Starting phenix.real_space_refine on Sat Feb 24 23:45:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7agx_11780/02_2024/7agx_11780.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7agx_11780/02_2024/7agx_11780.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7agx_11780/02_2024/7agx_11780.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7agx_11780/02_2024/7agx_11780.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7agx_11780/02_2024/7agx_11780.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7agx_11780/02_2024/7agx_11780.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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: 5 Type Number sf(0) Gaussians S 89 5.16 5 C 15373 2.51 5 N 3759 2.21 5 O 4439 1.98 5 H 24089 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "1A ASP 4": "OD1" <-> "OD2" Residue "1A PHE 13": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "1A PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "1A PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "1A PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "1A ASP 77": "OD1" <-> "OD2" Residue "1A GLU 78": "OE1" <-> "OE2" Residue "1A GLU 94": "OE1" <-> "OE2" Residue "1A TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "1A GLU 110": "OE1" <-> "OE2" Residue "1A PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "1A PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "1A GLU 154": "OE1" <-> "OE2" Residue "1A PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "1A TYR 164": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "1A PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "1B PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "1B PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "1B PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "1B TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "1B TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "1B PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "1B TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "1B TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "1B ARG 109": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "1B PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "1B GLU 139": "OE1" <-> "OE2" Residue "1B TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "1B GLU 154": "OE1" <-> "OE2" Residue "1B TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "1B PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "1C PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "1C PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "1C PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "1C TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "1C TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "1C PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "1C GLU 76": "OE1" <-> "OE2" Residue "1C PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "1C ASP 84": "OD1" <-> "OD2" Residue "1C GLU 94": "OE1" <-> "OE2" Residue "1C TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "1C PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "1C GLU 116": "OE1" <-> "OE2" Residue "1C PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "1C TYR 164": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "1C TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "1C PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "1C TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "1D ASP 4": "OD1" <-> "OD2" Residue "1D PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "1D PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "1D PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "1D PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "1D GLU 76": "OE1" <-> "OE2" Residue "1D GLU 78": "OE1" <-> "OE2" Residue "1D ARG 100": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "1D ASP 101": "OD1" <-> "OD2" Residue "1D TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "1D GLU 137": "OE1" <-> "OE2" Residue "1D TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "1D GLU 154": "OE1" <-> "OE2" Residue "1D TYR 164": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "1D TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "1D PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "1E ASP 4": "OD1" <-> "OD2" Residue "1E PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "1E PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "1E PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "1E PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "1E TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "1E TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "1E TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "1E GLU 110": "OE1" <-> "OE2" Residue "1E PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "1E ARG 122": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "1E GLU 154": "OE1" <-> "OE2" Residue "1E PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "1E TYR 164": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "1E PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "1F PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "1F PHE 7": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "1F PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "1F GLU 61": "OE1" <-> "OE2" Residue "1F PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "1F PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "1F ASP 115": "OD1" <-> "OD2" Residue "1F ASP 121": "OD1" <-> "OD2" Residue "1F TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "1F GLU 162": "OE1" <-> "OE2" Residue "1F PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "1F PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "1F PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "1F TYR 254": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "1F ARG 256": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "1G PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "1G PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "1G TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "1G GLU 69": "OE1" <-> "OE2" Residue "1G ARG 76": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "1H PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "1H TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "1H GLU 69": "OE1" <-> "OE2" Residue "1H ARG 76": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "1H PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "1I PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "1I TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "1I GLU 69": "OE1" <-> "OE2" Residue "1I ARG 76": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "1I PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "1J PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "1J TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "1J GLU 69": "OE1" <-> "OE2" Residue "1J ARG 76": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "1K ARG 32": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "1K ASP 47": "OD1" <-> "OD2" Residue "1K GLU 72": "OE1" <-> "OE2" Residue "1K TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "1L ARG 32": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "1L PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "1L ARG 54": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "1L ASP 57": "OD1" <-> "OD2" Residue "1L GLU 72": "OE1" <-> "OE2" Residue "1M GLU 56": "OE1" <-> "OE2" Residue "1M GLU 66": "OE1" <-> "OE2" Residue "1M GLU 72": "OE1" <-> "OE2" Residue "1M ARG 89": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "1M GLU 96": "OE1" <-> "OE2" Residue "1N ASP 31": "OD1" <-> "OD2" Residue "1N GLU 56": "OE1" <-> "OE2" Residue "1N ASP 57": "OD1" <-> "OD2" Residue "1N GLU 72": "OE1" <-> "OE2" Residue "1N ARG 100": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "1O ARG 32": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "1O TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "1O GLU 96": "OE1" <-> "OE2" Residue "1P ASP 30": "OD1" <-> "OD2" Residue "1P ASP 31": "OD1" <-> "OD2" Residue "1P GLU 72": "OE1" <-> "OE2" Residue "1P TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "2A ASP 32": "OD1" <-> "OD2" Residue "2A PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "2B PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "2C ASP 40": "OD1" <-> "OD2" Residue "2C PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "2D PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "2D PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "2E ASP 40": "OD1" <-> "OD2" Residue "2E ARG 58": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "2E PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "2F PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "2F ASP 21": "OD1" <-> "OD2" Residue "2F ASP 40": "OD1" <-> "OD2" Residue "2F PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "2F ASP 72": "OD1" <-> "OD2" Residue "2G PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "2G ASP 21": "OD1" <-> "OD2" Residue "2G GLU 53": "OE1" <-> "OE2" Residue "2G PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "2H GLU 53": "OE1" <-> "OE2" Residue "2H ARG 58": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "2H PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "2I ASP 17": "OD1" <-> "OD2" Residue "2I TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "2I ARG 58": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "2J PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "2J ASP 17": "OD1" <-> "OD2" Residue "2J GLU 29": "OE1" <-> "OE2" Residue "2J TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "2J ARG 58": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "2K PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "2K ASP 17": "OD1" <-> "OD2" Residue "2K PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "2L PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "2L ASP 17": "OD1" <-> "OD2" Residue "2L PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "2L ARG 80": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "2M PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "2M ASP 17": "OD1" <-> "OD2" Residue "2M ASP 21": "OD1" <-> "OD2" Residue "2M PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "2M PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "2N TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "2N PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "2N GLU 53": "OE1" <-> "OE2" Residue "2N PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "2O TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "2O PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "2O ASP 17": "OD1" <-> "OD2" Residue "2O ASP 21": "OD1" <-> "OD2" Residue "2P ASP 10": "OD1" <-> "OD2" Residue "2P ASP 11": "OD1" <-> "OD2" Residue "2P PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "2P ARG 80": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "2Q PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 47749 Number of models: 1 Model: "" Number of chains: 33 Chain: "1A" Number of atoms: 3196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 3196 Classifications: {'peptide': 200} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 191} Chain breaks: 1 Chain: "1B" Number of atoms: 3120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 3120 Classifications: {'peptide': 195} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 186} Chain breaks: 2 Chain: "1C" Number of atoms: 3100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 3100 Classifications: {'peptide': 194} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 185} Chain breaks: 2 Chain: "1D" Number of atoms: 3055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 3055 Classifications: {'peptide': 190} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 181} Chain breaks: 2 Chain: "1E" Number of atoms: 3203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 3203 Classifications: {'peptide': 199} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 190} Chain breaks: 2 Chain: "1F" Number of atoms: 3968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 3968 Classifications: {'peptide': 257} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 239} Chain: "1G" Number of atoms: 1160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1160 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 2, 'TRANS': 70} Chain breaks: 1 Chain: "1H" Number of atoms: 1320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 1320 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 2, 'TRANS': 80} Chain: "1I" Number of atoms: 1320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 1320 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 2, 'TRANS': 80} Chain: "1J" Number of atoms: 1320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 1320 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 2, 'TRANS': 80} Chain: "1K" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 1042 Classifications: {'peptide': 68} Link IDs: {'PCIS': 1, 'TRANS': 66} Chain breaks: 1 Chain: "1L" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1129 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 2, 'TRANS': 70} Chain: "1M" Number of atoms: 1118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 1118 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain: "1N" Number of atoms: 1140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1140 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Chain: "1O" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1129 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 2, 'TRANS': 70} Chain: "1P" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1129 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 2, 'TRANS': 70} Chain: "2A" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 937 Classifications: {'peptide': 59} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 56} Chain: "2B" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 964 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 2, 'TRANS': 58} Chain: "2C" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 937 Classifications: {'peptide': 59} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 56} Chain: "2D" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 949 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 57} Chain: "2E" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 949 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 57} Chain: "2F" Number of atoms: 1120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 1120 Classifications: {'peptide': 72} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain: "2G" Number of atoms: 1158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1158 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "2H" Number of atoms: 1159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1159 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "2I" Number of atoms: 1159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1159 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "2J" Number of atoms: 1159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1159 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "2K" Number of atoms: 1196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1196 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "2L" Number of atoms: 1033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 1033 Classifications: {'peptide': 66} Link IDs: {'TRANS': 65} Chain breaks: 1 Chain: "2M" Number of atoms: 992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 992 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain breaks: 1 Chain: "2N" Number of atoms: 901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 901 Classifications: {'peptide': 57} Modifications used: {'COO': 1} Link IDs: {'TRANS': 56} Chain breaks: 1 Chain: "2O" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 788 Classifications: {'peptide': 50} Modifications used: {'COO': 1} Link IDs: {'TRANS': 49} Chain breaks: 1 Chain: "2P" Number of atoms: 700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 700 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'TRANS': 43} Chain breaks: 1 Chain: "2Q" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 199 Classifications: {'peptide': 13} Link IDs: {'TRANS': 12} Time building chain proxies: 21.11, per 1000 atoms: 0.44 Number of scatterers: 47749 At special positions: 0 Unit cell: (109, 101.37, 206.01, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 89 16.00 O 4439 8.00 N 3759 7.00 C 15373 6.00 H 24089 1.00 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: 40.33 Conformation dependent library (CDL) restraints added in 4.7 seconds 5866 Ramachandran restraints generated. 2933 Oldfield, 0 Emsley, 2933 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5780 Finding SS restraints... Secondary structure from input PDB file: 127 helices and 1 sheets defined 89.5% alpha, 0.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.02 Creating SS restraints... Processing helix chain '1A' and resid 4 through 21 removed outlier: 4.228A pdb=" N LEU1A 10 " --> pdb=" O SER1A 6 " (cutoff:3.500A) Proline residue: 1A 18 - end of helix Processing helix chain '1A' and resid 26 through 41 removed outlier: 3.568A pdb=" N ILE1A 32 " --> pdb=" O VAL1A 28 " (cutoff:3.500A) Processing helix chain '1A' and resid 48 through 76 removed outlier: 3.527A pdb=" N LEU1A 57 " --> pdb=" O ASN1A 53 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N PHE1A 62 " --> pdb=" O LEU1A 58 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N VAL1A 63 " --> pdb=" O LEU1A 59 " (cutoff:3.500A) Proline residue: 1A 66 - end of helix removed outlier: 3.563A pdb=" N PHE1A 75 " --> pdb=" O ALA1A 71 " (cutoff:3.500A) Processing helix chain '1A' and resid 84 through 107 removed outlier: 3.807A pdb=" N GLY1A 95 " --> pdb=" O HIS1A 91 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU1A 96 " --> pdb=" O VAL1A 92 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASP1A 97 " --> pdb=" O ASP1A 93 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N GLY1A 98 " --> pdb=" O GLU1A 94 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N TYR1A 99 " --> pdb=" O GLY1A 95 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N TYR1A 102 " --> pdb=" O GLY1A 98 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS1A 105 " --> pdb=" O ASP1A 101 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N TYR1A 106 " --> pdb=" O TYR1A 102 " (cutoff:3.500A) Processing helix chain '1A' and resid 108 through 119 removed outlier: 3.505A pdb=" N VAL1A 112 " --> pdb=" O ASP1A 108 " (cutoff:3.500A) Processing helix chain '1A' and resid 142 through 183 Proline residue: 1A 148 - end of helix removed outlier: 4.105A pdb=" N SER1A 153 " --> pdb=" O ALA1A 149 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA1A 158 " --> pdb=" O GLU1A 154 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE1A 159 " --> pdb=" O ILE1A 155 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N TYR1A 164 " --> pdb=" O LYS1A 160 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LEU1A 165 " --> pdb=" O ILE1A 161 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU1A 167 " --> pdb=" O PHE1A 163 " (cutoff:3.500A) Proline residue: 1A 168 - end of helix Processing helix chain '1A' and resid 193 through 204 removed outlier: 4.110A pdb=" N ILE1A 197 " --> pdb=" O ILE1A 193 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU1A 199 " --> pdb=" O THR1A 195 " (cutoff:3.500A) Processing helix chain '1A' and resid 206 through 220 removed outlier: 4.032A pdb=" N GLN1A 218 " --> pdb=" O GLY1A 214 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N TYR1A 219 " --> pdb=" O LEU1A 215 " (cutoff:3.500A) Processing helix chain '1B' and resid 3 through 24 removed outlier: 3.619A pdb=" N ILE1B 8 " --> pdb=" O ASP1B 4 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA1B 9 " --> pdb=" O ILE1B 5 " (cutoff:3.500A) Proline residue: 1B 18 - end of helix Processing helix chain '1B' and resid 26 through 42 removed outlier: 3.617A pdb=" N ILE1B 32 " --> pdb=" O VAL1B 28 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE1B 34 " --> pdb=" O PHE1B 30 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL1B 35 " --> pdb=" O SER1B 31 " (cutoff:3.500A) Processing helix chain '1B' and resid 48 through 77 removed outlier: 3.629A pdb=" N MET1B 61 " --> pdb=" O LEU1B 57 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL1B 63 " --> pdb=" O LEU1B 59 " (cutoff:3.500A) Proline residue: 1B 66 - end of helix removed outlier: 3.740A pdb=" N TYR1B 74 " --> pdb=" O ASP1B 70 " (cutoff:3.500A) Processing helix chain '1B' and resid 85 through 107 removed outlier: 3.555A pdb=" N LYS1B 90 " --> pdb=" O SER1B 86 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU1B 94 " --> pdb=" O LYS1B 90 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLY1B 95 " --> pdb=" O HIS1B 91 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU1B 96 " --> pdb=" O VAL1B 92 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N GLY1B 98 " --> pdb=" O GLU1B 94 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N TYR1B 99 " --> pdb=" O GLY1B 95 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N TYR1B 102 " --> pdb=" O GLY1B 98 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N TYR1B 