Starting phenix.real_space_refine on Fri Mar 15 17:23:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jov_36463/03_2024/8jov_36463.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jov_36463/03_2024/8jov_36463.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jov_36463/03_2024/8jov_36463.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jov_36463/03_2024/8jov_36463.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jov_36463/03_2024/8jov_36463.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jov_36463/03_2024/8jov_36463.pdb" } resolution = 3.8 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= 1.650 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 540 5.16 5 C 80184 2.51 5 N 22716 2.21 5 O 24630 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "0 GLU 40": "OE1" <-> "OE2" Residue "0 GLU 56": "OE1" <-> "OE2" Residue "0 ASP 83": "OD1" <-> "OD2" Residue "0 ASP 127": "OD1" <-> "OD2" Residue "0 ASP 143": "OD1" <-> "OD2" Residue "0 ASP 223": "OD1" <-> "OD2" Residue "0 ASP 226": "OD1" <-> "OD2" Residue "0 GLU 227": "OE1" <-> "OE2" Residue "0 GLU 254": "OE1" <-> "OE2" Residue "0 ASP 258": "OD1" <-> "OD2" Residue "0 GLU 339": "OE1" <-> "OE2" Residue "0 ASP 362": "OD1" <-> "OD2" Residue "0 ASP 374": "OD1" <-> "OD2" Residue "0 ASP 398": "OD1" <-> "OD2" Residue "0 GLU 410": "OE1" <-> "OE2" Residue "0 ASP 432": "OD1" <-> "OD2" Residue "0 ASP 441": "OD1" <-> "OD2" Residue "0 GLU 512": "OE1" <-> "OE2" Residue "0 GLU 550": "OE1" <-> "OE2" Residue "0 GLU 563": "OE1" <-> "OE2" Residue "0 GLU 595": "OE1" <-> "OE2" Residue "1 PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 19": "OE1" <-> "OE2" Residue "2 ASP 35": "OD1" <-> "OD2" Residue "2 GLU 66": "OE1" <-> "OE2" Residue "2 ASP 92": "OD1" <-> "OD2" Residue "2 GLU 99": "OE1" <-> "OE2" Residue "2 TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ASP 118": "OD1" <-> "OD2" Residue "2 TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 138": "OE1" <-> "OE2" Residue "3 GLU 41": "OE1" <-> "OE2" Residue "3 ASP 143": "OD1" <-> "OD2" Residue "3 PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ASP 168": "OD1" <-> "OD2" Residue "3 GLU 184": "OE1" <-> "OE2" Residue "3 ASP 223": "OD1" <-> "OD2" Residue "3 ASP 362": "OD1" <-> "OD2" Residue "3 ASP 404": "OD1" <-> "OD2" Residue "3 GLU 411": "OE1" <-> "OE2" Residue "3 ASP 432": "OD1" <-> "OD2" Residue "3 GLU 512": "OE1" <-> "OE2" Residue "3 ARG 558": "NH1" <-> "NH2" Residue "3 ASP 582": "OD1" <-> "OD2" Residue "4 PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ASP 66": "OD1" <-> "OD2" Residue "4 GLU 75": "OE1" <-> "OE2" Residue "4 GLU 89": "OE1" <-> "OE2" Residue "4 PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ASP 35": "OD1" <-> "OD2" Residue "5 ASP 92": "OD1" <-> "OD2" Residue "5 TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ASP 118": "OD1" <-> "OD2" Residue "5 TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 GLU 138": "OE1" <-> "OE2" Residue "5 GLU 160": "OE1" <-> "OE2" Residue "6 ASP 72": "OD1" <-> "OD2" Residue "6 GLU 81": "OE1" <-> "OE2" Residue "6 ASP 157": "OD1" <-> "OD2" Residue "6 ASP 202": "OD1" <-> "OD2" Residue "6 PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ASP 223": "OD1" <-> "OD2" Residue "6 GLU 227": "OE1" <-> "OE2" Residue "6 GLU 248": "OE1" <-> "OE2" Residue "6 GLU 254": "OE1" <-> "OE2" Residue "6 ASP 258": "OD1" <-> "OD2" Residue "6 GLU 278": "OE1" <-> "OE2" Residue "6 ASP 362": "OD1" <-> "OD2" Residue "6 PHE 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 GLU 428": "OE1" <-> "OE2" Residue "6 GLU 512": "OE1" <-> "OE2" Residue "6 GLU 536": "OE1" <-> "OE2" Residue "6 ASP 552": "OD1" <-> "OD2" Residue "6 ARG 558": "NH1" <-> "NH2" Residue "6 ASP 594": "OD1" <-> "OD2" Residue "7 PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 56": "OE1" <-> "OE2" Residue "7 PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 12": "OE1" <-> "OE2" Residue "A ASP 23": "OD1" <-> "OD2" Residue "A PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 297": "OE1" <-> "OE2" Residue "A GLU 344": "OE1" <-> "OE2" Residue "A TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 480": "OE1" <-> "OE2" Residue "A GLU 517": "OE1" <-> "OE2" Residue "A PHE 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 553": "OE1" <-> "OE2" Residue "B TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 23": "OD1" <-> "OD2" Residue "B ASP 54": "OD1" <-> "OD2" Residue "B PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 297": "OE1" <-> "OE2" Residue "B GLU 344": "OE1" <-> "OE2" Residue "B ASP 351": "OD1" <-> "OD2" Residue "B PHE 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 12": "OE1" <-> "OE2" Residue "C ASP 23": "OD1" <-> "OD2" Residue "C PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 305": "OE1" <-> "OE2" Residue "C PHE 419": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 475": "OE1" <-> "OE2" Residue "D GLU 12": "OE1" <-> "OE2" Residue "D ASP 23": "OD1" <-> "OD2" Residue "D PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 344": "OE1" <-> "OE2" Residue "D TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 419": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 475": "OE1" <-> "OE2" Residue "D GLU 480": "OE1" <-> "OE2" Residue "D GLU 517": "OE1" <-> "OE2" Residue "D PHE 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 23": "OD1" <-> "OD2" Residue "E PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 305": "OE1" <-> "OE2" Residue "E GLU 344": "OE1" <-> "OE2" Residue "E ASP 351": "OD1" <-> "OD2" Residue "E PHE 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 12": "OE1" <-> "OE2" Residue "F ASP 23": "OD1" <-> "OD2" Residue "F GLU 220": "OE1" <-> "OE2" Residue "F PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 305": "OE1" <-> "OE2" Residue "F ASP 329": "OD1" <-> "OD2" Residue "F GLU 344": "OE1" <-> "OE2" Residue "F PHE 419": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 475": "OE1" <-> "OE2" Residue "G GLU 29": "OE1" <-> "OE2" Residue "G PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 45": "OD1" <-> "OD2" Residue "G GLU 46": "OE1" <-> "OE2" Residue "G GLU 67": "OE1" <-> "OE2" Residue "G PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 88": "OE1" <-> "OE2" Residue "G GLU 110": "OE1" <-> "OE2" Residue "G ASP 111": "OD1" <-> "OD2" Residue "G ASP 144": "OD1" <-> "OD2" Residue "G ASP 152": "OD1" <-> "OD2" Residue "G GLU 182": "OE1" <-> "OE2" Residue "G ASP 184": "OD1" <-> "OD2" Residue "H ASP 5": "OD1" <-> "OD2" Residue "H PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 45": "OD1" <-> "OD2" Residue "H ASP 52": "OD1" <-> "OD2" Residue "H GLU 56": "OE1" <-> "OE2" Residue "H GLU 67": "OE1" <-> "OE2" Residue "H ASP 92": "OD1" <-> "OD2" Residue "H TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 110": "OE1" <-> "OE2" Residue "H ASP 170": "OD1" <-> "OD2" Residue "H ASP 184": "OD1" <-> "OD2" Residue "I PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 36": "OE1" <-> "OE2" Residue "I ASP 45": "OD1" <-> "OD2" Residue "I GLU 56": "OE1" <-> "OE2" Residue "I GLU 69": "OE1" <-> "OE2" Residue "I GLU 88": "OE1" <-> "OE2" Residue "I GLU 119": "OE1" <-> "OE2" Residue "I ASP 140": "OD1" <-> "OD2" Residue "I ASP 180": "OD1" <-> "OD2" Residue "J GLU 29": "OE1" <-> "OE2" Residue "J PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 45": "OD1" <-> "OD2" Residue "J GLU 46": "OE1" <-> "OE2" Residue "J GLU 69": "OE1" <-> "OE2" Residue "J PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 88": "OE1" <-> "OE2" Residue "J ASP 111": "OD1" <-> "OD2" Residue "J ASP 152": "OD1" <-> "OD2" Residue "J GLU 182": "OE1" <-> "OE2" Residue "J ASP 184": "OD1" <-> "OD2" Residue "K ASP 5": "OD1" <-> "OD2" Residue "K PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 45": "OD1" <-> "OD2" Residue "K ASP 52": "OD1" <-> "OD2" Residue "K GLU 56": "OE1" <-> "OE2" Residue "K GLU 110": "OE1" <-> "OE2" Residue "K ASP 144": "OD1" <-> "OD2" Residue "K ASP 170": "OD1" <-> "OD2" Residue "K ASP 184": "OD1" <-> "OD2" Residue "L PHE 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 29": "OE1" <-> "OE2" Residue "L PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 36": "OE1" <-> "OE2" Residue "L ASP 52": "OD1" <-> "OD2" Residue "L GLU 110": "OE1" <-> "OE2" Residue "L PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 140": "OD1" <-> "OD2" Residue "L ASP 152": "OD1" <-> "OD2" Residue "L ASP 170": "OD1" <-> "OD2" Residue "L ASP 180": "OD1" <-> "OD2" Residue "M PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 52": "OD1" <-> "OD2" Residue "M GLU 75": "OE1" <-> "OE2" Residue "M GLU 96": "OE1" <-> "OE2" Residue "M PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 119": "OD1" <-> "OD2" Residue "N PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 66": "OD1" <-> "OD2" Residue "N GLU 75": "OE1" <-> "OE2" Residue "N PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 119": "OD1" <-> "OD2" Residue "O GLU 56": "OE1" <-> "OE2" Residue "O PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 86": "OD1" <-> "OD2" Residue "O ASP 99": "OD1" <-> "OD2" Residue "P PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 89": "OE1" <-> "OE2" Residue "P PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 119": "OD1" <-> "OD2" Residue "Q PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 66": "OD1" <-> "OD2" Residue "Q GLU 75": "OE1" <-> "OE2" Residue "Q ASP 86": "OD1" <-> "OD2" Residue "R PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 119": "OD1" <-> "OD2" Residue "S PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 45": "OD1" <-> "OD2" Residue "S PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 53": "OE1" <-> "OE2" Residue "S TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 69": "OE1" <-> "OE2" Residue "S PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 88": "OE1" <-> "OE2" Residue "S ASP 92": "OD1" <-> "OD2" Residue "S ASP 111": "OD1" <-> "OD2" Residue "S ASP 134": "OD1" <-> "OD2" Residue "S ASP 140": "OD1" <-> "OD2" Residue "S ASP 180": "OD1" <-> "OD2" Residue "T ASP 35": "OD1" <-> "OD2" Residue "T GLU 66": "OE1" <-> "OE2" Residue "T ASP 92": "OD1" <-> "OD2" Residue "T ASP 97": "OD1" <-> "OD2" Residue "T ASP 118": "OD1" <-> "OD2" Residue "T TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 153": "OD1" <-> "OD2" Residue "T GLU 160": "OE1" <-> "OE2" Residue "T GLU 179": "OE1" <-> "OE2" Residue "T ASP 195": "OD1" <-> "OD2" Residue "U GLU 44": "OE1" <-> "OE2" Residue "U ASP 72": "OD1" <-> "OD2" Residue "U GLU 81": "OE1" <-> "OE2" Residue "U GLU 89": "OE1" <-> "OE2" Residue "U GLU 111": "OE1" <-> "OE2" Residue "U ASP 127": "OD1" <-> "OD2" Residue "U PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 171": "OD1" <-> "OD2" Residue "U GLU 184": "OE1" <-> "OE2" Residue "U ASP 199": "OD1" <-> "OD2" Residue "U GLU 227": "OE1" <-> "OE2" Residue "U ASP 258": "OD1" <-> "OD2" Residue "U ASP 362": "OD1" <-> "OD2" Residue "U ASP 398": "OD1" <-> "OD2" Residue "U GLU 407": "OE1" <-> "OE2" Residue "U GLU 411": "OE1" <-> "OE2" Residue "U ASP 432": "OD1" <-> "OD2" Residue "U GLU 512": "OE1" <-> "OE2" Residue "U ASP 582": "OD1" <-> "OD2" Residue "U ASP 589": "OD1" <-> "OD2" Residue "U ASP 594": "OD1" <-> "OD2" Residue "V PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 52": "OD1" <-> "OD2" Residue "V GLU 96": "OE1" <-> "OE2" Residue "V ASP 119": "OD1" <-> "OD2" Residue "W PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 56": "OE1" <-> "OE2" Residue "W TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 136": "OD1" <-> "OD2" Residue "W ASP 140": "OD1" <-> "OD2" Residue "W ASP 184": "OD1" <-> "OD2" Residue "X GLU 19": "OE1" <-> "OE2" Residue "X ASP 20": "OD1" <-> "OD2" Residue "X GLU 22": "OE1" <-> "OE2" Residue "X ASP 35": "OD1" <-> "OD2" Residue "X GLU 66": "OE1" <-> "OE2" Residue "X ASP 67": "OD1" <-> "OD2" Residue "X ASP 92": "OD1" <-> "OD2" Residue "X GLU 99": "OE1" <-> "OE2" Residue "X ASP 102": "OD1" <-> "OD2" Residue "X TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 118": "OD1" <-> "OD2" Residue "X PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 153": "OD1" <-> "OD2" Residue "Y GLU 56": "OE1" <-> "OE2" Residue "Y GLU 81": "OE1" <-> "OE2" Residue "Y ASP 157": "OD1" <-> "OD2" Residue "Y ASP 223": "OD1" <-> "OD2" Residue "Y ASP 226": "OD1" <-> "OD2" Residue "Y GLU 339": "OE1" <-> "OE2" Residue "Y ASP 362": "OD1" <-> "OD2" Residue "Y ASP 374": "OD1" <-> "OD2" Residue "Y GLU 406": "OE1" <-> "OE2" Residue "Y GLU 407": "OE1" <-> "OE2" Residue "Y GLU 410": "OE1" <-> "OE2" Residue "Y GLU 411": "OE1" <-> "OE2" Residue "Y GLU 428": "OE1" <-> "OE2" Residue "Y ASP 441": "OD1" <-> "OD2" Residue "Y ASP 489": "OD1" <-> "OD2" Residue "Y PHE 493": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 512": "OE1" <-> "OE2" Residue "Y GLU 536": "OE1" <-> "OE2" Residue "Y ARG 558": "NH1" <-> "NH2" Residue "Y ASP 594": "OD1" <-> "OD2" Residue "Z PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 66": "OD1" <-> "OD2" Residue "Z GLU 89": "OE1" <-> "OE2" Residue "Z PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 29": "OE1" <-> "OE2" Residue "a PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 36": "OE1" <-> "OE2" Residue "a PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 67": "OE1" <-> "OE2" Residue "a GLU 69": "OE1" <-> "OE2" Residue "a TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 111": "OD1" <-> "OD2" Residue "a ASP 140": "OD1" <-> "OD2" Residue "a GLU 157": "OE1" <-> "OE2" Residue "a PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 184": "OD1" <-> "OD2" Residue "b ASP 20": "OD1" <-> "OD2" Residue "b ASP 35": "OD1" <-> "OD2" Residue "b GLU 39": "OE1" <-> "OE2" Residue "b ASP 102": "OD1" <-> "OD2" Residue "b TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 118": "OD1" <-> "OD2" Residue "b PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 81": "OE1" <-> "OE2" Residue "c PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 167": "OE1" <-> "OE2" Residue "c TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 184": "OE1" <-> "OE2" Residue "c GLU 254": "OE1" <-> "OE2" Residue "c PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ASP 398": "OD1" <-> "OD2" Residue "c ASP 432": "OD1" <-> "OD2" Residue "c GLU 512": "OE1" <-> "OE2" Residue "c GLU 513": "OE1" <-> "OE2" Residue "c ARG 558": "NH1" <-> "NH2" Residue "c ASP 582": "OD1" <-> "OD2" Residue "c ASP 594": "OD1" <-> "OD2" Residue "d PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 75": "OE1" <-> "OE2" Residue "d PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 86": "OD1" <-> "OD2" Residue "e PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ASP 45": "OD1" <-> "OD2" Residue "e PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 53": "OE1" <-> "OE2" Residue "e TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 88": "OE1" <-> "OE2" Residue "e ASP 92": "OD1" <-> "OD2" Residue "e GLU 110": "OE1" <-> "OE2" Residue "e ASP 111": "OD1" <-> "OD2" Residue "e ASP 134": "OD1" <-> "OD2" Residue "e ASP 140": "OD1" <-> "OD2" Residue "e TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 157": "OE1" <-> "OE2" Residue "f GLU 19": "OE1" <-> "OE2" Residue "f GLU 22": "OE1" <-> "OE2" Residue "f ASP 35": "OD1" <-> "OD2" Residue "f ASP 67": "OD1" <-> "OD2" Residue "f ASP 73": "OD1" <-> "OD2" Residue "f ASP 92": "OD1" <-> "OD2" Residue "f ASP 102": "OD1" <-> "OD2" Residue "f TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ASP 118": "OD1" <-> "OD2" Residue "f PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ASP 153": "OD1" <-> "OD2" Residue "f PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 56": "OE1" <-> "OE2" Residue "g GLU 81": "OE1" <-> "OE2" Residue "g GLU 132": "OE1" <-> "OE2" Residue "g ASP 143": "OD1" <-> "OD2" Residue "g GLU 167": "OE1" <-> "OE2" Residue "g TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 223": "OD1" <-> "OD2" Residue "g ASP 226": "OD1" <-> "OD2" Residue "g GLU 254": "OE1" <-> "OE2" Residue "g ASP 258": "OD1" <-> "OD2" Residue "g GLU 339": "OE1" <-> "OE2" Residue "g ASP 374": "OD1" <-> "OD2" Residue "g ASP 398": "OD1" <-> "OD2" Residue "g GLU 410": "OE1" <-> "OE2" Residue "g ASP 441": "OD1" <-> "OD2" Residue "g GLU 512": "OE1" <-> "OE2" Residue "g GLU 536": "OE1" <-> "OE2" Residue "g GLU 550": "OE1" <-> "OE2" Residue "g GLU 563": "OE1" <-> "OE2" Residue "g GLU 595": "OE1" <-> "OE2" Residue "h PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 75": "OE1" <-> "OE2" Residue "h PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ASP 119": "OD1" <-> "OD2" Residue "i PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i GLU 56": "OE1" <-> "OE2" Residue "i TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i GLU 67": "OE1" <-> "OE2" Residue "i GLU 69": "OE1" <-> "OE2" Residue "i ASP 92": "OD1" <-> "OD2" Residue "i GLU 110": "OE1" <-> "OE2" Residue "i ASP 111": "OD1" <-> "OD2" Residue "i ASP 134": "OD1" <-> "OD2" Residue "i ASP 136": "OD1" <-> "OD2" Residue "i ASP 140": "OD1" <-> "OD2" Residue "i ASP 180": "OD1" <-> "OD2" Residue "i ASP 184": "OD1" <-> "OD2" Residue "j ASP 35": "OD1" <-> "OD2" Residue "j ASP 67": "OD1" <-> "OD2" Residue "j ASP 92": "OD1" <-> "OD2" Residue "j ASP 97": "OD1" <-> "OD2" Residue "j ASP 118": "OD1" <-> "OD2" Residue "j ASP 153": "OD1" <-> "OD2" Residue "k GLU 41": "OE1" <-> "OE2" Residue "k GLU 44": "OE1" <-> "OE2" Residue "k ASP 72": "OD1" <-> "OD2" Residue "k TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ASP 127": "OD1" <-> "OD2" Residue "k PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k GLU 156": "OE1" <-> "OE2" Residue "k ASP 168": "OD1" <-> "OD2" Residue "k ASP 175": "OD1" <-> "OD2" Residue "k TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k GLU 184": "OE1" <-> "OE2" Residue "k ASP 223": "OD1" <-> "OD2" Residue "k ASP 251": "OD1" <-> "OD2" Residue "k ASP 362": "OD1" <-> "OD2" Residue "k ASP 398": "OD1" <-> "OD2" Residue "k ASP 404": "OD1" <-> "OD2" Residue "k GLU 407": "OE1" <-> "OE2" Residue "k GLU 411": "OE1" <-> "OE2" Residue "k ASP 432": "OD1" <-> "OD2" Residue "k ASP 489": "OD1" <-> "OD2" Residue "k GLU 512": "OE1" <-> "OE2" Residue "k ASP 582": "OD1" <-> "OD2" Residue "l PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ASP 66": "OD1" <-> "OD2" Residue "l GLU 75": "OE1" <-> "OE2" Residue "l PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ASP 119": "OD1" <-> "OD2" Residue "m PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m GLU 29": "OE1" <-> "OE2" Residue "m PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m GLU 36": "OE1" <-> "OE2" Residue "m ASP 45": "OD1" <-> "OD2" Residue "m PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m GLU 56": "OE1" <-> "OE2" Residue "m TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m GLU 67": "OE1" <-> "OE2" Residue "m GLU 69": "OE1" <-> "OE2" Residue "m PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ASP 92": "OD1" <-> "OD2" Residue "m ASP 111": "OD1" <-> "OD2" Residue "m GLU 157": "OE1" <-> "OE2" Residue "m ASP 184": "OD1" <-> "OD2" Residue "n ASP 20": "OD1" <-> "OD2" Residue "n ASP 35": "OD1" <-> "OD2" Residue "n GLU 66": "OE1" <-> "OE2" Residue "n ASP 97": "OD1" <-> "OD2" Residue "n GLU 99": "OE1" <-> "OE2" Residue "n ASP 102": "OD1" <-> "OD2" Residue "n TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ASP 118": "OD1" <-> "OD2" Residue "n PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o GLU 81": "OE1" <-> "OE2" Residue "o GLU 111": "OE1" <-> "OE2" Residue "o GLU 184": "OE1" <-> "OE2" Residue "o PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o GLU 227": "OE1" <-> "OE2" Residue "o ASP 247": "OD1" <-> "OD2" Residue "o GLU 254": "OE1" <-> "OE2" Residue "o ASP 258": "OD1" <-> "OD2" Residue "o GLU 278": "OE1" <-> "OE2" Residue "o GLU 399": "OE1" <-> "OE2" Residue "o GLU 428": "OE1" <-> "OE2" Residue "o GLU 512": "OE1" <-> "OE2" Residue "o GLU 536": "OE1" <-> "OE2" Residue "o GLU 550": "OE1" <-> "OE2" Residue "o ASP 552": "OD1" <-> "OD2" Residue "p PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p GLU 56": "OE1" <-> "OE2" Residue "p GLU 75": "OE1" <-> "OE2" Residue "p PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ASP 86": "OD1" <-> "OD2" Residue "p GLU 96": "OE1" <-> "OE2" Residue "p ASP 99": "OD1" <-> "OD2" Residue "p PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q GLU 19": "OE1" <-> "OE2" Residue "q GLU 28": "OE1" <-> "OE2" Residue "q ASP 35": "OD1" <-> "OD2" Residue "q GLU 66": "OE1" <-> "OE2" Residue "q ASP 92": "OD1" <-> "OD2" Residue "q TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ASP 118": "OD1" <-> "OD2" Residue "q TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r GLU 41": "OE1" <-> "OE2" Residue "r GLU 44": "OE1" <-> "OE2" Residue "r ASP 72": "OD1" <-> "OD2" Residue "r GLU 81": "OE1" <-> "OE2" Residue "r GLU 89": "OE1" <-> "OE2" Residue "r GLU 111": "OE1" <-> "OE2" Residue "r ASP 127": "OD1" <-> "OD2" Residue "r PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ASP 168": "OD1" <-> "OD2" Residue "r ASP 171": "OD1" <-> "OD2" Residue "r GLU 184": "OE1" <-> "OE2" Residue "r ASP 199": "OD1" <-> "OD2" Residue "r ASP 202": "OD1" <-> "OD2" Residue "r ASP 223": "OD1" <-> "OD2" Residue "r GLU 227": "OE1" <-> "OE2" Residue "r ASP 362": "OD1" <-> "OD2" Residue "r GLU 407": "OE1" <-> "OE2" Residue "r ASP 432": "OD1" <-> "OD2" Residue "r GLU 512": "OE1" <-> "OE2" Residue "r GLU 513": "OE1" <-> "OE2" Residue "r ARG 558": "NH1" <-> "NH2" Residue "r ASP 582": "OD1" <-> "OD2" Residue "r ASP 589": "OD1" <-> "OD2" Residue "r ASP 594": "OD1" <-> "OD2" Residue "s PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s GLU 96": "OE1" <-> "OE2" Residue "s PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ASP 119": "OD1" <-> "OD2" Residue "t GLU 19": "OE1" <-> "OE2" Residue "t ASP 35": "OD1" <-> "OD2" Residue "t GLU 39": "OE1" <-> "OE2" Residue "t GLU 66": "OE1" <-> "OE2" Residue "t ASP 92": "OD1" <-> "OD2" Residue "t GLU 99": "OE1" <-> "OE2" Residue "t TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t ASP 118": "OD1" <-> "OD2" Residue "t TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t GLU 138": "OE1" <-> "OE2" Residue "u GLU 62": "OE1" <-> "OE2" Residue "u GLU 81": "OE1" <-> "OE2" Residue "u ASP 143": "OD1" <-> "OD2" Residue "u ASP 199": "OD1" <-> "OD2" Residue "u TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ASP 223": "OD1" <-> "OD2" Residue "u ASP 226": "OD1" <-> "OD2" Residue "u GLU 339": "OE1" <-> "OE2" Residue "u ASP 362": "OD1" <-> "OD2" Residue "u GLU 407": "OE1" <-> "OE2" Residue "u GLU 428": "OE1" <-> "OE2" Residue "u ASP 432": "OD1" <-> "OD2" Residue "u PHE 493": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u GLU 512": "OE1" <-> "OE2" Residue "u GLU 536": "OE1" <-> "OE2" Residue "u ASP 552": "OD1" <-> "OD2" Residue "u ASP 594": "OD1" <-> "OD2" Residue "v PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v ASP 66": "OD1" <-> "OD2" Residue "v GLU 75": "OE1" <-> "OE2" Residue "v ASP 86": "OD1" <-> "OD2" Residue "v GLU 89": "OE1" <-> "OE2" Residue "v ASP 119": "OD1" <-> "OD2" Residue "w ASP 20": "OD1" <-> "OD2" Residue "w GLU 22": "OE1" <-> "OE2" Residue "w GLU 28": "OE1" <-> "OE2" Residue "w GLU 66": "OE1" <-> "OE2" Residue "w ASP 92": "OD1" <-> "OD2" Residue "w TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w ASP 118": "OD1" <-> "OD2" Residue "w TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x GLU 132": "OE1" <-> "OE2" Residue "x PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x GLU 184": "OE1" <-> "OE2" Residue "x GLU 254": "OE1" <-> "OE2" Residue "x PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x GLU 339": "OE1" <-> "OE2" Residue "x ASP 398": "OD1" <-> "OD2" Residue "x GLU 403": "OE1" <-> "OE2" Residue "x GLU 411": "OE1" <-> "OE2" Residue "x ASP 432": "OD1" <-> "OD2" Residue "x ASP 489": "OD1" <-> "OD2" Residue "x GLU 512": "OE1" <-> "OE2" Residue "x GLU 513": "OE1" <-> "OE2" Residue "x ARG 558": "NH1" <-> "NH2" Residue "x ASP 582": "OD1" <-> "OD2" Residue "x ASP 589": "OD1" <-> "OD2" Residue "x ASP 594": "OD1" <-> "OD2" Residue "y PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y GLU 96": "OE1" <-> "OE2" Residue "y PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y ASP 119": "OD1" <-> "OD2" Residue "z ASP 20": "OD1" <-> "OD2" Residue "z ASP 92": "OD1" <-> "OD2" Residue "z TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z ASP 118": "OD1" <-> "OD2" Residue "z TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z GLU 138": "OE1" <-> "OE2" Residue "z GLU 160": "OE1" <-> "OE2" Time to flip residues: 0.29s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 128070 Number of models: 1 Model: "" Number of chains: 60 Chain: "0" Number of atoms: 4297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 547, 4297 Classifications: {'peptide': 547} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 19, 'TRANS': 527} Chain breaks: 5 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 159 Unresolved non-hydrogen angles: 195 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 12, 'ASN:plan1': 1, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 105 Chain: "1" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 829 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 5, 'TRANS': 110} Chain: "2" Number of atoms: 1615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1615 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 200} Chain: "3" Number of atoms: 4297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 547, 4297 Classifications: {'peptide': 547} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 19, 'TRANS': 527} Chain breaks: 5 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 159 Unresolved non-hydrogen angles: 195 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 12, 'ASN:plan1': 1, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 105 Chain: "4" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 829 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 5, 'TRANS': 110} Chain: "5" Number of atoms: 1615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1615 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 200} Chain: "6" Number of atoms: 4297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 547, 4297 Classifications: {'peptide': 547} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 19, 'TRANS': 527} Chain breaks: 5 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 159 Unresolved non-hydrogen angles: 195 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 12, 'ASN:plan1': 1, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 105 Chain: "7" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 829 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 5, 'TRANS': 110} Chain: "A" Number of atoms: 3812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 518, 3812 Classifications: {'peptide': 518} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'PTRANS': 31, 'TRANS': 486} Chain breaks: 2 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 170 Unresolved non-hydrogen angles: 227 Unresolved non-hydrogen dihedrals: 140 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 4, 'GLU:plan': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 90 Chain: "B" Number of atoms: 3812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 518, 3812 Classifications: {'peptide': 518} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'PTRANS': 31, 'TRANS': 486} Chain breaks: 2 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 170 Unresolved non-hydrogen angles: 227 Unresolved non-hydrogen dihedrals: 140 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 4, 'GLU:plan': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 90 Chain: "C" Number of atoms: 3812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 518, 3812 Classifications: {'peptide': 518} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'PTRANS': 31, 'TRANS': 486} Chain breaks: 2 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 170 Unresolved non-hydrogen angles: 227 Unresolved non-hydrogen dihedrals: 140 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 4, 'GLU:plan': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 90 Chain: "D" Number of atoms: 3812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 518, 3812 Classifications: {'peptide': 518} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'PTRANS': 31, 'TRANS': 486} Chain breaks: 2 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 170 Unresolved non-hydrogen angles: 227 Unresolved non-hydrogen dihedrals: 140 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 4, 'GLU:plan': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 90 Chain: "E" Number of atoms: 3812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 518, 3812 Classifications: {'peptide': 518} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'PTRANS': 31, 'TRANS': 486} Chain breaks: 2 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 170 Unresolved non-hydrogen angles: 227 Unresolved non-hydrogen dihedrals: 140 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 4, 'GLU:plan': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 90 Chain: "F" Number of atoms: 3812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 518, 3812 Classifications: {'peptide': 518} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'PTRANS': 31, 'TRANS': 486} Chain breaks: 2 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 170 Unresolved non-hydrogen angles: 227 Unresolved non-hydrogen dihedrals: 140 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 4, 'GLU:plan': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 90 Chain: "G" Number of atoms: 1611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1611 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 13, 'TRANS': 190} Chain: "H" Number of atoms: 1611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1611 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 13, 'TRANS': 190} Chain: "I" Number of atoms: 1611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1611 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 13, 'TRANS': 190} Chain: "J" Number of atoms: 1611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1611 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 13, 'TRANS': 190} Chain: "K" Number of atoms: 1611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1611 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 13, 'TRANS': 190} Chain: "L" Number of atoms: 1611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1611 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 13, 'TRANS': 190} Chain: "M" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 829 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 5, 'TRANS': 110} Chain: "N" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 829 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 5, 'TRANS': 110} Chain: "O" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 829 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 5, 'TRANS': 110} Chain: "P" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 829 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 5, 'TRANS': 110} Chain: "Q" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 829 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 5, 'TRANS': 110} Chain: "R" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 829 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 5, 'TRANS': 110} Chain: "S" Number of atoms: 1611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1611 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 13, 'TRANS': 190} Chain: "T" Number of atoms: 1615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1615 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 200} Chain: "U" Number of atoms: 4297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 547, 4297 Classifications: {'peptide': 547} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 19, 'TRANS': 527} Chain breaks: 5 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 159 Unresolved non-hydrogen angles: 195 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 12, 'ASN:plan1': 1, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 105 Chain: "V" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 829 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 5, 'TRANS': 110} Chain: "W" Number of atoms: 1611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1611 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 13, 'TRANS': 190} Chain: "X" Number of atoms: 1615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1615 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 200} Chain: "Y" Number of atoms: 4297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 547, 4297 Classifications: {'peptide': 547} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 19, 'TRANS': 527} Chain breaks: 5 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 159 Unresolved non-hydrogen angles: 195 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 12, 'ASN:plan1': 1, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 105 Chain: "Z" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 829 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 5, 'TRANS': 110} Chain: "a" Number of atoms: 1611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1611 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 13, 'TRANS': 190} Chain: "b" Number of atoms: 1615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1615 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 200} Chain: "c" Number of atoms: 4297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 547, 4297 Classifications: {'peptide': 547} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 19, 'TRANS': 527} Chain breaks: 5 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 159 Unresolved non-hydrogen angles: 195 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 12, 'ASN:plan1': 1, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 105 Chain: "d" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 829 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 5, 'TRANS': 110} Chain: "e" Number of atoms: 1611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1611 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 13, 'TRANS': 190} Chain: "f" Number of atoms: 1615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1615 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 200} Chain: "g" Number of atoms: 4297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 547, 4297 Classifications: {'peptide': 547} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 19, 'TRANS': 527} Chain breaks: 5 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 159 Unresolved non-hydrogen angles: 195 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 12, 'ASN:plan1': 1, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 105 Chain: "h" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 829 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 5, 'TRANS': 110} Chain: "i" Number of atoms: 1611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1611 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 13, 'TRANS': 190} Chain: "j" Number of atoms: 1615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1615 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 200} Chain: "k" Number of atoms: 4297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 547, 4297 Classifications: {'peptide': 547} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 19, 'TRANS': 527} Chain breaks: 5 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 159 Unresolved non-hydrogen angles: 195 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 12, 'ASN:plan1': 1, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 105 Chain: "l" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 829 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 5, 'TRANS': 110} Chain: "m" Number of atoms: 1611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1611 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 13, 'TRANS': 190} Chain: "n" Number of atoms: 1615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1615 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 200} Chain: "o" Number of atoms: 4297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 547, 4297 Classifications: {'peptide': 547} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 19, 'TRANS': 527} Chain breaks: 5 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 159 Unresolved non-hydrogen angles: 195 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 12, 'ASN:plan1': 1, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 105 Chain: "p" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 829 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 5, 'TRANS': 110} Chain: "q" Number of atoms: 1615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1615 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 200} Chain: "r" Number of atoms: 4297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 547, 4297 Classifications: {'peptide': 547} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 19, 'TRANS': 527} Chain breaks: 5 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 159 Unresolved non-hydrogen angles: 195 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 12, 'ASN:plan1': 1, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 105 Chain: "s" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 829 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 5, 'TRANS': 110} Chain: "t" Number of atoms: 1615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1615 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 200} Chain: "u" Number of atoms: 4297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 547, 4297 Classifications: {'peptide': 547} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 19, 'TRANS': 527} Chain breaks: 5 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 159 Unresolved non-hydrogen angles: 195 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 12, 'ASN:plan1': 1, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 105 Chain: "v" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 829 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 5, 'TRANS': 110} Chain: "w" Number of atoms: 1615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1615 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 200} Chain: "x" Number of atoms: 4297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 547, 4297 Classifications: {'peptide': 547} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 19, 'TRANS': 527} Chain breaks: 5 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 159 Unresolved non-hydrogen angles: 195 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 12, 'ASN:plan1': 1, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 105 Chain: "y" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 829 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 5, 'TRANS': 110} Chain: "z" Number of atoms: 1615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1615 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 200} Time building chain proxies: 47.92, per 1000 atoms: 0.37 Number of scatterers: 128070 At special positions: 0 Unit cell: (201.93, 204.47, 394.97, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 540 16.00 O 24630 8.00 N 22716 7.00 C 80184 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: 38.11 Conformation dependent library (CDL) restraints added in 17.0 seconds 33000 Ramachandran restraints generated. 16500 Oldfield, 0 Emsley, 16500 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 31596 Finding SS restraints... Secondary structure from input PDB file: 471 helices and 204 sheets defined 41.3% alpha, 16.