excluded: chain h residue 76 THR Chi-restraints excluded: chain h residue 93 SER Chi-restraints excluded: chain h residue 106 ILE Chi-restraints excluded: chain h residue 113 GLU Chi-restraints excluded: chain s residue 184 PHE Chi-restraints excluded: chain s residue 194 MET Chi-restraints excluded: chain s residue 282 HIS Chi-restraints excluded: chain j residue 246 ILE Chi-restraints excluded: chain j residue 267 TYR Chi-restraints excluded: chain j residue 357 ILE Chi-restraints excluded: chain g residue 962 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1269 random chunks: chunk 799 optimal weight: 0.6980 chunk 1072 optimal weight: 9.9990 chunk 308 optimal weight: 0.0010 chunk 928 optimal weight: 7.9990 chunk 148 optimal weight: 6.9990 chunk 279 optimal weight: 7.9990 chunk 1008 optimal weight: 6.9990 chunk 421 optimal weight: 0.9990 chunk 1035 optimal weight: 10.0000 chunk 127 optimal weight: 20.0000 chunk 185 optimal weight: 7.9990 overall best weight: 3.1392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** u 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 155 GLN ** y 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 579 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 114 GLN ** H 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 62 GLN ** x 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 GLN ** E 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 89 GLN F 130 ASN ** J 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 293 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.166673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.134369 restraints weight = 269227.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.131716 restraints weight = 287283.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.132133 restraints weight = 172720.650| |-----------------------------------------------------------------------------| r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3740 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3740 r_free = 0.3740 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 216 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3740 r_free = 0.3740 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 235 | |-----------------------------------------------------------------------------| r_final: 0.3740 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.5735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 123665 Z= 0.358 Angle : 0.764 16.860 176203 Z= 0.395 Chirality : 0.044 0.408 21730 Planarity : 0.005 0.134 16084 Dihedral : 20.751 178.669 38690 Min Nonbonded Distance : 1.016 Molprobity Statistics. All-atom Clashscore : 17.43 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.03 % Favored : 92.93 % Rotamer: Outliers : 3.39 % Allowed : 29.20 % Favored : 67.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.57 (0.08), residues: 10949 helix: 0.08 (0.08), residues: 4325 sheet: -1.15 (0.13), residues: 1474 loop : -2.00 (0.08), residues: 5150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP u 149 HIS 0.014 0.001 HIS a 66 PHE 0.041 0.002 PHE x 33 TYR 0.038 0.002 TYR i 34 ARG 0.013 0.001 ARG L 121 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 37101.89 seconds wall clock time: 682 minutes 55.12 seconds (40975.12 seconds total)