106 " --> pdb=" O TYR1B 102 " (cutoff:3.500A) Processing helix chain '1B' and resid 108 through 119 removed outlier: 3.749A pdb=" N GLN1B 113 " --> pdb=" O ARG1B 109 " (cutoff:3.500A) Processing helix chain '1B' and resid 142 through 183 Proline residue: 1B 148 - end of helix removed outlier: 3.516A pdb=" N LYS1B 156 " --> pdb=" O LEU1B 152 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU1B 167 " --> pdb=" O PHE1B 163 " (cutoff:3.500A) Proline residue: 1B 168 - end of helix removed outlier: 3.698A pdb=" N VAL1B 172 " --> pdb=" O PRO1B 168 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER1B 177 " --> pdb=" O ASP1B 173 " (cutoff:3.500A) Processing helix chain '1B' and resid 190 through 205 Proline residue: 1B 196 - end of helix Processing helix chain '1B' and resid 206 through 218 removed outlier: 3.607A pdb=" N ILE1B 216 " --> pdb=" O SER1B 212 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN1B 218 " --> pdb=" O GLY1B 214 " (cutoff:3.500A) Processing helix chain '1C' and resid 3 through 24 removed outlier: 3.663A pdb=" N SER1C 14 " --> pdb=" O LEU1C 10 " (cutoff:3.500A) Proline residue: 1C 18 - end of helix removed outlier: 3.736A pdb=" N ALA1C 22 " --> pdb=" O PRO1C 18 " (cutoff:3.500A) Processing helix chain '1C' and resid 26 through 42 removed outlier: 3.604A pdb=" N PHE1C 30 " --> pdb=" O CYS1C 26 " (cutoff:3.500A) Processing helix chain '1C' and resid 48 through 73 removed outlier: 3.523A pdb=" N GLY1C 54 " --> pdb=" O MET1C 50 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU1C 57 " --> pdb=" O ASN1C 53 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N PHE1C 62 " --> pdb=" O LEU1C 58 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N VAL1C 63 " --> pdb=" O LEU1C 59 " (cutoff:3.500A) Proline residue: 1C 66 - end of helix removed outlier: 3.631A pdb=" N ALA1C 71 " --> pdb=" O ILE1C 67 " (cutoff:3.500A) Processing helix chain '1C' and resid 84 through 104 removed outlier: 3.543A pdb=" N LEU1C 96 " --> pdb=" O VAL1C 92 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N GLY1C 98 " --> pdb=" O GLU1C 94 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N TYR1C 99 " --> pdb=" O GLY1C 95 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N TYR1C 102 " --> pdb=" O GLY1C 98 " (cutoff:3.500A) Processing helix chain '1C' and resid 105 through 107 No H-bonds generated for 'chain '1C' and resid 105 through 107' Processing helix chain '1C' and resid 108 through 117 Processing helix chain '1C' and resid 142 through 184 Proline residue: 1C 148 - end of helix removed outlier: 4.113A pdb=" N TYR1C 164 " --> pdb=" O LYS1C 160 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU1C 167 " --> pdb=" O PHE1C 163 " (cutoff:3.500A) Proline residue: 1C 168 - end of helix removed outlier: 3.637A pdb=" N VAL1C 171 " --> pdb=" O LEU1C 167 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N VAL1C 172 " --> pdb=" O PRO1C 168 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA1C 182 " --> pdb=" O SER1C 178 " (cutoff:3.500A) Processing helix chain '1C' and resid 190 through 206 removed outlier: 3.525A pdb=" N THR1C 195 " --> pdb=" O VAL1C 191 " (cutoff:3.500A) Proline residue: 1C 196 - end of helix removed outlier: 3.539A pdb=" N LEU1C 199 " --> pdb=" O THR1C 195 " (cutoff:3.500A) Processing helix chain '1C' and resid 206 through 221 removed outlier: 3.694A pdb=" N ILE1C 216 " --> pdb=" O SER1C 212 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N TYR1C 219 " --> pdb=" O LEU1C 215 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASP1C 221 " --> pdb=" O LEU1C 217 " (cutoff:3.500A) Processing helix chain '1D' and resid 4 through 22 removed outlier: 3.536A pdb=" N PHE1D 13 " --> pdb=" O ALA1D 9 " (cutoff:3.500A) Proline residue: 1D 18 - end of helix Processing helix chain '1D' and resid 26 through 42 removed outlier: 3.727A pdb=" N ILE1D 32 " --> pdb=" O VAL1D 28 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL1D 33 " --> pdb=" O LYS1D 29 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE1D 34 " --> pdb=" O PHE1D 30 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL1D 35 " --> pdb=" O SER1D 31 " (cutoff:3.500A) Processing helix chain '1D' and resid 48 through 63 removed outlier: 3.653A pdb=" N LEU1D 52 " --> pdb=" O SER1D 48 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU1D 57 " --> pdb=" O ASN1D 53 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE1D 62 " --> pdb=" O LEU1D 58 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL1D 63 " --> pdb=" O LEU1D 59 " (cutoff:3.500A) Processing helix chain '1D' and resid 64 through 74 removed outlier: 3.647A pdb=" N ASP1D 70 " --> pdb=" O PRO1D 66 " (cutoff:3.500A) Processing helix chain '1D' and resid 86 through 104 removed outlier: 3.746A pdb=" N GLY1D 95 " --> pdb=" O HIS1D 91 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N GLY1D 98 " --> pdb=" O GLU1D 94 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N TYR1D 99 " --> pdb=" O GLY1D 95 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N TYR1D 102 " --> pdb=" O GLY1D 98 " (cutoff:3.500A) Processing helix chain '1D' and resid 108 through 113 Processing helix chain '1D' and resid 142 through 183 Proline residue: 1D 148 - end of helix removed outlier: 3.589A pdb=" N LYS1D 160 " --> pdb=" O LYS1D 156 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE1D 161 " --> pdb=" O SER1D 157 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU1D 167 " --> pdb=" O PHE1D 163 " (cutoff:3.500A) Proline residue: 1D 168 - end of helix removed outlier: 4.361A pdb=" N VAL1D 172 " --> pdb=" O PRO1D 168 " (cutoff:3.500A) Processing helix chain '1D' and resid 190 through 206 removed outlier: 3.877A pdb=" N THR1D 195 " --> pdb=" O VAL1D 191 " (cutoff:3.500A) Proline residue: 1D 196 - end of helix removed outlier: 3.537A pdb=" N LEU1D 205 " --> pdb=" O LEU1D 201 " (cutoff:3.500A) Processing helix chain '1D' and resid 206 through 218 removed outlier: 3.832A pdb=" N ILE1D 216 " --> pdb=" O SER1D 212 " (cutoff:3.500A) Processing helix chain '1E' and resid 3 through 24 removed outlier: 3.603A pdb=" N LEU1E 7 " --> pdb=" O ASN1E 3 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ILE1E 8 " --> pdb=" O ASP1E 4 " (cutoff:3.500A) Proline residue: 1E 18 - end of helix Processing helix chain '1E' and resid 26 through 42 removed outlier: 3.579A pdb=" N ILE1E 32 " --> pdb=" O VAL1E 28 " (cutoff:3.500A) Processing helix chain '1E' and resid 48 through 75 removed outlier: 3.846A pdb=" N GLY1E 54 " --> pdb=" O MET1E 50 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU1E 57 " --> pdb=" O ASN1E 53 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N PHE1E 62 " --> pdb=" O LEU1E 58 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N VAL1E 63 " --> pdb=" O LEU1E 59 " (cutoff:3.500A) Proline residue: 1E 66 - end of helix removed outlier: 3.546A pdb=" N ALA1E 71 " --> pdb=" O ILE1E 67 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL1E 73 " --> pdb=" O HIS1E 69 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TYR1E 74 " --> pdb=" O ASP1E 70 " (cutoff:3.500A) Processing helix chain '1E' and resid 84 through 107 