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.92 Creating SS restraints... Processing helix chain '0' and resid 41 through 60 Processing helix chain '0' and resid 60 through 75 removed outlier: 3.643A pdb=" N ASP 0 75 " --> pdb=" O GLU 0 71 " (cutoff:3.500A) Processing helix chain '0' and resid 80 through 91 Processing helix chain '0' and resid 98 through 114 removed outlier: 4.434A pdb=" N GLN 0 102 " --> pdb=" O ASN 0 98 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER 0 103 " --> pdb=" O VAL 0 99 " (cutoff:3.500A) Processing helix chain '0' and resid 127 through 146 Processing helix chain '0' and resid 146 through 161 Processing helix chain '0' and resid 214 through 221 Processing helix chain '0' and resid 224 through 231 removed outlier: 3.632A pdb=" N ILE 0 228 " --> pdb=" O ARG 0 224 " (cutoff:3.500A) Processing helix chain '0' and resid 247 through 260 Processing helix chain '0' and resid 368 through 392 removed outlier: 4.651A pdb=" N MET 0 372 " --> pdb=" O VAL 0 368 " (cutoff:3.500A) Processing helix chain '0' and resid 404 through 412 Processing helix chain '0' and resid 433 through 453 removed outlier: 3.945A pdb=" N ALA 0 437 " --> pdb=" O ARG 0 433 " (cutoff:3.500A) Processing helix chain '0' and resid 484 through 510 Processing helix chain '0' and resid 511 through 519 Processing helix chain '0' and resid 537 through 545 removed outlier: 3.681A pdb=" N ASP 0 545 " --> pdb=" O ARG 0 541 " (cutoff:3.500A) Processing helix chain '0' and resid 556 through 572 removed outlier: 3.747A pdb=" N ALA 0 560 " --> pdb=" O THR 0 556 " (cutoff:3.500A) Processing helix chain '0' and resid 576 through 588 removed outlier: 3.851A pdb=" N MET 0 580 " --> pdb=" O VAL 0 576 " (cutoff:3.500A) Processing helix chain '0' and resid 593 through 605 Processing helix chain '0' and resid 615 through 673 Processing helix chain '1' and resid 30 through 35 removed outlier: 4.248A pdb=" N ALA 1 33 " --> pdb=" O GLY 1 30 " (cutoff:3.500A) Processing helix chain '1' and resid 92 through 119 removed outlier: 3.805A pdb=" N GLU 1 96 " --> pdb=" O LEU 1 92 " (cutoff:3.500A) Processing helix chain '2' and resid 4 through 16 removed outlier: 4.228A pdb=" N VAL 2 8 " --> pdb=" O PRO 2 4 " (cutoff:3.500A) Processing helix chain '2' and resid 25 through 44 Processing helix chain '2' and resid 45 through 48 Processing helix chain '2' and resid 92 through 99 Processing helix chain '2' and resid 158 through 160 No H-bonds generated for 'chain '2' and resid 158 through 160' Processing helix chain '2' and resid 161 through 174 Processing helix chain '2' and resid 182 through 199 Processing helix chain '3' and resid 41 through 60 Processing helix chain '3' and resid 60 through 75 removed outlier: 3.647A pdb=" N ASP 3 75 " --> pdb=" O GLU 3 71 " (cutoff:3.500A) Processing helix chain '3' and resid 80 through 90 Processing helix chain '3' and resid 99 through 114 removed outlier: 3.660A pdb=" N SER 3 103 " --> pdb=" O VAL 3 99 " (cutoff:3.500A) Processing helix chain '3' and resid 127 through 146 Processing helix chain '3' and resid 146 through 161 removed outlier: 3.651A pdb=" N HIS 3 150 " --> pdb=" O ARG 3 146 " (cutoff:3.500A) Processing helix chain '3' and resid 214 through 221 Processing helix chain '3' and resid 224 through 231 removed outlier: 3.612A pdb=" N ILE 3 228 " --> pdb=" O ARG 3 224 " (cutoff:3.500A) Processing helix chain '3' and resid 247 through 260 removed outlier: 3.504A pdb=" N TYR 3 260 " --> pdb=" O ASP 3 256 " (cutoff:3.500A) Processing helix chain '3' and resid 368 through 392 removed outlier: 4.607A pdb=" N MET 3 372 " --> pdb=" O VAL 3 368 " (cutoff:3.500A) Processing helix chain '3' and resid 404 through 412 Processing helix chain '3' and resid 433 through 453 removed outlier: 3.657A pdb=" N ALA 3 437 " --> pdb=" O ARG 3 433 " (cutoff:3.500A) Processing helix chain '3' and resid 481 through 483 No H-bonds generated for 'chain '3' and resid 481 through 483' Processing helix chain '3' and resid 484 through 510 Processing helix chain '3' and resid 511 through 519 Processing helix chain '3' and resid 537 through 545 removed outlier: 3.764A pdb=" N ASP 3 545 " --> pdb=" O ARG 3 541 " (cutoff:3.500A) Processing helix chain '3' and resid 556 through 572 removed outlier: 3.686A pdb=" N ALA 3 560 " --> pdb=" O THR 3 556 " (cutoff:3.500A) Processing helix chain '3' and resid 576 through 588 removed outlier: 3.968A pdb=" N MET 3 580 " --> pdb=" O VAL 3 576 " (cutoff:3.500A) Processing helix chain '3' and resid 593 through 605 Processing helix chain '3' and resid 615 through 673 Processing helix chain '4' and resid 92 through 119 removed outlier: 3.611A pdb=" N GLU 4 96 " --> pdb=" O LEU 4 92 " (cutoff:3.500A) Processing helix chain '5' and resid 4 through 16 removed outlier: 4.287A pdb=" N VAL 5 8 " --> pdb=" O PRO 5 4 " (cutoff:3.500A) Processing helix chain '5' and resid 25 through 44 Processing helix chain '5' and resid 45 through 47 No H-bonds generated for 'chain '5' and resid 45 through 47' Processing helix chain '5' and resid 92 through 99 Processing helix chain '5' and resid 158 through 160 No H-bonds generated for 'chain '5' and resid 158 through 160' Processing helix chain '5' and resid 161 through 174 Processing helix chain '5' and resid 183 through 199 Processing helix chain '6' and resid 41 through 75 removed outlier: 5.299A pdb=" N GLU 6 62 " --> pdb=" O ASP 6 58 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N ASN 6 63 " --> pdb=" O ARG 6 59 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASP 6 75 " --> pdb=" O GLU 6 71 " (cutoff:3.500A) Processing helix chain '6' and resid 80 through 91 Processing helix chain '6' and resid 98 through 113 removed outlier: 4.478A pdb=" N GLN 6 102 " --> pdb=" O ASN 6 98 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER 6 103 " --> pdb=" O VAL 6 99 " (cutoff:3.500A) Processing helix chain '6' and resid 127 through 145 Processing helix chain '6' and resid 146 through 161 removed outlier: 3.568A pdb=" N HIS 6 150 " --> pdb=" O ARG 6 146 " (cutoff:3.500A) Processing helix chain '6' and resid 214 through 221 Processing helix chain '6' and resid 224 through 231 removed outlier: 3.649A pdb=" N ILE 6 228 " --> pdb=" O ARG 6 224 " (cutoff:3.500A) Processing helix chain '6' and resid 247 through 260 Processing helix chain '6' and resid 368 through 392 removed outlier: 4.693A pdb=" N MET 6 372 " --> pdb=" O VAL 6 368 " (cutoff:3.500A) Processing helix chain '6' and resid 404 through 411 Processing helix chain '6' and resid 433 through 453 removed outlier: 4.084A pdb=" N ALA 6 437 " --> pdb=" O ARG 6 433 " (cutoff:3.500A) Processing helix chain '6' and resid 484 through 510 removed outlier: 3.631A pdb=" N PHE 6 488 " --> pdb=" O THR 6 484 " (cutoff:3.500A) Processing helix chain '6' and resid 511 through 519 Processing helix chain '6' and resid 537 through 545 removed outlier: 3.702A pdb=" N ASP 6 545 " --> pdb=" O ARG 6 541 " (cutoff:3.500A) Processing helix chain '6' and resid 556 through 572 removed outlier: 3.663A pdb=" N ALA 6 560 " --> pdb=" O THR 6 556 " (cutoff:3.500A) Processing helix chain '6' and resid 576 through 588 removed outlier: 3.852A pdb=" N MET 6 580 " --> pdb=" O VAL 6 576 " (cutoff:3.500A) Processing helix chain '6' and resid 592 through 605 removed outlier: 4.095A pdb=" N ILE 6 596 " --> pdb=" O ASN 6 592 " (cutoff:3.500A) Processing helix chain '6' and resid 615 through 673 Processing helix chain '7' and resid 29 through 33 removed outlier: 3.654A pdb=" N GLY 7 32 " --> pdb=" O PRO 7 29 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ALA 7 33 " --> pdb=" O GLY 7 30 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 29 through 33' Processing helix chain '7' and resid 92 through 119 removed outlier: 3.747A pdb=" N GLU 7 96 " --> pdb=" O LEU 7 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 347 removed outlier: 4.019A pdb=" N GLN A 345 " --> pdb=" O VAL A 341 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU A 346 " --> pdb=" O ILE A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 356 Processing helix chain 'A' and resid 357 through 360 removed outlier: 3.866A pdb=" N ILE A 360 " --> pdb=" O PRO A 357 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 357 through 360' Processing helix chain 'A' and resid 466 through 488 Processing helix chain 'A' and resid 570 through 577 removed outlier: 3.531A pdb=" N VAL A 577 " --> pdb=" O GLU A 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 21 removed outlier: 3.597A pdb=" N LEU B 21 " --> pdb=" O PRO B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 347 Processing helix chain 'B' and resid 348 through 356 Processing helix chain 'B' and resid 466 through 488 Processing helix chain 'B' and resid 570 through 577 Processing helix chain 'C' and resid 342 through 347 removed outlier: 3.614A pdb=" N LEU C 346 " --> pdb=" O ILE C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 348 through 356 Processing helix chain 'C' and resid 357 through 360 removed outlier: 3.933A pdb=" N ILE C 360 " --> pdb=" O PRO C 357 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 357 through 360' Processing helix chain 'C' and resid 466 through 488 Processing helix chain 'C' and resid 570 through 577 Processing helix chain 'D' and resid 342 through 347 Processing helix chain 'D' and resid 348 through 356 Processing helix chain 'D' and resid 357 through 360 removed outlier: 3.868A pdb=" N ILE D 360 " --> pdb=" O PRO D 357 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 357 through 360' Processing helix chain 'D' and resid 466 through 488 Processing helix chain 'D' and resid 570 through 577 Processing helix chain 'E' and resid 17 through 21 removed outlier: 3.843A pdb=" N LEU E 21 " --> pdb=" O PRO E 18 " (cutoff:3.500A) Processing helix chain 'E' and resid 342 through 347 removed outlier: 3.704A pdb=" N LEU E 346 " --> pdb=" O ILE E 342 " (cutoff:3.500A) Processing helix chain 'E' and resid 348 through 356 Processing helix chain 'E' and resid 466 through 488 Processing helix chain 'E' and resid 570 through 577 Processing helix chain 'F' and resid 342 through 347 removed outlier: 3.598A pdb=" N LEU F 346 " --> pdb=" O ILE F 342 " (cutoff:3.500A) Processing helix chain 'F' and resid 348 through 356 Processing helix chain 'F' and resid 357 through 360 removed outlier: 3.910A pdb=" N ILE F 360 " --> pdb=" O PRO F 357 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 357 through 360' Processing helix chain 'F' and resid 466 through 488 Processing helix chain 'F' and resid 570 through 577 Processing helix chain 'G' and resid 3 through 6 removed outlier: 3.699A pdb=" N VAL G 6 " --> pdb=" O PRO G 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 3 through 6' Processing helix chain 'G' and resid 7 through 15 removed outlier: 3.707A pdb=" N ILE G 11 " --> pdb=" O PHE G 7 " (cutoff:3.500A) Processing helix chain 'G' and resid 19 through 39 Processing helix chain 'G' and resid 82 through 90 Processing helix chain 'G' and resid 139 through 146 Processing helix chain 'G' and resid 146 through 161 removed outlier: 3.760A pdb=" N ILE G 150 " --> pdb=" O TYR G 146 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE G 161 " --> pdb=" O GLU G 157 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 187 Processing helix chain 'G' and resid 188 through 193 Processing helix chain 'G' and resid 194 through 196 No H-bonds generated for 'chain 'G' and resid 194 through 196' Processing helix chain 'H' and resid 3 through 6 removed outlier: 3.672A pdb=" N VAL H 6 " --> pdb=" O PRO H 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 3 through 6' Processing helix chain 'H' and resid 7 through 15 removed outlier: 3.687A pdb=" N ILE H 11 " --> pdb=" O PHE H 7 " (cutoff:3.500A) Processing helix chain 'H' and resid 19 through 39 Processing helix chain 'H' and resid 82 through 90 Processing helix chain 'H' and resid 139 through 161 removed outlier: 3.850A pdb=" N THR H 145 " --> pdb=" O LEU H 141 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N LYS H 148 " --> pdb=" O ASP H 144 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N THR H 149 " --> pdb=" O THR H 145 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE H 150 " --> pdb=" O TYR H 146 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE H 161 " --> pdb=" O GLU H 157 " (cutoff:3.500A) Processing helix chain 'H' and resid 168 through 187 Processing helix chain 'H' and resid 188 through 193 Processing helix chain 'H' and resid 194 through 196 No H-bonds generated for 'chain 'H' and resid 194 through 196' Processing helix chain 'I' and resid 3 through 6 removed outlier: 3.663A pdb=" N VAL I 6 " --> pdb=" O PRO I 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 3 through 6' Processing helix chain 'I' and resid 7 through 15 removed outlier: 3.638A pdb=" N ILE I 11 " --> pdb=" O PHE I 7 " (cutoff:3.500A) Processing helix chain 'I' and resid 19 through 39 Processing helix chain 'I' and resid 82 through 90 Processing helix chain 'I' and resid 139 through 144 Processing helix chain 'I' and resid 146 through 161 removed outlier: 3.707A pdb=" N ILE I 150 " --> pdb=" O TYR I 146 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ILE I 161 " --> pdb=" O GLU I 157 " (cutoff:3.500A) Processing helix chain 'I' and resid 168 through 187 Processing helix chain 'I' and resid 188 through 193 Processing helix chain 'I' and resid 194 through 196 No H-bonds generated for 'chain 'I' and resid 194 through 196' Processing helix chain 'J' and resid 3 through 6 removed outlier: 3.717A pdb=" N VAL J 6 " --> pdb=" O PRO J 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 3 through 6' Processing helix chain 'J' and resid 7 through 15 removed outlier: 3.685A pdb=" N ILE J 11 " --> pdb=" O PHE J 7 " (cutoff:3.500A) Processing helix chain 'J' and resid 19 through 39 Processing helix chain 'J' and resid 82 through 90 Processing helix chain 'J' and resid 139 through 146 removed outlier: 3.584A pdb=" N THR J 145 " --> pdb=" O LEU J 141 " (cutoff:3.500A) Processing helix chain 'J' and resid 146 through 161 removed outlier: 3.740A pdb=" N ILE J 150 " --> pdb=" O TYR J 146 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE J 161 " --> pdb=" O GLU J 157 " (cutoff:3.500A) Processing helix chain 'J' and resid 168 through 187 Processing helix chain 'J' and resid 188 through 193 Processing helix chain 'J' and resid 194 through 196 No H-bonds generated for 'chain 'J' and resid 194 through 196' Processing helix chain 'K' and resid 3 through 6 removed outlier: 3.681A pdb=" N VAL K 6 " --> pdb=" O PRO K 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 3 through 6' Processing helix chain 'K' and resid 7 through 15 removed outlier: 3.669A pdb=" N ILE K 11 " --> pdb=" O PHE K 7 " (cutoff:3.500A) Processing helix chain 'K' and resid 19 through 39 Processing helix chain 'K' and resid 82 through 90 Processing helix chain 'K' and resid 139 through 144 Processing helix chain 'K' and resid 146 through 161 removed outlier: 3.748A pdb=" N ILE K 150 " --> pdb=" O TYR K 146 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE K 161 " --> pdb=" O GLU K 157 " (cutoff:3.500A) Processing helix chain 'K' and resid 168 through 187 Processing helix chain 'K' and resid 188 through 193 Processing helix chain 'K' and resid 194 through 196 No H-bonds generated for 'chain 'K' and resid 194 through 196' Processing helix chain 'L' and resid 3 through 6 removed outlier: 3.718A pdb=" N VAL L 6 " --> pdb=" O PRO L 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 3 through 6' Processing helix chain 'L' and resid 7 through 15 removed outlier: 3.803A pdb=" N ILE L 11 " --> pdb=" O PHE L 7 " (cutoff:3.500A) Processing helix chain 'L' and resid 19 through 39 Processing helix chain 'L' and resid 82 through 90 Processing helix chain 'L' and resid 139 through 145 removed outlier: 3.589A pdb=" N THR L 145 " --> pdb=" O LEU L 141 " (cutoff:3.500A) Processing helix chain 'L' and resid 146 through 161 removed outlier: 3.719A pdb=" N ILE L 150 " --> pdb=" O TYR L 146 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE L 161 " --> pdb=" O GLU L 157 " (cutoff:3.500A) Processing helix chain 'L' and resid 168 through 187 Processing helix chain 'L' and resid 188 through 193 Processing helix chain 'L' and resid 194 through 196 No H-bonds generated for 'chain 'L' and resid 194 through 196' Processing helix chain 'M' and resid 29 through 34 removed outlier: 3.687A pdb=" N GLY M 32 " --> pdb=" O PRO M 29 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ALA M 33 " --> pdb=" O GLY M 30 " (cutoff:3.500A) Processing helix chain 'M' and resid 93 through 119 Processing helix chain 'N' and resid 92 through 119 removed outlier: 4.711A pdb=" N GLU N 96 " --> pdb=" O LEU N 92 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU N 97 " --> pdb=" O THR N 93 " (cutoff:3.500A) Processing helix chain 'O' and resid 92 through 119 Processing helix chain 'P' and resid 31 through 35 removed outlier: 3.557A pdb=" N PHE P 35 " --> pdb=" O GLY P 32 " (cutoff:3.500A) Processing helix chain 'P' and resid 92 through 119 removed outlier: 3.807A pdb=" N GLU P 96 " --> pdb=" O LEU P 92 " (cutoff:3.500A) Processing helix chain 'Q' and resid 29 through 33 removed outlier: 3.512A pdb=" N GLY Q 32 " --> pdb=" O PRO Q 29 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ALA Q 33 " --> pdb=" O GLY Q 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 29 through 33' Processing helix chain 'Q' and resid 92 through 119 removed outlier: 3.615A pdb=" N GLU Q 96 " --> pdb=" O LEU Q 92 " (cutoff:3.500A) Processing helix chain 'R' and resid 29 through 33 removed outlier: 3.664A pdb=" N GLY R 32 " --> pdb=" O PRO R 29 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ALA R 33 " --> pdb=" O GLY R 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 29 through 33' Processing helix chain 'R' and resid 92 through 119 removed outlier: 3.749A pdb=" N GLU R 96 " --> pdb=" O LEU R 92 " (cutoff:3.500A) Processing helix chain 'S' and resid 7 through 15 removed outlier: 3.862A pdb=" N ILE S 11 " --> pdb=" O PHE S 7 " (cutoff:3.500A) Processing helix chain 'S' and resid 19 through 39 Processing helix chain 'S' and resid 82 through 90 Processing helix chain 'S' and resid 139 through 144 Processing helix chain 'S' and resid 146 through 161 removed outlier: 3.630A pdb=" N ILE S 150 " --> pdb=" O TYR S 146 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE S 161 " --> pdb=" O GLU S 157 " (cutoff:3.500A) Processing helix chain 'S' and resid 168 through 187 Processing helix chain 'S' and resid 188 through 193 Processing helix chain 'T' and resid 4 through 16 removed outlier: 4.150A pdb=" N VAL T 8 " --> pdb=" O PRO T 4 " (cutoff:3.500A) Processing helix chain 'T' and resid 25 through 44 Processing helix chain 'T' and resid 92 through 99 Processing helix chain 'T' and resid 160 through 175 Processing helix chain 'T' and resid 179 through 182 removed outlier: 3.530A pdb=" N ASN T 182 " --> pdb=" O GLU T 179 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 179 through 182' Processing helix chain 'T' and resid 183 through 199 Processing helix chain 'U' and resid 41 through 60 removed outlier: 3.552A pdb=" N GLN U 60 " --> pdb=" O GLU U 56 " (cutoff:3.500A) Processing helix chain 'U' and resid 60 through 75 removed outlier: 3.665A pdb=" N ASP U 75 " --> pdb=" O GLU U 71 " (cutoff:3.500A) Processing helix chain 'U' and resid 80 through 90 Processing helix chain 'U' and resid 98 through 114 removed outlier: 4.354A pdb=" N GLN U 102 " --> pdb=" O ASN U 98 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER U 103 " --> pdb=" O VAL U 99 " (cutoff:3.500A) Processing helix chain 'U' and resid 127 through 146 Processing helix chain 'U' and resid 146 through 161 Processing helix chain 'U' and resid 214 through 221 Processing helix chain 'U' and resid 224 through 231 removed outlier: 3.786A pdb=" N ILE U 228 " --> pdb=" O ARG U 224 " (cutoff:3.500A) Processing helix chain 'U' and resid 247 through 260 Processing helix chain 'U' and resid 368 through 392 removed outlier: 4.738A pdb=" N MET U 372 " --> pdb=" O VAL U 368 " (cutoff:3.500A) Processing helix chain 'U' and resid 404 through 412 Processing helix chain 'U' and resid 433 through 453 removed outlier: 4.036A pdb=" N ALA U 437 " --> pdb=" O ARG U 433 " (cutoff:3.500A) Processing helix chain 'U' and resid 484 through 510 removed outlier: 3.522A pdb=" N PHE U 488 " --> pdb=" O THR U 484 " (cutoff:3.500A) Processing helix chain 'U' and resid 511 through 519 Processing helix chain 'U' and resid 537 through 545 Processing helix chain 'U' and resid 556 through 572 removed outlier: 3.679A pdb=" N ALA U 560 " --> pdb=" O THR U 556 " (cutoff:3.500A) Processing helix chain 'U' and resid 576 through 588 removed outlier: 3.952A pdb=" N MET U 580 " --> pdb=" O VAL U 576 " (cutoff:3.500A) Processing helix chain 'U' and resid 593 through 605 Processing helix chain 'U' and resid 615 through 673 Processing helix chain 'V' and resid 31 through 35 Processing helix chain 'V' and resid 92 through 119 removed outlier: 4.379A pdb=" N GLU V 96 " --> pdb=" O LEU V 92 " (cutoff:3.500A) Processing helix chain 'W' and resid 7 through 15 removed outlier: 3.842A pdb=" N ILE W 11 " --> pdb=" O PHE W 7 " (cutoff:3.500A) Processing helix chain 'W' and resid 19 through 39 Processing helix chain 'W' and resid 82 through 90 Processing helix chain 'W' and resid 139 through 144 Processing helix chain 'W' and resid 146 through 161 removed outlier: 3.710A pdb=" N ILE W 150 " --> pdb=" O TYR W 146 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE W 161 " --> pdb=" O GLU W 157 " (cutoff:3.500A) Processing helix chain 'W' and resid 168 through 187 Processing helix chain 'W' and resid 188 through 193 Processing helix chain 'W' and resid 194 through 196 No H-bonds generated for 'chain 'W' and resid 194 through 196' Processing helix chain 'X' and resid 4 through 16 removed outlier: 4.199A pdb=" N VAL X 8 " --> pdb=" O PRO X 4 " (cutoff:3.500A) Processing helix chain 'X' and resid 25 through 44 Processing helix chain 'X' and resid 45 through 47 No H-bonds generated for 'chain 'X' and resid 45 through 47' Processing helix chain 'X' and resid 92 through 99 Processing helix chain 'X' and resid 160 through 175 Processing helix chain 'X' and resid 179 through 182 removed outlier: 3.616A pdb=" N ASN X 182 " --> pdb=" O GLU X 179 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 179 through 182' Processing helix chain 'X' and resid 183 through 199 Processing helix chain 'Y' and resid 41 through 60 Processing helix chain 'Y' and resid 60 through 75 removed outlier: 3.673A pdb=" N ASP Y 75 " --> pdb=" O GLU Y 71 " (cutoff:3.500A) Processing helix chain 'Y' and resid 80 through 91 Processing helix chain 'Y' and resid 98 through 113 removed outlier: 4.462A pdb=" N GLN Y 102 " --> pdb=" O ASN Y 98 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER Y 103 " --> pdb=" O VAL Y 99 " (cutoff:3.500A) Processing helix chain 'Y' and resid 127 through 146 Processing helix chain 'Y' and resid 146 through 161 Processing helix chain 'Y' and resid 214 through 221 Processing helix chain 'Y' and resid 224 through 231 removed outlier: 3.693A pdb=" N ILE Y 228 " --> pdb=" O ARG Y 224 " (cutoff:3.500A) Processing helix chain 'Y' and resid 247 through 260 Processing helix chain 'Y' and resid 368 through 392 removed outlier: 4.659A pdb=" N MET Y 372 " --> pdb=" O VAL Y 368 " (cutoff:3.500A) Processing helix chain 'Y' and resid 404 through 411 Processing helix chain 'Y' and resid 433 through 453 removed outlier: 4.006A pdb=" N ALA Y 437 " --> pdb=" O ARG Y 433 " (cutoff:3.500A) Processing helix chain 'Y' and resid 484 through 510 removed outlier: 3.591A pdb=" N PHE Y 488 " --> pdb=" O THR Y 484 " (cutoff:3.500A) Processing helix chain 'Y' and resid 511 through 519 Processing helix chain 'Y' and resid 537 through 545 removed outlier: 3.674A pdb=" N ASP Y 545 " --> pdb=" O ARG Y 541 " (cutoff:3.500A) Processing helix chain 'Y' and resid 556 through 572 removed outlier: 3.596A pdb=" N ALA Y 560 " --> pdb=" O THR Y 556 " (cutoff:3.500A) Processing helix chain 'Y' and resid 576 through 588 removed outlier: 3.739A pdb=" N MET Y 580 " --> pdb=" O VAL Y 576 " (cutoff:3.500A) Processing helix chain 'Y' and resid 592 through 605 removed outlier: 4.053A pdb=" N ILE Y 596 " --> pdb=" O ASN Y 592 " (cutoff:3.500A) Processing helix chain 'Y' and resid 615 through 673 Processing helix chain 'Z' and resid 92 through 119 removed outlier: 3.845A pdb=" N GLU Z 96 " --> pdb=" O LEU Z 92 " (cutoff:3.500A) Processing helix chain 'a' and resid 3 through 6 removed outlier: 3.543A pdb=" N VAL a 6 " --> pdb=" O PRO a 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 3 through 6' Processing helix chain 'a' and resid 7 through 15 removed outlier: 3.598A pdb=" N ILE a 11 " --> pdb=" O PHE a 7 " (cutoff:3.500A) Processing helix chain 'a' and resid 19 through 39 Processing helix chain 'a' and resid 82 through 90 Processing helix chain 'a' and resid 139 through 145 removed outlier: 4.016A pdb=" N THR a 145 " --> pdb=" O LEU a 141 " (cutoff:3.500A) Processing helix chain 'a' and resid 146 through 160 removed outlier: 3.658A pdb=" N ILE a 150 " --> pdb=" O TYR a 146 " (cutoff:3.500A) Processing helix chain 'a' and resid 168 through 187 Processing helix chain 'a' and resid 188 through 193 Processing helix chain 'b' and resid 4 through 16 removed outlier: 4.181A pdb=" N VAL b 8 " --> pdb=" O PRO b 4 " (cutoff:3.500A) Processing helix chain 'b' and resid 25 through 44 Processing helix chain 'b' and resid 45 through 48 removed outlier: 3.603A pdb=" N TYR b 48 " --> pdb=" O PRO b 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 45 through 48' Processing helix chain 'b' and resid 92 through 99 removed outlier: 3.601A pdb=" N LEU b 96 " --> pdb=" O ASP b 92 " (cutoff:3.500A) Processing helix chain 'b' and resid 160 through 175 Processing helix chain 'b' and resid 179 through 182 Processing helix chain 'b' and resid 183 through 199 Processing helix chain 'c' and resid 41 through 60 Processing helix chain 'c' and resid 60 through 75 removed outlier: 3.685A pdb=" N ASP c 75 " --> pdb=" O GLU c 71 " (cutoff:3.500A) Processing helix chain 'c' and resid 80 through 90 Processing helix chain 'c' and resid 98 through 114 removed outlier: 4.343A pdb=" N GLN c 102 " --> pdb=" O ASN c 98 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER c 103 " --> pdb=" O VAL c 99 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY c 114 " --> pdb=" O SER c 110 " (cutoff:3.500A) Processing helix chain 'c' and resid 127 through 146 Processing helix chain 'c' and resid 146 through 161 removed outlier: 3.612A pdb=" N HIS c 150 " --> pdb=" O ARG c 146 " (cutoff:3.500A) Processing helix chain 'c' and resid 214 through 221 Processing helix chain 'c' and resid 224 through 231 removed outlier: 3.731A pdb=" N ILE c 228 " --> pdb=" O ARG c 224 " (cutoff:3.500A) Processing helix chain 'c' and resid 247 through 260 Processing helix chain 'c' and resid 368 through 392 removed outlier: 4.711A pdb=" N MET c 372 " --> pdb=" O VAL c 368 " (cutoff:3.500A) Processing helix chain 'c' and resid 404 through 412 Processing helix chain 'c' and resid 433 through 453 removed outlier: 3.869A pdb=" N ALA c 437 " --> pdb=" O ARG c 433 " (cutoff:3.500A) Processing helix chain 'c' and resid 481 through 483 No H-bonds generated for 'chain 'c' and resid 481 through 483' Processing helix chain 'c' and resid 484 through 510 Processing helix chain 'c' and resid 511 through 519 Processing helix chain 'c' and resid 537 through 545 removed outlier: 3.722A pdb=" N ASP c 545 " --> pdb=" O ARG c 541 " (cutoff:3.500A) Processing helix chain 'c' and resid 556 through 572 removed outlier: 3.704A pdb=" N ALA c 560 " --> pdb=" O THR c 556 " (cutoff:3.500A) Processing helix chain 'c' and resid 576 through 588 removed outlier: 3.894A pdb=" N MET c 580 " --> pdb=" O VAL c 576 " (cutoff:3.500A) Processing helix chain 'c' and resid 593 through 605 Processing helix chain 'c' and resid 615 through 673 Processing helix chain 'd' and resid 29 through 33 removed outlier: 3.625A pdb=" N GLY d 32 " --> pdb=" O PRO d 29 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ALA d 33 " --> pdb=" O GLY d 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 29 through 33' Processing helix chain 'd' and resid 92 through 119 removed outlier: 3.724A pdb=" N GLU d 96 " --> pdb=" O LEU d 92 " (cutoff:3.500A) Processing helix chain 'e' and resid 7 through 15 removed outlier: 3.848A pdb=" N ILE e 11 " --> pdb=" O PHE e 7 " (cutoff:3.500A) Processing helix chain 'e' and resid 19 through 39 Processing helix chain 'e' and resid 82 through 90 Processing helix chain 'e' and resid 139 through 144 Processing helix chain 'e' and resid 146 through 161 removed outlier: 3.670A pdb=" N ILE e 150 " --> pdb=" O TYR e 146 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE e 161 " --> pdb=" O GLU e 157 " (cutoff:3.500A) Processing helix chain 'e' and resid 168 through 187 Processing helix chain 'e' and resid 188 through 190 No H-bonds generated for 'chain 'e' and resid 188 through 190' Processing helix chain 'f' and resid 4 through 16 removed outlier: 4.229A pdb=" N VAL f 8 " --> pdb=" O PRO f 4 " (cutoff:3.500A) Processing helix chain 'f' and resid 25 through 44 Processing helix chain 'f' and resid 45 through 48 removed outlier: 3.807A pdb=" N TYR f 48 " --> pdb=" O PRO f 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 45 through 48' Processing helix chain 'f' and resid 92 through 99 Processing helix chain 'f' and resid 160 through 175 Processing helix chain 'f' and resid 179 through 182 Processing helix chain 'f' and resid 183 through 199 Processing helix chain 'g' and resid 41 through 60 Processing helix chain 'g' and resid 60 through 75 removed outlier: 3.625A pdb=" N ASP g 75 " --> pdb=" O GLU g 71 " (cutoff:3.500A) Processing helix chain 'g' and resid 80 through 91 Processing helix chain 'g' and resid 98 through 113 removed outlier: 4.411A pdb=" N GLN g 102 " --> pdb=" O ASN g 98 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER g 103 " --> pdb=" O VAL g 99 " (cutoff:3.500A) Processing helix chain 'g' and resid 127 through 146 Processing helix chain 'g' and resid 146 through 161 Processing helix chain 'g' and resid 214 through 221 Processing helix chain 'g' and resid 224 through 231 removed outlier: 3.627A pdb=" N ILE g 228 " --> pdb=" O ARG g 224 " (cutoff:3.500A) Processing helix chain 'g' and resid 247 through 260 removed outlier: 3.509A pdb=" N TYR g 260 " --> pdb=" O ASP g 256 " (cutoff:3.500A) Processing helix chain 'g' and resid 368 through 392 removed outlier: 4.674A pdb=" N MET g 372 " --> pdb=" O VAL g 368 " (cutoff:3.500A) Processing helix chain 'g' and resid 404 through 412 Processing helix chain 'g' and resid 433 through 453 removed outlier: 4.181A pdb=" N ALA g 437 " --> pdb=" O ARG g 433 " (cutoff:3.500A) Processing helix chain 'g' and resid 484 through 510 removed outlier: 3.572A pdb=" N PHE g 488 " --> pdb=" O THR g 484 " (cutoff:3.500A) Processing helix chain 'g' and resid 511 through 519 Processing helix chain 'g' and resid 537 through 545 removed outlier: 3.721A pdb=" N ASP g 545 " --> pdb=" O ARG g 541 " (cutoff:3.500A) Processing helix chain 'g' and resid 556 through 572 removed outlier: 3.665A pdb=" N ALA g 560 " --> pdb=" O THR g 556 " (cutoff:3.500A) Processing helix chain 'g' and resid 576 through 588 removed outlier: 3.885A pdb=" N MET g 580 " --> pdb=" O VAL g 576 " (cutoff:3.500A) Processing helix chain 'g' and resid 593 through 605 Processing helix chain 'g' and resid 615 through 673 Processing helix chain 'h' and resid 30 through 34 removed outlier: 4.228A pdb=" N ALA h 33 " --> pdb=" O GLY h 30 " (cutoff:3.500A) Processing helix chain 'h' and resid 92 through 119 removed outlier: 4.283A pdb=" N GLU h 96 " --> pdb=" O LEU h 92 " (cutoff:3.500A) Processing helix chain 'i' and resid 7 through 15 removed outlier: 3.677A pdb=" N ILE i 11 " --> pdb=" O PHE i 7 " (cutoff:3.500A) Processing helix chain 'i' and resid 19 through 39 Processing helix chain 'i' and resid 82 through 90 Processing helix chain 'i' and resid 139 through 144 Processing helix chain 'i' and resid 146 through 161 removed outlier: 3.755A pdb=" N ILE i 150 " --> pdb=" O TYR i 146 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ILE i 161 " --> pdb=" O GLU i 157 " (cutoff:3.500A) Processing helix chain 'i' and resid 168 through 187 Processing helix chain 'i' and resid 188 through 193 Processing helix chain 'i' and resid 194 through 196 No H-bonds generated for 'chain 'i' and resid 194 through 196' Processing helix chain 'j' and resid 4 through 16 removed outlier: 4.118A pdb=" N VAL j 8 " --> pdb=" O PRO j 4 " (cutoff:3.500A) Processing helix chain 'j' and resid 25 through 44 Processing helix chain 'j' and resid 92 through 99 removed outlier: 3.703A pdb=" N GLU j 99 " --> pdb=" O LEU j 95 " (cutoff:3.500A) Processing helix chain 'j' and resid 160 through 175 Processing helix chain 'j' and resid 179 through 182 Processing helix chain 'j' and resid 183 through 199 Processing helix chain 'k' and resid 41 through 60 Processing helix chain 'k' and resid 60 through 75 removed outlier: 3.700A pdb=" N ASP k 75 " --> pdb=" O GLU k 71 " (cutoff:3.500A) Processing helix chain 'k' and resid 80 through 90 Processing helix chain 'k' and resid 99 through 114 Processing helix chain 'k' and resid 127 through 146 Processing helix chain 'k' and resid 146 through 161 removed outlier: 3.683A pdb=" N HIS k 150 " --> pdb=" O ARG k 146 " (cutoff:3.500A) Processing helix chain 'k' and resid 214 through 221 Processing helix chain 'k' and resid 224 through 231 removed outlier: 3.607A pdb=" N ILE k 228 " --> pdb=" O ARG k 224 " (cutoff:3.500A) Processing helix chain 'k' and resid 247 through 260 removed outlier: 3.508A pdb=" N ASP k 251 " --> pdb=" O ASP k 247 " (cutoff:3.500A) Processing helix chain 'k' and resid 368 through 392 removed outlier: 4.602A pdb=" N MET k 372 " --> pdb=" O VAL k 368 " (cutoff:3.500A) Processing helix chain 'k' and resid 404 through 412 Processing helix chain 'k' and resid 433 through 453 removed outlier: 3.764A pdb=" N ALA k 437 " --> pdb=" O ARG k 433 " (cutoff:3.500A) Processing helix chain 'k' and resid 481 through 483 No H-bonds generated for 'chain 'k' and resid 481 through 483' Processing helix chain 'k' and resid 484 through 510 Processing helix chain 'k' and resid 511 through 519 Processing helix chain 'k' and resid 537 through 545 removed outlier: 3.518A pdb=" N LYS k 543 " --> pdb=" O ILE k 539 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASP k 545 " --> pdb=" O ARG k 541 " (cutoff:3.500A) Processing helix chain 'k' and resid 556 through 572 removed outlier: 3.659A pdb=" N ALA k 560 " --> pdb=" O THR k 556 " (cutoff:3.500A) Processing helix chain 'k' and resid 576 through 588 removed outlier: 4.067A pdb=" N MET k 580 " --> pdb=" O VAL k 576 " (cutoff:3.500A) Processing helix chain 'k' and resid 593 through 605 Processing helix chain 'k' and resid 615 through 673 Processing helix chain 'l' and resid 92 through 119 removed outlier: 4.726A pdb=" N GLU l 96 " --> pdb=" O LEU l 92 " (cutoff:3.500A) Processing helix chain 'm' and resid 7 through 15 removed outlier: 3.661A pdb=" N ILE m 11 " --> pdb=" O PHE m 7 " (cutoff:3.500A) Processing helix chain 'm' and resid 19 through 39 Processing helix chain 'm' and resid 82 through 90 removed outlier: 3.525A pdb=" N LEU m 86 " --> pdb=" O SER m 82 " (cutoff:3.500A) Processing helix chain 'm' and resid 139 through 145 removed outlier: 3.992A pdb=" N THR m 145 " --> pdb=" O LEU m 141 " (cutoff:3.500A) Processing helix chain 'm' and resid 146 through 160 removed outlier: 3.648A pdb=" N ILE m 150 " --> pdb=" O TYR m 146 " (cutoff:3.500A) Processing helix chain 'm' and resid 168 through 187 Processing helix chain 'm' and resid 188 through 193 Processing helix chain 'n' and resid 4 through 16 removed outlier: 4.177A pdb=" N VAL n 8 " --> pdb=" O PRO n 4 " (cutoff:3.500A) Processing helix chain 'n' and resid 25 through 44 Processing helix chain 'n' and resid 45 through 47 No H-bonds generated for 'chain 'n' and resid 45 through 47' Processing helix chain 'n' and resid 92 through 99 removed outlier: 3.635A pdb=" N LEU n 96 " --> pdb=" O ASP n 92 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU n 99 " --> pdb=" O LEU n 95 " (cutoff:3.500A) Processing helix chain 'n' and resid 160 through 175 Processing helix chain 'n' and resid 179 through 182 Processing helix chain 'n' and resid 183 through 199 Processing helix chain 'o' and resid 41 through 60 Processing helix chain 'o' and resid 60 through 75 removed outlier: 3.620A pdb=" N ASP o 75 " --> pdb=" O GLU o 71 " (cutoff:3.500A) Processing helix chain 'o' and resid 80 through 91 Processing helix chain 'o' and resid 98 through 113 removed outlier: 4.498A pdb=" N GLN o 102 " --> pdb=" O ASN o 98 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER o 103 " --> pdb=" O VAL o 99 " (cutoff:3.500A) Processing helix chain 'o' and resid 127 through 146 Processing helix chain 'o' and resid 146 through 161 Processing helix chain 'o' and resid 214 through 221 Processing helix chain 'o' and resid 224 through 231 removed outlier: 3.647A pdb=" N ILE o 228 " --> pdb=" O ARG o 224 " (cutoff:3.500A) Processing helix chain 'o' and resid 247 through 260 Processing helix chain 'o' and resid 368 through 392 removed outlier: 4.581A pdb=" N MET o 372 " --> pdb=" O VAL o 368 " (cutoff:3.500A) Processing helix chain 'o' and resid 404 through 411 Processing helix chain 'o' and resid 433 through 453 removed outlier: 4.030A pdb=" N ALA o 437 " --> pdb=" O ARG o 433 " (cutoff:3.500A) Processing helix chain 'o' and resid 484 through 510 removed outlier: 3.617A pdb=" N PHE o 488 " --> pdb=" O THR o 484 " (cutoff:3.500A) Processing helix chain 'o' and resid 511 through 519 Processing helix chain 'o' and resid 537 through 545 removed outlier: 3.745A pdb=" N ASP o 545 " --> pdb=" O ARG o 541 " (cutoff:3.500A) Processing helix chain 'o' and resid 556 through 572 removed outlier: 3.662A pdb=" N ALA o 560 " --> pdb=" O THR o 556 " (cutoff:3.500A) Processing helix chain 'o' and resid 576 through 588 removed outlier: 3.755A pdb=" N MET o 580 " --> pdb=" O VAL o 576 " (cutoff:3.500A) Processing helix chain 'o' and resid 592 through 605 removed outlier: 4.130A pdb=" N ILE o 596 " --> pdb=" O ASN o 592 " (cutoff:3.500A) Processing helix chain 'o' and resid 615 through 673 Processing helix chain 'p' and resid 92 through 119 removed outlier: 3.576A pdb=" N GLU p 96 " --> pdb=" O LEU p 92 " (cutoff:3.500A) Processing helix chain 'q' and resid 4 through 16 removed outlier: 4.299A pdb=" N VAL q 8 " --> pdb=" O PRO q 4 " (cutoff:3.500A) Processing helix chain 'q' and resid 25 through 44 Processing helix chain 'q' and resid 45 through 48 removed outlier: 3.543A pdb=" N TYR q 48 " --> pdb=" O PRO q 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'q' and resid 45 through 48' Processing helix chain 'q' and resid 92 through 99 Processing helix chain 'q' and resid 158 through 160 No H-bonds generated for 'chain 'q' and resid 158 through 160' Processing helix chain 'q' and resid 161 through 175 Processing helix chain 'q' and resid 182 through 199 Processing helix chain 'r' and resid 41 through 60 removed outlier: 3.586A pdb=" N GLN r 60 " --> pdb=" O GLU r 56 " (cutoff:3.500A) Processing helix chain 'r' and resid 60 through 75 removed outlier: 3.547A pdb=" N ASP r 75 " --> pdb=" O GLU r 71 " (cutoff:3.500A) Processing helix chain 'r' and resid 80 through 90 Processing helix chain 'r' and resid 98 through 114 removed outlier: 4.469A pdb=" N GLN r 102 " --> pdb=" O ASN r 98 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER r 103 " --> pdb=" O VAL r 99 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY r 114 " --> pdb=" O SER r 110 " (cutoff:3.500A) Processing helix chain 'r' and resid 127 through 146 Processing helix chain 'r' and resid 146 through 161 removed outlier: 3.510A pdb=" N HIS r 150 " --> pdb=" O ARG r 146 " (cutoff:3.500A) Processing helix chain 'r' and resid 214 through 221 Processing helix chain 'r' and resid 224 through 231 removed outlier: 3.765A pdb=" N ILE r 228 " --> pdb=" O ARG r 224 " (cutoff:3.500A) Processing helix chain 'r' and resid 247 through 260 removed outlier: 3.516A pdb=" N TYR r 260 " --> pdb=" O ASP r 256 " (cutoff:3.500A) Processing helix chain 'r' and resid 368 through 392 removed outlier: 4.766A pdb=" N MET r 372 " --> pdb=" O VAL r 368 " (cutoff:3.500A) Processing helix chain 'r' and resid 404 through 412 Processing helix chain 'r' and resid 433 through 453 removed outlier: 3.928A pdb=" N ALA r 437 " --> pdb=" O ARG r 433 " (cutoff:3.500A) Processing helix chain 'r' and resid 481 through 483 No H-bonds generated for 'chain 'r' and resid 481 through 483' Processing helix chain 'r' and resid 484 through 510 removed outlier: 3.510A pdb=" N PHE r 488 " --> pdb=" O THR r 484 " (cutoff:3.500A) Processing helix chain 'r' and resid 511 through 519 Processing helix chain 'r' and resid 537 through 545 removed outlier: 3.844A pdb=" N ASP r 545 " --> pdb=" O ARG r 541 " (cutoff:3.500A) Processing helix chain 'r' and resid 556 through 572 removed outlier: 3.638A pdb=" N ALA r 560 " --> pdb=" O THR r 556 " (cutoff:3.500A) Processing helix chain 'r' and resid 576 through 588 removed outlier: 3.863A pdb=" N MET r 580 " --> pdb=" O VAL r 576 " (cutoff:3.500A) Processing helix chain 'r' and resid 593 through 605 Processing helix chain 'r' and resid 615 through 673 Processing helix chain 's' and resid 31 through 35 removed outlier: 3.564A pdb=" N PHE s 35 " --> pdb=" O GLY s 32 " (cutoff:3.500A) Processing helix chain 's' and resid 92 through 119 removed outlier: 4.010A pdb=" N GLU s 96 " --> pdb=" O LEU s 92 " (cutoff:3.500A) Processing helix chain 't' and resid 4 through 16 removed outlier: 4.216A pdb=" N VAL t 8 " --> pdb=" O PRO t 4 " (cutoff:3.500A) Processing helix chain 't' and resid 25 through 44 Processing helix chain 't' and resid 45 through 48 Processing helix chain 't' and resid 92 through 99 Processing helix chain 't' and resid 158 through 160 No H-bonds generated for 'chain 't' and resid 158 through 160' Processing helix chain 't' and resid 161 through 174 Processing helix chain 't' and resid 182 through 199 Processing helix chain 'u' and resid 41 through 60 Processing helix chain 'u' and resid 60 through 75 removed outlier: 3.668A pdb=" N ASP u 75 " --> pdb=" O GLU u 71 " (cutoff:3.500A) Processing helix chain 'u' and resid 80 through 91 Processing helix chain 'u' and resid 98 through 113 removed outlier: 4.462A pdb=" N GLN u 102 " --> pdb=" O ASN u 98 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER u 103 " --> pdb=" O VAL u 99 " (cutoff:3.500A) Processing helix chain 'u' and resid 127 through 146 Processing helix chain 'u' and resid 146 through 161 removed outlier: 3.571A pdb=" N HIS u 150 " --> pdb=" O ARG u 146 " (cutoff:3.500A) Processing helix chain 'u' and resid 214 through 221 Processing helix chain 'u' and resid 224 through 231 removed outlier: 3.684A pdb=" N ILE u 228 " --> pdb=" O ARG u 224 " (cutoff:3.500A) Processing helix chain 'u' and resid 247 through 260 Processing helix chain 'u' and resid 368 through 392 removed outlier: 4.573A pdb=" N MET u 372 " --> pdb=" O VAL u 368 " (cutoff:3.500A) Processing helix chain 'u' and resid 404 through 412 Processing helix chain 'u' and resid 433 through 453 removed outlier: 3.685A pdb=" N ALA u 437 " --> pdb=" O ARG u 433 " (cutoff:3.500A) Processing helix chain 'u' and resid 484 through 510 removed outlier: 3.586A pdb=" N PHE u 488 " --> pdb=" O THR u 484 " (cutoff:3.500A) Processing helix chain 'u' and resid 511 through 519 Processing helix chain 'u' and resid 537 through 545 removed outlier: 3.684A pdb=" N ASP u 545 " --> pdb=" O ARG u 541 " (cutoff:3.500A) Processing helix chain 'u' and resid 556 through 572 Processing helix chain 'u' and resid 576 through 588 removed outlier: 3.700A pdb=" N MET u 580 " --> pdb=" O VAL u 576 " (cutoff:3.500A) Processing helix chain 'u' and resid 592 through 605 removed outlier: 4.146A pdb=" N ILE u 596 " --> pdb=" O ASN u 592 " (cutoff:3.500A) Processing helix chain 'u' and resid 615 through 673 Processing helix chain 'v' and resid 28 through 33 removed outlier: 4.582A pdb=" N ALA v 33 " --> pdb=" O PRO v 29 " (cutoff:3.500A) Processing helix chain 'v' and resid 92 through 119 removed outlier: 3.969A pdb=" N GLU v 96 " --> pdb=" O LEU v 92 " (cutoff:3.500A) Processing helix chain 'w' and resid 4 through 16 removed outlier: 4.264A pdb=" N VAL w 8 " --> pdb=" O PRO w 4 " (cutoff:3.500A) Processing helix chain 'w' and resid 25 through 44 Processing helix chain 'w' and resid 45 through 48 removed outlier: 3.553A pdb=" N TYR w 48 " --> pdb=" O PRO w 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'w' and resid 45 through 48' Processing helix chain 'w' and resid 92 through 99 Processing helix chain 'w' and resid 158 through 160 No H-bonds generated for 'chain 'w' and resid 158 through 160' Processing helix chain 'w' and resid 161 through 175 Processing helix chain 'w' and resid 182 through 199 Processing helix chain 'x' and resid 41 through 60 Processing helix chain 'x' and resid 60 through 75 removed outlier: 3.682A pdb=" N ASP x 75 " --> pdb=" O GLU x 71 " (cutoff:3.500A) Processing helix chain 'x' and resid 80 through 90 Processing helix chain 'x' and resid 98 through 114 removed outlier: 4.326A pdb=" N GLN x 102 " --> pdb=" O ASN x 98 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER x 103 " --> pdb=" O VAL x 99 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY x 114 " --> pdb=" O SER x 110 " (cutoff:3.500A) Processing helix chain 'x' and resid 127 through 146 Processing helix chain 'x' and resid 146 through 161 removed outlier: 3.729A pdb=" N HIS x 150 " --> pdb=" O ARG