removed outlier: 3.681A pdb=" N GLY1E 95 " --> pdb=" O HIS1E 91 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU1E 96 " --> pdb=" O VAL1E 92 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N GLY1E 98 " --> pdb=" O GLU1E 94 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N TYR1E 99 " --> pdb=" O GLY1E 95 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N TYR1E 102 " --> pdb=" O GLY1E 98 " (cutoff:3.500A) Processing helix chain '1E' and resid 108 through 124 removed outlier: 3.765A pdb=" N ARG1E 122 " --> pdb=" O ALA1E 118 " (cutoff:3.500A) Processing helix chain '1E' and resid 142 through 184 Proline residue: 1E 148 - end of helix removed outlier: 3.532A pdb=" N TYR1E 164 " --> pdb=" O LYS1E 160 " (cutoff:3.500A) Proline residue: 1E 168 - end of helix removed outlier: 4.274A pdb=" N VAL1E 171 " --> pdb=" O LEU1E 167 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N VAL1E 172 " --> pdb=" O PRO1E 168 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU1E 181 " --> pdb=" O SER1E 177 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU1E 183 " --> pdb=" O VAL1E 179 " (cutoff:3.500A) Processing helix chain '1E' and resid 190 through 205 Proline residue: 1E 196 - end of helix Processing helix chain '1E' and resid 207 through 218 removed outlier: 3.821A pdb=" N LEU1E 211 " --> pdb=" O GLY1E 207 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLN1E 218 " --> pdb=" O GLY1E 214 " (cutoff:3.500A) Processing helix chain '1F' and resid 3 through 30 removed outlier: 3.706A pdb=" N HIS1F 10 " --> pdb=" O TYR1F 6 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LEU1F 12 " --> pdb=" O GLU1F 8 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU1F 18 " --> pdb=" O ALA1F 14 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ARG1F 22 " --> pdb=" O LEU1F 18 " (cutoff:3.500A) Proline residue: 1F 25 - end of helix removed outlier: 3.793A pdb=" N PHE1F 29 " --> pdb=" O PRO1F 25 " (cutoff:3.500A) Processing helix chain '1F' and resid 40 through 55 removed outlier: 3.949A pdb=" N ASN1F 44 " --> pdb=" O GLY1F 40 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ALA1F 45 " --> pdb=" O ALA1F 41 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ILE1F 48 " --> pdb=" O ASN1F 44 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TRP1F 55 " --> pdb=" O ALA1F 51 " (cutoff:3.500A) Processing helix chain '1F' and resid 63 through 68 removed outlier: 3.539A pdb=" N LEU1F 66 " --> pdb=" O PRO1F 63 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N SER1F 67 " --> pdb=" O PRO1F 64 " (cutoff:3.500A) Processing helix chain '1F' and resid 69 through 107 removed outlier: 3.694A pdb=" N LEU1F 73 " --> pdb=" O ALA1F 69 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN1F 76 " --> pdb=" O PRO1F 72 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA1F 79 " --> pdb=" O LEU1F 75 " (cutoff:3.500A) Proline residue: 1F 91 - end of helix removed outlier: 3.570A pdb=" N MET1F 95 " --> pdb=" O PRO1F 91 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE1F 102 " --> pdb=" O LEU1F 98 " (cutoff:3.500A) Processing helix chain '1F' and resid 123 through 140 removed outlier: 3.628A pdb=" N ASN1F 130 " --> pdb=" O ALA1F 126 " (cutoff:3.500A) Processing helix chain '1F' and resid 141 through 157 removed outlier: 4.008A pdb=" N THR1F 145 " --> pdb=" O GLY1F 141 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU1F 150 " --> pdb=" O MET1F 146 " (cutoff:3.500A) Processing helix chain '1F' and resid 158 through 162 Processing helix chain '1F' and resid 166 through 171 removed outlier: 3.522A pdb=" N LEU1F 170 " --> pdb=" O SER1F 166 " (cutoff:3.500A) Processing helix chain '1F' and resid 172 through 206 Proline residue: 1F 187 - end of helix removed outlier: 4.493A pdb=" N VAL1F 191 " --> pdb=" O PRO1F 187 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU1F 192 " --> pdb=" O VAL1F 188 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ARG1F 204 " --> pdb=" O GLY1F 200 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N PHE1F 205 " --> pdb=" O LEU1F 201 " (cutoff:3.500A) Processing helix chain '1F' and resid 210 through 240 removed outlier: 4.020A pdb=" N ILE1F 214 " --> pdb=" O ASN1F 210 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER1F 215 " --> pdb=" O ALA1F 211 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL1F 218 " --> pdb=" O ILE1F 214 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N SER1F 220 " --> pdb=" O LEU1F 216 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N GLY1F 221 " --> pdb=" O THR1F 217 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N VAL1F 224 " --> pdb=" O SER1F 220 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N TYR1F 230 " --> pdb=" O ILE1F 226 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N SER1F 232 " --> pdb=" O LEU1F 228 " (cutoff:3.500A) Proline residue: 1F 233 - end of helix Proline residue: 1F 236 - end of helix removed outlier: 3.565A pdb=" N VAL1F 239 " --> pdb=" O LEU1F 235 " (cutoff:3.500A) Processing helix chain '1F' and resid 245 through 247 No H-bonds generated for 'chain '1F' and resid 245 through 247' Processing helix chain '1F' and resid 248 through 252 Processing helix chain '1G' and resid 3 through 36 removed outlier: 3.648A pdb=" N ALA1G 11 " --> pdb=" O ALA1G 7 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU1G 12 " --> pdb=" O GLY1G 8 " (cutoff:3.500A) Proline residue: 1G 22 - end of helix Processing helix chain '1G' and resid 48 through 84 removed outlier: 3.943A pdb=" N CYS1G 59 " --> pdb=" O GLY1G 55 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU1G 60 " --> pdb=" O VAL1G 56 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N GLY1G 65 " --> pdb=" O PHE1G 61 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N TRP1G 66 " --> pdb=" O LEU1G 62 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL1G 70 " --> pdb=" O TRP1G 66 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER1G 73 " --> pdb=" O GLU1G 69 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLN1G 77 " --> pdb=" O SER1G 73 " (cutoff:3.500A) Processing helix chain '1H' and resid 3 through 40 removed outlier: 3.937A pdb=" N LEU1H 12 " --> pdb=" O GLY1H 8 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU1H 16 " --> pdb=" O LEU1H 12 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N TRP1H 21 " --> pdb=" O ILE1H 17 " (cutoff:3.500A) Proline residue: 1H 22 - end of helix removed outlier: 3.726A pdb=" N LEU1H 32 " --> pdb=" O ILE1H 28 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N THR1H 38 " --> pdb=" O GLY1H 34 " (cutoff:3.500A) Processing helix chain '1H' and resid 46 through 84 removed outlier: 3.550A pdb=" N GLY1H 50 " --> pdb=" O THR1H 46 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE1H 51 " --> pdb=" O LEU1H 47 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU1H 53 " --> pdb=" O PHE1H 49 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU1H 54 " --> pdb=" O GLY1H 50 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY1H 55 " --> pdb=" O ILE1H 51 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N GLY1H 65 " --> pdb=" O PHE1H 61 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N TRP1H 66 " --> pdb=" O LEU1H 62 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLY1H 68 " --> pdb=" O SER1H 64 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU1H 69 " --> pdb=" O GLY1H 65 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL1H 70 " --> pdb=" O TRP1H 66 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU1H 71 " --> pdb=" O TYR1H 67 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG1H 76 " --> pdb=" O LEU1H 72 " (cutoff:3.500A) Processing helix chain '1I' and resid 3 through 40 removed outlier: 3.582A pdb=" N ALA1I 7 " --> pdb=" O ASP1I 3 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU1I 12 " --> pdb=" O GLY1I 8 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N TRP1I 21 " --> pdb=" O ILE1I 17 " (cutoff:3.500A) Proline residue: 1I 22 - end of helix Processing helix chain '1I' and resid 45 through 84 removed outlier: 3.512A pdb=" N PHE1I 49 " --> pdb=" O GLN1I 45 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU1I 54 " --> pdb=" O GLY1I 50 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N GLY1I 65 " --> pdb=" O PHE1I 61 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N TRP1I 66 " --> pdb=" O LEU1I 62 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY1I 68 " --> pdb=" O SER1I 64 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU1I 69 " --> pdb=" O GLY1I 65 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE1I 79 " --> pdb=" O GLY1I 75 " (cutoff:3.500A) Processing helix chain '1J' and resid 4 through 40 removed outlier: 3.507A pdb=" N ALA1J 11 " --> pdb=" O ALA1J 7 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU1J 12 " --> pdb=" O GLY1J 8 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N TRP1J 21 " --> pdb=" O ILE1J 17 " (cutoff:3.500A) Proline residue: 1J 22 - end of helix removed outlier: 3.749A pdb=" N THR1J 40 " --> pdb=" O PHE1J 36 " (cutoff:3.500A) Processing helix chain '1J' and resid 45 through 84 removed outlier: 4.262A pdb=" N PHE1J 49 " --> pdb=" O GLN1J 45 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU1J 54 " --> pdb=" O GLY1J 50 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY1J 55 " --> pdb=" O ILE1J 51 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU1J 60 " --> pdb=" O VAL1J 56 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N GLY1J 65 " --> pdb=" O PHE1J 61 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N TRP1J 66 " --> pdb=" O LEU1J 62 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLY1J 68 " --> pdb=" O SER1J 64 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLU1J 69 " --> pdb=" O GLY1J 65 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ARG1J 76 " --> pdb=" O LEU1J 72 " (cutoff:3.500A) Processing helix chain '1K' and resid 30 through 34 Processing helix chain '1K' and resid 38 through 47 Processing helix chain '1K' and resid 64 through 101 removed outlier: 3.907A pdb=" N GLN1K 71 " --> pdb=" O LEU1K 67 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLU1K 72 " --> pdb=" O ALA1K 68 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N MET1K 73 " --> pdb=" O ILE1K 69 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N TYR1K 77 " --> pdb=" O MET1K 73 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN1K 78 " --> pdb=" O ILE1K 74 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER1K 82 " --> pdb=" O ASN1K 78 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N THR1K 86 " --> pdb=" O SER1K 82 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR1K 88 " --> pdb=" O VAL1K 84 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ARG1K 89 " --> pdb=" O SER1K 85 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N SER1K 101 " --> pdb=" O THR1K 97 " (cutoff:3.500A) Processing helix chain '1L' and resid 30 through 57 removed outlier: 3.773A pdb=" N GLN1L 35 " --> pdb=" O ASP1L 31 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA1L 45 " --> pdb=" O ALA1L 41 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASP1L 57 " --> pdb=" O ASN1L 53 " (cutoff:3.500A) Processing helix chain '1L' and resid 57 through 62 Processing helix chain '1L' and resid 63 through 101 removed outlier: 3.571A pdb=" N GLU1L 72 " --> pdb=" O ALA1L 68 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL1L 95 " --> pdb=" O GLY1L 91 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLU1L 96 " --> pdb=" O VAL1L 92 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N THR1L 97 " --> pdb=" O GLY1L 93 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU1L 98 " --> pdb=" O ALA1L 94 " (cutoff:3.500A) Processing helix chain '1M' and resid 30 through 57 removed outlier: 3.875A pdb=" N GLN1M 35 " --> pdb=" O ASP1M 31 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASP1M 47 " --> pdb=" O ALA1M 43 " (cutoff:3.500A) Processing helix chain '1M' and resid 57 through 62 removed outlier: 3.524A pdb=" N VAL1M 61 " --> pdb=" O ASP1M 57 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR1M 62 " --> pdb=" O PRO1M 58 " (cutoff:3.500A) No H-bonds generated for 'chain '1M' and resid 57 through 62' Processing helix chain '1M' and resid 63 through 100 removed outlier: 3.533A pdb=" N ILE1M 69 " --> pdb=" O LYS1M 65 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU1M 72 " --> pdb=" O ALA1M 68 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL1M 95 " --> pdb=" O GLY1M 91 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU1M 98 " --> pdb=" O ALA1M 94 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU1M 99 " --> pdb=" O VAL1M 95 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG1M 100 " --> pdb=" O GLU1M 96 " (cutoff:3.500A) Processing helix chain '1N' and resid 29 through 53 removed outlier: 4.087A pdb=" N LEU1N 33 " --> pdb=" O LEU1N 29 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N LEU1N 34 " --> pdb=" O ASP1N 30 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA1N 43 " --> pdb=" O GLY1N 39 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASP1N 47 " --> pdb=" O ALA1N 43 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASN1N 53 " --> pdb=" O GLN1N 49 " (cutoff:3.500A) Processing helix chain '1N' and resid 54 through 56 No H-bonds generated for 'chain '1N' and resid 54 through 56' Processing helix chain '1N' and resid 57 through 62 removed outlier: 3.854A pdb=" N THR1N 62 " --> pdb=" O PRO1N 58 " (cutoff:3.500A) Processing helix chain '1N' and resid 63 through 101 removed outlier: 3.815A pdb=" N ILE1N 69 " --> pdb=" O LYS1N 65 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU1N 72 " --> pdb=" O ALA1N 68 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER1N 75 " --> pdb=" O GLN1N 71 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL1N 95 " --> pdb=" O GLY1N 91 " (cutoff:3.500A) Processing helix chain '1O' and resid 30 through 57 removed outlier: 3.515A pdb=" N GLN1O 35 " --> pdb=" O ASP1O 31 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG1O 54 " --> pdb=" O THR1O 50 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE1O 55 " --> pdb=" O ILE1O 51 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU1O 56 " --> pdb=" O THR1O 52 