x 146 " (cutoff:3.500A) Processing helix chain 'x' and resid 214 through 221 Processing helix chain 'x' and resid 224 through 231 removed outlier: 3.728A pdb=" N ILE x 228 " --> pdb=" O ARG x 224 " (cutoff:3.500A) Processing helix chain 'x' and resid 247 through 260 removed outlier: 3.505A pdb=" N TYR x 260 " --> pdb=" O ASP x 256 " (cutoff:3.500A) Processing helix chain 'x' and resid 368 through 392 removed outlier: 4.556A pdb=" N MET x 372 " --> pdb=" O VAL x 368 " (cutoff:3.500A) Processing helix chain 'x' and resid 404 through 412 Processing helix chain 'x' and resid 433 through 453 removed outlier: 4.140A pdb=" N ALA x 437 " --> pdb=" O ARG x 433 " (cutoff:3.500A) Processing helix chain 'x' and resid 484 through 510 Processing helix chain 'x' and resid 511 through 519 Processing helix chain 'x' and resid 537 through 545 removed outlier: 3.791A pdb=" N ASP x 545 " --> pdb=" O ARG x 541 " (cutoff:3.500A) Processing helix chain 'x' and resid 556 through 572 removed outlier: 3.732A pdb=" N ALA x 560 " --> pdb=" O THR x 556 " (cutoff:3.500A) Processing helix chain 'x' and resid 576 through 588 removed outlier: 3.963A pdb=" N MET x 580 " --> pdb=" O VAL x 576 " (cutoff:3.500A) Processing helix chain 'x' and resid 593 through 605 Processing helix chain 'x' and resid 615 through 673 Processing helix chain 'y' and resid 29 through 33 removed outlier: 3.695A pdb=" N GLY y 32 " --> pdb=" O PRO y 29 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ALA y 33 " --> pdb=" O GLY y 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'y' and resid 29 through 33' Processing helix chain 'y' and resid 92 through 119 removed outlier: 3.823A pdb=" N GLU y 96 " --> pdb=" O LEU y 92 " (cutoff:3.500A) Processing helix chain 'z' and resid 4 through 16 removed outlier: 4.294A pdb=" N VAL z 8 " --> pdb=" O PRO z 4 " (cutoff:3.500A) Processing helix chain 'z' and resid 25 through 44 Processing helix chain 'z' and resid 45 through 48 Processing helix chain 'z' and resid 92 through 99 Processing helix chain 'z' and resid 158 through 160 No H-bonds generated for 'chain 'z' and resid 158 through 160' Processing helix chain 'z' and resid 161 through 175 Processing helix chain 'z' and resid 183 through 199 Processing sheet with id=AA1, first strand: chain '0' and resid 116 through 122 Processing sheet with id=AA2, first strand: chain '0' and resid 179 through 184 removed outlier: 3.752A pdb=" N TRP 0 165 " --> pdb=" O GLU 0 184 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '0' and resid 190 through 191 Processing sheet with id=AA4, first strand: chain '0' and resid 357 through 358 Processing sheet with id=AA5, first strand: chain '0' and resid 427 through 428 removed outlier: 6.439A pdb=" N VAL 0 395 " --> pdb=" O LEU 3 419 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N LYS 3 421 " --> pdb=" O VAL 0 395 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N MET 0 397 " --> pdb=" O LYS 3 421 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '0' and resid 418 through 421 Processing sheet with id=AA7, first strand: chain '1' and resid 11 through 13 removed outlier: 3.678A pdb=" N PHE 1 44 " --> pdb=" O VAL 1 60 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL 1 60 " --> pdb=" O PHE 1 44 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N VAL 1 60 " --> pdb=" O THR 1 71 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N THR 1 71 " --> pdb=" O VAL 1 60 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N SER 1 62 " --> pdb=" O SER 1 69 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain '2' and resid 50 through 55 removed outlier: 7.093A pdb=" N VAL 2 140 " --> pdb=" O ILE 2 72 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLN 2 70 " --> pdb=" O ALA 2 142 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain '2' and resid 59 through 63 removed outlier: 5.021A pdb=" N SER 2 60 " --> pdb=" O THR 2 127 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N VAL 2 124 " --> pdb=" O ASP 2 118 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N ASP 2 118 " --> pdb=" O VAL 2 124 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N THR 2 89 " --> pdb=" O TYR 2 115 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N TYR 2 117 " --> pdb=" O THR 2 89 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain '3' and resid 116 through 122 Processing sheet with id=AB2, first strand: chain '3' and resid 181 through 184 removed outlier: 3.570A pdb=" N GLU 3 184 " --> pdb=" O TRP 3 165 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N TRP 3 165 " --> pdb=" O GLU 3 184 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain '3' and resid 190 through 191 removed outlier: 8.218A pdb=" N VAL 3 326 " --> pdb=" O ALA 3 341 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N ALA 3 341 " --> pdb=" O VAL 3 326 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N VAL 3 328 " --> pdb=" O GLU 3 339 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N GLU 3 339 " --> pdb=" O VAL 3 328 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ILE 3 330 " --> pdb=" O LEU 3 337 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain '3' and resid 357 through 358 removed outlier: 3.623A pdb=" N PHE 3 357 " --> pdb=" O TYR 3 366 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain '3' and resid 427 through 428 removed outlier: 6.707A pdb=" N VAL 3 395 " --> pdb=" O LEU 6 419 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N LYS 6 421 " --> pdb=" O VAL 3 395 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N MET 3 397 " --> pdb=" O LYS 6 421 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain '4' and resid 12 through 13 removed outlier: 3.657A pdb=" N PHE 4 44 " --> pdb=" O VAL 4 60 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N VAL 4 60 " --> pdb=" O THR 4 71 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N THR 4 71 " --> pdb=" O VAL 4 60 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N SER 4 62 " --> pdb=" O SER 4 69 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain '5' and resid 49 through 55 removed outlier: 3.592A pdb=" N CYS 5 141 " --> pdb=" O LYS 5 50 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N VAL 5 140 " --> pdb=" O ILE 5 72 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLN 5 70 " --> pdb=" O ALA 5 142 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain '5' and resid 59 through 63 removed outlier: 4.956A pdb=" N SER 5 60 " --> pdb=" O THR 5 127 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N THR 5 89 " --> pdb=" O TYR 5 115 " (cutoff:3.500A) removed outlier: 8.298A pdb=" N TYR 5 117 " --> pdb=" O THR 5 89 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain '6' and resid 116 through 122 Processing sheet with id=AC1, first strand: chain '6' and resid 179 through 184 removed outlier: 3.628A pdb=" N TRP 6 165 " --> pdb=" O GLU 6 184 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain '6' and resid 190 through 191 Processing sheet with id=AC3, first strand: chain '6' and resid 357 through 358 Processing sheet with id=AC4, first strand: chain '6' and resid 427 through 428 removed outlier: 6.362A pdb=" N VAL 6 395 " --> pdb=" O LEU U 419 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N LYS U 421 " --> pdb=" O VAL 6 395 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N MET 6 397 " --> pdb=" O LYS U 421 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain '7' and resid 12 through 13 removed outlier: 3.878A pdb=" N ALA 7 46 " --> pdb=" O VAL 7 58 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL 7 58 " --> pdb=" O ALA 7 46 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain '7' and resid 24 through 26 Processing sheet with id=AC7, first strand: chain 'A' and resid 4 through 6 removed outlier: 3.566A pdb=" N VAL A 566 " --> pdb=" O LEU A 457 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 27 through 30 removed outlier: 4.758A pdb=" N ARG A 28 " --> pdb=" O ARG A 441 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ARG A 441 " --> pdb=" O ARG A 28 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER A 558 " --> pdb=" O LEU A 438 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N ARG A 550 " --> pdb=" O LEU A 447 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 27 through 30 removed outlier: 4.758A pdb=" N ARG A 28 " --> pdb=" O ARG A 441 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ARG A 441 " --> pdb=" O ARG A 28 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER A 558 " --> pdb=" O LEU A 438 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LYS A 532 " --> pdb=" O ILE A 524 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 32 through 33 removed outlier: 3.682A pdb=" N THR A 40 " --> pdb=" O ARG A 33 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 47 through 50 removed outlier: 6.531A pdb=" N PHE A 47 " --> pdb=" O GLU A 427 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N GLU A 427 " --> pdb=" O PHE A 47 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA A 49 " --> pdb=" O ILE A 425 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ALA A 416 " --> pdb=" O GLU A 411 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLU A 411 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA A 407 " --> pdb=" O LEU A 420 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 58 through 62 removed outlier: 3.842A pdb=" N THR A 58 " --> pdb=" O TRP A 69 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 75 through 77 removed outlier: 3.528A pdb=" N TYR A 86 " --> pdb=" O ALA A 76 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N TYR A 87 " --> pdb=" O LYS A 94 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LYS A 94 " --> pdb=" O TYR A 87 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 145 through 148 Processing sheet with id=AD6, first strand: chain 'A' and resid 232 through 233 Processing sheet with id=AD7, first strand: chain 'A' and resid 270 through 276 removed outlier: 3.603A pdb=" N ALA A 272 " --> pdb=" O MET A 283 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'A' and resid 317 through 318 Processing sheet with id=AD9, first strand: chain 'A' and resid 361 through 365 removed outlier: 3.731A pdb=" N ASP A 390 " --> pdb=" O PHE A 397 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE A 397 " --> pdb=" O ASP A 390 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 4 through 6 removed outlier: 4.431A pdb=" N ASP B 564 " --> pdb=" O GLU B 459 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU B 459 " --> pdb=" O ASP B 564 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N VAL B 566 " --> pdb=" O LEU B 457 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 27 through 30 removed outlier: 4.746A pdb=" N ARG B 28 " --> pdb=" O ARG B 441 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ARG B 441 " --> pdb=" O ARG B 28 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER B 558 " --> pdb=" O LEU B 438 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ARG B 550 " --> pdb=" O LEU B 447 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 27 through 30 removed outlier: 4.746A pdb=" N ARG B 28 " --> pdb=" O ARG B 441 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ARG B 441 " --> pdb=" O ARG B 28 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER B 558 " --> pdb=" O LEU B 438 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LYS B 532 " --> pdb=" O ILE B 524 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 32 through 33 removed outlier: 3.699A pdb=" N THR B 40 " --> pdb=" O ARG B 33 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 47 through 50 removed outlier: 6.959A pdb=" N PHE B 47 " --> pdb=" O GLU B 427 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N GLU B 427 " --> pdb=" O PHE B 47 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA B 49 " --> pdb=" O ILE B 425 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA B 416 " --> pdb=" O GLU B 411 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU B 411 " --> pdb=" O ALA B 416 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALA B 407 " --> pdb=" O LEU B 420 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 58 through 62 removed outlier: 3.646A pdb=" N THR B 58 " --> pdb=" O TRP B 69 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 75 through 77 removed outlier: 3.513A pdb=" N TYR B 86 " --> pdb=" O ALA B 76 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS B 94 " --> pdb=" O TYR B 87 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 145 through 148 Processing sheet with id=AE9, first strand: chain 'B' and resid 232 through 233 Processing sheet with id=AF1, first strand: chain 'B' and resid 270 through 276 removed outlier: 3.543A pdb=" N ALA B 272 " --> pdb=" O MET B 283 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'B' and resid 317 through 318 removed outlier: 3.694A pdb=" N VAL B 332 " --> pdb=" O TYR B 325 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLN B 340 " --> pdb=" O MET B 333 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'B' and resid 361 through 364 removed outlier: 3.596A pdb=" N ASP B 390 " --> pdb=" O PHE B 397 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 4 through 6 removed outlier: 3.516A pdb=" N VAL C 566 " --> pdb=" O LEU C 457 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 27 through 30 removed outlier: 4.739A pdb=" N ARG C 28 " --> pdb=" O ARG C 441 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG C 441 " --> pdb=" O ARG C 28 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER C 558 " --> pdb=" O LEU C 438 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ARG C 550 " --> pdb=" O LEU C 447 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 27 through 30 removed outlier: 4.739A pdb=" N ARG C 28 " --> pdb=" O ARG C 441 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG C 441 " --> pdb=" O ARG C 28 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER C 558 " --> pdb=" O LEU C 438 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LYS C 532 " --> pdb=" O ILE C 524 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 32 through 33 removed outlier: 3.627A pdb=" N THR C 40 " --> pdb=" O ARG C 33 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 47 through 50 removed outlier: 6.366A pdb=" N PHE C 47 " --> pdb=" O GLU C 427 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N GLU C 427 " --> pdb=" O PHE C 47 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA C 49 " --> pdb=" O ILE C 425 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA C 407 " --> pdb=" O LEU C 420 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 58 through 62 removed outlier: 3.726A pdb=" N THR C 58 " --> pdb=" O TRP C 69 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 75 through 77 removed outlier: 3.545A pdb=" N TYR C 87 " --> pdb=" O LYS C 94 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS C 94 " --> pdb=" O TYR C 87 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'C' and resid 145 through 148 Processing sheet with id=AG3, first strand: chain 'C' and resid 232 through 233 Processing sheet with id=AG4, first strand: chain 'C' and resid 270 through 276 removed outlier: 3.543A pdb=" N ALA C 272 " --> pdb=" O MET C 283 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'C' and resid 317 through 318 removed outlier: 3.640A pdb=" N VAL C 332 " --> pdb=" O TYR C 325 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'C' and resid 361 through 365 removed outlier: 3.565A pdb=" N ASP C 390 " --> pdb=" O PHE C 397 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'D' and resid 4 through 6 removed outlier: 3.525A pdb=" N VAL D 566 " --> pdb=" O LEU D 457 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'D' and resid 27 through 30 removed outlier: 4.800A pdb=" N ARG D 28 " --> pdb=" O ARG D 441 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ARG D 441 " --> pdb=" O ARG D 28 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER D 558 " --> pdb=" O LEU D 438 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ARG D 550 " --> pdb=" O LEU D 447 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'D' and resid 27 through 30 removed outlier: 4.800A pdb=" N ARG D 28 " --> pdb=" O ARG D 441 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ARG D 441 " --> pdb=" O ARG D 28 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER D 558 " --> pdb=" O LEU D 438 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LYS D 532 " --> pdb=" O ILE D 524 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'D' and resid 32 through 33 removed outlier: 3.656A pdb=" N THR D 40 " --> pdb=" O ARG D 33 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'D' and resid 47 through 50 removed outlier: 6.545A pdb=" N PHE D 47 " --> pdb=" O GLU D 427 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N GLU D 427 " --> pdb=" O PHE D 47 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA D 49 " --> pdb=" O ILE D 425 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ALA D 416 " --> pdb=" O GLU D 411 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLU D 411 " --> pdb=" O ALA D 416 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA D 407 " --> pdb=" O LEU D 420 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'D' and resid 58 through 62 removed outlier: 3.850A pdb=" N THR D 58 " --> pdb=" O TRP D 69 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'D' and resid 75 through 77 removed outlier: 3.599A pdb=" N TYR D 86 " --> pdb=" O ALA D 76 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS D 94 " --> pdb=" O TYR D 87 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'D' and resid 145 through 148 Processing sheet with id=AH6, first strand: chain 'D' and resid 232 through 233 Processing sheet with id=AH7, first strand: chain 'D' and resid 270 through 276 removed outlier: 3.528A pdb=" N ALA D 272 " --> pdb=" O MET D 283 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'D' and resid 317 through 318 removed outlier: 3.659A pdb=" N VAL D 332 " --> pdb=" O TYR D 325 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN D 340 " --> pdb=" O MET D 333 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'D' and resid 361 through 365 removed outlier: 3.732A pdb=" N ASP D 390 " --> pdb=" O PHE D 397 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE D 397 " --> pdb=" O ASP D 390 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'E' and resid 4 through 6 removed outlier: 4.453A pdb=" N ASP E 564 " --> pdb=" O GLU E 459 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU E 459 " --> pdb=" O ASP E 564 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL E 566 " --> pdb=" O LEU E 457 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'E' and resid 27 through 30 removed outlier: 4.741A pdb=" N ARG E 28 " --> pdb=" O ARG E 441 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ARG E 441 " --> pdb=" O ARG E 28 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER E 558 " --> pdb=" O LEU E 438 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ARG E 550 " --> pdb=" O LEU E 447 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'E' and resid 27 through 30 removed outlier: 4.741A pdb=" N ARG E 28 " --> pdb=" O ARG E 441 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ARG E 441 " --> pdb=" O ARG E 28 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER E 558 " --> pdb=" O LEU E 438 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LYS E 532 " --> pdb=" O ILE E 524 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'E' and resid 32 through 33 removed outlier: 3.737A pdb=" N THR E 40 " --> pdb=" O ARG E 33 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'E' and resid 47 through 50 removed outlier: 6.942A pdb=" N PHE E 47 " --> pdb=" O GLU E 427 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N GLU E 427 " --> pdb=" O PHE E 47 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA E 49 " --> pdb=" O ILE E 425 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ALA E 416 " --> pdb=" O GLU E 411 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLU E 411 " --> pdb=" O ALA E 416 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA E 407 " --> pdb=" O LEU E 420 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'E' and resid 58 through 62 removed outlier: 3.631A pdb=" N THR E 58 " --> pdb=" O TRP E 69 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'E' and resid 75 through 77 removed outlier: 3.652A pdb=" N LEU E 85 " --> pdb=" O ILE E 96 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS E 94 " --> pdb=" O TYR E 87 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'E' and resid 145 through 148 Processing sheet with id=AI9, first strand: chain 'E' and resid 232 through 233 removed outlier: 3.548A pdb=" N ILE E 232 " --> pdb=" O ALA E 240 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA E 240 " --> pdb=" O ILE E 232 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'E' and resid 270 through 276 removed outlier: 3.550A pdb=" N ALA E 272 " --> pdb=" O MET E 283 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'E' and resid 317 through 318 removed outlier: 3.682A pdb=" N VAL E 332 " --> pdb=" O TYR E 325 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'E' and resid 361 through 364 removed outlier: 3.706A pdb=" N ASP E 390 " --> pdb=" O PHE E 397 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N PHE E 397 " --> pdb=" O ASP E 390 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'F' and resid 4 through 6 removed outlier: 4.446A pdb=" N ASP F 564 " --> pdb=" O GLU F 459 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL F 566 " --> pdb=" O LEU F 457 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'F' and resid 27 through 30 removed outlier: 4.719A pdb=" N ARG F 28 " --> pdb=" O ARG F 441 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG F 441 " --> pdb=" O ARG F 28 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER F 558 " --> pdb=" O LEU F 438 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ARG F 550 " --> pdb=" O LEU F 447 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'F' and resid 27 through 30 removed outlier: 4.719A pdb=" N ARG F 28 " --> pdb=" O ARG F 441 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG F 441 " --> pdb=" O ARG F 28 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER F 558 " --> pdb=" O LEU F 438 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYS F 532 " --> pdb=" O ILE F 524 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'F' and resid 32 through 33 removed outlier: 3.614A pdb=" N THR F 40 " --> pdb=" O ARG F 33 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'F' and resid 47 through 50 removed outlier: 6.358A pdb=" N PHE F 47 " --> pdb=" O GLU F 427 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N GLU F 427 " --> pdb=" O PHE F 47 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA F 49 " --> pdb=" O ILE F 425 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA F 416 " --> pdb=" O GLU F 411 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU F 411 " --> pdb=" O ALA F 416 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA F 407 " --> pdb=" O LEU F 420 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'F' and resid 58 through 62 removed outlier: 3.566A pdb=" N THR F 58 " --> pdb=" O TRP F 69 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'F' and resid 75 through 77 removed outlier: 3.567A pdb=" N TYR F 87 " --> pdb=" O LYS F 94 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS F 94 " --> pdb=" O TYR F 87 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'F' and resid 145 through 148 Processing sheet with id=AK3, first strand: chain 'F' and resid 231 through 233 Processing sheet with id=AK4, first strand: chain 'F' and resid 270 through 276 removed outlier: 3.538A pdb=" N ALA F 272 " --> pdb=" O MET F 283 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'F' and resid 317 through 318 removed outlier: 3.631A pdb=" N VAL F 332 " --> pdb=" O TYR F 325 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'F' and resid 361 through 365 removed outlier: 3.562A pdb=" N ASP F 390 " --> pdb=" O PHE F 397 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'G' and resid 42 through 49 removed outlier: 7.045A pdb=" N SER G 122 " --> pdb=" O GLN G 72 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N GLN G 72 " --> pdb=" O SER G 122 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N ARG G 124 " --> pdb=" O LEU G 70 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N LEU G 70 " --> pdb=" O ARG G 124 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N TYR G 126 " --> pdb=" O MET G 68 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N MET G 68 " --> pdb=" O TYR G 126 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N LEU G 128 " --> pdb=" O TYR G 66 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'G' and resid 79 through 80 removed outlier: 6.873A pdb=" N ARG G 79 " --> pdb=" O VAL G 105 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'H' and resid 42 through 49 removed outlier: 6.981A pdb=" N SER H 122 " --> pdb=" O GLN H 72 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N GLN H 72 " --> pdb=" O SER H 122 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N ARG H 124 " --> pdb=" O LEU H 70 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N LEU H 70 " --> pdb=" O ARG H 124 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N TYR H 126 " --> pdb=" O MET H 68 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N MET H 68 " --> pdb=" O TYR H 126 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N LEU H 128 " --> pdb=" O TYR H 66 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'H' and resid 79 through 80 removed outlier: 6.915A pdb=" N ARG H 79 " --> pdb=" O VAL H 105 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'I' and resid 42 through 49 removed outlier: 7.062A pdb=" N SER I 122 " --> pdb=" O GLN I 72 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N GLN I 72 " --> pdb=" O SER I 122 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N ARG I 124 " --> pdb=" O LEU I 70 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N LEU I 70 " --> pdb=" O ARG I 124 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N TYR I 126 " --> pdb=" O MET I 68 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N MET I 68 " --> pdb=" O TYR I 126 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N LEU I 128 " --> pdb=" O TYR I 66 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'I' and resid 79 through 80 removed outlier: 6.873A pdb=" N ARG I 79 " --> pdb=" O VAL I 105 " (cutoff:3.500A) Processing sheet with id=AL4, first strand: chain 'J' and resid 42 through 49 removed outlier: 7.045A pdb=" N SER J 122 " --> pdb=" O GLN J 72 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N GLN J 72 " --> pdb=" O SER J 122 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ARG J 124 " --> pdb=" O LEU J 70 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N LEU J 70 " --> pdb=" O ARG J 124 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N TYR J 126 " --> pdb=" O MET J 68 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N MET J 68 " --> pdb=" O TYR J 126 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LEU J 128 " --> pdb=" O TYR J 66 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'J' and resid 79 through 80 removed outlier: 6.862A pdb=" N ARG J 79 " --> pdb=" O VAL J 105 " (cutoff:3.500A) Processing sheet with id=AL6, first strand: chain 'K' and resid 42 through 49 removed outlier: 6.990A pdb=" N SER K 122 " --> pdb=" O GLN K 72 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N GLN K 72 " --> pdb=" O SER K 122 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N ARG K 124 " --> pdb=" O LEU K 70 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N LEU K 70 " --> pdb=" O ARG K 124 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N TYR K 126 " --> pdb=" O MET K 68 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N MET K 68 " --> pdb=" O TYR K 126 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N LEU K 128 " --> pdb=" O TYR K 66 " (cutoff:3.500A) Processing sheet with id=AL7, first strand: chain 'K' and resid 79 through 80 removed outlier: 6.860A pdb=" N ARG K 79 " --> pdb=" O VAL K 105 " (cutoff:3.500A) Processing sheet with id=AL8, first strand: chain 'L' and resid 42 through 49 removed outlier: 7.090A pdb=" N SER L 122 " --> pdb=" O GLN L 72 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N GLN L 72 " --> pdb=" O SER L 122 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N ARG L 124 " --> pdb=" O LEU L 70 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N LEU L 70 " --> pdb=" O ARG L 124 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N TYR L 126 " --> pdb=" O MET L 68 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N MET L 68 " --> pdb=" O TYR L 126 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N LEU L 128 " --> pdb=" O TYR L 66 " (cutoff:3.500A) Processing sheet with id=AL9, first strand: chain 'L' and resid 79 through 80 removed outlier: 6.863A pdb=" N ARG L 79 " --> pdb=" O VAL L 105 " (cutoff:3.500A) Processing sheet with id=AM1, first strand: chain 'M' and resid 24 through 26 removed outlier: 6.825A pdb=" N ALA M 67 " --> pdb=" O ARG M 63 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N ARG M 63 " --> pdb=" O ALA M 67 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N SER M 69 " --> pdb=" O THR M 61 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N THR M 61 " --> pdb=" O SER M 69 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE M 44 " --> pdb=" O VAL M 60 " (cutoff:3.500A) Processing sheet with id=AM2, first strand: chain 'N' and resid 24 through 26 removed outlier: 3.946A pdb=" N SER N 62 " --> pdb=" O SER N 69 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N THR N 71 " --> pdb=" O VAL N 60 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N VAL N 60 " --> pdb=" O THR N 71 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N PHE N 44 " --> pdb=" O VAL N 60 " (cutoff:3.500A) Processing sheet with id=AM3, first strand: chain 'O' and resid 24 through 26 removed outlier: 4.199A pdb=" N SER O 62 " --> pdb=" O SER O 69 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N THR O 71 " --> pdb=" O VAL O 60 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N VAL O 60 " --> pdb=" O THR O 71 " (cutoff:3.500A) Processing sheet with id=AM4, first strand: chain 'O' and resid 55 through 57 removed outlier: 3.529A pdb=" N GLU O 89 " --> pdb=" O THR O 47 " (cutoff:3.500A) Processing sheet with id=AM5, first strand: chain 'P' and resid 11 through 12 removed outlier: 3.625A pdb=" N ARG P 87 " --> pdb=" O ILE P 49 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N PHE P 44 " --> pdb=" O VAL P 60 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N VAL P 60 " --> pdb=" O THR P 71 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N THR P 71 " --> pdb=" O VAL P 60 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N SER P 62 " --> pdb=" O SER P 69 " (cutoff:3.500A) Processing sheet with id=AM6, first strand: chain 'Q' and resid 24 through 26 removed outlier: 3.833A pdb=" N SER Q 62 " --> pdb=" O SER Q 69 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N THR Q 71 " --> pdb=" O VAL Q 60 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N VAL Q 60 " --> pdb=" O THR Q 71 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE Q 44 " --> pdb=" O VAL Q 60 " (cutoff:3.500A) Processing sheet with id=AM7, first strand: chain 'R' and resid 24 through 26 Processing sheet with id=AM8, first strand: chain 'R' and resid 71 through 72 removed outlier: 3.657A pdb=" N GLU R 89 " --> pdb=" O THR R 47 " (cutoff:3.500A) Processing sheet with id=AM9, first strand: chain 'S' and resid 42 through 48 removed outlier: 3.584A pdb=" N CYS S 43 " --> pdb=" O GLY S 127 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLY S 127 " --> pdb=" O CYS S 43 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N SER S 122 " --> pdb=" O PHE S 73 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N PHE S 73 " --> pdb=" O SER S 122 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ARG S 124 " --> pdb=" O VAL S 71 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N VAL S 71 " --> pdb=" O ARG S 124 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N TYR S 126 " --> pdb=" O GLU S 69 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N LYS S 130 " --> pdb=" O LEU S 65 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N LEU S 65 " --> pdb=" O LYS S 130 " (cutoff:3.500A) Processing sheet with id=AN1, first strand: chain 'S' and resid 79 through 80 removed outlier: 6.960A pdb=" N ARG S 79 " --> pdb=" O VAL S 105 " (cutoff:3.500A) Processing sheet with id=AN2, first strand: chain 'T' and resid 50 through 55 removed outlier: 3.815A pdb=" N LYS T 50 " --> pdb=" O CYS T 141 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N CYS T 141 " --> pdb=" O LYS T 50 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N VAL T 140 " --> pdb=" O ILE T 72 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLN T 70 " --> pdb=" O ALA T 142 " (cutoff:3.500A) Processing sheet with id=AN3, first strand: chain 'T' and resid 89 through 90 removed outlier: 6.227A pdb=" N THR T 89 " --> pdb=" O TYR T 115 " (cutoff:3.500A) Processing sheet with id=AN4, first strand: chain 'U' and resid 116 through 122 Processing sheet with id=AN5, first strand: chain 'U' and resid 179 through 184 removed outlier: 3.516A pdb=" N GLU U 184 " --> pdb=" O TRP U 165 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TRP U 165 " --> pdb=" O GLU U 184 " (cutoff:3.500A) Processing sheet with id=AN6, first strand: chain 'U' and resid 190 through 191 Processing sheet with id=AN7, first strand: chain 'U' and resid 357 through 358 Processing sheet with id=AN8, first strand: chain 'U' and resid 427 through 429 removed outlier: 6.431A pdb=" N VAL U 395 " --> pdb=" O LEU Y 419 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N LYS Y 421 " --> pdb=" O VAL U 395 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N MET U 397 " --> pdb=" O LYS Y 421 " (cutoff:3.500A) Processing sheet with id=AN9, first strand: chain 'V' and resid 11 through 13 removed outlier: 3.605A pdb=" N PHE V 44 " --> pdb=" O VAL V 60 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N VAL V 60 " --> pdb=" O THR V 71 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N THR V 71 " --> pdb=" O VAL V 60 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N SER V 62 " --> pdb=" O SER V 69 " (cutoff:3.500A) Processing sheet with id=AO1, first strand: chain 'W' and resid 42 through 49 removed outlier: 3.607A pdb=" N CYS W 43 " --> pdb=" O GLY W 127 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLY W 127 " --> pdb=" O CYS W 43 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N SER W 122 " --> pdb=" O PHE W 73 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N PHE W 73 " --> pdb=" O SER W 122 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ARG W 124 " --> pdb=" O VAL W 71 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N VAL W 71 " --> pdb=" O ARG W 124 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N TYR W 126 " --> pdb=" O GLU W 69 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU W 67 " --> pdb=" O LEU W 128 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N LYS W 130 " --> pdb=" O LEU W 65 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N LEU W 65 " --> pdb=" O LYS W 130 " (cutoff:3.500A) removed outlier: 11.026A pdb=" N GLU W 69 " --> pdb=" O PRO W 80 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N VAL W 71 " --> pdb=" O MET W 78 " (cutoff:3.500A) removed outlier: 8.842A pdb=" N VAL W 105 " --> pdb=" O ASN W 77 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ARG W 79 " --> pdb=" O VAL W 105 " (cutoff:3.500A) Processing sheet with id=AO2, first strand: chain 'X' and resid 49 through 55 removed outlier: 4.262A pdb=" N LYS X 50 " --> pdb=" O CYS X 141 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N CYS X 141 " --> pdb=" O LYS X 50 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N GLU X 138 " --> pdb=" O ASP X 73 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N ASP X 73 " --> pdb=" O GLU X 138 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N VAL X 140 " --> pdb=" O LEU X 71 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N LEU X 71 " --> pdb=" O VAL X 140 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ALA X 142 " --> pdb=" O ILE X 69 " (cutoff:3.500A) Processing sheet with id=AO3, first strand: chain 'X' and resid 59 through 63 removed outlier: 5.088A pdb=" N SER X 60 " --> pdb=" O THR X 127 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N THR X 89 " --> pdb=" O TYR X 115 " (cutoff:3.500A) Processing sheet with id=AO4, first strand: chain 'Y' and resid 116 through 122 Processing sheet with id=AO5, first strand: chain 'Y' and resid 183 through 184 removed outlier: 3.755A pdb=" N TRP Y 165 " --> pdb=" O GLU Y 184 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE Y 166 " --> pdb=" O THR Y 352 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR Y 352 " --> pdb=" O ILE Y 166 " (cutoff:3.500A) Processing sheet with id=AO6, first strand: chain 'Y' and resid 169 through 170 Processing sheet with id=AO7, first strand: chain 'Y' and resid 190 through 191 removed outlier: 3.686A pdb=" N GLU Y 278 " --> pdb=" O ARG Y 208 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS Y 283 " --> pdb=" O ARG Y 325 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG Y 325 " --> pdb=" O LYS Y 283 " (cutoff:3.500A) Processing sheet with id=AO8, first strand: chain 'Y' and resid 357 through 358 removed outlier: 3.556A pdb=" N PHE Y 357 " --> pdb=" O TYR Y 366 " (cutoff:3.500A) Processing sheet with id=AO9, first strand: chain 'Y' and resid 427 through 428 removed outlier: 6.397A pdb=" N VAL Y 395 " --> pdb=" O LEU c 419 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N LYS c 421 " --> pdb=" O VAL Y 395 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N MET Y 397 " --> pdb=" O LYS c 421 " (cutoff:3.500A) Processing sheet with id=AP1, first strand: chain 'Z' and resid 12 through 13 removed outlier: 3.679A pdb=" N PHE Z 44 " --> pdb=" O VAL Z 60 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N VAL Z 60 " --> pdb=" O THR Z 71 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N THR Z 71 " --> pdb=" O VAL Z 60 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N SER Z 62 " --> pdb=" O SER Z 69 " (cutoff:3.500A) Processing sheet with id=AP2, first strand: chain 'a' and resid 42 through 49 removed outlier: 3.669A pdb=" N GLY a 127 " --> pdb=" O CYS a 43 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N SER a 122 " --> pdb=" O PHE a 73 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N PHE a 73 " --> pdb=" O SER a 122 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ARG a 124 " --> pdb=" O VAL a 71 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N VAL a 71 " --> pdb=" O ARG a 124 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N TYR a 126 " --> pdb=" O GLU a 69 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU a 67 " --> pdb=" O LEU a 128 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N LYS a 130 " --> pdb=" O LEU a 65 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N LEU a 65 " --> pdb=" O LYS a 130 " (cutoff:3.500A) Processing sheet with id=AP3, first strand: chain 'a' and resid 79 through 80 removed outlier: 6.743A pdb=" N ARG a 79 " --> pdb=" O VAL a 105 " (cutoff:3.500A) Processing sheet with id=AP4, first strand: chain 'b' and resid 50 through 55 removed outlier: 3.692A pdb=" N LYS b 50 " --> pdb=" O CYS b 141 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N CYS b 141 " --> pdb=" O LYS b 50 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N VAL b 140 " --> pdb=" O ILE b 72 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLN b 70 " --> pdb=" O ALA b 142 " (cutoff:3.500A) Processing sheet with id=AP5, first strand: chain 'b' and resid 89 through 90 removed outlier: 6.425A pdb=" N THR b 89 " --> pdb=" O TYR b 115 " (cutoff:3.500A) Processing sheet with id=AP6, first strand: chain 'c' and resid 116 through 122 Processing sheet with id=AP7, first strand: chain 'c' and resid 179 through 184 removed outlier: 3.773A pdb=" N GLU c 184 " --> pdb=" O TRP c 165 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N TRP c 165 " --> pdb=" O GLU c 184 " (cutoff:3.500A) Processing sheet with id=AP8, first strand: chain 'c' and resid 190 through 191 removed outlier: 8.284A pdb=" N VAL c 326 " --> pdb=" O ALA c 341 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N ALA c 341 " --> pdb=" O VAL c 326 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N VAL c 328 " --> pdb=" O GLU c 339 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N GLU c 339 " --> pdb=" O VAL c 328 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ILE c 330 " --> pdb=" O LEU c 337 " (cutoff:3.500A) Processing sheet with id=AP9, first strand: chain 'c' and resid 357 through 358 removed outlier: 3.538A pdb=" N PHE c 357 " --> pdb=" O TYR c 366 " (cutoff:3.500A) Processing sheet with id=AQ1, first strand: chain 'c' and resid 427 through 429 removed outlier: 6.508A pdb=" N VAL c 395 " --> pdb=" O LEU g 419 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N LYS g 421 " --> pdb=" O VAL c 395 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N MET c 397 " --> pdb=" O LYS g 421 " (cutoff:3.500A) Processing sheet with id=AQ2, first strand: chain 'd' and resid 24 through 26 removed outlier: 4.108A pdb=" N SER d 62 " --> pdb=" O SER d 69 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N THR d 71 " --> pdb=" O VAL d 60 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N VAL d 60 " --> pdb=" O THR d 71 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU d 56 " --> pdb=" O LEU d 48 " (cutoff:3.500A) Processing sheet with id=AQ3, first strand: chain 'e' and resid 42 through 48 removed outlier: 3.536A pdb=" N CYS e 43 " --> pdb=" O GLY e 127 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY e 127 " --> pdb=" O CYS e 43 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N SER e 122 " --> pdb=" O PHE e 73 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N PHE e 73 " --> pdb=" O SER e 122 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ARG e 124 " --> pdb=" O VAL e 71 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N VAL e 71 " --> pdb=" O ARG e 124 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N TYR e 126 " --> pdb=" O GLU e 69 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N LYS e 130 " --> pdb=" O LEU e 65 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N LEU e 65 " --> pdb=" O LYS e 130 " (cutoff:3.500A) Processing sheet with id=AQ4, first strand: chain 'e' and resid 79 through 80 removed outlier: 7.090A pdb=" N ARG e 79 " --> pdb=" O VAL e 105 " (cutoff:3.500A) Processing sheet with id=AQ5, first strand: chain 'f' and resid 50 through 55 removed outlier: 4.220A pdb=" N LYS f 50 " --> pdb=" O CYS f 141 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N CYS f 141 " --> pdb=" O LYS f 50 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N GLU f 138 " --> pdb=" O ASP f 73 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N ASP f 73 " --> pdb=" O GLU f 138 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N VAL f 140 " --> pdb=" O LEU f 71 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N LEU f 71 " --> pdb=" O VAL f 140 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ALA f 142 " --> pdb=" O ILE f 69 " (cutoff:3.500A) Processing sheet with id=AQ6, first strand: chain 'f' and resid 59 through 63 removed outlier: 5.089A pdb=" N SER f 60 " --> pdb=" O THR f 127 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N THR f 89 " --> pdb=" O TYR f 115 " (cutoff:3.500A) Processing sheet with id=AQ7, first strand: chain 'g' and resid 116 through 122 Processing sheet with id=AQ8, first strand: chain 'g' and resid 179 through 184 removed outlier: 3.750A pdb=" N TRP g 165 " --> pdb=" O GLU g 184 " (cutoff:3.500A) Processing sheet with id=AQ9, first strand: chain 'g' and resid 190 through 191 Processing sheet with id=AR1, first strand: chain 'g' and resid 357 through 358 Processing sheet with id=AR2, first strand: chain 'g' and resid 427 through 428 removed outlier: 6.499A pdb=" N VAL g 395 " --> pdb=" O LEU k 419 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N LYS k 421 " --> pdb=" O VAL g 395 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N MET g 397 " --> pdb=" O LYS k 421 " (cutoff:3.500A) Processing sheet with id=AR3, first strand: chain 'h' and resid 24 through 26 removed outlier: 4.097A pdb=" N SER h 62 " --> pdb=" O SER h 69 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N THR h 71 " --> pdb=" O VAL h 60 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N VAL h 60 " --> pdb=" O THR h 71 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE h 44 " --> pdb=" O VAL h 60 " (cutoff:3.500A) Processing sheet with id=AR4, first strand: chain 'i' and resid 42 through 49 removed outlier: 3.621A pdb=" N CYS i 43 " --> pdb=" O GLY i 127 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLY i 127 " --> pdb=" O CYS i 43 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N SER i 122 " --> pdb=" O PHE i 73 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N PHE i 73 " --> pdb=" O SER i 122 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ARG i 124 " --> pdb=" O VAL i 71 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N VAL i 71 " --> pdb=" O ARG i 124 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N TYR i 126 " --> pdb=" O GLU i 69 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU i 67 " --> pdb=" O LEU i 128 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N LYS i 130 " --> pdb=" O LEU i 65 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N LEU i 65 " --> pdb=" O LYS i 130 " (cutoff:3.500A) Processing sheet with id=AR5, first strand: chain 'i' and resid 79 through 80 removed outlier: 7.138A pdb=" N ARG i 79 " --> pdb=" O VAL i 105 " (cutoff:3.500A) Processing sheet with id=AR6, first strand: chain 'j' and resid 50 through 55 removed outlier: 3.833A pdb=" N LYS j 50 " --> pdb=" O CYS j 141 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N CYS j 141 " --> pdb=" O LYS j 50 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N VAL j 140 " --> pdb=" O ILE j 72 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLN j 70 " --> pdb=" O ALA j 142 " (cutoff:3.500A) Processing sheet with id=AR7, first strand: chain 'j' and resid 89 through 90 removed outlier: 6.226A pdb=" N THR j 89 " --> pdb=" O TYR j 115 " (cutoff:3.500A) Processing sheet with id=AR8, first strand: chain 'k' and resid 116 through 122 Processing sheet with id=AR9, first strand: chain 'k' and resid 179 through 184 removed outlier: 3.596A pdb=" N GLU k 184 " --> pdb=" O TRP k 165 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N TRP k 165 " --> pdb=" O GLU k 184 " (cutoff:3.500A) Processing sheet with id=AS1, first strand: chain 'k' and resid 190 through 191 removed outlier: 8.207A pdb=" N VAL k 326 " --> pdb=" O ALA k 341 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N ALA k 341 " --> pdb=" O VAL k 326 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N VAL k 328 " --> pdb=" O GLU k 339 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N GLU k 339 " --> pdb=" O VAL k 328 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ILE k 330 " --> pdb=" O LEU k 337 " (cutoff:3.500A) Processing sheet with id=AS2, first strand: chain 'k' and resid 357 through 358 removed outlier: 3.624A pdb=" N PHE k 357 " --> pdb=" O TYR k 366 " (cutoff:3.500A) Processing sheet with id=AS3, first strand: chain 'k' and resid 427 through 429 removed outlier: 6.506A pdb=" N VAL k 395 " --> pdb=" O LEU o 419 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N LYS o 421 " --> pdb=" O VAL k 395 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N MET k 397 " --> pdb=" O LYS o 421 " (cutoff:3.500A) Processing sheet with id=AS4, first strand: chain 'l' and resid 24 through 26 removed outlier: 3.988A pdb=" N SER l 62 " --> pdb=" O SER l 69 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N THR l 71 " --> pdb=" O VAL l 60 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N VAL l 60 " --> pdb=" O THR l 71 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N PHE l 44 " --> pdb=" O VAL l 60 " (cutoff:3.500A) Processing sheet with id=AS5, first strand: chain 'm' and resid 42 through 49 removed outlier: 3.746A pdb=" N GLY m 127 " --> pdb=" O CYS m 43 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N LEU m 128 " --> pdb=" O MET m 68 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N MET m 68 " --> pdb=" O LEU m 128 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N LYS m 130 " --> pdb=" O TYR m 66 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N TYR m 66 " --> pdb=" O LYS m 130 " (cutoff:3.500A) Processing sheet with id=AS6, first strand: chain 'm' and resid 79 through 80 removed outlier: 6.793A pdb=" N ARG m 79 " --> pdb=" O VAL m 105 " (cutoff:3.500A) Processing sheet with id=AS7, first strand: chain 'n' and resid 49 through 55 removed outlier: 4.556A pdb=" N LYS n 50 " --> pdb=" O CYS n 141 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N CYS n 141 " --> pdb=" O LYS n 50 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N VAL n 140 " --> pdb=" O ILE n 72 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLN n 70 " --> pdb=" O ALA n 142 " (cutoff:3.500A) Processing sheet with id=AS8, first strand: chain 'n' and resid 59 through 63 removed outlier: 5.062A pdb=" N SER n 60 " --> pdb=" O THR n 127 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N THR n 89 " --> pdb=" O TYR n 115 " (cutoff:3.500A) Processing sheet with id=AS9, first strand: chain 'o' and resid 116 through 122 Processing sheet with id=AT1, first strand: chain 'o' and resid 183 through 184 removed outlier: 3.740A pdb=" N TRP o 165 " --> pdb=" O GLU o 184 " (cutoff:3.500A) Processing sheet with id=AT2, first strand: chain 'o' and resid 169 through 170 Processing sheet with id=AT3, first strand: chain 'o' and resid 190 through 191 removed outlier: 3.612A pdb=" N LYS o 283 " --> pdb=" O ARG o 325 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ARG o 325 " --> pdb=" O LYS o 283 " (cutoff:3.500A) Processing sheet with id=AT4, first strand: chain 'o' and resid 357 through 358 removed outlier: 3.522A pdb=" N PHE o 357 " --> pdb=" O TYR o 366 " (cutoff:3.500A) Processing sheet with id=AT5, first strand: chain 'o' and resid 427 through 428 removed outlier: 6.368A pdb=" N VAL o 395 " --> pdb=" O LEU r 419 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N LYS r 421 " --> pdb=" O VAL o 395 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N MET o 397 " --> pdb=" O LYS r 421 " (cutoff:3.500A) Processing sheet with id=AT6, first strand: chain 'p' and resid 12 through 13 removed outlier: 3.861A pdb=" N PHE p 44 " --> pdb=" O VAL p 60 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N VAL p 60 " --> pdb=" O THR p 71 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N THR p 71 " --> pdb=" O VAL p 60 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N SER p 62 " --> pdb=" O SER p 69 " (cutoff:3.500A) Processing sheet with id=AT7, first strand: chain 'q' and resid 50 through 55 removed outlier: 3.908A pdb=" N CYS q 141 " --> pdb=" O LYS q 50 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N VAL q 140 " --> pdb=" O ILE q 72 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLN q 70 " --> pdb=" O ALA q 142 " (cutoff:3.500A) Processing sheet with id=AT8, first strand: chain 'q' and resid 59 through 63 removed outlier: 5.041A pdb=" N SER q 60 " --> pdb=" O THR q 127 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N THR q 89 " --> pdb=" O TYR q 115 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N TYR q 117 " --> pdb=" O THR q 89 " (cutoff:3.500A) Processing sheet with id=AT9, first strand: chain 'r' and resid 116 through 122 Processing sheet with id=AU1, first strand: chain 'r' and resid 179 through 184 removed outlier: 3.671A pdb=" N TRP r 165 " --> pdb=" O GLU r 184 " (cutoff:3.500A) Processing sheet with id=AU2, first strand: chain 'r' and resid 190 through 191 removed outlier: 8.299A pdb=" N VAL r 326 " --> pdb=" O ALA r 341 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N ALA r 341 " --> pdb=" O VAL r 326 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N VAL r 328 " --> pdb=" O GLU r 339 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N GLU r 339 " --> pdb=" O VAL r 328 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ILE r 330 " --> pdb=" O LEU r 337 " (cutoff:3.500A) Processing sheet with id=AU3, first strand: chain 'r' and resid 357 through 358 removed outlier: 3.528A pdb=" N PHE r 357 " --> pdb=" O TYR r 366 " (cutoff:3.500A) Processing sheet with id=AU4, first strand: chain 'r' and resid 427 through 429 removed outlier: 6.584A pdb=" N VAL r 395 " --> pdb=" O LEU u 419 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N LYS u 421 " --> pdb=" O VAL r 395 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N MET r 397 " --> pdb=" O LYS u 421 " (cutoff:3.500A) Processing sheet with id=AU5, first strand: chain 's' and resid 11 through 12 removed outlier: 3.602A pdb=" N PHE s 44 " --> pdb=" O VAL s 60 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N VAL s 60 " --> pdb=" O THR s 71 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N THR s 71 " --> pdb=" O VAL s 60 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N SER s 62 " --> pdb=" O SER s 69 " (cutoff:3.500A) Processing sheet with id=AU6, first strand: chain 't' and resid 50 through 55 removed outlier: 3.714A pdb=" N CYS t 141 " --> pdb=" O LYS t 50 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N VAL t 140 " --> pdb=" O ILE t 72 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLN t 70 " --> pdb=" O ALA t 142 " (cutoff:3.500A) Processing sheet with id=AU7, first strand: chain 't' and resid 59 through 63 removed outlier: 5.031A pdb=" N SER t 60 " --> pdb=" O THR t 127 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N VAL t 124 " --> pdb=" O ASP t 118 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N ASP t 118 " --> pdb=" O VAL t 124 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N THR t 89 " --> pdb=" O TYR t 115 " (cutoff:3.500A) removed outlier: 8.327A pdb=" N TYR t 117 " --> pdb=" O THR t 89 " (cutoff:3.500A) Processing sheet with id=AU8, first strand: chain 'u' and resid 116 through 122 Processing sheet with id=AU9, first strand: chain 'u' and resid 183 through 184 removed outlier: 3.767A pdb=" N TRP u 165 " --> pdb=" O GLU u 184 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR u 352 " --> pdb=" O ILE u 166 " (cutoff:3.500A) Processing sheet with id=AV1, first strand: chain 'u' and resid 169 through 170 Processing sheet with id=AV2, first strand: chain 'u' and resid 190 through 191 removed outlier: 3.531A pdb=" N GLU u 278 " --> pdb=" O ARG u 208 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS u 283 " --> pdb=" O ARG u 325 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ARG u 325 " --> pdb=" O LYS u 283 " (cutoff:3.500A) Processing sheet with id=AV3, first strand: chain 'u' and resid 357 through 358 removed outlier: 3.574A pdb=" N PHE u 357 " --> pdb=" O TYR u 366 " (cutoff:3.500A) Processing sheet with id=AV4, first strand: chain 'u' and resid 427 through 428 removed outlier: 6.461A pdb=" N VAL u 395 " --> pdb=" O LEU x 419 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N LYS x 421 " --> pdb=" O VAL u 395 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N MET u 397 " --> pdb=" O LYS x 421 " (cutoff:3.500A) Processing sheet with id=AV5, first strand: chain 'v' and resid 11 through 12 removed outlier: 3.682A pdb=" N PHE v 44 " --> pdb=" O VAL v 60 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N VAL v 60 " --> pdb=" O THR v 71 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N THR v 71 " --> pdb=" O VAL v 60 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N SER v 62 " --> pdb=" O SER v 69 " (cutoff:3.500A) Processing sheet with id=AV6, first strand: chain 'w' and resid 50 through 55 removed outlier: 3.906A pdb=" N CYS w 141 " --> pdb=" O LYS w 50 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N VAL w 140 " --> pdb=" O ILE w 72 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N GLN w 70 " --> pdb=" O ALA w 142 " (cutoff:3.500A) Processing sheet with id=AV7, first strand: chain 'w' and resid 59 through 63 removed outlier: 5.030A pdb=" N SER w 60 " --> pdb=" O THR w 127 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N THR w 89 " --> pdb=" O TYR w 115 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N TYR w 117 " --> pdb=" O THR w 89 " (cutoff:3.500A) Processing sheet with id=AV8, first strand: chain 'x' and resid 116 through 122 Processing sheet with id=AV9, first strand: chain 'x' and resid 179 through 184 removed outlier: 3.885A pdb=" N GLU x 184 " --> pdb=" O TRP x 165 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N TRP x 165 " --> pdb=" O GLU x 184 " (cutoff:3.500A) Processing sheet with id=AW1, first strand: chain 'x' and resid 190 through 191 removed outlier: 7.970A pdb=" N VAL x 326 " --> pdb=" O ALA x 341 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N ALA x 341 " --> pdb=" O VAL x 326 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N VAL x 328 " --> pdb=" O GLU x 339 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLU x 339 " --> pdb=" O VAL x 328 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ILE x 330 " --> pdb=" O LEU x 337 " (cutoff:3.500A) Processing sheet with id=AW2, first strand: chain 'x' and resid 357 through 358 removed outlier: 3.557A pdb=" N PHE x 357 " --> pdb=" O TYR x 366 " (cutoff:3.500A) Processing sheet with id=AW3, first strand: chain 'y' and resid 24 through 26 Processing sheet with id=AW4, first strand: chain 'y' and resid 71 through 72 removed outlier: 3.502A pdb=" N PHE y 44 " --> pdb=" O VAL y 60 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU y 89 " --> pdb=" O THR y 47 " (cutoff:3.500A) Processing sheet with id=AW5, first strand: chain 'z' and resid 50 through 55 removed outlier: 3.575A pdb=" N CYS z 141 " --> pdb=" O LYS z 50 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N VAL z 140 " --> pdb=" O ILE z 72 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLN z 70 " --> pdb=" O ALA z 142 " (cutoff:3.500A) Processing sheet with id=AW6, first strand: chain 'z' and resid 59 through 63 removed outlier: 4.912A pdb=" N SER z 60 " --> pdb=" O THR z 127 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N THR z 89 " --> pdb=" O TYR z 115 " (cutoff:3.500A) removed outlier: 8.285A pdb=" N TYR z 117 " --> pdb=" O THR z 89 " (cutoff:3.500A) 6463 hydrogen bonds defined for protein. 18615 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 66.45 Time building geometry restraints manager: 42.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 41903 1.34 - 1.46: 21350 1.46 - 1.58: 66275 1.58 - 1.70: 6 1.70 - 1.82: 972 Bond restraints: 130506 Sorted by residual: bond pdb=" CB PRO 4 84 " pdb=" CG PRO 4 84 " ideal model delta sigma weight residual 1.492 1.613 -0.121 5.00e-02 4.00e+02 5.82e+00 bond pdb=" CB PRO Z 84 " pdb=" CG PRO Z 84 " ideal model delta sigma weight residual 1.492 1.611 -0.119 5.00e-02 4.00e+02 5.65e+00 bond pdb=" CB PRO i 91 " pdb=" CG PRO i 91 " ideal model delta sigma weight residual 1.492 1.609 -0.117 5.00e-02 4.00e+02 5.48e+00 bond pdb=" CB PRO W 91 " pdb=" CG PRO W 91 " ideal model delta sigma weight residual 1.492 1.606 -0.114 5.00e-02 4.00e+02 5.21e+00 bond pdb=" CB PRO v 84 " pdb=" CG PRO v 84 " ideal model delta sigma weight residual 1.492 1.593 -0.101 5.00e-02 4.00e+02 4.10e+00 ... (remaining 130501 not shown) Histogram of bond angle deviations from ideal: 97.26 - 104.68: 2372 104.68 - 112.11: 65205 112.11 - 119.53: 42991 119.53 - 126.95: 65050 126.95 - 134.38: 1628 Bond angle restraints: 177246 Sorted by residual: angle pdb=" N PRO A 113 " pdb=" CA PRO A 113 " pdb=" CB PRO A 113 " ideal model delta sigma weight residual 103.25 111.60 -8.35 1.05e+00 9.07e-01 6.33e+01 angle pdb=" N PRO E 113 " pdb=" CA PRO E 113 " pdb=" CB PRO E 113 " ideal model delta sigma weight residual 103.25 111.58 -8.33 1.05e+00 9.07e-01 6.29e+01 angle pdb=" N PRO B 113 " pdb=" CA PRO B 113 " pdb=" CB PRO B 113 " ideal model delta sigma weight residual 103.25 111.55 -8.30 1.05e+00 9.07e-01 6.25e+01 angle pdb=" N PRO C 113 " pdb=" CA PRO C 113 " pdb=" CB PRO C 113 " ideal model delta sigma weight residual 103.25 111.54 -8.29 1.05e+00 9.07e-01 6.23e+01 angle pdb=" N PRO D 113 " pdb=" CA PRO D 113 " pdb=" CB PRO D 113 " ideal model delta sigma weight residual 103.25 111.52 -8.27 1.05e+00 9.07e-01 6.20e+01 ... (remaining 177241 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.06: 71974 18.06 - 36.13: 5643 36.13 - 54.19: 916 54.19 - 72.26: 180 72.26 - 90.32: 127 Dihedral angle restraints: 78840 sinusoidal: 30198 harmonic: 48642 Sorted by residual: dihedral pdb=" CA VAL H 116 " pdb=" C VAL H 116 " pdb=" N PRO H 117 " pdb=" CA PRO H 117 " ideal model delta harmonic sigma weight residual 180.00 148.74 31.26 0 5.00e+00 4.00e-02 3.91e+01 dihedral pdb=" CA VAL F 80 " pdb=" C VAL F 80 " pdb=" N ALA F 81 " pdb=" CA ALA F 81 " ideal model delta harmonic sigma weight residual -180.00 -149.02 -30.98 0 5.00e+00 4.00e-02 3.84e+01 dihedral pdb=" CA VAL C 80 " pdb=" C VAL C 80 " pdb=" N ALA C 81 " pdb=" CA ALA C 81 " ideal model delta harmonic sigma weight residual -180.00 -151.08 -28.92 0 5.00e+00 4.00e-02 3.34e+01 ... (remaining 78837 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 16673 0.055 - 0.110: 2685 0.110 - 0.165: 454 0.165 - 0.220: 44 0.220 - 0.275: 34 Chirality restraints: 19890 Sorted by residual: chirality pdb=" CA THR 4 93 " pdb=" N THR 4 93 " pdb=" C THR 4 93 " pdb=" CB THR 4 93 " both_signs ideal model delta sigma weight residual False 2.53 2.25 0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CA PRO D 109 " pdb=" N PRO D 109 " pdb=" C PRO D 109 " pdb=" CB PRO D 109 " both_signs ideal model delta sigma weight residual False 2.72 2.45 0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" CA PRO F 109 " pdb=" N PRO F 109 " pdb=" C PRO F 109 " pdb=" CB PRO F 109 " both_signs ideal model delta sigma weight residual False 2.72 2.45 0.27 2.00e-01 2.50e+01 1.85e+00 ... (remaining 19887 not shown) Planarity restraints: 23400 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN 4 83 " -0.119 5.00e-02 4.00e+02 1.72e-01 4.73e+01 pdb=" N PRO 4 84 " 0.297 5.00e-02 4.00e+02 pdb=" CA PRO 4 84 " -0.094 5.00e-02 4.00e+02 pdb=" CD PRO 4 84 " -0.084 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN v 83 " -0.117 5.00e-02 4.00e+02 1.70e-01 4.63e+01 pdb=" N PRO v 84 " 0.294 5.00e-02 4.00e+02 pdb=" CA PRO v 84 " -0.094 5.00e-02 4.00e+02 pdb=" CD PRO v 84 " -0.084 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN Z 83 " -0.116 5.00e-02 4.00e+02 1.67e-01 4.49e+01 pdb=" N PRO Z 84 " 0.289 5.00e-02 4.00e+02 pdb=" CA PRO Z 84 " -0.091 5.00e-02 4.00e+02 pdb=" CD PRO Z 84 " -0.083 5.00e-02 4.00e+02 ... (remaining 23397 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 9799 2.74 - 3.28: 135500 3.28 - 3.82: 219773 3.82 - 4.36: 251703 4.36 - 4.90: 436870 Nonbonded interactions: 1053645 Sorted by model distance: nonbonded pdb=" N THR r 323 " pdb=" OG1 THR u 174 " model vdw 2.195 2.520 nonbonded pdb=" O SER j 175 " pdb=" OG SER j 178 " model vdw 2.197 2.440 nonbonded pdb=" OG1 THR Q 47 " pdb=" O GLU Q 89 " model vdw 2.197 2.440 nonbonded pdb=" OG SER U 391 " pdb=" O GLN W 204 " model vdw 2.198 2.440 nonbonded pdb=" O SER f 175 " pdb=" OG SER f 178 " model vdw 2.198 2.440 ... (remaining 1053640 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain '0' selection = chain '3' selection = chain '6' selection = chain 'U' selection = chain 'Y' selection = chain 'c' selection = chain 'g' selection = chain 'k' selection = chain 'o' selection = chain 'r' selection = chain 'u' selection = chain 'x' } ncs_group { reference = chain '1' selection = chain '4' selection = chain '7' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'V' selection = chain 'Z' selection = chain 'd' selection = chain 'h' selection = chain 'l' selection = chain 'p' selection = chain 's' selection = chain 'v' selection = chain 'y' } ncs_group { reference = chain '2' selection = chain '5' selection = chain 'T' selection = chain 'X' selection = chain 'b' selection = chain 'f' selection = chain 'j' selection = chain 'n' selection = chain 'q' selection = chain 't' selection = chain 'w' selection = chain 'z' } ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'S' selection = chain 'W' selection = chain 'a' selection = chain 'e' selection = chain 'i' selection = chain 'm' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.110 Extract box with map and model: 17.750 Check model and map are aligned: 1.400 Set scattering table: 0.880 Process input model: 272.490 Find NCS groups from input model: 7.840 Set up NCS constraints: 1.710 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:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 307.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 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 : 0.003 0.121 130506 Z= 0.230 Angle : 0.700 11.507 177246 Z= 0.403 Chirality : 0.044 0.275 19890 Planarity : 0.006 0.197 23400 Dihedral : 13.797 90.323 47244 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.44 % Allowed : 4.00 % Favored : 95.56 % Rotamer: Outliers : 0.09 % Allowed : 0.42 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 0.13 % 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: 0.47 (0.07), residues: 16500 helix: 2.20 (0.07), residues: 6252 sheet: -0.07 (0.11), residues: 2448 loop : -1.18 (0.06), residues: 7800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.002 TRP Y 553 HIS 0.009 0.001 HIS m 12 PHE 0.032 0.002 PHE s 6 TYR 0.026 0.001 TYR G 126 ARG 0.016 0.001 ARG O 63 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 33000 Ramachandran restraints generated. 16500 Oldfield, 0 Emsley, 16500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 33000 Ramachandran restraints generated. 16500 Oldfield, 0 Emsley, 16500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2334 residues out of total 13764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 2323 time to evaluate : 11.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 72 ASP cc_start: 0.6804 (t0) cc_final: 0.6416 (t0) REVERT: 0 184 GLU cc_start: 0.7328 (mm-30) cc_final: 0.7026 (mm-30) REVERT: 1 96 GLU cc_start: 0.7701 (mt-10) cc_final: 0.7368 (pt0) REVERT: 3 607 ARG cc_start: 0.6295 (mmt-90) cc_final: 0.5404 (mtp180) REVERT: 4 42 ASP cc_start: 0.6779 (t0) cc_final: 0.6152 (t0) REVERT: 6 580 MET cc_start: 0.7863 (mmt) cc_final: 0.7541 (mmp) REVERT: 7 45 MET cc_start: 0.6457 (mtm) cc_final: 0.5986 (mtm) REVERT: A 10 SER cc_start: 0.8858 (m) cc_final: 0.8584 (p) REVERT: A 299 MET cc_start: 0.7839 (mmt) cc_final: 0.7638 (mmt) REVERT: A 329 ASP cc_start: 0.6214 (m-30) cc_final: 0.5902 (t0) REVERT: B 283 MET cc_start: 0.7179 (mtm) cc_final: 0.6630 (mtm) REVERT: C 333 MET cc_start: 0.6966 (mtm) cc_final: 0.6563 (mtt) REVERT: D 10 SER cc_start: 0.8968 (m) cc_final: 0.8558 (p) REVERT: D 283 MET cc_start: 0.7493 (mpp) cc_final: 0.7057 (mtm) REVERT: D 353 MET cc_start: 0.8308 (mmt) cc_final: 0.7398 (mmt) REVERT: E 299 MET cc_start: 0.8181 (mmt) cc_final: 0.7949 (mmt) REVERT: E 473 ASP cc_start: 0.7497 (m-30) cc_final: 0.7295 (m-30) REVERT: F 333 MET cc_start: 0.6973 (mtm) cc_final: 0.6551 (mtt) REVERT: I 144 ASP cc_start: 0.5953 (t0) cc_final: 0.5683 (t70) REVERT: J 87 ASP cc_start: 0.7234 (m-30) cc_final: 0.6949 (m-30) REVERT: L 69 GLU cc_start: 0.7990 (tt0) cc_final: 0.7780 (tt0) REVERT: L 87 ASP cc_start: 0.7154 (m-30) cc_final: 0.6934 (m-30) REVERT: M 100 PHE cc_start: 0.8200 (m-80) cc_final: 0.7750 (m-80) REVERT: N 42 ASP cc_start: 0.7171 (t0) cc_final: 0.6697 (t0) REVERT: N 80 LEU cc_start: 0.7534 (pp) cc_final: 0.7268 (pp) REVERT: P 91 ARG cc_start: 0.3373 (mpp-170) cc_final: 0.2976 (mpp-170) REVERT: Q 26 THR cc_start: 0.8810 (m) cc_final: 0.8578 (m) REVERT: Q 87 ARG cc_start: 0.8554 (mmm-85) cc_final: 0.7483 (mtm180) REVERT: Q 99 ASP cc_start: 0.8797 (m-30) cc_final: 0.8584 (m-30) REVERT: S 116 VAL cc_start: 0.8210 (p) cc_final: 0.7838 (p) REVERT: U 156 GLU cc_start: 0.7687 (tt0) cc_final: 0.7249 (tm-30) REVERT: V 42 ASP cc_start: 0.5051 (t70) cc_final: 0.4760 (t70) REVERT: V 96 GLU cc_start: 0.7468 (mp0) cc_final: 0.6762 (mp0) REVERT: Y 362 ASP cc_start: 0.6216 (t0) cc_final: 0.5976 (t0) REVERT: Y 486 LYS cc_start: 0.7490 (tttp) cc_final: 0.7197 (tttp) REVERT: Y 563 GLU cc_start: 0.7332 (mp0) cc_final: 0.7024 (mp0) REVERT: Z 42 ASP cc_start: 0.6710 (t0) cc_final: 0.5993 (t0) REVERT: Z 99 ASP cc_start: 0.8610 (m-30) cc_final: 0.8367 (m-30) REVERT: a 49 VAL cc_start: 0.8156 (t) cc_final: 0.7618 (m) REVERT: c 397 MET cc_start: 0.7315 (ptt) cc_final: 0.7103 (ptt) REVERT: c 572 MET cc_start: 0.7635 (mmt) cc_final: 0.7262 (mmp) REVERT: d 45 MET cc_start: 0.6390 (mtm) cc_final: 0.5844 (mtm) REVERT: e 116 VAL cc_start: 0.8174 (p) cc_final: 0.7816 (p) REVERT: g 184 GLU cc_start: 0.7376 (mm-30) cc_final: 0.7077 (mm-30) REVERT: g 250 MET cc_start: 0.7279 (pmm) cc_final: 0.7015 (ptp) REVERT: g 382 ARG cc_start: 0.8617 (mmp80) cc_final: 0.8413 (mmp80) REVERT: g 442 MET cc_start: 0.7815 (mmm) cc_final: 0.7434 (mmm) REVERT: i 78 MET cc_start: 0.7711 (tpp) cc_final: 0.7294 (tpt) REVERT: j 69 ILE cc_start: 0.8582 (mp) cc_final: 0.8154 (mt) REVERT: l 42 ASP cc_start: 0.7139 (t0) cc_final: 0.6650 (t0) REVERT: m 78 MET cc_start: 0.7976 (tpp) cc_final: 0.7302 (mtp) REVERT: m 95 THR cc_start: 0.7847 (m) cc_final: 0.7641 (t) REVERT: m 136 ASP cc_start: 0.7517 (p0) cc_final: 0.7130 (p0) REVERT: o 250 MET cc_start: 0.7732 (pmm) cc_final: 0.6975 (ptp) REVERT: p 45 MET cc_start: 0.7178 (ptp) cc_final: 0.6801 (ptm) REVERT: p 100 PHE cc_start: 0.7808 (m-10) cc_final: 0.7500 (m-80) REVERT: u 362 ASP cc_start: 0.6093 (t0) cc_final: 0.5713 (t0) REVERT: u 543 LYS cc_start: 0.8096 (mmtp) cc_final: 0.7553 (mmmm) REVERT: v 26 THR cc_start: 0.8819 (m) cc_final: 0.8548 (m) REVERT: v 45 MET cc_start: 0.7389 (mmt) cc_final: 0.7009 (mmm) REVERT: v 49 ILE cc_start: 0.7538 (mt) cc_final: 0.7329 (mt) REVERT: w 3 PHE cc_start: 0.7709 (p90) cc_final: 0.7271 (p90) REVERT: y 18 LEU cc_start: 0.6215 (tp) cc_final: 0.5928 (tp) outliers start: 11 outliers final: 2 residues processed: 2330 average time/residue: 1.0498 time to fit residues: 4323.8873 Evaluate side-chains 1718 residues out of total 13764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1716 time to evaluate : 10.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 47 THR Chi-restraints excluded: chain l residue 47 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1644 random chunks: chunk 1388 optimal weight: 7.9990 chunk 1246 optimal weight: 9.9990 chunk 691 optimal weight: 4.9990 chunk 425 optimal weight: 9.9990 chunk 840 optimal weight: 0.0010 chunk 665 optimal weight: 10.0000 chunk 1288 optimal weight: 8.9990 chunk 498 optimal weight: 6.9990 chunk 783 optimal weight: 7.9990 chunk 959 optimal weight: 0.9980 chunk 1492 optimal weight: 7.9990 overall best weight: 4.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 54 HIS ** 1 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 376 GLN ** 3 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 485 ASN 4 9 ASN 5 17 GLN 6 54 HIS 6 430 ASN ** 7 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 403 HIS C 538 ASN ** D 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 403 HIS F 538 ASN ** H 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 9 ASN O 5 GLN ** O 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 8 ASN ** S 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 485 ASN ** V 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 54 HIS ** Y 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 9 ASN ** a 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 54 HIS g 430 ASN ** h 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 485 ASN ** k 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 9 ASN ** m 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 54 HIS o 430 ASN ** p 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 430 ASN ** s 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 54 HIS ** u 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 9 ASN ** w 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 130506 Z= 0.315 Angle : 0.644 9.317 177246 Z= 0.343 Chirality : 0.044 0.302 19890 Planarity : 0.005 0.111 23400 Dihedral : 4.912 30.480 18212 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.66 % Favored : 95.01 % Rotamer: Outliers : 1.58 % Allowed : 9.11 % Favored : 89.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.06), residues: 16500 helix: 2.27 (0.07), residues: 6258 sheet: -0.12 (0.10), residues: 2412 loop : -1.28 (0.06), residues: 7830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP 6 553 HIS 0.009 0.001 HIS x 346 PHE 0.024 0.002 PHE P 100 TYR 0.022 0.002 TYR q 128 ARG 0.010 0.001 ARG 6 593 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 33000 Ramachandran restraints generated. 16500 Oldfield, 0 Emsley, 16500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 33000 Ramachandran restraints generated. 16500 Oldfield, 0 Emsley, 16500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2024 residues out of total 13764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 205 poor density : 1819 time to evaluate : 11.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 72 ASP cc_start: 0.7233 (t0) cc_final: 0.6804 (t0) REVERT: 0 183 TYR cc_start: 0.8138 (OUTLIER) cc_final: 0.7237 (t80) REVERT: 0 374 ASP cc_start: 0.7110 (p0) cc_final: 0.6860 (p0) REVERT: 0 486 LYS cc_start: 0.8440 (ptmt) cc_final: 0.8212 (tptt) REVERT: 3 486 LYS cc_start: 0.8534 (tptm) cc_final: 0.8205 (tptt) REVERT: 3 607 ARG cc_start: 0.6295 (mmt-90) cc_final: 0.5420 (mtp180) REVERT: 4 42 ASP cc_start: 0.6911 (t0) cc_final: 0.6083 (t0) REVERT: 4 45 MET cc_start: 0.7686 (mmp) cc_final: 0.7443 (mmp) REVERT: 4 96 GLU cc_start: 0.6857 (mt-10) cc_final: 0.6187 (mt-10) REVERT: 6 489 ASP cc_start: 0.7652 (OUTLIER) cc_final: 0.7103 (t0) REVERT: 6 580 MET cc_start: 0.8053 (mmt) cc_final: 0.7678 (mmp) REVERT: 7 45 MET cc_start: 0.6346 (mtm) cc_final: 0.5923 (mtm) REVERT: 7 68 MET cc_start: 0.6695 (tpp) cc_final: 0.6399 (tpp) REVERT: A 10 SER cc_start: 0.8933 (m) cc_final: 0.8669 (p) REVERT: A 69 TRP cc_start: 0.7871 (m-90) cc_final: 0.7336 (m-90) REVERT: B 238 MET cc_start: 0.7231 (ptp) cc_final: 0.6995 (ptp) REVERT: C 276 TYR cc_start: 0.8289 (p90) cc_final: 0.7915 (p90) REVERT: C 339 MET cc_start: 0.7155 (tpp) cc_final: 0.6922 (tpp) REVERT: D 69 TRP cc_start: 0.7796 (m-90) cc_final: 0.7236 (m-90) REVERT: D 95 MET cc_start: 0.5963 (mtt) cc_final: 0.5670 (mtt) REVERT: D 283 MET cc_start: 0.7437 (mpp) cc_final: 0.7074 (mtm) REVERT: E 339 MET cc_start: 0.6746 (tpp) cc_final: 0.6455 (tpp) REVERT: F 66 TRP cc_start: 0.7808 (m100) cc_final: 0.7416 (m100) REVERT: F 276 TYR cc_start: 0.8314 (p90) cc_final: 0.7946 (p90) REVERT: F 339 MET cc_start: 0.6927 (tpp) cc_final: 0.6686 (tpp) REVERT: F 449 MET cc_start: 0.7730 (ppp) cc_final: 0.7507 (ppp) REVERT: G 182 GLU cc_start: 0.6434 (mm-30) cc_final: 0.6196 (mm-30) REVERT: H 5 ASP cc_start: 0.6404 (t0) cc_final: 0.6038 (t70) REVERT: K 5 ASP cc_start: 0.6465 (t0) cc_final: 0.6172 (t70) REVERT: L 5 ASP cc_start: 0.7018 (t0) cc_final: 0.6455 (t70) REVERT: L 87 ASP cc_start: 0.7293 (m-30) cc_final: 0.7019 (m-30) REVERT: M 97 LEU cc_start: 0.8336 (mp) cc_final: 0.8038 (mt) REVERT: M 100 PHE cc_start: 0.8093 (m-80) cc_final: 0.7638 (m-80) REVERT: N 5 GLN cc_start: 0.8395 (tm-30) cc_final: 0.7423 (tm-30) REVERT: N 42 ASP cc_start: 0.6878 (t0) cc_final: 0.6515 (t0) REVERT: N 80 LEU cc_start: 0.7744 (pp) cc_final: 0.7481 (pp) REVERT: N 87 ARG cc_start: 0.8083 (OUTLIER) cc_final: 0.7131 (mpp80) REVERT: O 82 PHE cc_start: 0.5290 (m-80) cc_final: 0.4899 (m-80) REVERT: Q 26 THR cc_start: 0.8688 (m) cc_final: 0.8480 (m) REVERT: R 68 MET cc_start: 0.6958 (tpp) cc_final: 0.6266 (tpp) REVERT: R 93 THR cc_start: 0.3904 (m) cc_final: 0.3633 (m) REVERT: S 66 TYR cc_start: 0.8436 (t80) cc_final: 0.7718 (t80) REVERT: S 134 ASP cc_start: 0.7623 (p0) cc_final: 0.7400 (p0) REVERT: U 568 MET cc_start: 0.8094 (tmm) cc_final: 0.7885 (tmm) REVERT: V 82 PHE cc_start: 0.7285 (m-80) cc_final: 0.6517 (m-10) REVERT: W 66 TYR cc_start: 0.8400 (t80) cc_final: 0.7906 (t80) REVERT: X 39 GLU cc_start: 0.7569 (tp30) cc_final: 0.7266 (tp30) REVERT: X 49 MET cc_start: 0.7469 (tpp) cc_final: 0.7004 (tpp) REVERT: Y 73 TYR cc_start: 0.8596 (OUTLIER) cc_final: 0.7960 (t80) REVERT: Z 5 GLN cc_start: 0.8632 (tm-30) cc_final: 0.7846 (tm-30) REVERT: Z 42 ASP cc_start: 0.6824 (t0) cc_final: 0.6104 (t0) REVERT: Z 45 MET cc_start: 0.7928 (mmp) cc_final: 0.7716 (mmp) REVERT: a 49 VAL cc_start: 0.8017 (t) cc_final: 0.7734 (m) REVERT: a 66 TYR cc_start: 0.8473 (t80) cc_final: 0.7977 (t80) REVERT: c 397 MET cc_start: 0.7434 (ptt) cc_final: 0.7121 (ptt) REVERT: d 45 MET cc_start: 0.6414 (mtm) cc_final: 0.5788 (mtm) REVERT: e 66 TYR cc_start: 0.8524 (t80) cc_final: 0.7869 (t80) REVERT: g 183 TYR cc_start: 0.8159 (OUTLIER) cc_final: 0.7194 (t80) REVERT: g 382 ARG cc_start: 0.8590 (mmp80) cc_final: 0.8242 (mmp80) REVERT: h 96 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7124 (mp0) REVERT: i 66 TYR cc_start: 0.8372 (t80) cc_final: 0.7910 (t80) REVERT: i 78 MET cc_start: 0.8122 (tpp) cc_final: 0.7538 (tpt) REVERT: j 69 ILE cc_start: 0.8573 (mp) cc_final: 0.8293 (mt) REVERT: k 486 LYS cc_start: 0.8549 (tptm) cc_final: 0.8270 (tptt) REVERT: l 42 ASP cc_start: 0.7155 (t0) cc_final: 0.6554 (t0) REVERT: l 89 GLU cc_start: 0.5808 (pp20) cc_final: 0.5513 (pp20) REVERT: l 91 ARG cc_start: 0.7508 (tmm160) cc_final: 0.6062 (mpp-170) REVERT: m 78 MET cc_start: 0.8109 (tpp) cc_final: 0.7392 (mtp) REVERT: m 95 THR cc_start: 0.7917 (m) cc_final: 0.7598 (t) REVERT: o 486 LYS cc_start: 0.7706 (tptt) cc_final: 0.7296 (tptt) REVERT: o 489 ASP cc_start: 0.7827 (OUTLIER) cc_final: 0.7488 (t0) REVERT: p 91 ARG cc_start: 0.4079 (mmp80) cc_final: 0.3814 (mmp80) REVERT: r 553 TRP cc_start: 0.7614 (t60) cc_final: 0.7342 (t60) REVERT: s 45 MET cc_start: 0.8167 (mmm) cc_final: 0.7915 (mmm) REVERT: u 73 TYR cc_start: 0.8609 (OUTLIER) cc_final: 0.7981 (t80) REVERT: u 184 GLU cc_start: 0.7237 (mm-30) cc_final: 0.6897 (mm-30) REVERT: u 440 MET cc_start: 0.8408 (mmt) cc_final: 0.8169 (mmt) REVERT: v 26 THR cc_start: 0.8668 (m) cc_final: 0.8432 (m) REVERT: w 3 PHE cc_start: 0.7807 (p90) cc_final: 0.7311 (p90) REVERT: x 572 MET cc_start: 0.7752 (mmt) cc_final: 0.7499 (mmp) REVERT: x 580 MET cc_start: 0.7712 (mmm) cc_final: 0.7181 (mmp) REVERT: y 18 LEU cc_start: 0.6251 (tp) cc_final: 0.5947 (tp) outliers start: 205 outliers final: 121 residues processed: 1941 average time/residue: 1.0317 time to fit residues: 3562.8631 Evaluate side-chains 1751 residues out of total 13764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 1622 time to evaluate : 10.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 183 TYR Chi-restraints excluded: chain 0 residue 450 LEU Chi-restraints excluded: chain 1 residue 61 THR Chi-restraints excluded: chain 3 residue 412 VAL Chi-restraints excluded: chain 3 residue 576 VAL Chi-restraints excluded: chain 4 residue 25 LEU Chi-restraints excluded: chain 4 residue 52 ASP Chi-restraints excluded: chain 4 residue 64 THR Chi-restraints excluded: chain 4 residue 71 THR Chi-restraints excluded: chain 6 residue 41 GLU Chi-restraints excluded: chain 6 residue 69 VAL Chi-restraints excluded: chain 6 residue 252 TRP Chi-restraints excluded: chain 6 residue 489 ASP Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 462 THR Chi-restraints excluded: chain C residue 553 GLU Chi-restraints excluded: chain E residue 333 MET Chi-restraints excluded: chain F residue 462 THR Chi-restraints excluded: chain G residue 116 VAL Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 33 LYS Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain H residue 122 SER Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain I residue 32 ILE Chi-restraints excluded: chain I residue 116 VAL Chi-restraints excluded: chain I residue 173 VAL Chi-restraints excluded: chain I residue 184 ASP Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain J residue 109 SER Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain K residue 32 ILE Chi-restraints excluded: chain K residue 33 LYS Chi-restraints excluded: chain K residue 116 VAL Chi-restraints excluded: chain L residue 32 ILE Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 186 LEU Chi-restraints excluded: chain M residue 61 THR Chi-restraints excluded: chain N residue 25 LEU Chi-restraints excluded: chain N residue 52 ASP Chi-restraints excluded: chain N residue 87 ARG Chi-restraints excluded: chain P residue 61 THR Chi-restraints excluded: chain Q residue 8 ASN Chi-restraints excluded: chain Q residue 24 SER Chi-restraints excluded: chain Q residue 25 LEU Chi-restraints excluded: chain Q residue 52 ASP Chi-restraints excluded: chain Q residue 64 THR Chi-restraints excluded: chain Q residue 71 THR Chi-restraints excluded: chain R residue 18 LEU Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain S residue 43 CYS Chi-restraints excluded: chain S residue 142 LEU Chi-restraints excluded: chain S residue 161 ILE Chi-restraints excluded: chain T residue 52 THR Chi-restraints excluded: chain T residue 149 THR Chi-restraints excluded: chain U residue 393 ASN Chi-restraints excluded: chain U residue 496 GLN Chi-restraints excluded: chain W residue 27 ILE Chi-restraints excluded: chain W residue 43 CYS Chi-restraints excluded: chain W residue 44 ASP Chi-restraints excluded: chain W residue 134 ASP Chi-restraints excluded: chain X residue 156 GLN Chi-restraints excluded: chain Y residue 73 TYR Chi-restraints excluded: chain Y residue 228 ILE Chi-restraints excluded: chain Y residue 252 TRP Chi-restraints excluded: chain Y residue 547 ILE Chi-restraints excluded: chain Z residue 25 LEU Chi-restraints excluded: chain Z residue 47 THR Chi-restraints excluded: chain Z residue 52 ASP Chi-restraints excluded: chain Z residue 64 THR Chi-restraints excluded: chain Z residue 71 THR Chi-restraints excluded: chain a residue 43 CYS Chi-restraints excluded: chain a residue 161 ILE Chi-restraints excluded: chain c residue 163 LEU Chi-restraints excluded: chain c residue 576 VAL Chi-restraints excluded: chain d residue 71 THR Chi-restraints excluded: chain e residue 43 CYS Chi-restraints excluded: chain e residue 44 ASP Chi-restraints excluded: chain e residue 161 ILE Chi-restraints excluded: chain f residue 14 THR Chi-restraints excluded: chain f residue 156 GLN Chi-restraints excluded: chain g residue 69 VAL Chi-restraints excluded: chain g residue 183 TYR Chi-restraints excluded: chain g residue 199 ASP Chi-restraints excluded: chain g residue 252 TRP Chi-restraints excluded: chain g residue 372 MET Chi-restraints excluded: chain g residue 450 LEU Chi-restraints excluded: chain h residue 15 VAL Chi-restraints excluded: chain h residue 96 GLU Chi-restraints excluded: chain i residue 43 CYS Chi-restraints excluded: chain i residue 44 ASP Chi-restraints excluded: chain i residue 93 TRP Chi-restraints excluded: chain i residue 158 LEU Chi-restraints excluded: chain i residue 161 ILE Chi-restraints excluded: chain j residue 52 THR Chi-restraints excluded: chain j residue 149 THR Chi-restraints excluded: chain k residue 216 VAL Chi-restraints excluded: chain k residue 412 VAL Chi-restraints excluded: chain k residue 576 VAL Chi-restraints excluded: chain l residue 25 LEU Chi-restraints excluded: chain l residue 52 ASP Chi-restraints excluded: chain m residue 43 CYS Chi-restraints excluded: chain m residue 161 ILE Chi-restraints excluded: chain o residue 41 GLU Chi-restraints excluded: chain o residue 69 VAL Chi-restraints excluded: chain o residue 252 TRP Chi-restraints excluded: chain o residue 450 LEU Chi-restraints excluded: chain o residue 489 ASP Chi-restraints excluded: chain q residue 152 ASN Chi-restraints excluded: chain r residue 391 SER Chi-restraints excluded: chain r residue 428 GLU Chi-restraints excluded: chain s residue 26 THR Chi-restraints excluded: chain s residue 61 THR Chi-restraints excluded: chain s residue 96 GLU Chi-restraints excluded: chain u residue 73 TYR Chi-restraints excluded: chain u residue 166 ILE Chi-restraints excluded: chain u residue 228 ILE Chi-restraints excluded: chain u residue 252 TRP Chi-restraints excluded: chain u residue 547 ILE Chi-restraints excluded: chain u residue 583 LEU Chi-restraints excluded: chain v residue 52 ASP Chi-restraints excluded: chain v residue 64 THR Chi-restraints excluded: chain v residue 71 THR Chi-restraints excluded: chain v residue 96 GLU Chi-restraints excluded: chain w residue 152 ASN Chi-restraints excluded: chain x residue 163 LEU Chi-restraints excluded: chain x residue 412 VAL Chi-restraints excluded: chain z residue 71 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1644 random chunks: chunk 829 optimal weight: 7.9990 chunk 463 optimal weight: 20.0000 chunk 1242 optimal weight: 9.9990 chunk 1016 optimal weight: 5.9990 chunk 411 optimal weight: 4.9990 chunk 1495 optimal weight: 0.6980 chunk 1615 optimal weight: 0.0070 chunk 1331 optimal weight: 9.9990 chunk 1483 optimal weight: 5.9990 chunk 509 optimal weight: 30.0000 chunk 1199 optimal weight: 10.0000 overall best weight: 3.5404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 54 HIS ** 1 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 485 ASN 4 9 ASN 6 54 HIS 6 430 ASN ** 7 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 486 ASN ** E 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 572 GLN ** H 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 485 ASN V 74 GLN ** V 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 9 ASN ** a 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 54 HIS g 60 GLN ** g 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 485 ASN ** k 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 9 ASN ** m 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 89 GLN ** m 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 54 HIS ** o 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 54 HIS u 63 ASN u 430 ASN ** u 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 9 ASN v 108 GLN ** w 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 130506 Z= 0.271 Angle : 0.606 9.486 177246 Z= 0.320 Chirality : 0.043 0.313 19890 Planarity : 0.005 0.085 23400 Dihedral : 4.846 26.217 18210 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.69 % Favored : 94.99 % Rotamer: Outliers : 2.13 % Allowed : 12.38 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.07), residues: 16500 helix: 2.32 (0.07), residues: 6264 sheet: -0.34 (0.10), residues: 2604 loop : -1.25 (0.07), residues: 7632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP u 553 HIS 0.009 0.001 HIS W 12 PHE 0.028 0.002 PHE 1 44 TYR 0.023 0.002 TYR w 128 ARG 0.010 0.000 ARG r 558 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 33000 Ramachandran restraints generated. 16500 Oldfield, 0 Emsley, 16500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 33000 Ramachandran restraints generated. 16500 Oldfield, 0 Emsley, 16500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2024 residues out of total 13764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 276 poor density : 1748 time to evaluate : 10.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 72 ASP cc_start: 0.7454 (t0) cc_final: 0.7063 (t0) REVERT: 0 183 TYR cc_start: 0.8150 (OUTLIER) cc_final: 0.7673 (t80) REVERT: 0 374 ASP cc_start: 0.7114 (p0) cc_final: 0.6808 (p0) REVERT: 3 486 LYS cc_start: 0.8530 (tptm) cc_final: 0.8252 (tptt) REVERT: 3 568 MET cc_start: 0.8168 (tmm) cc_final: 0.7631 (tmm) REVERT: 3 607 ARG cc_start: 0.6311 (mmt-90) cc_final: 0.5377 (mtp180) REVERT: 4 5 GLN cc_start: 0.8618 (tm-30) cc_final: 0.7650 (tm-30) REVERT: 4 42 ASP cc_start: 0.6814 (t0) cc_final: 0.5939 (t0) REVERT: 4 45 MET cc_start: 0.7857 (mmp) cc_final: 0.7655 (mmp) REVERT: 4 59 LYS cc_start: 0.7701 (mtpt) cc_final: 0.7451 (mtpp) REVERT: 4 99 ASP cc_start: 0.8096 (p0) cc_final: 0.7843 (p0) REVERT: 6 489 ASP cc_start: 0.7522 (OUTLIER) cc_final: 0.6942 (t0) REVERT: 7 45 MET cc_start: 0.6565 (mtm) cc_final: 0.6216 (mtm) REVERT: A 10 SER cc_start: 0.8891 (m) cc_final: 0.8648 (p) REVERT: A 283 MET cc_start: 0.7984 (tpp) cc_final: 0.7640 (mmp) REVERT: A 510 MET cc_start: 0.1519 (mtm) cc_final: 0.1095 (mtt) REVERT: B 239 MET cc_start: 0.6730 (mmm) cc_final: 0.6452 (mmm) REVERT: C 276 TYR cc_start: 0.8207 (p90) cc_final: 0.7869 (p90) REVERT: C 353 MET cc_start: 0.8509 (mmt) cc_final: 0.7882 (mmt) REVERT: E 283 MET cc_start: 0.7919 (mtm) cc_final: 0.7697 (mtt) REVERT: E 565 ILE cc_start: 0.9263 (mm) cc_final: 0.8966 (mp) REVERT: F 66 TRP cc_start: 0.7887 (m100) cc_final: 0.7404 (m100) REVERT: F 276 TYR cc_start: 0.8270 (p90) cc_final: 0.7965 (p90) REVERT: H 5 ASP cc_start: 0.6749 (t0) cc_final: 0.6444 (t70) REVERT: H 164 LYS cc_start: 0.7952 (mtpp) cc_final: 0.7666 (ttpt) REVERT: I 5 ASP cc_start: 0.7315 (t0) cc_final: 0.7093 (t70) REVERT: I 113 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8251 (pp) REVERT: I 144 ASP cc_start: 0.5952 (t0) cc_final: 0.5750 (t70) REVERT: J 87 ASP cc_start: 0.7384 (m-30) cc_final: 0.7090 (m-30) REVERT: K 5 ASP cc_start: 0.6777 (t0) cc_final: 0.6502 (t70) REVERT: L 5 ASP cc_start: 0.7042 (t0) cc_final: 0.6799 (t70) REVERT: L 87 ASP cc_start: 0.7337 (m-30) cc_final: 0.7112 (m-30) REVERT: L 113 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8201 (pp) REVERT: M 96 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.7153 (mp0) REVERT: M 100 PHE cc_start: 0.8031 (m-80) cc_final: 0.7617 (m-80) REVERT: N 42 ASP cc_start: 0.6991 (t0) cc_final: 0.6595 (t0) REVERT: N 80 LEU cc_start: 0.7666 (pp) cc_final: 0.7319 (pp) REVERT: N 87 ARG cc_start: 0.8069 (OUTLIER) cc_final: 0.7258 (mpp80) REVERT: O 82 PHE cc_start: 0.5305 (m-80) cc_final: 0.4929 (m-80) REVERT: Q 26 THR cc_start: 0.8660 (m) cc_final: 0.8419 (m) REVERT: Q 72 ARG cc_start: 0.6903 (mtp180) cc_final: 0.6058 (mtp180) REVERT: R 45 MET cc_start: 0.5939 (mtm) cc_final: 0.5489 (ptt) REVERT: R 68 MET cc_start: 0.6997 (tpp) cc_final: 0.6721 (tpp) REVERT: R 91 ARG cc_start: 0.2442 (mtt90) cc_final: 0.1243 (mmt180) REVERT: S 66 TYR cc_start: 0.8519 (t80) cc_final: 0.8056 (t80) REVERT: S 134 ASP cc_start: 0.7613 (p0) cc_final: 0.7374 (p0) REVERT: V 38 LEU cc_start: 0.5928 (mt) cc_final: 0.5638 (mt) REVERT: V 82 PHE cc_start: 0.7366 (m-80) cc_final: 0.6447 (m-10) REVERT: W 66 TYR cc_start: 0.8409 (t80) cc_final: 0.8052 (t80) REVERT: X 39 GLU cc_start: 0.7574 (tp30) cc_final: 0.7258 (tp30) REVERT: Y 73 TYR cc_start: 0.8670 (OUTLIER) cc_final: 0.8023 (t80) REVERT: Y 258 ASP cc_start: 0.7312 (t0) cc_final: 0.7054 (m-30) REVERT: Y 362 ASP cc_start: 0.6169 (t0) cc_final: 0.5956 (t0) REVERT: Z 5 GLN cc_start: 0.8699 (tm-30) cc_final: 0.7708 (tm-30) REVERT: Z 42 ASP cc_start: 0.6766 (t0) cc_final: 0.5952 (t0) REVERT: Z 45 MET cc_start: 0.7972 (mmp) cc_final: 0.7728 (mmp) REVERT: Z 99 ASP cc_start: 0.8460 (m-30) cc_final: 0.8238 (m-30) REVERT: a 49 VAL cc_start: 0.8039 (t) cc_final: 0.7756 (m) REVERT: a 103 GLN cc_start: 0.7716 (OUTLIER) cc_final: 0.6963 (mp10) REVERT: b 165 LEU cc_start: 0.8717 (mm) cc_final: 0.8386 (mt) REVERT: c 168 ASP cc_start: 0.7682 (OUTLIER) cc_final: 0.7170 (m-30) REVERT: c 372 MET cc_start: 0.6682 (ptp) cc_final: 0.6455 (ptt) REVERT: c 397 MET cc_start: 0.7354 (ptt) cc_final: 0.7091 (ptt) REVERT: c 432 ASP cc_start: 0.6229 (p0) cc_final: 0.5943 (p0) REVERT: c 572 MET cc_start: 0.7496 (mmp) cc_final: 0.7227 (mmt) REVERT: d 45 MET cc_start: 0.6395 (mtm) cc_final: 0.5768 (mtm) REVERT: d 59 LYS cc_start: 0.6819 (tptt) cc_final: 0.6220 (tptt) REVERT: e 66 TYR cc_start: 0.8547 (t80) cc_final: 0.8094 (t80) REVERT: e 134 ASP cc_start: 0.7642 (OUTLIER) cc_final: 0.7346 (p0) REVERT: f 40 ILE cc_start: 0.9501 (tt) cc_final: 0.9191 (tt) REVERT: g 183 TYR cc_start: 0.8159 (OUTLIER) cc_final: 0.7721 (t80) REVERT: g 382 ARG cc_start: 0.8607 (mmp80) cc_final: 0.8268 (mmp80) REVERT: h 96 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7169 (mp0) REVERT: i 83 THR cc_start: 0.8656 (OUTLIER) cc_final: 0.8121 (m) REVERT: i 134 ASP cc_start: 0.7517 (OUTLIER) cc_final: 0.7238 (p0) REVERT: j 69 ILE cc_start: 0.8666 (mp) cc_final: 0.8445 (mt) REVERT: k 486 LYS cc_start: 0.8549 (tptm) cc_final: 0.8260 (tptt) REVERT: k 572 MET cc_start: 0.7969 (mmp) cc_final: 0.7696 (mmt) REVERT: l 5 GLN cc_start: 0.8630 (tm-30) cc_final: 0.7364 (tm-30) REVERT: l 42 ASP cc_start: 0.6916 (t0) cc_final: 0.6445 (t0) REVERT: l 91 ARG cc_start: 0.7823 (tmm160) cc_final: 0.6271 (mpp-170) REVERT: o 486 LYS cc_start: 0.7809 (tptt) cc_final: 0.7548 (tptt) REVERT: o 489 ASP cc_start: 0.7867 (OUTLIER) cc_final: 0.7486 (t0) REVERT: q 128 TYR cc_start: 0.8718 (t80) cc_final: 0.8474 (t80) REVERT: r 553 TRP cc_start: 0.7658 (t60) cc_final: 0.7363 (t60) REVERT: s 45 MET cc_start: 0.8198 (mmm) cc_final: 0.7938 (mmm) REVERT: u 73 TYR cc_start: 0.8685 (OUTLIER) cc_final: 0.7992 (t80) REVERT: u 184 GLU cc_start: 0.7454 (mm-30) cc_final: 0.7072 (mm-30) REVERT: u 258 ASP cc_start: 0.7160 (t0) cc_final: 0.6936 (m-30) REVERT: v 5 GLN cc_start: 0.8095 (tm-30) cc_final: 0.7584 (tm-30) REVERT: w 3 PHE cc_start: 0.7755 (p90) cc_final: 0.7291 (p90) REVERT: x 177 GLU cc_start: 0.7977 (pp20) cc_final: 0.7704 (pp20) REVERT: x 432 ASP cc_start: 0.6391 (p0) cc_final: 0.6138 (p0) REVERT: y 18 LEU cc_start: 0.6257 (tp) cc_final: 0.5936 (tp) outliers start: 276 outliers final: 169 residues processed: 1913 average time/residue: 1.0242 time to fit residues: 3458.8773 Evaluate side-chains 1793 residues out of total 13764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 1608 time to evaluate : 10.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 183 TYR Chi-restraints excluded: chain 0 residue 450 LEU Chi-restraints excluded: chain 0 residue 583 LEU Chi-restraints excluded: chain 1 residue 61 THR Chi-restraints excluded: chain 2 residue 42 VAL Chi-restraints excluded: chain 3 residue 83 ASP Chi-restraints excluded: chain 3 residue 377 ASP Chi-restraints excluded: chain 3 residue 412 VAL Chi-restraints excluded: chain 3 residue 431 VAL Chi-restraints excluded: chain 3 residue 576 VAL Chi-restraints excluded: chain 4 residue 25 LEU Chi-restraints excluded: chain 4 residue 47 THR Chi-restraints excluded: chain 4 residue 52 ASP Chi-restraints excluded: chain 4 residue 68 MET Chi-restraints excluded: chain 4 residue 71 THR Chi-restraints excluded: chain 5 residue 71 LEU Chi-restraints excluded: chain 6 residue 41 GLU Chi-restraints excluded: chain 6 residue 69 VAL Chi-restraints excluded: chain 6 residue 183 TYR Chi-restraints excluded: chain 6 residue 252 TRP Chi-restraints excluded: chain 6 residue 330 ILE Chi-restraints excluded: chain 6 residue 390 LEU Chi-restraints excluded: chain 6 residue 450 LEU Chi-restraints excluded: chain 6 residue 489 ASP Chi-restraints excluded: chain 6 residue 583 LEU Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 384 SER Chi-restraints excluded: chain C residue 462 THR Chi-restraints excluded: chain E residue 333 MET Chi-restraints excluded: chain E residue 537 MET Chi-restraints excluded: chain F residue 384 SER Chi-restraints excluded: chain F residue 462 THR Chi-restraints excluded: chain F residue 540 MET Chi-restraints excluded: chain G residue 103 GLN Chi-restraints excluded: chain G residue 108 GLN Chi-restraints excluded: chain G residue 116 VAL Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 33 LYS Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain H residue 122 SER Chi-restraints excluded: chain I residue 32 ILE Chi-restraints excluded: chain I residue 113 LEU Chi-restraints excluded: chain I residue 116 VAL Chi-restraints excluded: chain I residue 122 SER Chi-restraints excluded: chain I residue 173 VAL Chi-restraints excluded: chain I residue 184 ASP Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain J residue 32 ILE Chi-restraints excluded: chain J residue 108 GLN Chi-restraints excluded: chain J residue 109 SER Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain K residue 32 ILE Chi-restraints excluded: chain K residue 33 LYS Chi-restraints excluded: chain K residue 116 VAL Chi-restraints excluded: chain K residue 122 SER Chi-restraints excluded: chain L residue 32 ILE Chi-restraints excluded: chain L residue 113 LEU Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 171 LEU Chi-restraints excluded: chain L residue 186 LEU Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 61 THR Chi-restraints excluded: chain M residue 71 THR Chi-restraints excluded: chain M residue 96 GLU Chi-restraints excluded: chain N residue 25 LEU Chi-restraints excluded: chain N residue 26 THR Chi-restraints excluded: chain N residue 49 ILE Chi-restraints excluded: chain N residue 52 ASP Chi-restraints excluded: chain N residue 87 ARG Chi-restraints excluded: chain O residue 71 THR Chi-restraints excluded: chain P residue 26 THR Chi-restraints excluded: chain P residue 61 THR Chi-restraints excluded: chain Q residue 24 SER Chi-restraints excluded: chain Q residue 25 LEU Chi-restraints excluded: chain Q residue 52 ASP Chi-restraints excluded: chain Q residue 64 THR Chi-restraints excluded: chain Q residue 71 THR Chi-restraints excluded: chain R residue 18 LEU Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain S residue 43 CYS Chi-restraints excluded: chain S residue 45 ASP Chi-restraints excluded: chain S residue 142 LEU Chi-restraints excluded: chain S residue 160 ILE Chi-restraints excluded: chain S residue 161 ILE Chi-restraints excluded: chain S residue 166 TRP Chi-restraints excluded: chain T residue 149 THR Chi-restraints excluded: chain U residue 83 ASP Chi-restraints excluded: chain U residue 377 ASP Chi-restraints excluded: chain U residue 393 ASN Chi-restraints excluded: chain U residue 427 ILE Chi-restraints excluded: chain U residue 496 GLN Chi-restraints excluded: chain U residue 506 ILE Chi-restraints excluded: chain V residue 80 LEU Chi-restraints excluded: chain W residue 27 ILE Chi-restraints excluded: chain W residue 43 CYS Chi-restraints excluded: chain W residue 44 ASP Chi-restraints excluded: chain W residue 83 THR Chi-restraints excluded: chain W residue 134 ASP Chi-restraints excluded: chain X residue 156 GLN Chi-restraints excluded: chain Y residue 73 TYR Chi-restraints excluded: chain Y residue 228 ILE Chi-restraints excluded: chain Y residue 252 TRP Chi-restraints excluded: chain Y residue 563 GLU Chi-restraints excluded: chain Y residue 583 LEU Chi-restraints excluded: chain Z residue 25 LEU Chi-restraints excluded: chain Z residue 47 THR Chi-restraints excluded: chain Z residue 52 ASP Chi-restraints excluded: chain Z residue 68 MET Chi-restraints excluded: chain a residue 43 CYS Chi-restraints excluded: chain a residue 44 ASP Chi-restraints excluded: chain a residue 93 TRP Chi-restraints excluded: chain a residue 103 GLN Chi-restraints excluded: chain a residue 161 ILE Chi-restraints excluded: chain c residue 83 ASP Chi-restraints excluded: chain c residue 168 ASP Chi-restraints excluded: chain c residue 377 ASP Chi-restraints excluded: chain c residue 412 VAL Chi-restraints excluded: chain c residue 427 ILE Chi-restraints excluded: chain c residue 443 MET Chi-restraints excluded: chain c residue 506 ILE Chi-restraints excluded: chain e residue 43 CYS Chi-restraints excluded: chain e residue 44 ASP Chi-restraints excluded: chain e residue 78 MET Chi-restraints excluded: chain e residue 134 ASP Chi-restraints excluded: chain e residue 161 ILE Chi-restraints excluded: chain e residue 166 TRP Chi-restraints excluded: chain f residue 14 THR Chi-restraints excluded: chain f residue 156 GLN Chi-restraints excluded: chain f residue 197 LEU Chi-restraints excluded: chain g residue 69 VAL Chi-restraints excluded: chain g residue 183 TYR Chi-restraints excluded: chain g residue 199 ASP Chi-restraints excluded: chain g residue 450 LEU Chi-restraints excluded: chain h residue 14 LEU Chi-restraints excluded: chain h residue 96 GLU Chi-restraints excluded: chain i residue 43 CYS Chi-restraints excluded: chain i residue 44 ASP Chi-restraints excluded: chain i residue 83 THR Chi-restraints excluded: chain i residue 93 TRP Chi-restraints excluded: chain i residue 134 ASP Chi-restraints excluded: chain i residue 158 LEU Chi-restraints excluded: chain i residue 161 ILE Chi-restraints excluded: chain j residue 149 THR Chi-restraints excluded: chain k residue 83 ASP Chi-restraints excluded: chain k residue 377 ASP Chi-restraints excluded: chain k residue 412 VAL Chi-restraints excluded: chain k residue 576 VAL Chi-restraints excluded: chain l residue 25 LEU Chi-restraints excluded: chain l residue 47 THR Chi-restraints excluded: chain l residue 49 ILE Chi-restraints excluded: chain l residue 52 ASP Chi-restraints excluded: chain m residue 43 CYS Chi-restraints excluded: chain m residue 78 MET Chi-restraints excluded: chain m residue 161 ILE Chi-restraints excluded: chain o residue 41 GLU Chi-restraints excluded: chain o residue 69 VAL Chi-restraints excluded: chain o residue 183 TYR Chi-restraints excluded: chain o residue 252 TRP Chi-restraints excluded: chain o residue 330 ILE Chi-restraints excluded: chain o residue 450 LEU Chi-restraints excluded: chain o residue 489 ASP Chi-restraints excluded: chain o residue 583 LEU Chi-restraints excluded: chain q residue 152 ASN Chi-restraints excluded: chain r residue 83 ASP Chi-restraints excluded: chain r residue 391 SER Chi-restraints excluded: chain r residue 428 GLU Chi-restraints excluded: chain s residue 15 VAL Chi-restraints excluded: chain s residue 61 THR Chi-restraints excluded: chain s residue 96 GLU Chi-restraints excluded: chain u residue 73 TYR Chi-restraints excluded: chain u residue 166 ILE Chi-restraints excluded: chain u residue 228 ILE Chi-restraints excluded: chain u residue 252 TRP Chi-restraints excluded: chain u residue 547 ILE Chi-restraints excluded: chain u residue 583 LEU Chi-restraints excluded: chain v residue 14 LEU Chi-restraints excluded: chain v residue 52 ASP Chi-restraints excluded: chain v residue 64 THR Chi-restraints excluded: chain v residue 71 THR Chi-restraints excluded: chain v residue 96 GLU Chi-restraints excluded: chain w residue 152 ASN Chi-restraints excluded: chain x residue 83 ASP Chi-restraints excluded: chain x residue 412 VAL Chi-restraints excluded: chain z residue 71 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1644 random chunks: chunk 1477 optimal weight: 5.9990 chunk 1124 optimal weight: 2.9990 chunk 776 optimal weight: 0.6980 chunk 165 optimal weight: 6.9990 chunk 713 optimal weight: 9.9990 chunk 1004 optimal weight: 10.0000 chunk 1500 optimal weight: 9.9990 chunk 1589 optimal weight: 5.9990 chunk 784 optimal weight: 9.9990 chunk 1422 optimal weight: 0.9980 chunk 428 optimal weight: 20.0000 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 496 GLN ** 1 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 485 ASN 4 9 ASN ** 6 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 486 ASN ** D 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 486 ASN E 62 HIS ** E 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 452 ASN F 486 ASN ** H 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 8 ASN Q 108 GLN ** S 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 485 ASN ** V 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 63 ASN Y 430 ASN Z 9 ASN a 89 GLN ** a 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 8 ASN ** d 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 208 GLN g 54 HIS g 60 GLN ** h 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 208 GLN ** k 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 485 ASN ** k 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 9 ASN ** m 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 208 GLN ** o 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 5 GLN ** s 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 156 GLN u 92 GLN ** u 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 9 ASN ** v 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 502 GLN ** y 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 108 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 130506 Z= 0.258 Angle : 0.590 9.146 177246 Z= 0.311 Chirality : 0.043 0.316 19890 Planarity : 0.005 0.078 23400 Dihedral : 4.778 25.781 18210 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.87 % Favored : 94.81 % Rotamer: Outliers : 2.67 % Allowed : 14.05 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.07), residues: 16500 helix: 2.38 (0.07), residues: 6264 sheet: -0.29 (0.10), residues: 2556 loop : -1.30 (0.07), residues: 7680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.001 TRP u 553 HIS 0.008 0.001 HIS W 12 PHE 0.020 0.002 PHE 1 44 TYR 0.024 0.002 TYR J 104 ARG 0.007 0.000 ARG Y 554 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 33000 Ramachandran restraints generated. 16500 Oldfield, 0 Emsley, 16500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 33000 Ramachandran restraints generated. 16500 Oldfield, 0 Emsley, 16500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2071 residues out of total 13764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 346 poor density : 1725 time to evaluate : 10.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 72 ASP cc_start: 0.7419 (t0) cc_final: 0.7172 (t0) REVERT: 0 374 ASP cc_start: 0.7143 (p0) cc_final: 0.6811 (p0) REVERT: 2 33 LEU cc_start: 0.9141 (tp) cc_final: 0.8871 (tt) REVERT: 3 443 MET cc_start: 0.8049 (ttm) cc_final: 0.7821 (ttp) REVERT: 3 486 LYS cc_start: 0.8553 (tptm) cc_final: 0.8287 (tptt) REVERT: 3 607 ARG cc_start: 0.6381 (mmt-90) cc_final: 0.5703 (mtp180) REVERT: 4 42 ASP cc_start: 0.6829 (t0) cc_final: 0.5865 (t0) REVERT: 4 45 MET cc_start: 0.7860 (mmp) cc_final: 0.7580 (mmp) REVERT: 4 83 ASN cc_start: 0.8188 (t0) cc_final: 0.7758 (m-40) REVERT: 4 99 ASP cc_start: 0.8145 (p0) cc_final: 0.7872 (p0) REVERT: 6 110 SER cc_start: 0.9469 (m) cc_final: 0.9222 (p) REVERT: 6 489 ASP cc_start: 0.7495 (OUTLIER) cc_final: 0.6944 (t0) REVERT: 6 506 ILE cc_start: 0.8542 (OUTLIER) cc_final: 0.8271 (mp) REVERT: 7 45 MET cc_start: 0.6581 (mtm) cc_final: 0.6244 (mtm) REVERT: 7 68 MET cc_start: 0.7037 (tpp) cc_final: 0.6323 (tpp) REVERT: A 10 SER cc_start: 0.8869 (m) cc_final: 0.8648 (p) REVERT: A 283 MET cc_start: 0.8042 (tpp) cc_final: 0.7660 (mmp) REVERT: A 510 MET cc_start: 0.1300 (mtm) cc_final: 0.0967 (mtt) REVERT: B 238 MET cc_start: 0.7167 (ptp) cc_final: 0.6894 (ptp) REVERT: B 239 MET cc_start: 0.7315 (mmm) cc_final: 0.7103 (mmm) REVERT: B 565 ILE cc_start: 0.9203 (mm) cc_final: 0.8844 (mp) REVERT: C 276 TYR cc_start: 0.8130 (p90) cc_final: 0.7904 (p90) REVERT: D 95 MET cc_start: 0.5731 (mtt) cc_final: 0.5219 (mtm) REVERT: D 276 TYR cc_start: 0.7886 (p90) cc_final: 0.7639 (p90) REVERT: D 510 MET cc_start: 0.1308 (mtm) cc_final: 0.0984 (mtt) REVERT: E 565 ILE cc_start: 0.9268 (mm) cc_final: 0.8934 (mp) REVERT: F 66 TRP cc_start: 0.7920 (m100) cc_final: 0.7417 (m100) REVERT: F 276 TYR cc_start: 0.8095 (p90) cc_final: 0.7889 (p90) REVERT: H 5 ASP cc_start: 0.6913 (t0) cc_final: 0.6624 (t70) REVERT: H 164 LYS cc_start: 0.8087 (mtpp) cc_final: 0.7741 (ttpt) REVERT: I 113 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8235 (pp) REVERT: L 87 ASP cc_start: 0.7274 (m-30) cc_final: 0.7027 (m-30) REVERT: L 113 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8194 (pp) REVERT: M 96 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.7103 (mp0) REVERT: M 108 GLN cc_start: 0.8394 (OUTLIER) cc_final: 0.8122 (mp10) REVERT: N 42 ASP cc_start: 0.6772 (t0) cc_final: 0.6308 (t0) REVERT: N 80 LEU cc_start: 0.7771 (pp) cc_final: 0.7471 (pp) REVERT: N 87 ARG cc_start: 0.8021 (OUTLIER) cc_final: 0.7182 (mpp80) REVERT: O 82 PHE cc_start: 0.5295 (m-80) cc_final: 0.4940 (m-80) REVERT: Q 26 THR cc_start: 0.8650 (m) cc_final: 0.8418 (m) REVERT: Q 72 ARG cc_start: 0.6935 (mtp180) cc_final: 0.6314 (mtp180) REVERT: Q 100 PHE cc_start: 0.7740 (m-10) cc_final: 0.7477 (m-10) REVERT: R 91 ARG cc_start: 0.2587 (mtt90) cc_final: 0.1389 (mmt180) REVERT: S 66 TYR cc_start: 0.8522 (t80) cc_final: 0.8179 (t80) REVERT: S 134 ASP cc_start: 0.7662 (p0) cc_final: 0.7457 (p0) REVERT: X 39 GLU cc_start: 0.7480 (tp30) cc_final: 0.7191 (tp30) REVERT: Y 73 TYR cc_start: 0.8698 (OUTLIER) cc_final: 0.8110 (t80) REVERT: Y 250 MET cc_start: 0.8069 (OUTLIER) cc_final: 0.7294 (ptp) REVERT: Y 258 ASP cc_start: 0.7266 (t0) cc_final: 0.7026 (m-30) REVERT: Z 5 GLN cc_start: 0.8736 (tm-30) cc_final: 0.7789 (tm-30) REVERT: Z 42 ASP cc_start: 0.6876 (t0) cc_final: 0.5896 (t0) REVERT: Z 45 MET cc_start: 0.8016 (mmp) cc_final: 0.7705 (mmp) REVERT: Z 99 ASP cc_start: 0.8453 (m-30) cc_final: 0.8212 (m-30) REVERT: a 49 VAL cc_start: 0.8089 (t) cc_final: 0.7808 (m) REVERT: b 128 TYR cc_start: 0.8990 (t80) cc_final: 0.8760 (t80) REVERT: c 168 ASP cc_start: 0.7527 (OUTLIER) cc_final: 0.6981 (m-30) REVERT: c 372 MET cc_start: 0.6857 (ptp) cc_final: 0.6639 (ptt) REVERT: c 397 MET cc_start: 0.7346 (ptt) cc_final: 0.7085 (ptt) REVERT: c 432 ASP cc_start: 0.6341 (p0) cc_final: 0.6054 (p0) REVERT: d 45 MET cc_start: 0.6372 (mtm) cc_final: 0.5947 (mtm) REVERT: d 59 LYS cc_start: 0.6939 (tptt) cc_final: 0.6442 (ttmt) REVERT: e 66 TYR cc_start: 0.8513 (t80) cc_final: 0.8109 (t80) REVERT: e 134 ASP cc_start: 0.7694 (OUTLIER) cc_final: 0.7245 (p0) REVERT: g 382 ARG cc_start: 0.8632 (mmp80) cc_final: 0.8244 (mmp80) REVERT: g 583 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8645 (mm) REVERT: h 52 ASP cc_start: 0.7549 (m-30) cc_final: 0.7330 (m-30) REVERT: h 96 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7196 (mp0) REVERT: j 165 LEU cc_start: 0.8866 (mm) cc_final: 0.8639 (mm) REVERT: k 486 LYS cc_start: 0.8534 (tptm) cc_final: 0.8262 (tptt) REVERT: k 568 MET cc_start: 0.7670 (tmm) cc_final: 0.7446 (tmm) REVERT: l 42 ASP cc_start: 0.6739 (t0) cc_final: 0.6207 (t0) REVERT: l 91 ARG cc_start: 0.7853 (tmm160) cc_final: 0.6557 (ptt-90) REVERT: o 486 LYS cc_start: 0.7909 (tptt) cc_final: 0.7697 (tptt) REVERT: o 489 ASP cc_start: 0.7870 (OUTLIER) cc_final: 0.7515 (t0) REVERT: p 45 MET cc_start: 0.6646 (ptm) cc_final: 0.6225 (ptt) REVERT: q 128 TYR cc_start: 0.8850 (t80) cc_final: 0.8618 (t80) REVERT: r 553 TRP cc_start: 0.7695 (t60) cc_final: 0.7386 (t60) REVERT: u 73 TYR cc_start: 0.8705 (OUTLIER) cc_final: 0.8134 (t80) REVERT: u 184 GLU cc_start: 0.7545 (mm-30) cc_final: 0.7322 (mm-30) REVERT: u 199 ASP cc_start: 0.7875 (OUTLIER) cc_final: 0.7332 (m-30) REVERT: v 5 GLN cc_start: 0.8268 (tm-30) cc_final: 0.7552 (tm-30) REVERT: w 3 PHE cc_start: 0.7764 (p90) cc_final: 0.7291 (p90) REVERT: x 432 ASP cc_start: 0.6541 (p0) cc_final: 0.6260 (p0) REVERT: x 442 MET cc_start: 0.7588 (mmm) cc_final: 0.7372 (mmm) REVERT: y 18 LEU cc_start: 0.6298 (tp) cc_final: 0.5960 (tp) outliers start: 346 outliers final: 224 residues processed: 1941 average time/residue: 0.9961 time to fit residues: 3445.8133 Evaluate side-chains 1848 residues out of total 13764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 240 poor density : 1608 time to evaluate : 10.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 69 VAL Chi-restraints excluded: chain 0 residue 199 ASP Chi-restraints excluded: chain 0 residue 330 ILE Chi-restraints excluded: chain 0 residue 450 LEU Chi-restraints excluded: chain 0 residue 484 THR Chi-restraints excluded: chain 0 residue 583 LEU Chi-restraints excluded: chain 1 residue 12 SER Chi-restraints excluded: chain 1 residue 61 THR Chi-restraints excluded: chain 1 residue 80 LEU Chi-restraints excluded: chain 2 residue 42 VAL Chi-restraints excluded: chain 2 residue 80 THR Chi-restraints excluded: chain 3 residue 83 ASP Chi-restraints excluded: chain 3 residue 377 ASP Chi-restraints excluded: chain 3 residue 412 VAL Chi-restraints excluded: chain 3 residue 431 VAL Chi-restraints excluded: chain 3 residue 576 VAL Chi-restraints excluded: chain 4 residue 25 LEU Chi-restraints excluded: chain 4 residue 52 ASP Chi-restraints excluded: chain 4 residue 68 MET Chi-restraints excluded: chain 5 residue 71 LEU Chi-restraints excluded: chain 6 residue 41 GLU Chi-restraints excluded: chain 6 residue 69 VAL Chi-restraints excluded: chain 6 residue 183 TYR Chi-restraints excluded: chain 6 residue 252 TRP Chi-restraints excluded: chain 6 residue 330 ILE Chi-restraints excluded: chain 6 residue 390 LEU Chi-restraints excluded: chain 6 residue 450 LEU Chi-restraints excluded: chain 6 residue 489 ASP Chi-restraints excluded: chain 6 residue 506 ILE Chi-restraints excluded: chain 6 residue 583 LEU Chi-restraints excluded: chain B residue 537 MET Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 384 SER Chi-restraints excluded: chain C residue 462 THR Chi-restraints excluded: chain E residue 333 MET Chi-restraints excluded: chain E residue 339 MET Chi-restraints excluded: chain E residue 346 LEU Chi-restraints excluded: chain E residue 537 MET Chi-restraints excluded: chain F residue 384 SER Chi-restraints excluded: chain F residue 462 THR Chi-restraints excluded: chain F residue 540 MET Chi-restraints excluded: chain F residue 553 GLU Chi-restraints excluded: chain G residue 32 ILE Chi-restraints excluded: chain G residue 103 GLN Chi-restraints excluded: chain G residue 108 GLN Chi-restraints excluded: chain G residue 116 VAL Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 33 LYS Chi-restraints excluded: chain H residue 67 GLU Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain H residue 122 SER Chi-restraints excluded: chain I residue 32 ILE Chi-restraints excluded: chain I residue 113 LEU Chi-restraints excluded: chain I residue 116 VAL Chi-restraints excluded: chain I residue 122 SER Chi-restraints excluded: chain I residue 173 VAL Chi-restraints excluded: chain I residue 184 ASP Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain J residue 32 ILE Chi-restraints excluded: chain J residue 108 GLN Chi-restraints excluded: chain J residue 109 SER Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain K residue 32 ILE Chi-restraints excluded: chain K residue 33 LYS Chi-restraints excluded: chain K residue 67 GLU Chi-restraints excluded: chain K residue 116 VAL Chi-restraints excluded: chain K residue 122 SER Chi-restraints excluded: chain K residue 184 ASP Chi-restraints excluded: chain L residue 32 ILE Chi-restraints excluded: chain L residue 113 LEU Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 171 LEU Chi-restraints excluded: chain L residue 186 LEU Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain M residue 71 THR Chi-restraints excluded: chain M residue 80 LEU Chi-restraints excluded: chain M residue 96 GLU Chi-restraints excluded: chain M residue 108 GLN Chi-restraints excluded: chain N residue 25 LEU Chi-restraints excluded: chain N residue 26 THR Chi-restraints excluded: chain N residue 49 ILE Chi-restraints excluded: chain N residue 52 ASP Chi-restraints excluded: chain N residue 87 ARG Chi-restraints excluded: chain O residue 18 LEU Chi-restraints excluded: chain O residue 71 THR Chi-restraints excluded: chain P residue 61 THR Chi-restraints excluded: chain P residue 80 LEU Chi-restraints excluded: chain Q residue 24 SER Chi-restraints excluded: chain Q residue 25 LEU Chi-restraints excluded: chain Q residue 47 THR Chi-restraints excluded: chain Q residue 52 ASP Chi-restraints excluded: chain Q residue 64 THR Chi-restraints excluded: chain Q residue 71 THR Chi-restraints excluded: chain R residue 18 LEU Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain R residue 93 THR Chi-restraints excluded: chain S residue 43 CYS Chi-restraints excluded: chain S residue 44 ASP Chi-restraints excluded: chain S residue 45 ASP Chi-restraints excluded: chain S residue 142 LEU Chi-restraints excluded: chain S residue 160 ILE Chi-restraints excluded: chain S residue 161 ILE Chi-restraints excluded: chain S residue 166 TRP Chi-restraints excluded: chain T residue 15 LEU Chi-restraints excluded: chain T residue 149 THR Chi-restraints excluded: chain U residue 83 ASP Chi-restraints excluded: chain U residue 377 ASP Chi-restraints excluded: chain U residue 393 ASN Chi-restraints excluded: chain U residue 412 VAL Chi-restraints excluded: chain U residue 427 ILE Chi-restraints excluded: chain U residue 496 GLN Chi-restraints excluded: chain V residue 80 LEU Chi-restraints excluded: chain W residue 27 ILE Chi-restraints excluded: chain W residue 43 CYS Chi-restraints excluded: chain W residue 44 ASP Chi-restraints excluded: chain W residue 83 THR Chi-restraints excluded: chain W residue 93 TRP Chi-restraints excluded: chain W residue 134 ASP Chi-restraints excluded: chain W residue 161 ILE Chi-restraints excluded: chain X residue 156 GLN Chi-restraints excluded: chain Y residue 63 ASN Chi-restraints excluded: chain Y residue 73 TYR Chi-restraints excluded: chain Y residue 228 ILE Chi-restraints excluded: chain Y residue 248 GLU Chi-restraints excluded: chain Y residue 250 MET Chi-restraints excluded: chain Y residue 330 ILE Chi-restraints excluded: chain Y residue 563 GLU Chi-restraints excluded: chain Y residue 583 LEU Chi-restraints excluded: chain Y residue 590 LEU Chi-restraints excluded: chain Z residue 25 LEU Chi-restraints excluded: chain Z residue 47 THR Chi-restraints excluded: chain Z residue 52 ASP Chi-restraints excluded: chain Z residue 68 MET Chi-restraints excluded: chain a residue 43 CYS Chi-restraints excluded: chain a residue 161 ILE Chi-restraints excluded: chain a residue 180 ASP Chi-restraints excluded: chain c residue 83 ASP Chi-restraints excluded: chain c residue 168 ASP Chi-restraints excluded: chain c residue 377 ASP Chi-restraints excluded: chain c residue 427 ILE Chi-restraints excluded: chain d residue 58 VAL Chi-restraints excluded: chain e residue 43 CYS Chi-restraints excluded: chain e residue 44 ASP Chi-restraints excluded: chain e residue 78 MET Chi-restraints excluded: chain e residue 134 ASP Chi-restraints excluded: chain e residue 149 THR Chi-restraints excluded: chain e residue 161 ILE Chi-restraints excluded: chain e residue 166 TRP Chi-restraints excluded: chain f residue 14 THR Chi-restraints excluded: chain f residue 156 GLN Chi-restraints excluded: chain g residue 69 VAL Chi-restraints excluded: chain g residue 199 ASP Chi-restraints excluded: chain g residue 330 ILE Chi-restraints excluded: chain g residue 450 LEU Chi-restraints excluded: chain g residue 583 LEU Chi-restraints excluded: chain h residue 14 LEU Chi-restraints excluded: chain h residue 15 VAL Chi-restraints excluded: chain h residue 80 LEU Chi-restraints excluded: chain h residue 96 GLU Chi-restraints excluded: chain i residue 43 CYS Chi-restraints excluded: chain i residue 44 ASP Chi-restraints excluded: chain i residue 45 ASP Chi-restraints excluded: chain i residue 93 TRP Chi-restraints excluded: chain i residue 158 LEU Chi-restraints excluded: chain i residue 160 ILE Chi-restraints excluded: chain i residue 161 ILE Chi-restraints excluded: chain i residue 183 LEU Chi-restraints excluded: chain j residue 16 LEU Chi-restraints excluded: chain j residue 52 THR Chi-restraints excluded: chain j residue 149 THR Chi-restraints excluded: chain k residue 83 ASP Chi-restraints excluded: chain k residue 377 ASP Chi-restraints excluded: chain k residue 412 VAL Chi-restraints excluded: chain k residue 576 VAL Chi-restraints excluded: chain k residue 590 LEU Chi-restraints excluded: chain l residue 25 LEU Chi-restraints excluded: chain l residue 47 THR Chi-restraints excluded: chain l residue 49 ILE Chi-restraints excluded: chain l residue 52 ASP Chi-restraints excluded: chain l residue 80 LEU Chi-restraints excluded: chain m residue 43 CYS Chi-restraints excluded: chain m residue 44 ASP Chi-restraints excluded: chain m residue 71 VAL Chi-restraints excluded: chain m residue 78 MET Chi-restraints excluded: chain m residue 160 ILE Chi-restraints excluded: chain m residue 161 ILE Chi-restraints excluded: chain n residue 121 VAL Chi-restraints excluded: chain o residue 41 GLU Chi-restraints excluded: chain o residue 69 VAL Chi-restraints excluded: chain o residue 177 GLU Chi-restraints excluded: chain o residue 183 TYR Chi-restraints excluded: chain o residue 199 ASP Chi-restraints excluded: chain o residue 252 TRP Chi-restraints excluded: chain o residue 330 ILE Chi-restraints excluded: chain o residue 352 THR Chi-restraints excluded: chain o residue 450 LEU Chi-restraints excluded: chain o residue 489 ASP Chi-restraints excluded: chain o residue 583 LEU Chi-restraints excluded: chain q residue 53 THR Chi-restraints excluded: chain q residue 80 THR Chi-restraints excluded: chain q residue 152 ASN Chi-restraints excluded: chain r residue 83 ASP Chi-restraints excluded: chain r residue 391 SER Chi-restraints excluded: chain r residue 412 VAL Chi-restraints excluded: chain r residue 428 GLU Chi-restraints excluded: chain r residue 489 ASP Chi-restraints excluded: chain r residue 547 ILE Chi-restraints excluded: chain s residue 15 VAL Chi-restraints excluded: chain s residue 26 THR Chi-restraints excluded: chain s residue 61 THR Chi-restraints excluded: chain s residue 80 LEU Chi-restraints excluded: chain s residue 96 GLU Chi-restraints excluded: chain t residue 80 THR Chi-restraints excluded: chain u residue 73 TYR Chi-restraints excluded: chain u residue 166 ILE Chi-restraints excluded: chain u residue 183 TYR Chi-restraints excluded: chain u residue 199 ASP Chi-restraints excluded: chain u residue 228 ILE Chi-restraints excluded: chain u residue 252 TRP Chi-restraints excluded: chain u residue 330 ILE Chi-restraints excluded: chain u residue 563 GLU Chi-restraints excluded: chain u residue 583 LEU Chi-restraints excluded: chain u residue 590 LEU Chi-restraints excluded: chain v residue 26 THR Chi-restraints excluded: chain v residue 52 ASP Chi-restraints excluded: chain v residue 64 THR Chi-restraints excluded: chain v residue 71 THR Chi-restraints excluded: chain v residue 96 GLU Chi-restraints excluded: chain w residue 53 THR Chi-restraints excluded: chain w residue 73 ASP Chi-restraints excluded: chain w residue 80 THR Chi-restraints excluded: chain w residue 152 ASN Chi-restraints excluded: chain x residue 83 ASP Chi-restraints excluded: chain x residue 168 ASP Chi-restraints excluded: chain x residue 412 VAL Chi-restraints excluded: chain y residue 119 ASP Chi-restraints excluded: chain z residue 71 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1644 random chunks: chunk 1323 optimal weight: 0.9990 chunk 902 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 1183 optimal weight: 0.7980 chunk 655 optimal weight: 10.0000 chunk 1356 optimal weight: 3.9990 chunk 1098 optimal weight: 0.9980 chunk 1 optimal weight: 10.0000 chunk 811 optimal weight: 10.0000 chunk 1426 optimal weight: 7.9990 chunk 400 optimal weight: 0.0980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 74 GLN 2 145 HIS ** 3 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 485 ASN 4 9 ASN ** 6 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 340 GLN ** D 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 486 ASN ** E 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 486 ASN ** H 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 204 GLN ** L 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 8 ASN Q 108 GLN ** S 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 430 ASN ** V 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 60 GLN Y 63 ASN Z 9 ASN ** a 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 502 GLN ** d 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 54 HIS g 60 GLN ** g 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 485 ASN ** k 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 63 ASN ** p 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 430 ASN r 485 ASN r 502 GLN ** s 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 92 GLN u 430 ASN ** u 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 9 ASN ** v 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 130506 Z= 0.170 Angle : 0.564 9.895 177246 Z= 0.295 Chirality : 0.042 0.319 19890 Planarity : 0.004 0.076 23400 Dihedral : 4.627 27.730 18210 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.70 % Favored : 94.98 % Rotamer: Outliers : 2.61 % Allowed : 15.33 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.07), residues: 16500 helix: 2.51 (0.07), residues: 6258 sheet: -0.33 (0.10), residues: 2502 loop : -1.27 (0.07), residues: 7740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.001 TRP u 553 HIS 0.006 0.001 HIS i 12 PHE 0.022 0.001 PHE s 6 TYR 0.020 0.001 TYR 2 171 ARG 0.007 0.000 ARG Y 359 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 33000 Ramachandran restraints generated. 16500 Oldfield, 0 Emsley, 16500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 33000 Ramachandran restraints generated. 16500 Oldfield, 0 Emsley, 16500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2148 residues out of total 13764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 338 poor density : 1810 time to evaluate : 11.201 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: 0 72 ASP cc_start: 0.7263 (t0) cc_final: 0.6969 (t0) REVERT: 0 374 ASP cc_start: 0.7071 (p0) cc_final: 0.6740 (p0) REVERT: 0 441 ASP cc_start: 0.7204 (t70) cc_final: 0.6981 (m-30) REVERT: 2 33 LEU cc_start: 0.9075 (tp) cc_final: 0.8764 (tt) REVERT: 3 324 MET cc_start: 0.7042 (tpp) cc_final: 0.6141 (mtp) REVERT: 3 607 ARG cc_start: 0.6282 (mmt-90) cc_final: 0.5610 (mtp180) REVERT: 4 42 ASP cc_start: 0.6896 (t0) cc_final: 0.5960 (t0) REVERT: 4 45 MET cc_start: 0.7827 (mmp) cc_final: 0.7527 (mmp) REVERT: 6 110 SER cc_start: 0.9375 (m) cc_final: 0.9158 (p) REVERT: 6 489 ASP cc_start: 0.7496 (OUTLIER) cc_final: 0.6949 (t0) REVERT: 7 45 MET cc_start: 0.6650 (mtm) cc_final: 0.6343 (mtm) REVERT: 7 68 MET cc_start: 0.7015 (tpp) cc_final: 0.6458 (tpp) REVERT: A 10 SER cc_start: 0.8752 (m) cc_final: 0.8520 (p) REVERT: A 510 MET cc_start: 0.1410 (mtm) cc_final: 0.0920 (mtt) REVERT: B 238 MET cc_start: 0.7148 (ptp) cc_final: 0.6864 (ptp) REVERT: B 339 MET cc_start: 0.6611 (tpp) cc_final: 0.6085 (tpp) REVERT: B 565 ILE cc_start: 0.9271 (mm) cc_final: 0.8911 (mp) REVERT: D 10 SER cc_start: 0.8910 (m) cc_final: 0.8705 (m) REVERT: D 95 MET cc_start: 0.5698 (mtt) cc_final: 0.5062 (mtm) REVERT: D 283 MET cc_start: 0.7682 (mtm) cc_final: 0.7475 (mtm) REVERT: D 339 MET cc_start: 0.6982 (tpp) cc_final: 0.6778 (tpp) REVERT: D 510 MET cc_start: 0.1410 (mtm) cc_final: 0.1082 (mtt) REVERT: E 565 ILE cc_start: 0.9292 (mm) cc_final: 0.8956 (mp) REVERT: F 66 TRP cc_start: 0.7824 (m100) cc_final: 0.7375 (m100) REVERT: F 239 MET cc_start: 0.7246 (mpp) cc_final: 0.6921 (mpp) REVERT: G 106 THR cc_start: 0.8038 (m) cc_final: 0.7838 (p) REVERT: H 39 ARG cc_start: 0.9078 (mtt-85) cc_final: 0.8551 (mtt-85) REVERT: H 164 LYS cc_start: 0.7955 (mtpp) cc_final: 0.7652 (ttpt) REVERT: I 88 GLU cc_start: 0.7704 (tm-30) cc_final: 0.7366 (tm-30) REVERT: I 113 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8171 (pp) REVERT: J 87 ASP cc_start: 0.7410 (m-30) cc_final: 0.7098 (m-30) REVERT: L 87 ASP cc_start: 0.6918 (m-30) cc_final: 0.6698 (m-30) REVERT: L 88 GLU cc_start: 0.7569 (tm-30) cc_final: 0.7106 (tm-30) REVERT: L 113 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8144 (pp) REVERT: M 96 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7081 (mp0) REVERT: M 108 GLN cc_start: 0.8407 (OUTLIER) cc_final: 0.8034 (mp10) REVERT: N 42 ASP cc_start: 0.6751 (t0) cc_final: 0.6290 (t0) REVERT: N 80 LEU cc_start: 0.7715 (pp) cc_final: 0.7498 (pp) REVERT: N 87 ARG cc_start: 0.8006 (OUTLIER) cc_final: 0.7509 (mpp80) REVERT: O 13 ARG cc_start: 0.7199 (mmp80) cc_final: 0.6759 (tpp80) REVERT: O 82 PHE cc_start: 0.5265 (m-80) cc_final: 0.4934 (m-10) REVERT: P 96 GLU cc_start: 0.7746 (mp0) cc_final: 0.7467 (pt0) REVERT: Q 26 THR cc_start: 0.8567 (m) cc_final: 0.8344 (m) REVERT: Q 100 PHE cc_start: 0.7805 (m-10) cc_final: 0.7564 (m-10) REVERT: R 45 MET cc_start: 0.5993 (mtm) cc_final: 0.5589 (ptt) REVERT: R 68 MET cc_start: 0.6839 (tpp) cc_final: 0.6152 (tpp) REVERT: R 91 ARG cc_start: 0.2570 (mtt90) cc_final: 0.1128 (mmp80) REVERT: S 66 TYR cc_start: 0.8373 (t80) cc_final: 0.7953 (t80) REVERT: S 134 ASP cc_start: 0.7585 (p0) cc_final: 0.7319 (p0) REVERT: U 411 GLU cc_start: 0.7510 (mm-30) cc_final: 0.7165 (mt-10) REVERT: U 442 MET cc_start: 0.7699 (mmm) cc_final: 0.7402 (mmm) REVERT: V 96 GLU cc_start: 0.7283 (mp0) cc_final: 0.6802 (mp0) REVERT: W 66 TYR cc_start: 0.8399 (t80) cc_final: 0.7955 (t80) REVERT: Y 60 GLN cc_start: 0.8069 (OUTLIER) cc_final: 0.7838 (mm-40) REVERT: Y 73 TYR cc_start: 0.8605 (OUTLIER) cc_final: 0.8333 (t80) REVERT: Y 250 MET cc_start: 0.7899 (OUTLIER) cc_final: 0.7190 (ptp) REVERT: Y 258 ASP cc_start: 0.7202 (t0) cc_final: 0.6955 (m-30) REVERT: Z 5 GLN cc_start: 0.8723 (tm-30) cc_final: 0.7702 (tm-30) REVERT: Z 42 ASP cc_start: 0.6863 (t0) cc_final: 0.5899 (t0) REVERT: Z 45 MET cc_start: 0.8023 (mmp) cc_final: 0.7690 (mmp) REVERT: a 49 VAL cc_start: 0.8036 (t) cc_final: 0.7798 (m) REVERT: c 168 ASP cc_start: 0.7428 (OUTLIER) cc_final: 0.6903 (m-30) REVERT: c 372 MET cc_start: 0.6706 (ptp) cc_final: 0.6409 (ptt) REVERT: c 411 GLU cc_start: 0.7137 (mm-30) cc_final: 0.6867 (mt-10) REVERT: c 432 ASP cc_start: 0.6332 (p0) cc_final: 0.6036 (p0) REVERT: d 45 MET cc_start: 0.5970 (mtm) cc_final: 0.5703 (mtm) REVERT: d 59 LYS cc_start: 0.7223 (tptt) cc_final: 0.6832 (ttmt) REVERT: e 66 TYR cc_start: 0.8417 (t80) cc_final: 0.7896 (t80) REVERT: e 134 ASP cc_start: 0.7536 (OUTLIER) cc_final: 0.7172 (p0) REVERT: f 28 GLU cc_start: 0.7955 (tm-30) cc_final: 0.7745 (tm-30) REVERT: f 49 MET cc_start: 0.7578 (mmm) cc_final: 0.7347 (tpp) REVERT: g 250 MET cc_start: 0.7900 (pmm) cc_final: 0.7028 (ptp) REVERT: g 374 ASP cc_start: 0.7099 (p0) cc_final: 0.6887 (p0) REVERT: g 382 ARG cc_start: 0.8591 (mmp80) cc_final: 0.8281 (mmp80) REVERT: h 96 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7232 (mp0) REVERT: i 83 THR cc_start: 0.8691 (OUTLIER) cc_final: 0.8134 (m) REVERT: j 62 GLN cc_start: 0.8602 (mm-40) cc_final: 0.8268 (mm-40) REVERT: j 165 LEU cc_start: 0.8782 (mm) cc_final: 0.8527 (mm) REVERT: k 443 MET cc_start: 0.8013 (ttp) cc_final: 0.7680 (ttt) REVERT: k 486 LYS cc_start: 0.8499 (tptm) cc_final: 0.8262 (tptt) REVERT: k 568 MET cc_start: 0.7764 (tmm) cc_final: 0.7560 (tmm) REVERT: l 5 GLN cc_start: 0.8532 (tm-30) cc_final: 0.7220 (tm-30) REVERT: l 42 ASP cc_start: 0.6897 (t0) cc_final: 0.6408 (t0) REVERT: l 91 ARG cc_start: 0.7787 (tmm160) cc_final: 0.6394 (mpp-170) REVERT: o 486 LYS cc_start: 0.7893 (tptt) cc_final: 0.7675 (tptt) REVERT: o 489 ASP cc_start: 0.7747 (OUTLIER) cc_final: 0.7437 (t0) REVERT: q 128 TYR cc_start: 0.8791 (t80) cc_final: 0.8588 (t80) REVERT: u 73 TYR cc_start: 0.8594 (OUTLIER) cc_final: 0.8352 (t80) REVERT: u 146 ARG cc_start: 0.8329 (mtt-85) cc_final: 0.7912 (mtt180) REVERT: u 184 GLU cc_start: 0.7567 (mm-30) cc_final: 0.7360 (mm-30) REVERT: u 250 MET cc_start: 0.7868 (OUTLIER) cc_final: 0.7192 (ptp) REVERT: u 363 ASN cc_start: 0.7760 (t0) cc_final: 0.7202 (t0) REVERT: v 5 GLN cc_start: 0.8237 (tm-30) cc_final: 0.7511 (tm-30) REVERT: w 3 PHE cc_start: 0.7810 (p90) cc_final: 0.7442 (p90) REVERT: x 432 ASP cc_start: 0.6512 (p0) cc_final: 0.6219 (p0) REVERT: y 18 LEU cc_start: 0.6280 (tp) cc_final: 0.5944 (tp) REVERT: z 33 LEU cc_start: 0.9135 (tt) cc_final: 0.8906 (tt) outliers start: 338 outliers final: 213 residues processed: 2032 average time/residue: 1.1618 time to fit residues: 4234.5050 Evaluate side-chains 1869 residues out of total 13764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 229 poor density : 1640 time to evaluate : 11.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 199 ASP Chi-restraints excluded: chain 0 residue 330 ILE Chi-restraints excluded: chain 0 residue 450 LEU Chi-restraints excluded: chain 0 residue 484 THR Chi-restraints excluded: chain 0 residue 583 LEU Chi-restraints excluded: chain 1 residue 12 SER Chi-restraints excluded: chain 1 residue 61 THR Chi-restraints excluded: chain 1 residue 80 LEU Chi-restraints excluded: chain 2 residue 53 THR Chi-restraints excluded: chain 2 residue 80 THR Chi-restraints excluded: chain 3 residue 412 VAL Chi-restraints excluded: chain 3 residue 576 VAL Chi-restraints excluded: chain 4 residue 25 LEU Chi-restraints excluded: chain 4 residue 52 ASP Chi-restraints excluded: chain 4 residue 68 MET Chi-restraints excluded: chain 4 residue 71 THR Chi-restraints excluded: chain 5 residue 53 THR Chi-restraints excluded: chain 5 residue 73 ASP Chi-restraints excluded: chain 5 residue 157 MET Chi-restraints excluded: chain 6 residue 41 GLU Chi-restraints excluded: chain 6 residue 183 TYR Chi-restraints excluded: chain 6 residue 199 ASP Chi-restraints excluded: chain 6 residue 252 TRP Chi-restraints excluded: chain 6 residue 330 ILE Chi-restraints excluded: chain 6 residue 374 ASP Chi-restraints excluded: chain 6 residue 390 LEU Chi-restraints excluded: chain 6 residue 412 VAL Chi-restraints excluded: chain 6 residue 450 LEU Chi-restraints excluded: chain 6 residue 489 ASP Chi-restraints excluded: chain 6 residue 576 VAL Chi-restraints excluded: chain 6 residue 583 LEU Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 384 SER Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 332 VAL Chi-restraints excluded: chain E residue 332 VAL Chi-restraints excluded: chain E residue 333 MET Chi-restraints excluded: chain E residue 339 MET Chi-restraints excluded: chain E residue 346 LEU Chi-restraints excluded: chain F residue 384 SER Chi-restraints excluded: chain G residue 45 ASP Chi-restraints excluded: chain G residue 103 GLN Chi-restraints excluded: chain G residue 108 GLN Chi-restraints excluded: chain G residue 116 VAL Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 67 GLU Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain H residue 142 LEU Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain I residue 32 ILE Chi-restraints excluded: chain I residue 113 LEU Chi-restraints excluded: chain I residue 116 VAL Chi-restraints excluded: chain I residue 173 VAL Chi-restraints excluded: chain I residue 184 ASP Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain J residue 108 GLN Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain K residue 32 ILE Chi-restraints excluded: chain K residue 67 GLU Chi-restraints excluded: chain K residue 116 VAL Chi-restraints excluded: chain K residue 122 SER Chi-restraints excluded: chain K residue 184 ASP Chi-restraints excluded: chain L residue 32 ILE Chi-restraints excluded: chain L residue 113 LEU Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 122 SER Chi-restraints excluded: chain L residue 171 LEU Chi-restraints excluded: chain L residue 186 LEU Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain M residue 80 LEU Chi-restraints excluded: chain M residue 96 GLU Chi-restraints excluded: chain M residue 108 GLN Chi-restraints excluded: chain N residue 25 LEU Chi-restraints excluded: chain N residue 49 ILE Chi-restraints excluded: chain N residue 52 ASP Chi-restraints excluded: chain N residue 87 ARG Chi-restraints excluded: chain O residue 71 THR Chi-restraints excluded: chain P residue 26 THR Chi-restraints excluded: chain P residue 34 LEU Chi-restraints excluded: chain P residue 61 THR Chi-restraints excluded: chain P residue 80 LEU Chi-restraints excluded: chain Q residue 25 LEU Chi-restraints excluded: chain Q residue 47 THR Chi-restraints excluded: chain Q residue 52 ASP Chi-restraints excluded: chain Q residue 71 THR Chi-restraints excluded: chain Q residue 108 GLN Chi-restraints excluded: chain R residue 18 LEU Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain S residue 43 CYS Chi-restraints excluded: chain S residue 45 ASP Chi-restraints excluded: chain S residue 93 TRP Chi-restraints excluded: chain S residue 142 LEU Chi-restraints excluded: chain S residue 149 THR Chi-restraints excluded: chain S residue 160 ILE Chi-restraints excluded: chain S residue 161 ILE Chi-restraints excluded: chain S residue 166 TRP Chi-restraints excluded: chain T residue 149 THR Chi-restraints excluded: chain U residue 83 ASP Chi-restraints excluded: chain U residue 252 TRP Chi-restraints excluded: chain U residue 377 ASP Chi-restraints excluded: chain U residue 393 ASN Chi-restraints excluded: chain U residue 412 VAL Chi-restraints excluded: chain U residue 427 ILE Chi-restraints excluded: chain U residue 496 GLN Chi-restraints excluded: chain V residue 26 THR Chi-restraints excluded: chain V residue 61 THR Chi-restraints excluded: chain V residue 80 LEU Chi-restraints excluded: chain W residue 43 CYS Chi-restraints excluded: chain W residue 44 ASP Chi-restraints excluded: chain W residue 45 ASP Chi-restraints excluded: chain W residue 77 ASN Chi-restraints excluded: chain W residue 78 MET Chi-restraints excluded: chain W residue 83 THR Chi-restraints excluded: chain W residue 93 TRP Chi-restraints excluded: chain W residue 134 ASP Chi-restraints excluded: chain W residue 141 LEU Chi-restraints excluded: chain X residue 156 GLN Chi-restraints excluded: chain Y residue 60 GLN Chi-restraints excluded: chain Y residue 73 TYR Chi-restraints excluded: chain Y residue 183 TYR Chi-restraints excluded: chain Y residue 250 MET Chi-restraints excluded: chain Y residue 252 TRP Chi-restraints excluded: chain Y residue 330 ILE Chi-restraints excluded: chain Y residue 485 ASN Chi-restraints excluded: chain Y residue 563 GLU Chi-restraints excluded: chain Y residue 576 VAL Chi-restraints excluded: chain Y residue 583 LEU Chi-restraints excluded: chain Y residue 590 LEU Chi-restraints excluded: chain Z residue 25 LEU Chi-restraints excluded: chain Z residue 47 THR Chi-restraints excluded: chain Z residue 52 ASP Chi-restraints excluded: chain Z residue 68 MET Chi-restraints excluded: chain a residue 43 CYS Chi-restraints excluded: chain a residue 44 ASP Chi-restraints excluded: chain a residue 71 VAL Chi-restraints excluded: chain a residue 93 TRP Chi-restraints excluded: chain b residue 157 MET Chi-restraints excluded: chain c residue 168 ASP Chi-restraints excluded: chain c residue 377 ASP Chi-restraints excluded: chain c residue 412 VAL Chi-restraints excluded: chain c residue 427 ILE Chi-restraints excluded: chain d residue 71 THR Chi-restraints excluded: chain e residue 78 MET Chi-restraints excluded: chain e residue 93 TRP Chi-restraints excluded: chain e residue 134 ASP Chi-restraints excluded: chain e residue 149 THR Chi-restraints excluded: chain e residue 166 TRP Chi-restraints excluded: chain f residue 156 GLN Chi-restraints excluded: chain f residue 197 LEU Chi-restraints excluded: chain g residue 199 ASP Chi-restraints excluded: chain g residue 252 TRP Chi-restraints excluded: chain g residue 330 ILE Chi-restraints excluded: chain g residue 450 LEU Chi-restraints excluded: chain h residue 15 VAL Chi-restraints excluded: chain h residue 58 VAL Chi-restraints excluded: chain h residue 61 THR Chi-restraints excluded: chain h residue 80 LEU Chi-restraints excluded: chain h residue 96 GLU Chi-restraints excluded: chain i residue 43 CYS Chi-restraints excluded: chain i residue 44 ASP Chi-restraints excluded: chain i residue 45 ASP Chi-restraints excluded: chain i residue 83 THR Chi-restraints excluded: chain i residue 93 TRP Chi-restraints excluded: chain i residue 158 LEU Chi-restraints excluded: chain i residue 160 ILE Chi-restraints excluded: chain j residue 16 LEU Chi-restraints excluded: chain j residue 149 THR Chi-restraints excluded: chain k residue 252 TRP Chi-restraints excluded: chain k residue 377 ASP Chi-restraints excluded: chain k residue 412 VAL Chi-restraints excluded: chain k residue 576 VAL Chi-restraints excluded: chain k residue 590 LEU Chi-restraints excluded: chain l residue 47 THR Chi-restraints excluded: chain l residue 49 ILE Chi-restraints excluded: chain l residue 52 ASP Chi-restraints excluded: chain l residue 80 LEU Chi-restraints excluded: chain m residue 43 CYS Chi-restraints excluded: chain m residue 44 ASP Chi-restraints excluded: chain m residue 71 VAL Chi-restraints excluded: chain m residue 78 MET Chi-restraints excluded: chain m residue 160 ILE Chi-restraints excluded: chain n residue 121 VAL Chi-restraints excluded: chain o residue 41 GLU Chi-restraints excluded: chain o residue 183 TYR Chi-restraints excluded: chain o residue 252 TRP Chi-restraints excluded: chain o residue 330 ILE Chi-restraints excluded: chain o residue 412 VAL Chi-restraints excluded: chain o residue 489 ASP Chi-restraints excluded: chain o residue 583 LEU Chi-restraints excluded: chain o residue 588 THR Chi-restraints excluded: chain r residue 83 ASP Chi-restraints excluded: chain r residue 391 SER Chi-restraints excluded: chain r residue 412 VAL Chi-restraints excluded: chain s residue 6 PHE Chi-restraints excluded: chain s residue 15 VAL Chi-restraints excluded: chain s residue 26 THR Chi-restraints excluded: chain s residue 61 THR Chi-restraints excluded: chain s residue 80 LEU Chi-restraints excluded: chain s residue 96 GLU Chi-restraints excluded: chain t residue 15 LEU Chi-restraints excluded: chain t residue 42 VAL Chi-restraints excluded: chain t residue 80 THR Chi-restraints excluded: chain u residue 73 TYR Chi-restraints excluded: chain u residue 138 LEU Chi-restraints excluded: chain u residue 166 ILE Chi-restraints excluded: chain u residue 250 MET Chi-restraints excluded: chain u residue 252 TRP Chi-restraints excluded: chain u residue 330 ILE Chi-restraints excluded: chain u residue 563 GLU Chi-restraints excluded: chain u residue 576 VAL Chi-restraints excluded: chain u residue 583 LEU Chi-restraints excluded: chain u residue 590 LEU Chi-restraints excluded: chain v residue 14 LEU Chi-restraints excluded: chain v residue 47 THR Chi-restraints excluded: chain v residue 52 ASP Chi-restraints excluded: chain v residue 64 THR Chi-restraints excluded: chain v residue 71 THR Chi-restraints excluded: chain w residue 152 ASN Chi-restraints excluded: chain x residue 168 ASP Chi-restraints excluded: chain x residue 412 VAL Chi-restraints excluded: chain y residue 119 ASP Chi-restraints excluded: chain z residue 73 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1644 random chunks: chunk 534 optimal weight: 1.9990 chunk 1431 optimal weight: 5.9990 chunk 314 optimal weight: 20.0000 chunk 932 optimal weight: 5.9990 chunk 392 optimal weight: 10.0000 chunk 1590 optimal weight: 4.9990 chunk 1320 optimal weight: 5.9990 chunk 736 optimal weight: 4.9990 chunk 132 optimal weight: 0.9990 chunk 526 optimal weight: 20.0000 chunk 835 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 54 HIS ** 0 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 60 GLN ** 3 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 485 ASN 4 9 ASN ** 4 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 108 GLN 6 54 HIS ** 6 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 486 ASN B 572 GLN C 340 GLN ** D 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 486 ASN ** E 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 486 ASN G 72 GLN G 204 GLN ** H 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 108 GLN ** O 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 8 ASN ** S 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 490 ASN Z 9 ASN ** a 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 182 ASN ** c 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 502 GLN ** d 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 54 HIS ** h 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 60 GLN ** k 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 108 GLN m 194 GLN o 54 HIS o 63 ASN ** p 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 430 ASN ** r 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 502 GLN ** s 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 54 HIS u 92 GLN ** u 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 485 ASN ** x 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 130506 Z= 0.284 Angle : 0.605 11.785 177246 Z= 0.317 Chirality : 0.043 0.355 19890 Planarity : 0.005 0.075 23400 Dihedral : 4.695 26.835 18210 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.18 % Favored : 94.50 % Rotamer: Outliers : 2.91 % Allowed : 16.21 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.07), residues: 16500 helix: 2.42 (0.07), residues: 6282 sheet: -0.36 (0.10), residues: 2556 loop : -1.29 (0.07), residues: 7662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP u 553 HIS 0.008 0.001 HIS W 12 PHE 0.040 0.002 PHE V 44 TYR 0.021 0.002 TYR 2 171 ARG 0.007 0.000 ARG o 599 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 33000 Ramachandran restraints generated. 16500 Oldfield, 0 Emsley, 16500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 33000 Ramachandran restraints generated. 16500 Oldfield, 0 Emsley, 16500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2042 residues out of total 13764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 377 poor density : 1665 time to evaluate : 11.082 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: 0 374 ASP cc_start: 0.7125 (p0) cc_final: 0.6824 (p0) REVERT: 1 8 ASN cc_start: 0.8043 (t0) cc_final: 0.7080 (p0) REVERT: 2 33 LEU cc_start: 0.9157 (tp) cc_final: 0.8897 (tt) REVERT: 3 324 MET cc_start: 0.7091 (tpp) cc_final: 0.6202 (mtp) REVERT: 3 607 ARG cc_start: 0.6295 (mmt-90) cc_final: 0.5676 (mtp180) REVERT: 4 42 ASP cc_start: 0.6926 (t0) cc_final: 0.5903 (t0) REVERT: 4 45 MET cc_start: 0.7865 (mmp) cc_final: 0.7518 (mmp) REVERT: 6 110 SER cc_start: 0.9455 (m) cc_final: 0.9219 (p) REVERT: 6 489 ASP cc_start: 0.7468 (OUTLIER) cc_final: 0.6947 (t0) REVERT: 7 13 ARG cc_start: 0.5728 (tpp80) cc_final: 0.5458 (tpp80) REVERT: 7 45 MET cc_start: 0.6737 (mtm) cc_final: 0.6438 (mtm) REVERT: 7 68 MET cc_start: 0.7087 (tpp) cc_final: 0.6557 (tpp) REVERT: A 267 ASP cc_start: 0.7209 (OUTLIER) cc_final: 0.6964 (m-30) REVERT: A 510 MET cc_start: 0.1750 (mtm) cc_final: 0.1313 (mtt) REVERT: B 339 MET cc_start: 0.7106 (tpp) cc_final: 0.6896 (tpp) REVERT: B 565 ILE cc_start: 0.9255 (mm) cc_final: 0.8907 (mp) REVERT: C 69 TRP cc_start: 0.8193 (m-90) cc_final: 0.7917 (m-90) REVERT: C 540 MET cc_start: 0.8545 (ppp) cc_final: 0.8240 (ptm) REVERT: D 95 MET cc_start: 0.5805 (mtt) cc_final: 0.5265 (mtm) REVERT: D 510 MET cc_start: 0.1417 (mtm) cc_final: 0.1083 (mtt) REVERT: E 565 ILE cc_start: 0.9310 (mm) cc_final: 0.8989 (mp) REVERT: F 66 TRP cc_start: 0.7970 (m100) cc_final: 0.7351 (m100) REVERT: F 239 MET cc_start: 0.7058 (mpp) cc_final: 0.6685 (mpp) REVERT: H 164 LYS cc_start: 0.8102 (mtpp) cc_final: 0.7625 (ttpt) REVERT: I 88 GLU cc_start: 0.7651 (tm-30) cc_final: 0.7250 (tm-30) REVERT: I 113 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8269 (pp) REVERT: L 88 GLU cc_start: 0.7715 (tm-30) cc_final: 0.7250 (tm-30) REVERT: L 113 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8228 (pp) REVERT: L 134 ASP cc_start: 0.5977 (p0) cc_final: 0.5774 (p0) REVERT: M 96 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7130 (mp0) REVERT: M 108 GLN cc_start: 0.8473 (OUTLIER) cc_final: 0.8197 (mp10) REVERT: N 42 ASP cc_start: 0.6854 (t0) cc_final: 0.6395 (t0) REVERT: O 13 ARG cc_start: 0.7381 (mmp80) cc_final: 0.6864 (mmp-170) REVERT: O 45 MET cc_start: 0.5633 (ptm) cc_final: 0.4427 (ptt) REVERT: O 82 PHE cc_start: 0.5275 (m-80) cc_final: 0.4943 (m-80) REVERT: Q 26 THR cc_start: 0.8560 (m) cc_final: 0.8336 (m) REVERT: Q 100 PHE cc_start: 0.7899 (m-10) cc_final: 0.7603 (m-10) REVERT: R 45 MET cc_start: 0.6011 (mtm) cc_final: 0.5710 (ptt) REVERT: R 68 MET cc_start: 0.6946 (tpp) cc_final: 0.6716 (tpp) REVERT: R 91 ARG cc_start: 0.2959 (mtt90) cc_final: 0.1156 (mmp80) REVERT: S 66 TYR cc_start: 0.8550 (t80) cc_final: 0.8245 (t80) REVERT: V 96 GLU cc_start: 0.7324 (mp0) cc_final: 0.6756 (mp0) REVERT: X 39 GLU cc_start: 0.7538 (tp30) cc_final: 0.7195 (tp30) REVERT: X 136 GLN cc_start: 0.8084 (pm20) cc_final: 0.7838 (pm20) REVERT: Y 73 TYR cc_start: 0.8709 (OUTLIER) cc_final: 0.8153 (t80) REVERT: Y 250 MET cc_start: 0.8079 (OUTLIER) cc_final: 0.7376 (ptp) REVERT: Y 486 LYS cc_start: 0.8191 (tptt) cc_final: 0.7613 (tttp) REVERT: Z 5 GLN cc_start: 0.8687 (tm-30) cc_final: 0.7721 (tm-30) REVERT: Z 42 ASP cc_start: 0.7087 (t0) cc_final: 0.6033 (t0) REVERT: Z 45 MET cc_start: 0.8166 (mmp) cc_final: 0.7767 (mmp) REVERT: a 49 VAL cc_start: 0.8103 (t) cc_final: 0.7840 (m) REVERT: b 128 TYR cc_start: 0.8980 (t80) cc_final: 0.8710 (t80) REVERT: c 372 MET cc_start: 0.6857 (ptp) cc_final: 0.6627 (ptt) REVERT: c 432 ASP cc_start: 0.6431 (p0) cc_final: 0.6224 (p0) REVERT: d 45 MET cc_start: 0.6078 (mtm) cc_final: 0.5816 (mtm) REVERT: d 59 LYS cc_start: 0.7060 (tptt) cc_final: 0.6713 (ttmt) REVERT: e 66 TYR cc_start: 0.8542 (t80) cc_final: 0.8129 (t80) REVERT: e 134 ASP cc_start: 0.7747 (OUTLIER) cc_final: 0.7322 (p0) REVERT: f 11 ARG cc_start: 0.7939 (OUTLIER) cc_final: 0.7503 (mpt-90) REVERT: g 250 MET cc_start: 0.8024 (pmm) cc_final: 0.7116 (ptp) REVERT: g 374 ASP cc_start: 0.7063 (p0) cc_final: 0.6725 (p0) REVERT: g 382 ARG cc_start: 0.8651 (mmp80) cc_final: 0.8130 (mmp80) REVERT: h 96 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7172 (mp0) REVERT: i 83 THR cc_start: 0.8696 (OUTLIER) cc_final: 0.8168 (m) REVERT: j 165 LEU cc_start: 0.8876 (mm) cc_final: 0.8647 (mm) REVERT: k 486 LYS cc_start: 0.8552 (tptm) cc_final: 0.8254 (tptt) REVERT: k 568 MET cc_start: 0.7822 (tmm) cc_final: 0.7576 (tmm) REVERT: l 42 ASP cc_start: 0.6732 (t0) cc_final: 0.6198 (t0) REVERT: l 91 ARG cc_start: 0.7912 (tmm160) cc_final: 0.6601 (ptt-90) REVERT: o 486 LYS cc_start: 0.7985 (tptt) cc_final: 0.7754 (tptt) REVERT: o 489 ASP cc_start: 0.7875 (OUTLIER) cc_final: 0.7511 (t0) REVERT: p 100 PHE cc_start: 0.7815 (m-10) cc_final: 0.7543 (m-80) REVERT: u 73 TYR cc_start: 0.8679 (OUTLIER) cc_final: 0.8055 (t80) REVERT: u 146 ARG cc_start: 0.8360 (mtt-85) cc_final: 0.7967 (mtt180) REVERT: u 199 ASP cc_start: 0.7997 (OUTLIER) cc_final: 0.7258 (m-30) REVERT: u 250 MET cc_start: 0.8053 (OUTLIER) cc_final: 0.7313 (ptp) REVERT: v 5 GLN cc_start: 0.8165 (tm-30) cc_final: 0.7389 (tm-30) REVERT: w 3 PHE cc_start: 0.7717 (p90) cc_final: 0.7208 (p90) REVERT: x 432 ASP cc_start: 0.6428 (p0) cc_final: 0.6144 (p0) REVERT: y 18 LEU cc_start: 0.6312 (tp) cc_final: 0.5956 (tp) REVERT: y 91 ARG cc_start: 0.3432 (mtt90) cc_final: 0.2775 (ptp90) REVERT: y 96 GLU cc_start: 0.7006 (mm-30) cc_final: 0.5249 (mt-10) outliers start: 377 outliers final: 267 residues processed: 1919 average time/residue: 1.0021 time to fit residues: 3436.0140 Evaluate side-chains 1852 residues out of total 13764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 283 poor density : 1569 time to evaluate : 11.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 69 VAL Chi-restraints excluded: chain 0 residue 183 TYR Chi-restraints excluded: chain 0 residue 199 ASP Chi-restraints excluded: chain 0 residue 330 ILE Chi-restraints excluded: chain 0 residue 450 LEU Chi-restraints excluded: chain 0 residue 484 THR Chi-restraints excluded: chain 0 residue 583 LEU Chi-restraints excluded: chain 1 residue 26 THR Chi-restraints excluded: chain 1 residue 61 THR Chi-restraints excluded: chain 1 residue 80 LEU Chi-restraints excluded: chain 2 residue 42 VAL Chi-restraints excluded: chain 2 residue 80 THR Chi-restraints excluded: chain 2 residue 148 LEU Chi-restraints excluded: chain 3 residue 83 ASP Chi-restraints excluded: chain 3 residue 166 ILE Chi-restraints excluded: chain 3 residue 397 MET Chi-restraints excluded: chain 3 residue 412 VAL Chi-restraints excluded: chain 3 residue 427 ILE Chi-restraints excluded: chain 3 residue 576 VAL Chi-restraints excluded: chain 4 residue 25 LEU Chi-restraints excluded: chain 4 residue 52 ASP Chi-restraints excluded: chain 4 residue 64 THR Chi-restraints excluded: chain 4 residue 68 MET Chi-restraints excluded: chain 4 residue 71 THR Chi-restraints excluded: chain 5 residue 71 LEU Chi-restraints excluded: chain 6 residue 41 GLU Chi-restraints excluded: chain 6 residue 69 VAL Chi-restraints excluded: chain 6 residue 183 TYR Chi-restraints excluded: chain 6 residue 199 ASP Chi-restraints excluded: chain 6 residue 252 TRP Chi-restraints excluded: chain 6 residue 330 ILE Chi-restraints excluded: chain 6 residue 374 ASP Chi-restraints excluded: chain 6 residue 390 LEU Chi-restraints excluded: chain 6 residue 412 VAL Chi-restraints excluded: chain 6 residue 450 LEU Chi-restraints excluded: chain 6 residue 489 ASP Chi-restraints excluded: chain 6 residue 576 VAL Chi-restraints excluded: chain 6 residue 583 LEU Chi-restraints excluded: chain 7 residue 35 PHE Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 384 SER Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain E residue 332 VAL Chi-restraints excluded: chain E residue 333 MET Chi-restraints excluded: chain E residue 339 MET Chi-restraints excluded: chain E residue 346 LEU Chi-restraints excluded: chain E residue 537 MET Chi-restraints excluded: chain F residue 384 SER Chi-restraints excluded: chain F residue 540 MET Chi-restraints excluded: chain F residue 553 GLU Chi-restraints excluded: chain G residue 32 ILE Chi-restraints excluded: chain G residue 103 GLN Chi-restraints excluded: chain G residue 108 GLN Chi-restraints excluded: chain G residue 116 VAL Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 33 LYS Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain H residue 122 SER Chi-restraints excluded: chain H residue 142 LEU Chi-restraints excluded: chain H residue 145 THR Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain I residue 32 ILE Chi-restraints excluded: chain I residue 113 LEU Chi-restraints excluded: chain I residue 116 VAL Chi-restraints excluded: chain I residue 173 VAL Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain J residue 108 GLN Chi-restraints excluded: chain J residue 109 SER Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain K residue 32 ILE Chi-restraints excluded: chain K residue 33 LYS Chi-restraints excluded: chain K residue 67 GLU Chi-restraints excluded: chain K residue 116 VAL Chi-restraints excluded: chain K residue 122 SER Chi-restraints excluded: chain K residue 184 ASP Chi-restraints excluded: chain L residue 32 ILE Chi-restraints excluded: chain L residue 113 LEU Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 122 SER Chi-restraints excluded: chain L residue 171 LEU Chi-restraints excluded: chain L residue 186 LEU Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain M residue 80 LEU Chi-restraints excluded: chain M residue 96 GLU Chi-restraints excluded: chain M residue 108 GLN Chi-restraints excluded: chain N residue 25 LEU Chi-restraints excluded: chain N residue 26 THR Chi-restraints excluded: chain N residue 49 ILE Chi-restraints excluded: chain N residue 52 ASP Chi-restraints excluded: chain O residue 18 LEU Chi-restraints excluded: chain O residue 71 THR Chi-restraints excluded: chain P residue 26 THR Chi-restraints excluded: chain P residue 34 LEU Chi-restraints excluded: chain P residue 58 VAL Chi-restraints excluded: chain P residue 61 THR Chi-restraints excluded: chain P residue 80 LEU Chi-restraints excluded: chain P residue 92 LEU Chi-restraints excluded: chain Q residue 8 ASN Chi-restraints excluded: chain Q residue 24 SER Chi-restraints excluded: chain Q residue 25 LEU Chi-restraints excluded: chain Q residue 47 THR Chi-restraints excluded: chain Q residue 52 ASP Chi-restraints excluded: chain Q residue 71 THR Chi-restraints excluded: chain R residue 18 LEU Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain S residue 43 CYS Chi-restraints excluded: chain S residue 44 ASP Chi-restraints excluded: chain S residue 45 ASP Chi-restraints excluded: chain S residue 93 TRP Chi-restraints excluded: chain S residue 116 VAL Chi-restraints excluded: chain S residue 142 LEU Chi-restraints excluded: chain S residue 149 THR Chi-restraints excluded: chain S residue 160 ILE Chi-restraints excluded: chain S residue 161 ILE Chi-restraints excluded: chain S residue 166 TRP Chi-restraints excluded: chain T residue 42 VAL Chi-restraints excluded: chain T residue 53 THR Chi-restraints excluded: chain T residue 149 THR Chi-restraints excluded: chain U residue 83 ASP Chi-restraints excluded: chain U residue 252 TRP Chi-restraints excluded: chain U residue 377 ASP Chi-restraints excluded: chain U residue 393 ASN Chi-restraints excluded: chain U residue 412 VAL Chi-restraints excluded: chain U residue 427 ILE Chi-restraints excluded: chain U residue 496 GLN Chi-restraints excluded: chain U residue 506 ILE Chi-restraints excluded: chain V residue 26 THR Chi-restraints excluded: chain V residue 80 LEU Chi-restraints excluded: chain W residue 43 CYS Chi-restraints excluded: chain W residue 44 ASP Chi-restraints excluded: chain W residue 45 ASP Chi-restraints excluded: chain W residue 77 ASN Chi-restraints excluded: chain W residue 78 MET Chi-restraints excluded: chain W residue 83 THR Chi-restraints excluded: chain W residue 93 TRP Chi-restraints excluded: chain W residue 134 ASP Chi-restraints excluded: chain W residue 141 LEU Chi-restraints excluded: chain W residue 161 ILE Chi-restraints excluded: chain X residue 156 GLN Chi-restraints excluded: chain X residue 162 VAL Chi-restraints excluded: chain Y residue 73 TYR Chi-restraints excluded: chain Y residue 183 TYR Chi-restraints excluded: chain Y residue 250 MET Chi-restraints excluded: chain Y residue 330 ILE Chi-restraints excluded: chain Y residue 485 ASN Chi-restraints excluded: chain Y residue 563 GLU Chi-restraints excluded: chain Y residue 576 VAL Chi-restraints excluded: chain Y residue 583 LEU Chi-restraints excluded: chain Y residue 590 LEU Chi-restraints excluded: chain Z residue 25 LEU Chi-restraints excluded: chain Z residue 47 THR Chi-restraints excluded: chain Z residue 52 ASP Chi-restraints excluded: chain Z residue 68 MET Chi-restraints excluded: chain Z residue 71 THR Chi-restraints excluded: chain a residue 43 CYS Chi-restraints excluded: chain a residue 44 ASP Chi-restraints excluded: chain a residue 71 VAL Chi-restraints excluded: chain a residue 93 TRP Chi-restraints excluded: chain a residue 161 ILE Chi-restraints excluded: chain b residue 70 GLN Chi-restraints excluded: chain c residue 83 ASP Chi-restraints excluded: chain c residue 377 ASP Chi-restraints excluded: chain c residue 412 VAL Chi-restraints excluded: chain c residue 427 ILE Chi-restraints excluded: chain d residue 58 VAL Chi-restraints excluded: chain d residue 71 THR Chi-restraints excluded: chain e residue 43 CYS Chi-restraints excluded: chain e residue 44 ASP Chi-restraints excluded: chain e residue 78 MET Chi-restraints excluded: chain e residue 93 TRP Chi-restraints excluded: chain e residue 106 THR Chi-restraints excluded: chain e residue 134 ASP Chi-restraints excluded: chain e residue 149 THR Chi-restraints excluded: chain e residue 161 ILE Chi-restraints excluded: chain e residue 166 TRP Chi-restraints excluded: chain f residue 11 ARG Chi-restraints excluded: chain f residue 156 GLN Chi-restraints excluded: chain f residue 197 LEU Chi-restraints excluded: chain g residue 69 VAL Chi-restraints excluded: chain g residue 183 TYR Chi-restraints excluded: chain g residue 199 ASP Chi-restraints excluded: chain g residue 330 ILE Chi-restraints excluded: chain g residue 450 LEU Chi-restraints excluded: chain h residue 14 LEU Chi-restraints excluded: chain h residue 15 VAL Chi-restraints excluded: chain h residue 58 VAL Chi-restraints excluded: chain h residue 61 THR Chi-restraints excluded: chain h residue 80 LEU Chi-restraints excluded: chain h residue 96 GLU Chi-restraints excluded: chain i residue 43 CYS Chi-restraints excluded: chain i residue 44 ASP Chi-restraints excluded: chain i residue 45 ASP Chi-restraints excluded: chain i residue 83 THR Chi-restraints excluded: chain i residue 93 TRP Chi-restraints excluded: chain i residue 158 LEU Chi-restraints excluded: chain i residue 160 ILE Chi-restraints excluded: chain i residue 161 ILE Chi-restraints excluded: chain j residue 16 LEU Chi-restraints excluded: chain j residue 53 THR Chi-restraints excluded: chain j residue 149 THR Chi-restraints excluded: chain k residue 83 ASP Chi-restraints excluded: chain k residue 166 ILE Chi-restraints excluded: chain k residue 252 TRP Chi-restraints excluded: chain k residue 377 ASP Chi-restraints excluded: chain k residue 412 VAL Chi-restraints excluded: chain k residue 576 VAL Chi-restraints excluded: chain k residue 590 LEU Chi-restraints excluded: chain l residue 25 LEU Chi-restraints excluded: chain l residue 47 THR Chi-restraints excluded: chain l residue 49 ILE Chi-restraints excluded: chain l residue 52 ASP Chi-restraints excluded: chain l residue 80 LEU Chi-restraints excluded: chain l residue 88 ILE Chi-restraints excluded: chain m residue 43 CYS Chi-restraints excluded: chain m residue 44 ASP Chi-restraints excluded: chain m residue 71 VAL Chi-restraints excluded: chain m residue 78 MET Chi-restraints excluded: chain m residue 93 TRP Chi-restraints excluded: chain m residue 161 ILE Chi-restraints excluded: chain n residue 121 VAL Chi-restraints excluded: chain o residue 41 GLU Chi-restraints excluded: chain o residue 63 ASN Chi-restraints excluded: chain o residue 183 TYR Chi-restraints excluded: chain o residue 199 ASP Chi-restraints excluded: chain o residue 330 ILE Chi-restraints excluded: chain o residue 374 ASP Chi-restraints excluded: chain o residue 412 VAL Chi-restraints excluded: chain o residue 450 LEU Chi-restraints excluded: chain o residue 489 ASP Chi-restraints excluded: chain o residue 576 VAL Chi-restraints excluded: chain o residue 583 LEU Chi-restraints excluded: chain o residue 588 THR Chi-restraints excluded: chain p residue 34 LEU Chi-restraints excluded: chain q residue 80 THR Chi-restraints excluded: chain q residue 152 ASN Chi-restraints excluded: chain r residue 391 SER Chi-restraints excluded: chain r residue 412 VAL Chi-restraints excluded: chain s residue 6 PHE Chi-restraints excluded: chain s residue 15 VAL Chi-restraints excluded: chain s residue 26 THR Chi-restraints excluded: chain s residue 61 THR Chi-restraints excluded: chain s residue 80 LEU Chi-restraints excluded: chain s residue 96 GLU Chi-restraints excluded: chain t residue 15 LEU Chi-restraints excluded: chain t residue 42 VAL Chi-restraints excluded: chain t residue 80 THR Chi-restraints excluded: chain u residue 73 TYR Chi-restraints excluded: chain u residue 138 LEU Chi-restraints excluded: chain u residue 166 ILE Chi-restraints excluded: chain u residue 183 TYR Chi-restraints excluded: chain u residue 199 ASP Chi-restraints excluded: chain u residue 250 MET Chi-restraints excluded: chain u residue 330 ILE Chi-restraints excluded: chain u residue 396 VAL Chi-restraints excluded: chain u residue 563 GLU Chi-restraints excluded: chain u residue 576 VAL Chi-restraints excluded: chain u residue 583 LEU Chi-restraints excluded: chain u residue 590 LEU Chi-restraints excluded: chain v residue 14 LEU Chi-restraints excluded: chain v residue 47 THR Chi-restraints excluded: chain v residue 52 ASP Chi-restraints excluded: chain v residue 57 ILE Chi-restraints excluded: chain v residue 64 THR Chi-restraints excluded: chain v residue 71 THR Chi-restraints excluded: chain v residue 96 GLU Chi-restraints excluded: chain w residue 80 THR Chi-restraints excluded: chain w residue 152 ASN Chi-restraints excluded: chain x residue 83 ASP Chi-restraints excluded: chain x residue 168 ASP Chi-restraints excluded: chain x residue 250 MET Chi-restraints excluded: chain x residue 412 VAL Chi-restraints excluded: chain y residue 61 THR Chi-restraints excluded: chain y residue 68 MET Chi-restraints excluded: chain z residue 71 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1644 random chunks: chunk 1533 optimal weight: 6.9990 chunk 179 optimal weight: 6.9990 chunk 906 optimal weight: 0.7980 chunk 1161 optimal weight: 9.9990 chunk 899 optimal weight: 7.9990 chunk 1338 optimal weight: 5.9990 chunk 888 optimal weight: 3.9990 chunk 1584 optimal weight: 0.9990 chunk 991 optimal weight: 10.0000 chunk 966 optimal weight: 4.9990 chunk 731 optimal weight: 5.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 54 HIS 1 5 GLN 3 60 GLN 3 485 ASN 4 9 ASN ** 4 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 108 GLN 6 54 HIS ** 6 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 486 ASN ** D 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 486 ASN G 12 HIS ** H 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 92 GLN ** a 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 54 HIS ** h 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 89 GLN k 60 GLN ** k 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 485 ASN ** k 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 54 HIS o 63 ASN o 92 GLN ** p 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 54 HIS u 92 GLN ** u 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 130506 Z= 0.257 Angle : 0.599 10.355 177246 Z= 0.313 Chirality : 0.043 0.387 19890 Planarity : 0.005 0.075 23400 Dihedral : 4.706 29.217 18210 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.07 % Favored : 94.61 % Rotamer: Outliers : 2.82 % Allowed : 16.97 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.07), residues: 16500 helix: 2.42 (0.07), residues: 6282 sheet: -0.43 (0.10), residues: 2586 loop : -1.34 (0.07), residues: 7632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.001 TRP u 553 HIS 0.008 0.001 HIS W 12 PHE 0.037 0.002 PHE V 44 TYR 0.021 0.001 TYR w 128 ARG 0.009 0.000 ARG o 599 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 33000 Ramachandran restraints generated. 16500 Oldfield, 0 Emsley, 16500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 33000 Ramachandran restraints generated. 16500 Oldfield, 0 Emsley, 16500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1996 residues out of total 13764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 365 poor density : 1631 time to evaluate : 11.238 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: 0 374 ASP cc_start: 0.7152 (p0) cc_final: 0.6834 (p0) REVERT: 1 8 ASN cc_start: 0.7739 (t0) cc_final: 0.7014 (p0) REVERT: 1 91 ARG cc_start: 0.2490 (mpp-170) cc_final: 0.2082 (mpp-170) REVERT: 2 33 LEU cc_start: 0.9132 (tp) cc_final: 0.8820 (tt) REVERT: 3 324 MET cc_start: 0.7113 (tpp) cc_final: 0.6192 (mtp) REVERT: 3 607 ARG cc_start: 0.6325 (mmt-90) cc_final: 0.5797 (mtp180) REVERT: 4 5 GLN cc_start: 0.8684 (tm-30) cc_final: 0.7685 (tm-30) REVERT: 4 42 ASP cc_start: 0.7048 (t0) cc_final: 0.6066 (t0) REVERT: 4 45 MET cc_start: 0.7836 (mmp) cc_final: 0.7495 (mmp) REVERT: 6 110 SER cc_start: 0.9470 (m) cc_final: 0.9232 (p) REVERT: 6 489 ASP cc_start: 0.7498 (OUTLIER) cc_final: 0.7002 (t0) REVERT: 7 68 MET cc_start: 0.7111 (tpp) cc_final: 0.6641 (tpp) REVERT: A 510 MET cc_start: 0.1640 (mtm) cc_final: 0.1292 (mtt) REVERT: B 239 MET cc_start: 0.7072 (mpp) cc_final: 0.6732 (mmm) REVERT: B 565 ILE cc_start: 0.9253 (mm) cc_final: 0.8915 (mp) REVERT: C 69 TRP cc_start: 0.8202 (m-90) cc_final: 0.7925 (m-90) REVERT: C 333 MET cc_start: 0.6303 (mtm) cc_final: 0.6056 (mtm) REVERT: C 540 MET cc_start: 0.8527 (ppp) cc_final: 0.8273 (ptm) REVERT: D 10 SER cc_start: 0.8969 (m) cc_final: 0.8726 (m) REVERT: D 283 MET cc_start: 0.7836 (mtm) cc_final: 0.7164 (mtm) REVERT: D 510 MET cc_start: 0.1471 (mtm) cc_final: 0.1093 (mtt) REVERT: E 565 ILE cc_start: 0.9313 (mm) cc_final: 0.8986 (mp) REVERT: F 66 TRP cc_start: 0.7844 (m100) cc_final: 0.7339 (m100) REVERT: F 239 MET cc_start: 0.6966 (mpp) cc_final: 0.6656 (mpp) REVERT: G 106 THR cc_start: 0.8675 (OUTLIER) cc_final: 0.8338 (p) REVERT: H 164 LYS cc_start: 0.8149 (mtpp) cc_final: 0.7677 (ttpt) REVERT: I 88 GLU cc_start: 0.7664 (tm-30) cc_final: 0.7277 (tm-30) REVERT: I 113 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8267 (pp) REVERT: L 88 GLU cc_start: 0.7648 (tm-30) cc_final: 0.7223 (tm-30) REVERT: L 113 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8238 (pp) REVERT: M 96 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7265 (mp0) REVERT: M 108 GLN cc_start: 0.8454 (OUTLIER) cc_final: 0.8117 (mp10) REVERT: N 5 GLN cc_start: 0.8434 (tm-30) cc_final: 0.6999 (tm-30) REVERT: N 42 ASP cc_start: 0.6860 (t0) cc_final: 0.6365 (t0) REVERT: O 13 ARG cc_start: 0.7401 (mmp80) cc_final: 0.6890 (mmp-170) REVERT: O 82 PHE cc_start: 0.5256 (m-80) cc_final: 0.4941 (m-80) REVERT: Q 26 THR cc_start: 0.8512 (m) cc_final: 0.8270 (m) REVERT: Q 68 MET cc_start: 0.8611 (mpp) cc_final: 0.8400 (mpp) REVERT: R 91 ARG cc_start: 0.3009 (mtt90) cc_final: 0.1152 (mmp80) REVERT: S 66 TYR cc_start: 0.8425 (t80) cc_final: 0.8112 (t80) REVERT: U 545 ASP cc_start: 0.6956 (m-30) cc_final: 0.6703 (m-30) REVERT: V 96 GLU cc_start: 0.7269 (mp0) cc_final: 0.6756 (mp0) REVERT: W 66 TYR cc_start: 0.8467 (t80) cc_final: 0.8159 (t80) REVERT: W 83 THR cc_start: 0.8656 (OUTLIER) cc_final: 0.8014 (m) REVERT: X 39 GLU cc_start: 0.7534 (tp30) cc_final: 0.7184 (tp30) REVERT: X 136 GLN cc_start: 0.8086 (pm20) cc_final: 0.7842 (pm20) REVERT: Y 73 TYR cc_start: 0.8725 (OUTLIER) cc_final: 0.8151 (t80) REVERT: Y 199 ASP cc_start: 0.7847 (OUTLIER) cc_final: 0.7267 (m-30) REVERT: Y 250 MET cc_start: 0.7989 (OUTLIER) cc_final: 0.7321 (ptp) REVERT: Y 486 LYS cc_start: 0.8139 (tptt) cc_final: 0.7672 (tttp) REVERT: Z 5 GLN cc_start: 0.8655 (tm-30) cc_final: 0.7694 (tm-30) REVERT: Z 42 ASP cc_start: 0.7119 (t0) cc_final: 0.6073 (t0) REVERT: Z 45 MET cc_start: 0.8181 (mmp) cc_final: 0.7690 (mmp) REVERT: a 49 VAL cc_start: 0.8175 (t) cc_final: 0.7864 (p) REVERT: a 66 TYR cc_start: 0.8527 (t80) cc_final: 0.8279 (t80) REVERT: b 128 TYR cc_start: 0.8962 (t80) cc_final: 0.8676 (t80) REVERT: c 362 ASP cc_start: 0.7968 (p0) cc_final: 0.7727 (p0) REVERT: c 372 MET cc_start: 0.6841 (ptp) cc_final: 0.6615 (ptt) REVERT: c 432 ASP cc_start: 0.6574 (p0) cc_final: 0.6322 (p0) REVERT: d 45 MET cc_start: 0.6297 (mtm) cc_final: 0.5946 (mtm) REVERT: d 59 LYS cc_start: 0.7014 (tptt) cc_final: 0.6665 (ttmt) REVERT: e 66 TYR cc_start: 0.8475 (t80) cc_final: 0.8108 (t80) REVERT: f 11 ARG cc_start: 0.7933 (OUTLIER) cc_final: 0.7615 (mpt-90) REVERT: g 250 MET cc_start: 0.8022 (pmm) cc_final: 0.7156 (ptp) REVERT: g 374 ASP cc_start: 0.7027 (p0) cc_final: 0.6763 (p0) REVERT: g 382 ARG cc_start: 0.8615 (mmp80) cc_final: 0.8168 (mmp80) REVERT: g 486 LYS cc_start: 0.8290 (ptmt) cc_final: 0.8079 (ttpp) REVERT: h 86 ASP cc_start: 0.6882 (OUTLIER) cc_final: 0.6234 (t70) REVERT: h 96 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7156 (mp0) REVERT: i 83 THR cc_start: 0.8705 (OUTLIER) cc_final: 0.8186 (m) REVERT: j 19 GLU cc_start: 0.7982 (mm-30) cc_final: 0.7758 (mm-30) REVERT: j 165 LEU cc_start: 0.8860 (mm) cc_final: 0.8640 (mm) REVERT: k 486 LYS cc_start: 0.8578 (tptm) cc_final: 0.8298 (tptt) REVERT: k 568 MET cc_start: 0.7856 (tmm) cc_final: 0.7453 (tmm) REVERT: k 572 MET cc_start: 0.7883 (mmp) cc_final: 0.7593 (mmt) REVERT: l 5 GLN cc_start: 0.8538 (tm-30) cc_final: 0.7206 (tm-30) REVERT: l 42 ASP cc_start: 0.6740 (t0) cc_final: 0.6236 (t0) REVERT: l 91 ARG cc_start: 0.7758 (tmm160) cc_final: 0.6597 (ptt-90) REVERT: o 486 LYS cc_start: 0.8019 (tptt) cc_final: 0.7767 (tptt) REVERT: o 489 ASP cc_start: 0.7799 (OUTLIER) cc_final: 0.7468 (t0) REVERT: p 100 PHE cc_start: 0.7781 (m-10) cc_final: 0.7495 (m-80) REVERT: q 3 PHE cc_start: 0.7780 (p90) cc_final: 0.7341 (p90) REVERT: u 73 TYR cc_start: 0.8709 (OUTLIER) cc_final: 0.8100 (t80) REVERT: u 146 ARG cc_start: 0.8368 (mtt-85) cc_final: 0.7970 (mtt180) REVERT: u 199 ASP cc_start: 0.8000 (OUTLIER) cc_final: 0.7298 (m-30) REVERT: u 250 MET cc_start: 0.7955 (OUTLIER) cc_final: 0.7307 (ptp) REVERT: v 5 GLN cc_start: 0.8134 (tm-30) cc_final: 0.7392 (tm-30) REVERT: w 3 PHE cc_start: 0.7693 (p90) cc_final: 0.7271 (p90) REVERT: y 18 LEU cc_start: 0.6374 (tp) cc_final: 0.6028 (tp) REVERT: y 91 ARG cc_start: 0.3489 (mtt90) cc_final: 0.1711 (mmt180) REVERT: y 96 GLU cc_start: 0.6967 (mm-30) cc_final: 0.5184 (mt-10) outliers start: 365 outliers final: 281 residues processed: 1870 average time/residue: 0.9935 time to fit residues: 3327.5669 Evaluate side-chains 1864 residues out of total 13764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 299 poor density : 1565 time to evaluate : 11.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 183 TYR Chi-restraints excluded: chain 0 residue 199 ASP Chi-restraints excluded: chain 0 residue 330 ILE Chi-restraints excluded: chain 0 residue 450 LEU Chi-restraints excluded: chain 0 residue 484 THR Chi-restraints excluded: chain 0 residue 583 LEU Chi-restraints excluded: chain 1 residue 61 THR Chi-restraints excluded: chain 1 residue 80 LEU Chi-restraints excluded: chain 2 residue 15 LEU Chi-restraints excluded: chain 2 residue 42 VAL Chi-restraints excluded: chain 2 residue 80 THR Chi-restraints excluded: chain 2 residue 148 LEU Chi-restraints excluded: chain 3 residue 83 ASP Chi-restraints excluded: chain 3 residue 166 ILE Chi-restraints excluded: chain 3 residue 397 MET Chi-restraints excluded: chain 3 residue 412 VAL Chi-restraints excluded: chain 3 residue 427 ILE Chi-restraints excluded: chain 3 residue 431 VAL Chi-restraints excluded: chain 3 residue 576 VAL Chi-restraints excluded: chain 4 residue 25 LEU Chi-restraints excluded: chain 4 residue 52 ASP Chi-restraints excluded: chain 4 residue 64 THR Chi-restraints excluded: chain 4 residue 68 MET Chi-restraints excluded: chain 4 residue 71 THR Chi-restraints excluded: chain 5 residue 71 LEU Chi-restraints excluded: chain 6 residue 41 GLU Chi-restraints excluded: chain 6 residue 183 TYR Chi-restraints excluded: chain 6 residue 199 ASP Chi-restraints excluded: chain 6 residue 330 ILE Chi-restraints excluded: chain 6 residue 374 ASP Chi-restraints excluded: chain 6 residue 412 VAL Chi-restraints excluded: chain 6 residue 450 LEU Chi-restraints excluded: chain 6 residue 489 ASP Chi-restraints excluded: chain 6 residue 576 VAL Chi-restraints excluded: chain 6 residue 583 LEU Chi-restraints excluded: chain 6 residue 588 THR Chi-restraints excluded: chain 7 residue 35 PHE Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 537 MET Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 384 SER Chi-restraints excluded: chain C residue 462 THR Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 332 VAL Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 332 VAL Chi-restraints excluded: chain E residue 333 MET Chi-restraints excluded: chain E residue 339 MET Chi-restraints excluded: chain E residue 346 LEU Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 384 SER Chi-restraints excluded: chain F residue 540 MET Chi-restraints excluded: chain F residue 553 GLU Chi-restraints excluded: chain G residue 32 ILE Chi-restraints excluded: chain G residue 103 GLN Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 108 GLN Chi-restraints excluded: chain G residue 116 VAL Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain H residue 11 ILE Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 33 LYS Chi-restraints excluded: chain H residue 67 GLU Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain H residue 122 SER Chi-restraints excluded: chain H residue 142 LEU Chi-restraints excluded: chain H residue 145 THR Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain I residue 32 ILE Chi-restraints excluded: chain I residue 113 LEU Chi-restraints excluded: chain I residue 116 VAL Chi-restraints excluded: chain I residue 173 VAL Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain J residue 32 ILE Chi-restraints excluded: chain J residue 108 GLN Chi-restraints excluded: chain J residue 109 SER Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain K residue 32 ILE Chi-restraints excluded: chain K residue 33 LYS Chi-restraints excluded: chain K residue 67 GLU Chi-restraints excluded: chain K residue 116 VAL Chi-restraints excluded: chain K residue 122 SER Chi-restraints excluded: chain K residue 184 ASP Chi-restraints excluded: chain L residue 32 ILE Chi-restraints excluded: chain L residue 113 LEU Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 122 SER Chi-restraints excluded: chain L residue 171 LEU Chi-restraints excluded: chain L residue 186 LEU Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain M residue 71 THR Chi-restraints excluded: chain M residue 80 LEU Chi-restraints excluded: chain M residue 96 GLU Chi-restraints excluded: chain M residue 108 GLN Chi-restraints excluded: chain N residue 25 LEU Chi-restraints excluded: chain N residue 26 THR Chi-restraints excluded: chain N residue 49 ILE Chi-restraints excluded: chain N residue 52 ASP Chi-restraints excluded: chain O residue 18 LEU Chi-restraints excluded: chain O residue 71 THR Chi-restraints excluded: chain P residue 26 THR Chi-restraints excluded: chain P residue 34 LEU Chi-restraints excluded: chain P residue 61 THR Chi-restraints excluded: chain P residue 80 LEU Chi-restraints excluded: chain P residue 92 LEU Chi-restraints excluded: chain Q residue 24 SER Chi-restraints excluded: chain Q residue 25 LEU Chi-restraints excluded: chain Q residue 47 THR Chi-restraints excluded: chain Q residue 52 ASP Chi-restraints excluded: chain Q residue 64 THR Chi-restraints excluded: chain Q residue 71 THR Chi-restraints excluded: chain R residue 18 LEU Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain S residue 43 CYS Chi-restraints excluded: chain S residue 44 ASP Chi-restraints excluded: chain S residue 45 ASP Chi-restraints excluded: chain S residue 93 TRP Chi-restraints excluded: chain S residue 116 VAL Chi-restraints excluded: chain S residue 142 LEU Chi-restraints excluded: chain S residue 149 THR Chi-restraints excluded: chain S residue 160 ILE Chi-restraints excluded: chain S residue 161 ILE Chi-restraints excluded: chain S residue 166 TRP Chi-restraints excluded: chain T residue 42 VAL Chi-restraints excluded: chain T residue 53 THR Chi-restraints excluded: chain T residue 149 THR Chi-restraints excluded: chain U residue 83 ASP Chi-restraints excluded: chain U residue 252 TRP Chi-restraints excluded: chain U residue 377 ASP Chi-restraints excluded: chain U residue 393 ASN Chi-restraints excluded: chain U residue 412 VAL Chi-restraints excluded: chain U residue 427 ILE Chi-restraints excluded: chain U residue 496 GLN Chi-restraints excluded: chain U residue 506 ILE Chi-restraints excluded: chain V residue 58 VAL Chi-restraints excluded: chain V residue 61 THR Chi-restraints excluded: chain V residue 80 LEU Chi-restraints excluded: chain W residue 43 CYS Chi-restraints excluded: chain W residue 44 ASP Chi-restraints excluded: chain W residue 45 ASP Chi-restraints excluded: chain W residue 77 ASN Chi-restraints excluded: chain W residue 78 MET Chi-restraints excluded: chain W residue 83 THR Chi-restraints excluded: chain W residue 93 TRP Chi-restraints excluded: chain W residue 134 ASP Chi-restraints excluded: chain X residue 156 GLN Chi-restraints excluded: chain Y residue 73 TYR Chi-restraints excluded: chain Y residue 183 TYR Chi-restraints excluded: chain Y residue 199 ASP Chi-restraints excluded: chain Y residue 250 MET Chi-restraints excluded: chain Y residue 330 ILE Chi-restraints excluded: chain Y residue 440 MET Chi-restraints excluded: chain Y residue 485 ASN Chi-restraints excluded: chain Y residue 563 GLU Chi-restraints excluded: chain Y residue 576 VAL Chi-restraints excluded: chain Y residue 583 LEU Chi-restraints excluded: chain Y residue 590 LEU Chi-restraints excluded: chain Z residue 25 LEU Chi-restraints excluded: chain Z residue 47 THR Chi-restraints excluded: chain Z residue 52 ASP Chi-restraints excluded: chain Z residue 68 MET Chi-restraints excluded: chain Z residue 71 THR Chi-restraints excluded: chain a residue 43 CYS Chi-restraints excluded: chain a residue 44 ASP Chi-restraints excluded: chain a residue 71 VAL Chi-restraints excluded: chain a residue 93 TRP Chi-restraints excluded: chain a residue 161 ILE Chi-restraints excluded: chain a residue 180 ASP Chi-restraints excluded: chain b residue 42 VAL Chi-restraints excluded: chain b residue 70 GLN Chi-restraints excluded: chain b residue 121 VAL Chi-restraints excluded: chain c residue 83 ASP Chi-restraints excluded: chain c residue 250 MET Chi-restraints excluded: chain c residue 377 ASP Chi-restraints excluded: chain c residue 412 VAL Chi-restraints excluded: chain c residue 427 ILE Chi-restraints excluded: chain c residue 443 MET Chi-restraints excluded: chain d residue 58 VAL Chi-restraints excluded: chain d residue 71 THR Chi-restraints excluded: chain e residue 43 CYS Chi-restraints excluded: chain e residue 44 ASP Chi-restraints excluded: chain e residue 78 MET Chi-restraints excluded: chain e residue 93 TRP Chi-restraints excluded: chain e residue 106 THR Chi-restraints excluded: chain e residue 116 VAL Chi-restraints excluded: chain e residue 134 ASP Chi-restraints excluded: chain e residue 149 THR Chi-restraints excluded: chain e residue 161 ILE Chi-restraints excluded: chain e residue 166 TRP Chi-restraints excluded: chain f residue 11 ARG Chi-restraints excluded: chain f residue 156 GLN Chi-restraints excluded: chain f residue 197 LEU Chi-restraints excluded: chain g residue 69 VAL Chi-restraints excluded: chain g residue 127 ASP Chi-restraints excluded: chain g residue 183 TYR Chi-restraints excluded: chain g residue 199 ASP Chi-restraints excluded: chain g residue 330 ILE Chi-restraints excluded: chain g residue 450 LEU Chi-restraints excluded: chain h residue 14 LEU Chi-restraints excluded: chain h residue 15 VAL Chi-restraints excluded: chain h residue 58 VAL Chi-restraints excluded: chain h residue 61 THR Chi-restraints excluded: chain h residue 80 LEU Chi-restraints excluded: chain h residue 86 ASP Chi-restraints excluded: chain h residue 96 GLU Chi-restraints excluded: chain i residue 43 CYS Chi-restraints excluded: chain i residue 44 ASP Chi-restraints excluded: chain i residue 45 ASP Chi-restraints excluded: chain i residue 83 THR Chi-restraints excluded: chain i residue 93 TRP Chi-restraints excluded: chain i residue 105 VAL Chi-restraints excluded: chain i residue 158 LEU Chi-restraints excluded: chain i residue 160 ILE Chi-restraints excluded: chain i residue 161 ILE Chi-restraints excluded: chain j residue 16 LEU Chi-restraints excluded: chain j residue 148 LEU Chi-restraints excluded: chain j residue 149 THR Chi-restraints excluded: chain k residue 83 ASP Chi-restraints excluded: chain k residue 166 ILE Chi-restraints excluded: chain k residue 252 TRP Chi-restraints excluded: chain k residue 377 ASP Chi-restraints excluded: chain k residue 412 VAL Chi-restraints excluded: chain k residue 576 VAL Chi-restraints excluded: chain k residue 590 LEU Chi-restraints excluded: chain l residue 25 LEU Chi-restraints excluded: chain l residue 47 THR Chi-restraints excluded: chain l residue 49 ILE Chi-restraints excluded: chain l residue 52 ASP Chi-restraints excluded: chain l residue 80 LEU Chi-restraints excluded: chain l residue 88 ILE Chi-restraints excluded: chain m residue 43 CYS Chi-restraints excluded: chain m residue 44 ASP Chi-restraints excluded: chain m residue 71 VAL Chi-restraints excluded: chain m residue 78 MET Chi-restraints excluded: chain m residue 93 TRP Chi-restraints excluded: chain m residue 161 ILE Chi-restraints excluded: chain n residue 69 ILE Chi-restraints excluded: chain n residue 121 VAL Chi-restraints excluded: chain o residue 41 GLU Chi-restraints excluded: chain o residue 138 LEU Chi-restraints excluded: chain o residue 183 TYR Chi-restraints excluded: chain o residue 199 ASP Chi-restraints excluded: chain o residue 330 ILE Chi-restraints excluded: chain o residue 374 ASP Chi-restraints excluded: chain o residue 412 VAL Chi-restraints excluded: chain o residue 450 LEU Chi-restraints excluded: chain o residue 489 ASP Chi-restraints excluded: chain o residue 576 VAL Chi-restraints excluded: chain o residue 583 LEU Chi-restraints excluded: chain o residue 588 THR Chi-restraints excluded: chain p residue 34 LEU Chi-restraints excluded: chain q residue 152 ASN Chi-restraints excluded: chain r residue 391 SER Chi-restraints excluded: chain r residue 412 VAL Chi-restraints excluded: chain s residue 6 PHE Chi-restraints excluded: chain s residue 15 VAL Chi-restraints excluded: chain s residue 26 THR Chi-restraints excluded: chain s residue 61 THR Chi-restraints excluded: chain s residue 80 LEU Chi-restraints excluded: chain s residue 96 GLU Chi-restraints excluded: chain t residue 15 LEU Chi-restraints excluded: chain t residue 42 VAL Chi-restraints excluded: chain t residue 80 THR Chi-restraints excluded: chain u residue 73 TYR Chi-restraints excluded: chain u residue 138 LEU Chi-restraints excluded: chain u residue 166 ILE Chi-restraints excluded: chain u residue 183 TYR Chi-restraints excluded: chain u residue 199 ASP Chi-restraints excluded: chain u residue 250 MET Chi-restraints excluded: chain u residue 330 ILE Chi-restraints excluded: chain u residue 396 VAL Chi-restraints excluded: chain u residue 563 GLU Chi-restraints excluded: chain u residue 576 VAL Chi-restraints excluded: chain u residue 583 LEU Chi-restraints excluded: chain u residue 590 LEU Chi-restraints excluded: chain v residue 14 LEU Chi-restraints excluded: chain v residue 25 LEU Chi-restraints excluded: chain v residue 47 THR Chi-restraints excluded: chain v residue 52 ASP Chi-restraints excluded: chain v residue 57 ILE Chi-restraints excluded: chain v residue 64 THR Chi-restraints excluded: chain v residue 71 THR Chi-restraints excluded: chain w residue 80 THR Chi-restraints excluded: chain w residue 152 ASN Chi-restraints excluded: chain x residue 83 ASP Chi-restraints excluded: chain x residue 168 ASP Chi-restraints excluded: chain x residue 250 MET Chi-restraints excluded: chain x residue 412 VAL Chi-restraints excluded: chain x residue 443 MET Chi-restraints excluded: chain z residue 53 THR Chi-restraints excluded: chain z residue 71 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1644 random chunks: chunk 980 optimal weight: 0.9980 chunk 632 optimal weight: 7.9990 chunk 946 optimal weight: 8.9990 chunk 477 optimal weight: 9.9990 chunk 311 optimal weight: 7.9990 chunk 306 optimal weight: 0.1980 chunk 1007 optimal weight: 5.9990 chunk 1079 optimal weight: 4.9990 chunk 783 optimal weight: 10.0000 chunk 147 optimal weight: 20.0000 chunk 1245 optimal weight: 8.9990 overall best weight: 4.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 54 HIS ** 1 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 60 GLN 3 520 ASN ** 4 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 54 HIS 6 63 ASN 6 92 GLN ** 6 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 403 HIS B 486 ASN ** D 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 403 HIS E 433 GLN H 12 HIS ** H 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 12 HIS ** K 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 89 GLN ** S 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 452 GLN ** V 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 92 GLN Y 485 ASN Z 108 GLN ** a 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 54 HIS ** h 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 89 GLN ** i 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 60 GLN k 430 ASN ** k 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 54 HIS o 63 ASN ** p 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 83 ASN ** q 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 452 GLN r 485 ASN ** s 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 54 HIS u 92 GLN ** u 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 130506 Z= 0.295 Angle : 0.620 11.939 177246 Z= 0.324 Chirality : 0.043 0.414 19890 Planarity : 0.005 0.076 23400 Dihedral : 4.765 28.884 18210 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.32 % Favored : 94.36 % Rotamer: Outliers : 3.02 % Allowed : 17.27 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.07), residues: 16500 helix: 2.37 (0.07), residues: 6270 sheet: -0.47 (0.10), residues: 2556 loop : -1.40 (0.07), residues: 7674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP u 553 HIS 0.008 0.001 HIS W 12 PHE 0.036 0.002 PHE V 44 TYR 0.025 0.002 TYR 2 171 ARG 0.017 0.000 ARG k 345 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 33000 Ramachandran restraints generated. 16500 Oldfield, 0 Emsley, 16500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 33000 Ramachandran restraints generated. 16500 Oldfield, 0 Emsley, 16500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1979 residues out of total 13764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 391 poor density : 1588 time to evaluate : 11.317 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: 0 374 ASP cc_start: 0.7171 (p0) cc_final: 0.6895 (p0) REVERT: 1 8 ASN cc_start: 0.7720 (t0) cc_final: 0.7066 (p0) REVERT: 1 91 ARG cc_start: 0.2848 (mpp-170) cc_final: 0.2468 (mpp-170) REVERT: 2 33 LEU cc_start: 0.9162 (tp) cc_final: 0.8851 (tt) REVERT: 3 607 ARG cc_start: 0.6320 (mmt-90) cc_final: 0.5826 (mtp180) REVERT: 4 5 GLN cc_start: 0.8653 (tm-30) cc_final: 0.7903 (tm-30) REVERT: 4 45 MET cc_start: 0.7864 (mmp) cc_final: 0.7499 (mmp) REVERT: 6 110 SER cc_start: 0.9487 (m) cc_final: 0.9235 (p) REVERT: 6 489 ASP cc_start: 0.7520 (OUTLIER) cc_final: 0.7025 (t0) REVERT: 7 68 MET cc_start: 0.7151 (tpp) cc_final: 0.6684 (tpp) REVERT: A 283 MET cc_start: 0.7847 (mtm) cc_final: 0.7615 (mtm) REVERT: A 510 MET cc_start: 0.1753 (mtm) cc_final: 0.1391 (mtt) REVERT: B 239 MET cc_start: 0.7014 (mpp) cc_final: 0.6664 (mmm) REVERT: B 565 ILE cc_start: 0.9268 (mm) cc_final: 0.8925 (mp) REVERT: C 69 TRP cc_start: 0.8092 (m-90) cc_final: 0.7826 (m-90) REVERT: C 540 MET cc_start: 0.8518 (ppp) cc_final: 0.8298 (ptm) REVERT: D 10 SER cc_start: 0.8816 (m) cc_final: 0.8567 (m) REVERT: D 95 MET cc_start: 0.5893 (mtt) cc_final: 0.5658 (mtm) REVERT: D 283 MET cc_start: 0.7844 (mtm) cc_final: 0.7196 (mtm) REVERT: D 510 MET cc_start: 0.1191 (mtm) cc_final: 0.0849 (mtt) REVERT: E 565 ILE cc_start: 0.9318 (mm) cc_final: 0.8992 (mp) REVERT: F 66 TRP cc_start: 0.7924 (m100) cc_final: 0.7328 (m100) REVERT: F 239 MET cc_start: 0.6971 (mpp) cc_final: 0.6766 (mpp) REVERT: G 106 THR cc_start: 0.8734 (OUTLIER) cc_final: 0.8409 (p) REVERT: I 113 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8319 (pp) REVERT: I 182 GLU cc_start: 0.6795 (mm-30) cc_final: 0.6447 (mm-30) REVERT: L 113 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8300 (pp) REVERT: M 5 GLN cc_start: 0.7004 (mt0) cc_final: 0.6443 (mt0) REVERT: M 52 ASP cc_start: 0.7519 (m-30) cc_final: 0.7276 (m-30) REVERT: M 96 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7250 (mp0) REVERT: M 108 GLN cc_start: 0.8337 (OUTLIER) cc_final: 0.8062 (mp10) REVERT: N 42 ASP cc_start: 0.6725 (t0) cc_final: 0.6169 (t0) REVERT: O 82 PHE cc_start: 0.5300 (m-80) cc_final: 0.4999 (m-80) REVERT: Q 50 ARG cc_start: 0.6864 (ptm160) cc_final: 0.6488 (ptm-80) REVERT: Q 68 MET cc_start: 0.8600 (mpp) cc_final: 0.8377 (mpp) REVERT: R 45 MET cc_start: 0.6178 (mtm) cc_final: 0.5768 (ptt) REVERT: R 68 MET cc_start: 0.6700 (tpp) cc_final: 0.6132 (tpp) REVERT: R 91 ARG cc_start: 0.3054 (mtt90) cc_final: 0.1178 (mmp80) REVERT: T 49 MET cc_start: 0.7777 (tpp) cc_final: 0.7514 (tpp) REVERT: U 545 ASP cc_start: 0.7195 (m-30) cc_final: 0.6912 (m-30) REVERT: V 96 GLU cc_start: 0.7385 (mp0) cc_final: 0.6908 (mp0) REVERT: W 66 TYR cc_start: 0.8495 (t80) cc_final: 0.8193 (t80) REVERT: W 83 THR cc_start: 0.8690 (OUTLIER) cc_final: 0.8077 (m) REVERT: X 39 GLU cc_start: 0.7557 (tp30) cc_final: 0.7211 (tp30) REVERT: X 136 GLN cc_start: 0.8088 (pm20) cc_final: 0.7852 (pm20) REVERT: Y 73 TYR cc_start: 0.8754 (OUTLIER) cc_final: 0.8075 (t80) REVERT: Y 113 ARG cc_start: 0.7566 (mmt180) cc_final: 0.7362 (mmt180) REVERT: Y 199 ASP cc_start: 0.7900 (OUTLIER) cc_final: 0.7312 (m-30) REVERT: Y 250 MET cc_start: 0.8051 (OUTLIER) cc_final: 0.7368 (ptp) REVERT: Y 485 ASN cc_start: 0.8245 (OUTLIER) cc_final: 0.7892 (t0) REVERT: Z 5 GLN cc_start: 0.8688 (tm-30) cc_final: 0.7804 (tm-30) REVERT: Z 42 ASP cc_start: 0.7194 (t0) cc_final: 0.6192 (t0) REVERT: Z 45 MET cc_start: 0.8121 (mmp) cc_final: 0.7688 (mmp) REVERT: a 49 VAL cc_start: 0.8217 (t) cc_final: 0.7914 (p) REVERT: b 128 TYR cc_start: 0.8975 (t80) cc_final: 0.8706 (t80) REVERT: c 372 MET cc_start: 0.6885 (ptp) cc_final: 0.6645 (ptt) REVERT: c 432 ASP cc_start: 0.6560 (p0) cc_final: 0.6325 (p0) REVERT: c 572 MET cc_start: 0.7570 (mmp) cc_final: 0.7343 (mmp) REVERT: d 59 LYS cc_start: 0.7076 (tptt) cc_final: 0.6695 (ttmt) REVERT: e 66 TYR cc_start: 0.8527 (t80) cc_final: 0.8182 (t80) REVERT: g 250 MET cc_start: 0.8071 (pmm) cc_final: 0.7205 (ptp) REVERT: g 374 ASP cc_start: 0.7053 (p0) cc_final: 0.6758 (p0) REVERT: g 382 ARG cc_start: 0.8670 (mmp80) cc_final: 0.8031 (mmp80) REVERT: g 486 LYS cc_start: 0.8328 (ptmt) cc_final: 0.8116 (ttpp) REVERT: h 86 ASP cc_start: 0.6841 (OUTLIER) cc_final: 0.6168 (t70) REVERT: i 83 THR cc_start: 0.8720 (OUTLIER) cc_final: 0.8214 (m) REVERT: j 165 LEU cc_start: 0.8881 (mm) cc_final: 0.8668 (mm) REVERT: k 486 LYS cc_start: 0.8587 (tptm) cc_final: 0.8290 (tptt) REVERT: k 568 MET cc_start: 0.7901 (tmm) cc_final: 0.7468 (tmm) REVERT: k 572 MET cc_start: 0.7954 (mmp) cc_final: 0.7714 (mmt) REVERT: l 42 ASP cc_start: 0.6788 (t0) cc_final: 0.6234 (t0) REVERT: l 91 ARG cc_start: 0.7659 (tmm160) cc_final: 0.6479 (ptt-90) REVERT: m 49 VAL cc_start: 0.7779 (t) cc_final: 0.7518 (m) REVERT: o 486 LYS cc_start: 0.8070 (tptt) cc_final: 0.7785 (tptt) REVERT: o 489 ASP cc_start: 0.7803 (OUTLIER) cc_final: 0.7469 (t0) REVERT: p 100 PHE cc_start: 0.7801 (m-10) cc_final: 0.7503 (m-80) REVERT: u 73 TYR cc_start: 0.8783 (OUTLIER) cc_final: 0.8024 (t80) REVERT: u 125 LYS cc_start: 0.7180 (ttmt) cc_final: 0.6950 (ttmm) REVERT: u 146 ARG cc_start: 0.8371 (mtt-85) cc_final: 0.7978 (mtt180) REVERT: u 199 ASP cc_start: 0.8040 (OUTLIER) cc_final: 0.7335 (m-30) REVERT: u 250 MET cc_start: 0.8066 (OUTLIER) cc_final: 0.7404 (ptp) REVERT: v 5 GLN cc_start: 0.8118 (tm-30) cc_final: 0.7383 (tm-30) REVERT: w 3 PHE cc_start: 0.7626 (p90) cc_final: 0.7105 (p90) REVERT: y 18 LEU cc_start: 0.6378 (tp) cc_final: 0.6030 (tp) REVERT: y 91 ARG cc_start: 0.3581 (mtt90) cc_final: 0.1840 (mmt180) REVERT: y 96 GLU cc_start: 0.7176 (mm-30) cc_final: 0.5419 (mt-10) outliers start: 391 outliers final: 304 residues processed: 1852 average time/residue: 1.0462 time to fit residues: 3468.0506 Evaluate side-chains 1859 residues out of total 13764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 321 poor density : 1538 time to evaluate : 10.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 69 VAL Chi-restraints excluded: chain 0 residue 96 VAL Chi-restraints excluded: chain 0 residue 183 TYR Chi-restraints excluded: chain 0 residue 199 ASP Chi-restraints excluded: chain 0 residue 330 ILE Chi-restraints excluded: chain 0 residue 450 LEU Chi-restraints excluded: chain 1 residue 26 THR Chi-restraints excluded: chain 1 residue 61 THR Chi-restraints excluded: chain 1 residue 80 LEU Chi-restraints excluded: chain 2 residue 42 VAL Chi-restraints excluded: chain 2 residue 80 THR Chi-restraints excluded: chain 2 residue 148 LEU Chi-restraints excluded: chain 3 residue 83 ASP Chi-restraints excluded: chain 3 residue 166 ILE Chi-restraints excluded: chain 3 residue 397 MET Chi-restraints excluded: chain 3 residue 412 VAL Chi-restraints excluded: chain 3 residue 431 VAL Chi-restraints excluded: chain 3 residue 576 VAL Chi-restraints excluded: chain 4 residue 25 LEU Chi-restraints excluded: chain 4 residue 47 THR Chi-restraints excluded: chain 4 residue 52 ASP Chi-restraints excluded: chain 4 residue 64 THR Chi-restraints excluded: chain 4 residue 68 MET Chi-restraints excluded: chain 4 residue 71 THR Chi-restraints excluded: chain 5 residue 67 ASP Chi-restraints excluded: chain 5 residue 71 LEU Chi-restraints excluded: chain 6 residue 41 GLU Chi-restraints excluded: chain 6 residue 63 ASN Chi-restraints excluded: chain 6 residue 183 TYR Chi-restraints excluded: chain 6 residue 199 ASP Chi-restraints excluded: chain 6 residue 330 ILE Chi-restraints excluded: chain 6 residue 371 TRP Chi-restraints excluded: chain 6 residue 374 ASP Chi-restraints excluded: chain 6 residue 412 VAL Chi-restraints excluded: chain 6 residue 450 LEU Chi-restraints excluded: chain 6 residue 489 ASP Chi-restraints excluded: chain 6 residue 576 VAL Chi-restraints excluded: chain 6 residue 583 LEU Chi-restraints excluded: chain 6 residue 588 THR Chi-restraints excluded: chain 7 residue 35 PHE Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 537 MET Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 384 SER Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 332 VAL Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 332 VAL Chi-restraints excluded: chain E residue 333 MET Chi-restraints excluded: chain E residue 339 MET Chi-restraints excluded: chain E residue 346 LEU Chi-restraints excluded: chain E residue 537 MET Chi-restraints excluded: chain E residue 551 ILE Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 384 SER Chi-restraints excluded: chain F residue 540 MET Chi-restraints excluded: chain F residue 553 GLU Chi-restraints excluded: chain G residue 32 ILE Chi-restraints excluded: chain G residue 36 GLU Chi-restraints excluded: chain G residue 103 GLN Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 108 GLN Chi-restraints excluded: chain G residue 116 VAL Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain H residue 11 ILE Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 33 LYS Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain H residue 122 SER Chi-restraints excluded: chain H residue 142 LEU Chi-restraints excluded: chain H residue 145 THR Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain I residue 32 ILE Chi-restraints excluded: chain I residue 113 LEU Chi-restraints excluded: chain I residue 116 VAL Chi-restraints excluded: chain I residue 122 SER Chi-restraints excluded: chain I residue 173 VAL Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain J residue 32 ILE Chi-restraints excluded: chain J residue 108 GLN Chi-restraints excluded: chain J residue 109 SER Chi-restraints excluded: chain K residue 11 ILE Chi-restraints excluded: chain K residue 32 ILE Chi-restraints excluded: chain K residue 33 LYS Chi-restraints excluded: chain K residue 67 GLU Chi-restraints excluded: chain K residue 116 VAL Chi-restraints excluded: chain K residue 122 SER Chi-restraints excluded: chain K residue 184 ASP Chi-restraints excluded: chain L residue 32 ILE Chi-restraints excluded: chain L residue 113 LEU Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 122 SER Chi-restraints excluded: chain L residue 171 LEU Chi-restraints excluded: chain L residue 186 LEU Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain M residue 71 THR Chi-restraints excluded: chain M residue 80 LEU Chi-restraints excluded: chain M residue 96 GLU Chi-restraints excluded: chain M residue 108 GLN Chi-restraints excluded: chain N residue 25 LEU Chi-restraints excluded: chain N residue 26 THR Chi-restraints excluded: chain N residue 49 ILE Chi-restraints excluded: chain N residue 52 ASP Chi-restraints excluded: chain O residue 18 LEU Chi-restraints excluded: chain O residue 71 THR Chi-restraints excluded: chain P residue 26 THR Chi-restraints excluded: chain P residue 34 LEU Chi-restraints excluded: chain P residue 58 VAL Chi-restraints excluded: chain P residue 61 THR Chi-restraints excluded: chain P residue 80 LEU Chi-restraints excluded: chain P residue 92 LEU Chi-restraints excluded: chain Q residue 25 LEU Chi-restraints excluded: chain Q residue 47 THR Chi-restraints excluded: chain Q residue 52 ASP Chi-restraints excluded: chain Q residue 64 THR Chi-restraints excluded: chain Q residue 71 THR Chi-restraints excluded: chain R residue 18 LEU Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain S residue 43 CYS Chi-restraints excluded: chain S residue 44 ASP Chi-restraints excluded: chain S residue 45 ASP Chi-restraints excluded: chain S residue 93 TRP Chi-restraints excluded: chain S residue 116 VAL Chi-restraints excluded: chain S residue 142 LEU Chi-restraints excluded: chain S residue 149 THR Chi-restraints excluded: chain S residue 160 ILE Chi-restraints excluded: chain S residue 161 ILE Chi-restraints excluded: chain S residue 166 TRP Chi-restraints excluded: chain T residue 16 LEU Chi-restraints excluded: chain T residue 42 VAL Chi-restraints excluded: chain T residue 53 THR Chi-restraints excluded: chain T residue 148 LEU Chi-restraints excluded: chain T residue 149 THR Chi-restraints excluded: chain T residue 165 LEU Chi-restraints excluded: chain U residue 252 TRP Chi-restraints excluded: chain U residue 377 ASP Chi-restraints excluded: chain U residue 393 ASN Chi-restraints excluded: chain U residue 412 VAL Chi-restraints excluded: chain U residue 427 ILE Chi-restraints excluded: chain U residue 496 GLN Chi-restraints excluded: chain U residue 506 ILE Chi-restraints excluded: chain V residue 26 THR Chi-restraints excluded: chain V residue 58 VAL Chi-restraints excluded: chain V residue 61 THR Chi-restraints excluded: chain V residue 80 LEU Chi-restraints excluded: chain V residue 108 GLN Chi-restraints excluded: chain W residue 43 CYS Chi-restraints excluded: chain W residue 44 ASP Chi-restraints excluded: chain W residue 45 ASP Chi-restraints excluded: chain W residue 78 MET Chi-restraints excluded: chain W residue 83 THR Chi-restraints excluded: chain W residue 93 TRP Chi-restraints excluded: chain W residue 134 ASP Chi-restraints excluded: chain W residue 160 ILE Chi-restraints excluded: chain W residue 161 ILE Chi-restraints excluded: chain X residue 156 GLN Chi-restraints excluded: chain X residue 162 VAL Chi-restraints excluded: chain Y residue 73 TYR Chi-restraints excluded: chain Y residue 183 TYR Chi-restraints excluded: chain Y residue 199 ASP Chi-restraints excluded: chain Y residue 250 MET Chi-restraints excluded: chain Y residue 371 TRP Chi-restraints excluded: chain Y residue 440 MET Chi-restraints excluded: chain Y residue 485 ASN Chi-restraints excluded: chain Y residue 563 GLU Chi-restraints excluded: chain Y residue 576 VAL Chi-restraints excluded: chain Y residue 579 VAL Chi-restraints excluded: chain Y residue 583 LEU Chi-restraints excluded: chain Y residue 590 LEU Chi-restraints excluded: chain Z residue 25 LEU Chi-restraints excluded: chain Z residue 47 THR Chi-restraints excluded: chain Z residue 52 ASP Chi-restraints excluded: chain Z residue 68 MET Chi-restraints excluded: chain Z residue 71 THR Chi-restraints excluded: chain a residue 43 CYS Chi-restraints excluded: chain a residue 44 ASP Chi-restraints excluded: chain a residue 71 VAL Chi-restraints excluded: chain a residue 93 TRP Chi-restraints excluded: chain a residue 96 THR Chi-restraints excluded: chain a residue 161 ILE Chi-restraints excluded: chain a residue 180 ASP Chi-restraints excluded: chain b residue 42 VAL Chi-restraints excluded: chain b residue 70 GLN Chi-restraints excluded: chain c residue 83 ASP Chi-restraints excluded: chain c residue 377 ASP Chi-restraints excluded: chain c residue 412 VAL Chi-restraints excluded: chain c residue 427 ILE Chi-restraints excluded: chain c residue 443 MET Chi-restraints excluded: chain d residue 35 PHE Chi-restraints excluded: chain d residue 58 VAL Chi-restraints excluded: chain d residue 71 THR Chi-restraints excluded: chain e residue 43 CYS Chi-restraints excluded: chain e residue 44 ASP Chi-restraints excluded: chain e residue 78 MET Chi-restraints excluded: chain e residue 93 TRP Chi-restraints excluded: chain e residue 106 THR Chi-restraints excluded: chain e residue 116 VAL Chi-restraints excluded: chain e residue 134 ASP Chi-restraints excluded: chain e residue 149 THR Chi-restraints excluded: chain e residue 161 ILE Chi-restraints excluded: chain e residue 166 TRP Chi-restraints excluded: chain f residue 156 GLN Chi-restraints excluded: chain f residue 197 LEU Chi-restraints excluded: chain g residue 69 VAL Chi-restraints excluded: chain g residue 127 ASP Chi-restraints excluded: chain g residue 183 TYR Chi-restraints excluded: chain g residue 199 ASP Chi-restraints excluded: chain g residue 330 ILE Chi-restraints excluded: chain g residue 450 LEU Chi-restraints excluded: chain h residue 14 LEU Chi-restraints excluded: chain h residue 15 VAL Chi-restraints excluded: chain h residue 58 VAL Chi-restraints excluded: chain h residue 61 THR Chi-restraints excluded: chain h residue 80 LEU Chi-restraints excluded: chain h residue 86 ASP Chi-restraints excluded: chain i residue 43 CYS Chi-restraints excluded: chain i residue 44 ASP Chi-restraints excluded: chain i residue 45 ASP Chi-restraints excluded: chain i residue 83 THR Chi-restraints excluded: chain i residue 93 TRP Chi-restraints excluded: chain i residue 105 VAL Chi-restraints excluded: chain i residue 158 LEU Chi-restraints excluded: chain i residue 160 ILE Chi-restraints excluded: chain i residue 161 ILE Chi-restraints excluded: chain j residue 16 LEU Chi-restraints excluded: chain j residue 53 THR Chi-restraints excluded: chain j residue 148 LEU Chi-restraints excluded: chain j residue 149 THR Chi-restraints excluded: chain k residue 83 ASP Chi-restraints excluded: chain k residue 166 ILE Chi-restraints excluded: chain k residue 252 TRP Chi-restraints excluded: chain k residue 377 ASP Chi-restraints excluded: chain k residue 412 VAL Chi-restraints excluded: chain k residue 576 VAL Chi-restraints excluded: chain k residue 590 LEU Chi-restraints excluded: chain l residue 25 LEU Chi-restraints excluded: chain l residue 47 THR Chi-restraints excluded: chain l residue 49 ILE Chi-restraints excluded: chain l residue 52 ASP Chi-restraints excluded: chain l residue 80 LEU Chi-restraints excluded: chain l residue 88 ILE Chi-restraints excluded: chain m residue 43 CYS Chi-restraints excluded: chain m residue 44 ASP Chi-restraints excluded: chain m residue 71 VAL Chi-restraints excluded: chain m residue 78 MET Chi-restraints excluded: chain m residue 93 TRP Chi-restraints excluded: chain m residue 161 ILE Chi-restraints excluded: chain n residue 25 THR Chi-restraints excluded: chain n residue 42 VAL Chi-restraints excluded: chain n residue 121 VAL Chi-restraints excluded: chain o residue 41 GLU Chi-restraints excluded: chain o residue 63 ASN Chi-restraints excluded: chain o residue 138 LEU Chi-restraints excluded: chain o residue 183 TYR Chi-restraints excluded: chain o residue 199 ASP Chi-restraints excluded: chain o residue 330 ILE Chi-restraints excluded: chain o residue 374 ASP Chi-restraints excluded: chain o residue 412 VAL Chi-restraints excluded: chain o residue 450 LEU Chi-restraints excluded: chain o residue 489 ASP Chi-restraints excluded: chain o residue 576 VAL Chi-restraints excluded: chain o residue 583 LEU Chi-restraints excluded: chain o residue 588 THR Chi-restraints excluded: chain p residue 34 LEU Chi-restraints excluded: chain p residue 83 ASN Chi-restraints excluded: chain q residue 52 THR Chi-restraints excluded: chain q residue 152 ASN Chi-restraints excluded: chain r residue 391 SER Chi-restraints excluded: chain r residue 412 VAL Chi-restraints excluded: chain r residue 450 LEU Chi-restraints excluded: chain s residue 6 PHE Chi-restraints excluded: chain s residue 26 THR Chi-restraints excluded: chain s residue 34 LEU Chi-restraints excluded: chain s residue 61 THR Chi-restraints excluded: chain s residue 80 LEU Chi-restraints excluded: chain s residue 96 GLU Chi-restraints excluded: chain t residue 15 LEU Chi-restraints excluded: chain t residue 42 VAL Chi-restraints excluded: chain t residue 80 THR Chi-restraints excluded: chain t residue 148 LEU Chi-restraints excluded: chain u residue 73 TYR Chi-restraints excluded: chain u residue 138 LEU Chi-restraints excluded: chain u residue 166 ILE Chi-restraints excluded: chain u residue 183 TYR Chi-restraints excluded: chain u residue 199 ASP Chi-restraints excluded: chain u residue 250 MET Chi-restraints excluded: chain u residue 330 ILE Chi-restraints excluded: chain u residue 396 VAL Chi-restraints excluded: chain u residue 563 GLU Chi-restraints excluded: chain u residue 576 VAL Chi-restraints excluded: chain u residue 583 LEU Chi-restraints excluded: chain u residue 590 LEU Chi-restraints excluded: chain v residue 14 LEU Chi-restraints excluded: chain v residue 47 THR Chi-restraints excluded: chain v residue 52 ASP Chi-restraints excluded: chain v residue 57 ILE Chi-restraints excluded: chain v residue 64 THR Chi-restraints excluded: chain v residue 71 THR Chi-restraints excluded: chain v residue 96 GLU Chi-restraints excluded: chain w residue 52 THR Chi-restraints excluded: chain w residue 152 ASN Chi-restraints excluded: chain x residue 83 ASP Chi-restraints excluded: chain x residue 168 ASP Chi-restraints excluded: chain x residue 250 MET Chi-restraints excluded: chain x residue 412 VAL Chi-restraints excluded: chain x residue 433 ARG Chi-restraints excluded: chain x residue 443 MET Chi-restraints excluded: chain y residue 25 LEU Chi-restraints excluded: chain y residue 35 PHE Chi-restraints excluded: chain z residue 71 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1644 random chunks: chunk 1441 optimal weight: 3.9990 chunk 1518 optimal weight: 6.9990 chunk 1385 optimal weight: 7.9990 chunk 1476 optimal weight: 9.9990 chunk 1517 optimal weight: 0.8980 chunk 888 optimal weight: 3.9990 chunk 643 optimal weight: 5.9990 chunk 1159 optimal weight: 3.9990 chunk 453 optimal weight: 50.0000 chunk 1334 optimal weight: 3.9990 chunk 1396 optimal weight: 8.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 54 HIS 3 60 GLN 6 54 HIS 6 63 ASN 6 92 GLN ** 6 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 486 ASN ** D 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 92 GLN Y 490 ASN ** a 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 54 HIS ** h 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 60 GLN ** k 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 54 HIS o 63 ASN ** p 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 83 ASN ** q 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 54 HIS ** u 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 108 GLN ** w 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 130506 Z= 0.261 Angle : 0.616 12.947 177246 Z= 0.321 Chirality : 0.043 0.470 19890 Planarity : 0.005 0.075 23400 Dihedral : 4.753 29.273 18210 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.18 % Favored : 94.50 % Rotamer: Outliers : 2.79 % Allowed : 17.88 % Favored : 79.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.07), residues: 16500 helix: 2.37 (0.07), residues: 6270 sheet: -0.48 (0.10), residues: 2574 loop : -1.42 (0.07), residues: 7656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP u 553 HIS 0.007 0.001 HIS S 12 PHE 0.035 0.002 PHE V 44 TYR 0.023 0.002 TYR q 128 ARG 0.009 0.000 ARG f 11 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 33000 Ramachandran restraints generated. 16500 Oldfield, 0 Emsley, 16500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 33000 Ramachandran restraints generated. 16500 Oldfield, 0 Emsley, 16500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1942 residues out of total 13764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 361 poor density : 1581 time to evaluate : 11.154 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: 0 374 ASP cc_start: 0.7170 (p0) cc_final: 0.6888 (p0) REVERT: 1 8 ASN cc_start: 0.7743 (t0) cc_final: 0.7052 (p0) REVERT: 1 91 ARG cc_start: 0.2853 (mpp-170) cc_final: 0.2495 (mpp-170) REVERT: 2 33 LEU cc_start: 0.9140 (tp) cc_final: 0.8856 (tt) REVERT: 2 148 LEU cc_start: 0.7578 (OUTLIER) cc_final: 0.7268 (mm) REVERT: 3 607 ARG cc_start: 0.6292 (mmt-90) cc_final: 0.5816 (mtp180) REVERT: 4 5 GLN cc_start: 0.8654 (tm-30) cc_final: 0.7942 (tm-30) REVERT: 4 45 MET cc_start: 0.8048 (mmp) cc_final: 0.7673 (mmp) REVERT: 6 110 SER cc_start: 0.9482 (m) cc_final: 0.9230 (p) REVERT: 6 489 ASP cc_start: 0.7499 (OUTLIER) cc_final: 0.7016 (t0) REVERT: 7 68 MET cc_start: 0.7159 (tpp) cc_final: 0.6672 (tpp) REVERT: A 510 MET cc_start: 0.1663 (mtm) cc_final: 0.1280 (mtt) REVERT: B 30 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.8131 (tt) REVERT: B 239 MET cc_start: 0.7050 (mpp) cc_final: 0.6716 (mmm) REVERT: B 565 ILE cc_start: 0.9260 (mm) cc_final: 0.8910 (mp) REVERT: C 69 TRP cc_start: 0.8097 (m-90) cc_final: 0.7826 (m-90) REVERT: D 10 SER cc_start: 0.8793 (m) cc_final: 0.8554 (m) REVERT: D 95 MET cc_start: 0.5915 (mtt) cc_final: 0.5673 (mtm) REVERT: D 283 MET cc_start: 0.7868 (mtm) cc_final: 0.7216 (mtm) REVERT: D 510 MET cc_start: 0.1086 (mtm) cc_final: 0.0683 (mtt) REVERT: E 565 ILE cc_start: 0.9308 (mm) cc_final: 0.8989 (mp) REVERT: F 66 TRP cc_start: 0.7987 (m100) cc_final: 0.7358 (m100) REVERT: F 239 MET cc_start: 0.6925 (mpp) cc_final: 0.6706 (mpp) REVERT: G 106 THR cc_start: 0.8599 (OUTLIER) cc_final: 0.8291 (p) REVERT: I 113 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8319 (pp) REVERT: I 182 GLU cc_start: 0.6758 (mm-30) cc_final: 0.6383 (mm-30) REVERT: L 113 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8245 (pp) REVERT: M 5 GLN cc_start: 0.7019 (mt0) cc_final: 0.6477 (mt0) REVERT: M 96 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7305 (mp0) REVERT: M 108 GLN cc_start: 0.8356 (OUTLIER) cc_final: 0.8027 (mp10) REVERT: N 5 GLN cc_start: 0.8327 (tm-30) cc_final: 0.6932 (tm-30) REVERT: N 42 ASP cc_start: 0.6717 (t0) cc_final: 0.6177 (t0) REVERT: O 82 PHE cc_start: 0.5386 (m-80) cc_final: 0.5123 (m-10) REVERT: Q 50 ARG cc_start: 0.6874 (ptm160) cc_final: 0.6479 (ptm-80) REVERT: Q 68 MET cc_start: 0.8590 (mpp) cc_final: 0.8368 (mpp) REVERT: T 49 MET cc_start: 0.7777 (tpp) cc_final: 0.7514 (tpp) REVERT: U 545 ASP cc_start: 0.7327 (m-30) cc_final: 0.7071 (m-30) REVERT: V 45 MET cc_start: 0.7894 (mmm) cc_final: 0.7247 (mmm) REVERT: V 96 GLU cc_start: 0.7450 (mp0) cc_final: 0.6927 (mp0) REVERT: W 66 TYR cc_start: 0.8494 (t80) cc_final: 0.8179 (t80) REVERT: W 83 THR cc_start: 0.8657 (OUTLIER) cc_final: 0.8083 (m) REVERT: X 39 GLU cc_start: 0.7532 (tp30) cc_final: 0.7184 (tp30) REVERT: X 136 GLN cc_start: 0.8089 (pm20) cc_final: 0.7884 (pm20) REVERT: Y 73 TYR cc_start: 0.8740 (OUTLIER) cc_final: 0.8063 (t80) REVERT: Y 113 ARG cc_start: 0.7618 (mmt180) cc_final: 0.7401 (mmt180) REVERT: Y 199 ASP cc_start: 0.7875 (OUTLIER) cc_final: 0.7318 (m-30) REVERT: Y 250 MET cc_start: 0.7994 (OUTLIER) cc_final: 0.7328 (ptp) REVERT: Y 485 ASN cc_start: 0.8314 (OUTLIER) cc_final: 0.8052 (t0) REVERT: Z 5 GLN cc_start: 0.8781 (tm-30) cc_final: 0.8195 (tm-30) REVERT: Z 45 MET cc_start: 0.8157 (mmp) cc_final: 0.7701 (mmp) REVERT: b 128 TYR cc_start: 0.8945 (t80) cc_final: 0.8684 (t80) REVERT: c 372 MET cc_start: 0.6795 (ptp) cc_final: 0.6555 (ptt) REVERT: c 411 GLU cc_start: 0.7248 (mm-30) cc_final: 0.6904 (mt-10) REVERT: c 572 MET cc_start: 0.7635 (mmp) cc_final: 0.7411 (mmp) REVERT: d 59 LYS cc_start: 0.7288 (tptt) cc_final: 0.6935 (ttmt) REVERT: e 66 TYR cc_start: 0.8484 (t80) cc_final: 0.8097 (t80) REVERT: g 250 MET cc_start: 0.7914 (pmm) cc_final: 0.7013 (ptp) REVERT: g 374 ASP cc_start: 0.7028 (p0) cc_final: 0.6770 (p0) REVERT: g 382 ARG cc_start: 0.8659 (mmp80) cc_final: 0.8040 (mmp80) REVERT: h 86 ASP cc_start: 0.6838 (OUTLIER) cc_final: 0.6147 (t70) REVERT: h 96 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7196 (mp0) REVERT: i 83 THR cc_start: 0.8729 (OUTLIER) cc_final: 0.8282 (m) REVERT: j 19 GLU cc_start: 0.8032 (mm-30) cc_final: 0.7766 (mm-30) REVERT: j 165 LEU cc_start: 0.8851 (mm) cc_final: 0.8629 (mm) REVERT: k 443 MET cc_start: 0.8052 (ttp) cc_final: 0.7791 (ttt) REVERT: k 486 LYS cc_start: 0.8584 (tptm) cc_final: 0.8283 (tptt) REVERT: k 568 MET cc_start: 0.7926 (tmm) cc_final: 0.7654 (tmm) REVERT: l 5 GLN cc_start: 0.8514 (tm-30) cc_final: 0.7964 (tm-30) REVERT: l 42 ASP cc_start: 0.6816 (t0) cc_final: 0.6240 (t0) REVERT: l 91 ARG cc_start: 0.7685 (tmm160) cc_final: 0.6598 (ptt-90) REVERT: m 49 VAL cc_start: 0.7781 (t) cc_final: 0.7546 (m) REVERT: o 486 LYS cc_start: 0.8036 (tptt) cc_final: 0.7771 (tptt) REVERT: o 489 ASP cc_start: 0.7803 (OUTLIER) cc_final: 0.7480 (t0) REVERT: p 100 PHE cc_start: 0.7813 (m-10) cc_final: 0.7514 (m-80) REVERT: t 148 LEU cc_start: 0.7700 (OUTLIER) cc_final: 0.7362 (mm) REVERT: u 73 TYR cc_start: 0.8768 (OUTLIER) cc_final: 0.8028 (t80) REVERT: u 125 LYS cc_start: 0.7274 (ttmt) cc_final: 0.7007 (ttmm) REVERT: u 146 ARG cc_start: 0.8344 (mtt-85) cc_final: 0.7934 (mtt180) REVERT: u 199 ASP cc_start: 0.8066 (OUTLIER) cc_final: 0.7347 (m-30) REVERT: u 250 MET cc_start: 0.7963 (OUTLIER) cc_final: 0.7323 (ptp) REVERT: v 5 GLN cc_start: 0.8132 (tm-30) cc_final: 0.7422 (tm-30) REVERT: w 3 PHE cc_start: 0.7688 (p90) cc_final: 0.7183 (p90) REVERT: y 18 LEU cc_start: 0.6380 (tp) cc_final: 0.6029 (tp) REVERT: y 75 GLU cc_start: 0.6598 (tm-30) cc_final: 0.6366 (pp20) REVERT: y 91 ARG cc_start: 0.3594 (mtt90) cc_final: 0.1798 (mmt180) REVERT: y 96 GLU cc_start: 0.7375 (mm-30) cc_final: 0.5674 (mt-10) outliers start: 361 outliers final: 302 residues processed: 1820 average time/residue: 0.9853 time to fit residues: 3204.3844 Evaluate side-chains 1851 residues out of total 13764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 323 poor density : 1528 time to evaluate : 10.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 69 VAL Chi-restraints excluded: chain 0 residue 96 VAL Chi-restraints excluded: chain 0 residue 183 TYR Chi-restraints excluded: chain 0 residue 199 ASP Chi-restraints excluded: chain 0 residue 330 ILE Chi-restraints excluded: chain 0 residue 450 LEU Chi-restraints excluded: chain 0 residue 484 THR Chi-restraints excluded: chain 1 residue 26 THR Chi-restraints excluded: chain 1 residue 61 THR Chi-restraints excluded: chain 1 residue 80 LEU Chi-restraints excluded: chain 2 residue 42 VAL Chi-restraints excluded: chain 2 residue 80 THR Chi-restraints excluded: chain 2 residue 148 LEU Chi-restraints excluded: chain 3 residue 83 ASP Chi-restraints excluded: chain 3 residue 166 ILE Chi-restraints excluded: chain 3 residue 397 MET Chi-restraints excluded: chain 3 residue 412 VAL Chi-restraints excluded: chain 3 residue 431 VAL Chi-restraints excluded: chain 3 residue 576 VAL Chi-restraints excluded: chain 4 residue 25 LEU Chi-restraints excluded: chain 4 residue 47 THR Chi-restraints excluded: chain 4 residue 52 ASP Chi-restraints excluded: chain 4 residue 64 THR Chi-restraints excluded: chain 4 residue 68 MET Chi-restraints excluded: chain 4 residue 71 THR Chi-restraints excluded: chain 5 residue 67 ASP Chi-restraints excluded: chain 5 residue 71 LEU Chi-restraints excluded: chain 6 residue 41 GLU Chi-restraints excluded: chain 6 residue 63 ASN Chi-restraints excluded: chain 6 residue 69 VAL Chi-restraints excluded: chain 6 residue 138 LEU Chi-restraints excluded: chain 6 residue 183 TYR Chi-restraints excluded: chain 6 residue 199 ASP Chi-restraints excluded: chain 6 residue 330 ILE Chi-restraints excluded: chain 6 residue 371 TRP Chi-restraints excluded: chain 6 residue 374 ASP Chi-restraints excluded: chain 6 residue 412 VAL Chi-restraints excluded: chain 6 residue 450 LEU Chi-restraints excluded: chain 6 residue 489 ASP Chi-restraints excluded: chain 6 residue 576 VAL Chi-restraints excluded: chain 6 residue 583 LEU Chi-restraints excluded: chain 6 residue 588 THR Chi-restraints excluded: chain 7 residue 35 PHE Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 537 MET Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 384 SER Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 332 VAL Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 332 VAL Chi-restraints excluded: chain E residue 339 MET Chi-restraints excluded: chain E residue 346 LEU Chi-restraints excluded: chain E residue 537 MET Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 384 SER Chi-restraints excluded: chain F residue 540 MET Chi-restraints excluded: chain F residue 553 GLU Chi-restraints excluded: chain G residue 32 ILE Chi-restraints excluded: chain G residue 103 GLN Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 108 GLN Chi-restraints excluded: chain G residue 116 VAL Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain H residue 11 ILE Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 67 GLU Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain H residue 122 SER Chi-restraints excluded: chain H residue 142 LEU Chi-restraints excluded: chain H residue 145 THR Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain I residue 32 ILE Chi-restraints excluded: chain I residue 113 LEU Chi-restraints excluded: chain I residue 116 VAL Chi-restraints excluded: chain I residue 122 SER Chi-restraints excluded: chain I residue 173 VAL Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain J residue 32 ILE Chi-restraints excluded: chain J residue 108 GLN Chi-restraints excluded: chain J residue 109 SER Chi-restraints excluded: chain J residue 160 ILE Chi-restraints excluded: chain K residue 11 ILE Chi-restraints excluded: chain K residue 32 ILE Chi-restraints excluded: chain K residue 33 LYS Chi-restraints excluded: chain K residue 67 GLU Chi-restraints excluded: chain K residue 116 VAL Chi-restraints excluded: chain K residue 122 SER Chi-restraints excluded: chain K residue 173 VAL Chi-restraints excluded: chain K residue 184 ASP Chi-restraints excluded: chain L residue 32 ILE Chi-restraints excluded: chain L residue 113 LEU Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 122 SER Chi-restraints excluded: chain L residue 171 LEU Chi-restraints excluded: chain L residue 186 LEU Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain M residue 71 THR Chi-restraints excluded: chain M residue 80 LEU Chi-restraints excluded: chain M residue 96 GLU Chi-restraints excluded: chain M residue 108 GLN Chi-restraints excluded: chain N residue 25 LEU Chi-restraints excluded: chain N residue 26 THR Chi-restraints excluded: chain N residue 49 ILE Chi-restraints excluded: chain N residue 52 ASP Chi-restraints excluded: chain O residue 18 LEU Chi-restraints excluded: chain O residue 71 THR Chi-restraints excluded: chain P residue 26 THR Chi-restraints excluded: chain P residue 34 LEU Chi-restraints excluded: chain P residue 58 VAL Chi-restraints excluded: chain P residue 61 THR Chi-restraints excluded: chain P residue 80 LEU Chi-restraints excluded: chain P residue 92 LEU Chi-restraints excluded: chain Q residue 25 LEU Chi-restraints excluded: chain Q residue 47 THR Chi-restraints excluded: chain Q residue 52 ASP Chi-restraints excluded: chain Q residue 71 THR Chi-restraints excluded: chain R residue 18 LEU Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain S residue 43 CYS Chi-restraints excluded: chain S residue 44 ASP Chi-restraints excluded: chain S residue 45 ASP Chi-restraints excluded: chain S residue 93 TRP Chi-restraints excluded: chain S residue 116 VAL Chi-restraints excluded: chain S residue 142 LEU Chi-restraints excluded: chain S residue 149 THR Chi-restraints excluded: chain S residue 160 ILE Chi-restraints excluded: chain S residue 161 ILE Chi-restraints excluded: chain S residue 166 TRP Chi-restraints excluded: chain T residue 16 LEU Chi-restraints excluded: chain T residue 42 VAL Chi-restraints excluded: chain T residue 53 THR Chi-restraints excluded: chain T residue 148 LEU Chi-restraints excluded: chain T residue 149 THR Chi-restraints excluded: chain T residue 165 LEU Chi-restraints excluded: chain U residue 252 TRP Chi-restraints excluded: chain U residue 377 ASP Chi-restraints excluded: chain U residue 393 ASN Chi-restraints excluded: chain U residue 412 VAL Chi-restraints excluded: chain U residue 427 ILE Chi-restraints excluded: chain U residue 496 GLN Chi-restraints excluded: chain U residue 506 ILE Chi-restraints excluded: chain V residue 26 THR Chi-restraints excluded: chain V residue 58 VAL Chi-restraints excluded: chain V residue 61 THR Chi-restraints excluded: chain V residue 80 LEU Chi-restraints excluded: chain W residue 43 CYS Chi-restraints excluded: chain W residue 44 ASP Chi-restraints excluded: chain W residue 45 ASP Chi-restraints excluded: chain W residue 78 MET Chi-restraints excluded: chain W residue 83 THR Chi-restraints excluded: chain W residue 93 TRP Chi-restraints excluded: chain W residue 134 ASP Chi-restraints excluded: chain W residue 160 ILE Chi-restraints excluded: chain W residue 161 ILE Chi-restraints excluded: chain X residue 156 GLN Chi-restraints excluded: chain X residue 162 VAL Chi-restraints excluded: chain Y residue 73 TYR Chi-restraints excluded: chain Y residue 183 TYR Chi-restraints excluded: chain Y residue 199 ASP Chi-restraints excluded: chain Y residue 250 MET Chi-restraints excluded: chain Y residue 330 ILE Chi-restraints excluded: chain Y residue 440 MET Chi-restraints excluded: chain Y residue 485 ASN Chi-restraints excluded: chain Y residue 563 GLU Chi-restraints excluded: chain Y residue 576 VAL Chi-restraints excluded: chain Y residue 583 LEU Chi-restraints excluded: chain Y residue 590 LEU Chi-restraints excluded: chain Z residue 25 LEU Chi-restraints excluded: chain Z residue 47 THR Chi-restraints excluded: chain Z residue 52 ASP Chi-restraints excluded: chain Z residue 68 MET Chi-restraints excluded: chain Z residue 71 THR Chi-restraints excluded: chain a residue 43 CYS Chi-restraints excluded: chain a residue 44 ASP Chi-restraints excluded: chain a residue 71 VAL Chi-restraints excluded: chain a residue 93 TRP Chi-restraints excluded: chain a residue 96 THR Chi-restraints excluded: chain a residue 161 ILE Chi-restraints excluded: chain b residue 42 VAL Chi-restraints excluded: chain b residue 70 GLN Chi-restraints excluded: chain b residue 121 VAL Chi-restraints excluded: chain c residue 83 ASP Chi-restraints excluded: chain c residue 377 ASP Chi-restraints excluded: chain c residue 412 VAL Chi-restraints excluded: chain c residue 427 ILE Chi-restraints excluded: chain d residue 35 PHE Chi-restraints excluded: chain d residue 58 VAL Chi-restraints excluded: chain d residue 71 THR Chi-restraints excluded: chain e residue 43 CYS Chi-restraints excluded: chain e residue 44 ASP Chi-restraints excluded: chain e residue 78 MET Chi-restraints excluded: chain e residue 93 TRP Chi-restraints excluded: chain e residue 106 THR Chi-restraints excluded: chain e residue 116 VAL Chi-restraints excluded: chain e residue 134 ASP Chi-restraints excluded: chain e residue 149 THR Chi-restraints excluded: chain e residue 161 ILE Chi-restraints excluded: chain e residue 166 TRP Chi-restraints excluded: chain f residue 156 GLN Chi-restraints excluded: chain f residue 197 LEU Chi-restraints excluded: chain g residue 69 VAL Chi-restraints excluded: chain g residue 127 ASP Chi-restraints excluded: chain g residue 183 TYR Chi-restraints excluded: chain g residue 199 ASP Chi-restraints excluded: chain g residue 330 ILE Chi-restraints excluded: chain g residue 450 LEU Chi-restraints excluded: chain h residue 14 LEU Chi-restraints excluded: chain h residue 15 VAL Chi-restraints excluded: chain h residue 58 VAL Chi-restraints excluded: chain h residue 61 THR Chi-restraints excluded: chain h residue 80 LEU Chi-restraints excluded: chain h residue 86 ASP Chi-restraints excluded: chain h residue 96 GLU Chi-restraints excluded: chain i residue 43 CYS Chi-restraints excluded: chain i residue 44 ASP Chi-restraints excluded: chain i residue 45 ASP Chi-restraints excluded: chain i residue 83 THR Chi-restraints excluded: chain i residue 93 TRP Chi-restraints excluded: chain i residue 105 VAL Chi-restraints excluded: chain i residue 158 LEU Chi-restraints excluded: chain i residue 160 ILE Chi-restraints excluded: chain i residue 161 ILE Chi-restraints excluded: chain i residue 192 LYS Chi-restraints excluded: chain j residue 16 LEU Chi-restraints excluded: chain j residue 53 THR Chi-restraints excluded: chain j residue 148 LEU Chi-restraints excluded: chain j residue 149 THR Chi-restraints excluded: chain k residue 83 ASP Chi-restraints excluded: chain k residue 166 ILE Chi-restraints excluded: chain k residue 252 TRP Chi-restraints excluded: chain k residue 377 ASP Chi-restraints excluded: chain k residue 412 VAL Chi-restraints excluded: chain k residue 576 VAL Chi-restraints excluded: chain k residue 590 LEU Chi-restraints excluded: chain l residue 25 LEU Chi-restraints excluded: chain l residue 26 THR Chi-restraints excluded: chain l residue 47 THR Chi-restraints excluded: chain l residue 49 ILE Chi-restraints excluded: chain l residue 52 ASP Chi-restraints excluded: chain l residue 88 ILE Chi-restraints excluded: chain m residue 43 CYS Chi-restraints excluded: chain m residue 44 ASP Chi-restraints excluded: chain m residue 71 VAL Chi-restraints excluded: chain m residue 78 MET Chi-restraints excluded: chain m residue 93 TRP Chi-restraints excluded: chain m residue 161 ILE Chi-restraints excluded: chain n residue 25 THR Chi-restraints excluded: chain n residue 42 VAL Chi-restraints excluded: chain n residue 71 LEU Chi-restraints excluded: chain n residue 121 VAL Chi-restraints excluded: chain o residue 41 GLU Chi-restraints excluded: chain o residue 63 ASN Chi-restraints excluded: chain o residue 138 LEU Chi-restraints excluded: chain o residue 183 TYR Chi-restraints excluded: chain o residue 199 ASP Chi-restraints excluded: chain o residue 330 ILE Chi-restraints excluded: chain o residue 374 ASP Chi-restraints excluded: chain o residue 412 VAL Chi-restraints excluded: chain o residue 450 LEU Chi-restraints excluded: chain o residue 489 ASP Chi-restraints excluded: chain o residue 576 VAL Chi-restraints excluded: chain o residue 583 LEU Chi-restraints excluded: chain o residue 588 THR Chi-restraints excluded: chain p residue 34 LEU Chi-restraints excluded: chain p residue 83 ASN Chi-restraints excluded: chain q residue 52 THR Chi-restraints excluded: chain q residue 152 ASN Chi-restraints excluded: chain r residue 83 ASP Chi-restraints excluded: chain r residue 391 SER Chi-restraints excluded: chain r residue 412 VAL Chi-restraints excluded: chain r residue 450 LEU Chi-restraints excluded: chain s residue 6 PHE Chi-restraints excluded: chain s residue 26 THR Chi-restraints excluded: chain s residue 34 LEU Chi-restraints excluded: chain s residue 61 THR Chi-restraints excluded: chain s residue 80 LEU Chi-restraints excluded: chain s residue 96 GLU Chi-restraints excluded: chain t residue 42 VAL Chi-restraints excluded: chain t residue 80 THR Chi-restraints excluded: chain t residue 148 LEU Chi-restraints excluded: chain u residue 73 TYR Chi-restraints excluded: chain u residue 138 LEU Chi-restraints excluded: chain u residue 166 ILE Chi-restraints excluded: chain u residue 183 TYR Chi-restraints excluded: chain u residue 199 ASP Chi-restraints excluded: chain u residue 250 MET Chi-restraints excluded: chain u residue 330 ILE Chi-restraints excluded: chain u residue 396 VAL Chi-restraints excluded: chain u residue 563 GLU Chi-restraints excluded: chain u residue 576 VAL Chi-restraints excluded: chain u residue 583 LEU Chi-restraints excluded: chain u residue 590 LEU Chi-restraints excluded: chain v residue 14 LEU Chi-restraints excluded: chain v residue 47 THR Chi-restraints excluded: chain v residue 52 ASP Chi-restraints excluded: chain v residue 57 ILE Chi-restraints excluded: chain v residue 64 THR Chi-restraints excluded: chain v residue 71 THR Chi-restraints excluded: chain w residue 52 THR Chi-restraints excluded: chain w residue 152 ASN Chi-restraints excluded: chain x residue 83 ASP Chi-restraints excluded: chain x residue 168 ASP Chi-restraints excluded: chain x residue 250 MET Chi-restraints excluded: chain x residue 412 VAL Chi-restraints excluded: chain x residue 443 MET Chi-restraints excluded: chain x residue 485 ASN Chi-restraints excluded: chain y residue 25 LEU Chi-restraints excluded: chain y residue 35 PHE Chi-restraints excluded: chain y residue 63 ARG Chi-restraints excluded: chain z residue 71 LEU Chi-restraints excluded: chain z residue 165 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1644 random chunks: chunk 1471 optimal weight: 0.0470 chunk 969 optimal weight: 4.9990 chunk 1561 optimal weight: 0.9980 chunk 953 optimal weight: 10.0000 chunk 740 optimal weight: 0.0870 chunk 1085 optimal weight: 6.9990 chunk 1637 optimal weight: 4.9990 chunk 1507 optimal weight: 9.9990 chunk 1304 optimal weight: 7.9990 chunk 135 optimal weight: 20.0000 chunk 1007 optimal weight: 3.9990 overall best weight: 2.0260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 54 HIS 3 60 GLN ** 3 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 54 HIS 6 63 ASN ** 6 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 300 GLN ** D 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 108 GLN ** P 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 208 GLN ** W 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 92 GLN Y 485 ASN ** a 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 208 GLN ** c 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 54 HIS ** h 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 60 GLN ** k 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 54 HIS o 63 ASN ** p 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 54 HIS u 92 GLN ** u 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 130506 Z= 0.205 Angle : 0.603 12.853 177246 Z= 0.312 Chirality : 0.043 0.478 19890 Planarity : 0.005 0.075 23400 Dihedral : 4.659 28.405 18210 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.20 % Favored : 94.52 % Rotamer: Outliers : 2.44 % Allowed : 18.35 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.07), residues: 16500 helix: 2.43 (0.07), residues: 6282 sheet: -0.42 (0.10), residues: 2406 loop : -1.41 (0.07), residues: 7812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP u 553 HIS 0.007 0.001 HIS S 12 PHE 0.037 0.001 PHE V 44 TYR 0.022 0.001 TYR 2 171 ARG 0.014 0.000 ARG 6 64 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 33000 Ramachandran restraints generated. 16500 Oldfield, 0 Emsley, 16500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 33000 Ramachandran restraints generated. 16500 Oldfield, 0 Emsley, 16500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1934 residues out of total 13764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 315 poor density : 1619 time to evaluate : 11.235 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: 0 374 ASP cc_start: 0.7142 (p0) cc_final: 0.6854 (p0) REVERT: 1 8 ASN cc_start: 0.7718 (t0) cc_final: 0.7034 (p0) REVERT: 1 91 ARG cc_start: 0.2870 (mpp-170) cc_final: 0.2557 (mpp-170) REVERT: 2 31 GLU cc_start: 0.7845 (tp30) cc_final: 0.7439 (tp30) REVERT: 2 33 LEU cc_start: 0.9077 (tp) cc_final: 0.8825 (tt) REVERT: 2 148 LEU cc_start: 0.7551 (OUTLIER) cc_final: 0.7231 (mm) REVERT: 3 607 ARG cc_start: 0.6388 (mmt-90) cc_final: 0.5871 (mtp180) REVERT: 4 5 GLN cc_start: 0.8654 (tm-30) cc_final: 0.7875 (tm-30) REVERT: 4 45 MET cc_start: 0.7938 (mmp) cc_final: 0.7500 (mmp) REVERT: 6 110 SER cc_start: 0.9433 (m) cc_final: 0.9205 (p) REVERT: 6 489 ASP cc_start: 0.7384 (OUTLIER) cc_final: 0.6946 (t0) REVERT: 7 68 MET cc_start: 0.7140 (tpp) cc_final: 0.6651 (tpp) REVERT: A 510 MET cc_start: 0.1696 (mtm) cc_final: 0.1292 (mtt) REVERT: B 30 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8159 (tt) REVERT: B 239 MET cc_start: 0.7001 (mpp) cc_final: 0.6661 (mmm) REVERT: B 347 MET cc_start: 0.7337 (ttp) cc_final: 0.7024 (mtm) REVERT: B 565 ILE cc_start: 0.9262 (mm) cc_final: 0.8905 (mp) REVERT: C 69 TRP cc_start: 0.7945 (m-90) cc_final: 0.7711 (m-90) REVERT: C 239 MET cc_start: 0.6346 (mpp) cc_final: 0.5852 (mpp) REVERT: D 95 MET cc_start: 0.5911 (mtt) cc_final: 0.5463 (mtm) REVERT: D 283 MET cc_start: 0.7789 (mtm) cc_final: 0.7503 (mtm) REVERT: D 510 MET cc_start: 0.1124 (mtm) cc_final: 0.0755 (mtt) REVERT: E 565 ILE cc_start: 0.9287 (mm) cc_final: 0.8968 (mp) REVERT: F 66 TRP cc_start: 0.7949 (m100) cc_final: 0.7337 (m100) REVERT: I 113 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8289 (pp) REVERT: K 39 ARG cc_start: 0.9108 (mtt-85) cc_final: 0.8576 (mtt-85) REVERT: K 166 TRP cc_start: 0.7165 (m-10) cc_final: 0.6408 (m-10) REVERT: L 113 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8226 (pp) REVERT: M 5 GLN cc_start: 0.7011 (mt0) cc_final: 0.6437 (mt0) REVERT: M 96 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7247 (mp0) REVERT: M 108 GLN cc_start: 0.8277 (OUTLIER) cc_final: 0.7880 (mp10) REVERT: N 5 GLN cc_start: 0.8114 (tm-30) cc_final: 0.6960 (tm-30) REVERT: N 42 ASP cc_start: 0.6657 (t0) cc_final: 0.6118 (t0) REVERT: O 82 PHE cc_start: 0.5373 (m-80) cc_final: 0.5091 (m-10) REVERT: Q 50 ARG cc_start: 0.6863 (ptm160) cc_final: 0.6472 (ptm-80) REVERT: Q 68 MET cc_start: 0.8546 (mpp) cc_final: 0.8327 (mpp) REVERT: T 49 MET cc_start: 0.7672 (tpp) cc_final: 0.7417 (tpp) REVERT: U 102 GLN cc_start: 0.7803 (tm-30) cc_final: 0.7135 (tm-30) REVERT: U 411 GLU cc_start: 0.7642 (mm-30) cc_final: 0.7257 (mt-10) REVERT: U 545 ASP cc_start: 0.7211 (m-30) cc_final: 0.6980 (m-30) REVERT: V 45 MET cc_start: 0.7796 (mmm) cc_final: 0.7234 (mmm) REVERT: V 96 GLU cc_start: 0.7318 (mp0) cc_final: 0.6859 (mp0) REVERT: W 83 THR cc_start: 0.8660 (OUTLIER) cc_final: 0.8115 (m) REVERT: X 136 GLN cc_start: 0.8074 (pm20) cc_final: 0.7841 (pm20) REVERT: Y 73 TYR cc_start: 0.8694 (OUTLIER) cc_final: 0.8183 (t80) REVERT: Y 113 ARG cc_start: 0.7537 (mmt180) cc_final: 0.7299 (mmt180) REVERT: Y 250 MET cc_start: 0.7878 (OUTLIER) cc_final: 0.7238 (ptp) REVERT: Z 5 GLN cc_start: 0.8780 (tm-30) cc_final: 0.7981 (tm-30) REVERT: Z 6 PHE cc_start: 0.8289 (m-80) cc_final: 0.8016 (m-80) REVERT: Z 42 ASP cc_start: 0.7225 (t0) cc_final: 0.6178 (t0) REVERT: Z 45 MET cc_start: 0.8157 (mmp) cc_final: 0.7727 (mmp) REVERT: Z 99 ASP cc_start: 0.8492 (m-30) cc_final: 0.8254 (m-30) REVERT: a 48 ASN cc_start: 0.8160 (m110) cc_final: 0.7769 (m-40) REVERT: a 134 ASP cc_start: 0.7373 (p0) cc_final: 0.7114 (p0) REVERT: b 128 TYR cc_start: 0.8918 (t80) cc_final: 0.8690 (t80) REVERT: c 372 MET cc_start: 0.6698 (ptp) cc_final: 0.6450 (ptt) REVERT: c 411 GLU cc_start: 0.7439 (mm-30) cc_final: 0.7136 (mt-10) REVERT: c 572 MET cc_start: 0.7569 (mmp) cc_final: 0.7355 (mmp) REVERT: d 59 LYS cc_start: 0.7252 (tptt) cc_final: 0.6937 (ttmt) REVERT: e 66 TYR cc_start: 0.8439 (t80) cc_final: 0.8020 (t80) REVERT: g 250 MET cc_start: 0.7863 (pmm) cc_final: 0.6987 (ptp) REVERT: g 382 ARG cc_start: 0.8645 (mmp80) cc_final: 0.8265 (mmp80) REVERT: i 83 THR cc_start: 0.8698 (OUTLIER) cc_final: 0.8224 (m) REVERT: j 165 LEU cc_start: 0.8800 (mm) cc_final: 0.8550 (mm) REVERT: k 443 MET cc_start: 0.8003 (ttp) cc_final: 0.7744 (ttt) REVERT: k 486 LYS cc_start: 0.8527 (tptm) cc_final: 0.8274 (tptt) REVERT: l 5 GLN cc_start: 0.8605 (tm-30) cc_final: 0.8094 (tm-30) REVERT: l 42 ASP cc_start: 0.6830 (t0) cc_final: 0.6239 (t0) REVERT: l 91 ARG cc_start: 0.7633 (tmm160) cc_final: 0.6640 (ptt-90) REVERT: m 49 VAL cc_start: 0.7793 (t) cc_final: 0.7572 (p) REVERT: o 221 VAL cc_start: 0.8027 (t) cc_final: 0.7750 (p) REVERT: o 486 LYS cc_start: 0.8023 (tptt) cc_final: 0.7761 (tptt) REVERT: o 489 ASP cc_start: 0.7788 (OUTLIER) cc_final: 0.7420 (t0) REVERT: p 83 ASN cc_start: 0.5479 (OUTLIER) cc_final: 0.5018 (m110) REVERT: p 100 PHE cc_start: 0.7794 (m-10) cc_final: 0.7507 (m-80) REVERT: t 73 ASP cc_start: 0.7277 (m-30) cc_final: 0.6988 (m-30) REVERT: t 148 LEU cc_start: 0.7717 (OUTLIER) cc_final: 0.7345 (mm) REVERT: u 73 TYR cc_start: 0.8723 (OUTLIER) cc_final: 0.8251 (t80) REVERT: u 125 LYS cc_start: 0.7262 (ttmt) cc_final: 0.7012 (ttmm) REVERT: u 146 ARG cc_start: 0.8308 (mtt-85) cc_final: 0.7931 (mtt180) REVERT: u 199 ASP cc_start: 0.7990 (OUTLIER) cc_final: 0.7278 (m-30) REVERT: u 250 MET cc_start: 0.7875 (OUTLIER) cc_final: 0.7239 (ptp) REVERT: v 5 GLN cc_start: 0.8155 (tm-30) cc_final: 0.7395 (tm-30) REVERT: w 3 PHE cc_start: 0.7573 (p90) cc_final: 0.7085 (p90) REVERT: y 18 LEU cc_start: 0.6302 (tp) cc_final: 0.5995 (tp) REVERT: y 75 GLU cc_start: 0.6703 (tm-30) cc_final: 0.6463 (pp20) REVERT: y 91 ARG cc_start: 0.3605 (mtt90) cc_final: 0.1864 (mmt180) REVERT: y 96 GLU cc_start: 0.7270 (mm-30) cc_final: 0.5643 (mt-10) outliers start: 315 outliers final: 266 residues processed: 1824 average time/residue: 1.0242 time to fit residues: 3330.4997 Evaluate side-chains 1847 residues out of total 13764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 283 poor density : 1564 time to evaluate : 9.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 69 VAL Chi-restraints excluded: chain 0 residue 96 VAL Chi-restraints excluded: chain 0 residue 183 TYR Chi-restraints excluded: chain 0 residue 199 ASP Chi-restraints excluded: chain 0 residue 330 ILE Chi-restraints excluded: chain 0 residue 450 LEU Chi-restraints excluded: chain 0 residue 484 THR Chi-restraints excluded: chain 1 residue 26 THR Chi-restraints excluded: chain 1 residue 61 THR Chi-restraints excluded: chain 1 residue 80 LEU Chi-restraints excluded: chain 2 residue 42 VAL Chi-restraints excluded: chain 2 residue 80 THR Chi-restraints excluded: chain 2 residue 148 LEU Chi-restraints excluded: chain 3 residue 83 ASP Chi-restraints excluded: chain 3 residue 166 ILE Chi-restraints excluded: chain 3 residue 397 MET Chi-restraints excluded: chain 3 residue 412 VAL Chi-restraints excluded: chain 3 residue 427 ILE Chi-restraints excluded: chain 3 residue 435 LEU Chi-restraints excluded: chain 3 residue 576 VAL Chi-restraints excluded: chain 4 residue 25 LEU Chi-restraints excluded: chain 4 residue 52 ASP Chi-restraints excluded: chain 4 residue 68 MET Chi-restraints excluded: chain 4 residue 71 THR Chi-restraints excluded: chain 5 residue 67 ASP Chi-restraints excluded: chain 6 residue 41 GLU Chi-restraints excluded: chain 6 residue 63 ASN Chi-restraints excluded: chain 6 residue 138 LEU Chi-restraints excluded: chain 6 residue 183 TYR Chi-restraints excluded: chain 6 residue 199 ASP Chi-restraints excluded: chain 6 residue 252 TRP Chi-restraints excluded: chain 6 residue 330 ILE Chi-restraints excluded: chain 6 residue 371 TRP Chi-restraints excluded: chain 6 residue 374 ASP Chi-restraints excluded: chain 6 residue 412 VAL Chi-restraints excluded: chain 6 residue 443 MET Chi-restraints excluded: chain 6 residue 450 LEU Chi-restraints excluded: chain 6 residue 489 ASP Chi-restraints excluded: chain 6 residue 576 VAL Chi-restraints excluded: chain 6 residue 583 LEU Chi-restraints excluded: chain 6 residue 588 THR Chi-restraints excluded: chain 7 residue 35 PHE Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 384 SER Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 332 VAL Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 332 VAL Chi-restraints excluded: chain E residue 339 MET Chi-restraints excluded: chain E residue 346 LEU Chi-restraints excluded: chain E residue 537 MET Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 384 SER Chi-restraints excluded: chain F residue 540 MET Chi-restraints excluded: chain F residue 553 GLU Chi-restraints excluded: chain G residue 32 ILE Chi-restraints excluded: chain G residue 103 GLN Chi-restraints excluded: chain G residue 116 VAL Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 67 GLU Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain H residue 122 SER Chi-restraints excluded: chain H residue 142 LEU Chi-restraints excluded: chain H residue 145 THR Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain I residue 32 ILE Chi-restraints excluded: chain I residue 113 LEU Chi-restraints excluded: chain I residue 116 VAL Chi-restraints excluded: chain I residue 173 VAL Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain J residue 32 ILE Chi-restraints excluded: chain J residue 195 GLN Chi-restraints excluded: chain K residue 11 ILE Chi-restraints excluded: chain K residue 32 ILE Chi-restraints excluded: chain K residue 116 VAL Chi-restraints excluded: chain K residue 122 SER Chi-restraints excluded: chain K residue 184 ASP Chi-restraints excluded: chain L residue 32 ILE Chi-restraints excluded: chain L residue 113 LEU Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 122 SER Chi-restraints excluded: chain L residue 171 LEU Chi-restraints excluded: chain L residue 186 LEU Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain M residue 71 THR Chi-restraints excluded: chain M residue 80 LEU Chi-restraints excluded: chain M residue 96 GLU Chi-restraints excluded: chain M residue 108 GLN Chi-restraints excluded: chain N residue 49 ILE Chi-restraints excluded: chain N residue 52 ASP Chi-restraints excluded: chain O residue 71 THR Chi-restraints excluded: chain P residue 34 LEU Chi-restraints excluded: chain P residue 58 VAL Chi-restraints excluded: chain P residue 61 THR Chi-restraints excluded: chain P residue 80 LEU Chi-restraints excluded: chain P residue 92 LEU Chi-restraints excluded: chain Q residue 25 LEU Chi-restraints excluded: chain Q residue 47 THR Chi-restraints excluded: chain Q residue 52 ASP Chi-restraints excluded: chain Q residue 71 THR Chi-restraints excluded: chain R residue 18 LEU Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain S residue 43 CYS Chi-restraints excluded: chain S residue 44 ASP Chi-restraints excluded: chain S residue 45 ASP Chi-restraints excluded: chain S residue 93 TRP Chi-restraints excluded: chain S residue 116 VAL Chi-restraints excluded: chain S residue 142 LEU Chi-restraints excluded: chain S residue 149 THR Chi-restraints excluded: chain S residue 160 ILE Chi-restraints excluded: chain S residue 161 ILE Chi-restraints excluded: chain S residue 166 TRP Chi-restraints excluded: chain T residue 16 LEU Chi-restraints excluded: chain T residue 42 VAL Chi-restraints excluded: chain T residue 53 THR Chi-restraints excluded: chain T residue 148 LEU Chi-restraints excluded: chain T residue 149 THR Chi-restraints excluded: chain T residue 165 LEU Chi-restraints excluded: chain U residue 252 TRP Chi-restraints excluded: chain U residue 377 ASP Chi-restraints excluded: chain U residue 393 ASN Chi-restraints excluded: chain U residue 412 VAL Chi-restraints excluded: chain U residue 427 ILE Chi-restraints excluded: chain U residue 496 GLN Chi-restraints excluded: chain U residue 506 ILE Chi-restraints excluded: chain V residue 26 THR Chi-restraints excluded: chain V residue 58 VAL Chi-restraints excluded: chain V residue 61 THR Chi-restraints excluded: chain V residue 80 LEU Chi-restraints excluded: chain V residue 108 GLN Chi-restraints excluded: chain W residue 43 CYS Chi-restraints excluded: chain W residue 44 ASP Chi-restraints excluded: chain W residue 45 ASP Chi-restraints excluded: chain W residue 78 MET Chi-restraints excluded: chain W residue 83 THR Chi-restraints excluded: chain W residue 93 TRP Chi-restraints excluded: chain W residue 134 ASP Chi-restraints excluded: chain X residue 156 GLN Chi-restraints excluded: chain Y residue 73 TYR Chi-restraints excluded: chain Y residue 183 TYR Chi-restraints excluded: chain Y residue 250 MET Chi-restraints excluded: chain Y residue 330 ILE Chi-restraints excluded: chain Y residue 563 GLU Chi-restraints excluded: chain Y residue 576 VAL Chi-restraints excluded: chain Y residue 583 LEU Chi-restraints excluded: chain Y residue 590 LEU Chi-restraints excluded: chain Z residue 25 LEU Chi-restraints excluded: chain Z residue 47 THR Chi-restraints excluded: chain Z residue 52 ASP Chi-restraints excluded: chain Z residue 71 THR Chi-restraints excluded: chain a residue 43 CYS Chi-restraints excluded: chain a residue 44 ASP Chi-restraints excluded: chain a residue 71 VAL Chi-restraints excluded: chain a residue 93 TRP Chi-restraints excluded: chain a residue 96 THR Chi-restraints excluded: chain a residue 161 ILE Chi-restraints excluded: chain b residue 70 GLN Chi-restraints excluded: chain c residue 83 ASP Chi-restraints excluded: chain c residue 377 ASP Chi-restraints excluded: chain c residue 412 VAL Chi-restraints excluded: chain c residue 427 ILE Chi-restraints excluded: chain c residue 443 MET Chi-restraints excluded: chain c residue 576 VAL Chi-restraints excluded: chain d residue 35 PHE Chi-restraints excluded: chain d residue 58 VAL Chi-restraints excluded: chain d residue 71 THR Chi-restraints excluded: chain e residue 43 CYS Chi-restraints excluded: chain e residue 44 ASP Chi-restraints excluded: chain e residue 78 MET Chi-restraints excluded: chain e residue 93 TRP Chi-restraints excluded: chain e residue 106 THR Chi-restraints excluded: chain e residue 116 VAL Chi-restraints excluded: chain e residue 134 ASP Chi-restraints excluded: chain e residue 149 THR Chi-restraints excluded: chain e residue 161 ILE Chi-restraints excluded: chain e residue 166 TRP Chi-restraints excluded: chain f residue 197 LEU Chi-restraints excluded: chain g residue 69 VAL Chi-restraints excluded: chain g residue 127 ASP Chi-restraints excluded: chain g residue 183 TYR Chi-restraints excluded: chain g residue 199 ASP Chi-restraints excluded: chain g residue 330 ILE Chi-restraints excluded: chain g residue 450 LEU Chi-restraints excluded: chain h residue 14 LEU Chi-restraints excluded: chain h residue 15 VAL Chi-restraints excluded: chain h residue 58 VAL Chi-restraints excluded: chain h residue 61 THR Chi-restraints excluded: chain h residue 80 LEU Chi-restraints excluded: chain h residue 96 GLU Chi-restraints excluded: chain i residue 43 CYS Chi-restraints excluded: chain i residue 44 ASP Chi-restraints excluded: chain i residue 45 ASP Chi-restraints excluded: chain i residue 83 THR Chi-restraints excluded: chain i residue 93 TRP Chi-restraints excluded: chain i residue 158 LEU Chi-restraints excluded: chain i residue 160 ILE Chi-restraints excluded: chain j residue 16 LEU Chi-restraints excluded: chain j residue 53 THR Chi-restraints excluded: chain j residue 148 LEU Chi-restraints excluded: chain j residue 149 THR Chi-restraints excluded: chain k residue 83 ASP Chi-restraints excluded: chain k residue 166 ILE Chi-restraints excluded: chain k residue 252 TRP Chi-restraints excluded: chain k residue 377 ASP Chi-restraints excluded: chain k residue 412 VAL Chi-restraints excluded: chain k residue 576 VAL Chi-restraints excluded: chain k residue 590 LEU Chi-restraints excluded: chain l residue 26 THR Chi-restraints excluded: chain l residue 49 ILE Chi-restraints excluded: chain l residue 52 ASP Chi-restraints excluded: chain l residue 88 ILE Chi-restraints excluded: chain m residue 43 CYS Chi-restraints excluded: chain m residue 44 ASP Chi-restraints excluded: chain m residue 71 VAL Chi-restraints excluded: chain m residue 78 MET Chi-restraints excluded: chain m residue 93 TRP Chi-restraints excluded: chain m residue 161 ILE Chi-restraints excluded: chain n residue 42 VAL Chi-restraints excluded: chain n residue 121 VAL Chi-restraints excluded: chain o residue 41 GLU Chi-restraints excluded: chain o residue 63 ASN Chi-restraints excluded: chain o residue 183 TYR Chi-restraints excluded: chain o residue 199 ASP Chi-restraints excluded: chain o residue 330 ILE Chi-restraints excluded: chain o residue 374 ASP Chi-restraints excluded: chain o residue 412 VAL Chi-restraints excluded: chain o residue 433 ARG Chi-restraints excluded: chain o residue 450 LEU Chi-restraints excluded: chain o residue 489 ASP Chi-restraints excluded: chain o residue 576 VAL Chi-restraints excluded: chain o residue 583 LEU Chi-restraints excluded: chain o residue 588 THR Chi-restraints excluded: chain p residue 34 LEU Chi-restraints excluded: chain p residue 83 ASN Chi-restraints excluded: chain q residue 52 THR Chi-restraints excluded: chain q residue 152 ASN Chi-restraints excluded: chain r residue 391 SER Chi-restraints excluded: chain r residue 412 VAL Chi-restraints excluded: chain s residue 6 PHE Chi-restraints excluded: chain s residue 26 THR Chi-restraints excluded: chain s residue 34 LEU Chi-restraints excluded: chain s residue 61 THR Chi-restraints excluded: chain s residue 80 LEU Chi-restraints excluded: chain s residue 96 GLU Chi-restraints excluded: chain t residue 42 VAL Chi-restraints excluded: chain t residue 80 THR Chi-restraints excluded: chain t residue 148 LEU Chi-restraints excluded: chain u residue 73 TYR Chi-restraints excluded: chain u residue 166 ILE Chi-restraints excluded: chain u residue 183 TYR Chi-restraints excluded: chain u residue 199 ASP Chi-restraints excluded: chain u residue 250 MET Chi-restraints excluded: chain u residue 330 ILE Chi-restraints excluded: chain u residue 396 VAL Chi-restraints excluded: chain u residue 563 GLU Chi-restraints excluded: chain u residue 576 VAL Chi-restraints excluded: chain u residue 583 LEU Chi-restraints excluded: chain u residue 590 LEU Chi-restraints excluded: chain v residue 14 LEU Chi-restraints excluded: chain v residue 47 THR Chi-restraints excluded: chain v residue 52 ASP Chi-restraints excluded: chain v residue 57 ILE Chi-restraints excluded: chain v residue 64 THR Chi-restraints excluded: chain v residue 71 THR Chi-restraints excluded: chain w residue 52 THR Chi-restraints excluded: chain w residue 152 ASN Chi-restraints excluded: chain x residue 83 ASP Chi-restraints excluded: chain x residue 168 ASP Chi-restraints excluded: chain x residue 250 MET Chi-restraints excluded: chain x residue 412 VAL Chi-restraints excluded: chain y residue 63 ARG Chi-restraints excluded: chain z residue 165 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1644 random chunks: chunk 799 optimal weight: 0.9990 chunk 1035 optimal weight: 40.0000 chunk 1389 optimal weight: 8.9990 chunk 399 optimal weight: 10.0000 chunk 1202 optimal weight: 9.9990 chunk 192 optimal weight: 5.9990 chunk 362 optimal weight: 2.9990 chunk 1306 optimal weight: 0.9980 chunk 546 optimal weight: 6.9990 chunk 1341 optimal weight: 4.9990 chunk 165 optimal weight: 7.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 54 HIS 3 60 GLN ** 5 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 54 HIS 6 63 ASN ** 6 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 433 GLN ** D 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 300 GLN F 433 GLN F 538 ASN ** H 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 156 GLN Y 92 GLN a 48 ASN ** a 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 54 HIS ** g 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 60 GLN ** k 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 54 HIS o 63 ASN ** p 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 54 HIS u 92 GLN ** u 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.115845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.097788 restraints weight = 379044.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.096803 restraints weight = 372789.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.097310 restraints weight = 303422.685| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 130506 Z= 0.255 Angle : 0.615 12.818 177246 Z= 0.319 Chirality : 0.043 0.497 19890 Planarity : 0.005 0.075 23400 Dihedral : 4.680 27.942 18210 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.37 % Favored : 94.33 % Rotamer: Outliers : 2.52 % Allowed : 18.51 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.07), residues: 16500 helix: 2.39 (0.07), residues: 6270 sheet: -0.46 (0.10), residues: 2406 loop : -1.42 (0.07), residues: 7824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP o 553 HIS 0.008 0.001 HIS S 12 PHE 0.035 0.001 PHE V 44 TYR 0.032 0.002 TYR r 74 ARG 0.009 0.000 ARG F 84 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 44598.36 seconds wall clock time: 770 minutes 35.78 seconds (46235.78 seconds total)