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP1O 57 " --> pdb=" O ASN1O 53 " (cutoff:3.500A) Processing helix chain '1O' and resid 57 through 62 removed outlier: 3.555A pdb=" N THR1O 62 " --> pdb=" O PRO1O 58 " (cutoff:3.500A) Processing helix chain '1O' and resid 63 through 100 removed outlier: 4.098A pdb=" N ILE1O 69 " --> pdb=" O LYS1O 65 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER1O 70 " --> pdb=" O GLU1O 66 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLU1O 72 " --> pdb=" O ALA1O 68 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASN1O 78 " --> pdb=" O ILE1O 74 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARG1O 89 " --> pdb=" O SER1O 85 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU1O 98 " --> pdb=" O ALA1O 94 " (cutoff:3.500A) Processing helix chain '1P' and resid 31 through 57 removed outlier: 3.769A pdb=" N GLN1P 35 " --> pdb=" O ASP1P 31 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE1P 42 " --> pdb=" O SER1P 38 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE1P 55 " --> pdb=" O ILE1P 51 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASP1P 57 " --> pdb=" O ASN1P 53 " (cutoff:3.500A) Processing helix chain '1P' and resid 63 through 100 removed outlier: 3.667A pdb=" N ASP1P 76 " --> pdb=" O GLU1P 72 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N TYR1P 77 " --> pdb=" O MET1P 73 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASN1P 78 " --> pdb=" O ILE1P 74 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N THR1P 97 " --> pdb=" O GLY1P 93 " (cutoff:3.500A) Processing helix chain '2A' and resid 23 through 36 removed outlier: 3.714A pdb=" N ALA2A 36 " --> pdb=" O ASP2A 32 " (cutoff:3.500A) Processing helix chain '2A' and resid 40 through 79 removed outlier: 3.919A pdb=" N SER2A 49 " --> pdb=" O ALA2A 45 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LYS2A 50 " --> pdb=" O ALA2A 46 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR2A 64 " --> pdb=" O ALA2A 60 " (cutoff:3.500A) Processing helix chain '2B' and resid 21 through 35 removed outlier: 3.753A pdb=" N GLN2B 26 " --> pdb=" O ASN2B 22 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU2B 31 " --> pdb=" O VAL2B 27 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP2B 32 " --> pdb=" O THR2B 28 " (cutoff:3.500A) Processing helix chain '2B' and resid 40 through 80 removed outlier: 3.628A pdb=" N SER2B 49 " --> pdb=" O ALA2B 45 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LYS2B 50 " --> pdb=" O ALA2B 46 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU2B 56 " --> pdb=" O SER2B 52 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TYR2B 57 " --> pdb=" O GLU2B 53 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N THR2B 64 " --> pdb=" O ALA2B 60 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASP2B 72 " --> pdb=" O PHE2B 68 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE2B 79 " --> pdb=" O ILE2B 75 " (cutoff:3.500A) Processing helix chain '2C' and resid 23 through 37 removed outlier: 3.853A pdb=" N ALA2C 36 " --> pdb=" O ASP2C 32 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS2C 37 " --> pdb=" O LYS2C 33 " (cutoff:3.500A) Processing helix chain '2C' and resid 40 through 80 removed outlier: 3.721A pdb=" N ALA2C 46 " --> pdb=" O ALA2C 42 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N SER2C 49 " --> pdb=" O ALA2C 45 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER2C 62 " --> pdb=" O ARG2C 58 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE2C 76 " --> pdb=" O ASP2C 72 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN2C 78 " --> pdb=" O ALA2C 74 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N PHE2C 79 " --> pdb=" O ILE2C 75 " (cutoff:3.500A) Processing helix chain '2D' and resid 22 through 37 removed outlier: 3.588A pdb=" N LYS2D 33 " --> pdb=" O GLU2D 29 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA2D 36 " --> pdb=" O ASP2D 32 " (cutoff:3.500A) Processing helix chain '2D' and resid 40 through 78 removed outlier: 4.009A pdb=" N ALA2D 46 " --> pdb=" O ALA2D 42 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU2D 56 " --> pdb=" O SER2D 52 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N SER2D 62 " --> pdb=" O ARG2D 58 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR2D 64 " --> pdb=" O ALA2D 60 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA2D 73 " --> pdb=" O LYS2D 69 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ILE2D 76 " --> pdb=" O ASP2D 72 " (cutoff:3.500A) Processing helix chain '2E' and resid 22 through 37 removed outlier: 3.502A pdb=" N THR2E 28 " --> pdb=" O GLN2E 24 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA2E 36 " --> pdb=" O ASP2E 32 " (cutoff:3.500A) Processing helix chain '2E' and resid 40 through 79 removed outlier: 3.539A pdb=" N ALA2E 45 " --> pdb=" O PRO2E 41 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA2E 46 " --> pdb=" O ALA2E 42 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N TYR2E 57 " --> pdb=" O GLU2E 53 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ALA2E 73 " --> pdb=" O LYS2E 69 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE2E 76 " --> pdb=" O ASP2E 72 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N PHE2E 79 " --> pdb=" O ILE2E 75 " (cutoff:3.500A) Processing helix chain '2F' and resid 11 through 18 removed outlier: 3.861A pdb=" N PHE2F 16 " --> pdb=" O VAL2F 12 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASP2F 17 " --> pdb=" O SER2F 13 " (cutoff:3.500A) Processing helix chain '2F' and resid 22 through 35 removed outlier: 4.485A pdb=" N THR2F 28 " --> pdb=" O GLN2F 24 " (cutoff:3.500A) Processing helix chain '2F' and resid 40 through 79 removed outlier: 3.589A pdb=" N ALA2F 46 " --> pdb=" O ALA2F 42 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER2F 49 " --> pdb=" O ALA2F 45 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR2F 64 " --> pdb=" O ALA2F 60 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL2F 65 " --> pdb=" O GLN2F 61 " (cutoff:3.500A) Processing helix chain '2G' and resid 8 through 20 removed outlier: 3.918A pdb=" N PHE2G 16 " --> pdb=" O VAL2G 12 " (cutoff:3.500A) Processing helix chain '2G' and resid 22 through 35 removed outlier: 3.703A pdb=" N THR2G 28 " --> pdb=" O GLN2G 24 " (cutoff:3.500A) Processing helix chain '2G' and resid 40 through 76 removed outlier: 3.575A pdb=" N LEU2G 44 " --> pdb=" O ASP2G 40 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ALA2G 46 " --> pdb=" O ALA2G 42 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER2G 49 " --> pdb=" O ALA2G 45 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER2G 62 " --> pdb=" O ARG2G 58 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR2G 64 " --> pdb=" O ALA2G 60 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL2G 65 " --> pdb=" O GLN2G 61 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASP2G 70 " --> pdb=" O LYS2G 66 " (cutoff:3.500A) Processing helix chain '2H' and resid 7 through 20 removed outlier: 3.533A pdb=" N ASP2H 11 " --> pdb=" O GLY2H 7 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N PHE2H 16 " --> pdb=" O VAL2H 12 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY2H 19 " --> pdb=" O LYS2H 15 " (cutoff:3.500A) Processing helix chain '2H' and resid 22 through 35 removed outlier: 3.842A pdb=" N THR2H 28 " --> pdb=" O GLN2H 24 " (cutoff:3.500A) Processing helix chain '2H' and resid 40 through 76 removed outlier: 3.511A pdb=" N ALA2H 46 " --> pdb=" O ALA2H 42 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N SER2H 49 " --> pdb=" O ALA2H 45 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS2H 50 " --> pdb=" O ALA2H 46 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N TYR2H 57 " --> pdb=" O GLU2H 53 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE2H 75 " --> pdb=" O ILE2H 71 " (cutoff:3.500A) Processing helix chain '2I' and resid 7 through 20 removed outlier: 3.855A pdb=" N ASP2I 11 " --> pdb=" O GLY2I 7 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N PHE2I 16 " --> pdb=" O VAL2I 12 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLY2I 19 " --> pdb=" O LYS2I 15 " (cutoff:3.500A) Processing helix chain '2I' and resid 22 through 37 removed outlier: 3.540A pdb=" N ASP2I 32 " --> pdb=" O THR2I 28 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA2I 36 " --> pdb=" O ASP2I 32 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LYS2I 37 " --> pdb=" O LYS2I 33 " (cutoff:3.500A) Processing helix chain '2I' and resid 40 through 77 removed outlier: 3.768A pdb=" N ALA2I 46 " --> pdb=" O ALA2I 42 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER2I 49 " --> pdb=" O ALA2I 45 " (cutoff:3.500A) Processing helix chain '2I' and resid 78 through 80 No H-bonds generated for 'chain '2I' and resid 78 through 80' Processing helix chain '2J' and resid 7 through 20 removed outlier: 3.659A pdb=" N ASP2J 11 " --> pdb=" O GLY2J 7 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N PHE2J 16 " --> pdb=" O VAL2J 12 " (cutoff:3.500A) Processing helix chain '2J' and resid 22 through 37 removed outlier: 4.086A pdb=" N THR2J 28 " --> pdb=" O GLN2J 24 " (cutoff:3.500A) Processing helix chain '2J' and resid 40 through 78 removed outlier: 3.965A pdb=" N ALA2J 46 " --> pdb=" O ALA2J 42 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N SER2J 49 " --> pdb=" O ALA2J 45 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL2J 65 " --> pdb=" O GLN2J 61 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE2J 75 " --> pdb=" O ILE2J 71 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLN2J 77 " --> pdb=" O ALA2J 73 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASN2J 78 " --> pdb=" O ALA2J 74 " (cutoff:3.500A) Processing helix chain '2K' and resid 7 through 18 removed outlier: 3.859A pdb=" N ASP2K 11 " --> pdb=" O GLY2K 7 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N PHE2K 16 " --> pdb=" O VAL2K 12 " (cutoff:3.500A) Processing helix chain '2K' and resid 20 through 37 removed outlier: 3.541A pdb=" N GLN2K 24 " --> pdb=" O VAL2K 20 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N THR2K 25 " --> pdb=" O ASP2K 21 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLN2K 26 " --> pdb=" O ASN2K 22 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N THR2K 28 " --> pdb=" O GLN2K 24 " (cutoff:3.500A) Processing helix chain '2K' and resid 40 through 76 removed outlier: 3.617A pdb=" N GLN2K 48 " --> pdb=" O LEU2K 44 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N SER2K 49 " --> pdb=" O ALA2K 45 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR2K 64 " --> pdb=" O ALA2K 60 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LYS2K 69 " --> pdb=" O VAL2K 65 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA2K 74 " --> pdb=" O ASP2K 70 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE2K 75 " --> pdb=" O ILE2K 71 " (cutoff:3.500A) Processing helix chain '2L' and resid 7 through 20 removed outlier: 3.880A pdb=" N PHE2L 16 " --> pdb=" O VAL2L 12 " (cutoff:3.500A) Processing helix chain '2L' and resid 22 through 32 removed outlier: 3.622A pdb=" N THR2L 28 " --> pdb=" O GLN2L 24 " (cutoff:3.500A) Processing helix chain '2L' and resid 45 through 76 removed outlier: 3.595A pdb=" N ASN2L 63 " --> pdb=" O ASN2L 59 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR2L 64 " --> pdb=" O ALA2L 60 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL2L 65 " --> pdb=" O GLN2L 61 " (cutoff:3.500A) Processing helix chain '2L' and resid 77 through 79 No H-bonds generated for 'chain '2L' and resid 77 through 79' Processing helix chain '2M' and resid 8 through 18 removed outlier: 4.017A pdb=" N PHE2M 16 " --> pdb=" O VAL2M 12 " (cutoff:3.500A) Processing helix chain '2M' and resid 22 through 31 removed outlier: 3.889A pdb=" N THR2M 28 " --> pdb=" O GLN2M 24 " (cutoff:3.500A) Processing helix chain '2M' and resid 47 through 77 removed outlier: 3.506A pdb=" N TYR2M 57 " --> pdb=" O GLU2M 53 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL2M 65 " --> pdb=" O GLN2M 61 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA2M 74 " --> pdb=" O ASP2M 70 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE2M 75 " --> pdb=" O ILE2M 71 " (cutoff:3.500A) Processing helix chain '2M' and resid 78 through 80 No H-bonds generated for 'chain '2M' and resid 78 through 80' Processing helix chain '2N' and resid 7 through 20 removed outlier: 3.503A pdb=" N SER2N 13 " --> pdb=" O LEU2N 9 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE2N 16 " --> pdb=" O VAL2N 12 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY2N 19 " --> pdb=" O LYS2N 15 " (cutoff:3.500A) Processing helix chain '2N' and resid 20 through 27 removed outlier: 3.521A pdb=" N GLN2N 24 " --> pdb=" O VAL2N 20 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N THR2N 25 " --> pdb=" O ASP2N 21 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN2N 26 " --> pdb=" O ASN2N 22 " (cutoff:3.500A) Processing helix chain '2N' and resid 50 through 77 removed outlier: 3.731A pdb=" N VAL2N 65 " --> pdb=" O GLN2N 61 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASP2N 72 " --> pdb=" O PHE2N 68 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ILE2N 75 " --> pdb=" O ILE2N 71 " (cutoff:3.500A) Processing helix chain '2N' and resid 78 through 80 No H-bonds generated for 'chain '2N' and resid 78 through 80' Processing helix chain '2O' and resid 7 through 20 removed outlier: 3.600A pdb=" N SER2O 13 " --> pdb=" O LEU2O 9 " (cutoff:3.500A) Processing helix chain '2O' and resid 21 through 23 No H-bonds generated for 'chain '2O' and resid 21 through 23' Processing helix chain '2O' and resid 53 through 78 removed outlier: 3.645A pdb=" N ALA2O 74 " --> pdb=" O ASP2O 70 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE2O 75 " --> pdb=" O ILE2O 71 " (cutoff:3.500A) Processing helix chain '2P' and resid 7 through 20 removed outlier: 4.053A pdb=" N LYS2P 15 " --> pdb=" O ASP2P 11 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE2P 16 " --> pdb=" O VAL2P 12 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP2P 17 " --> pdb=" O SER2P 13 " (cutoff:3.500A) Processing helix chain '2P' and resid 55 through 79 removed outlier: 3.505A pdb=" N LYS2P 69 " --> pdb=" O VAL2P 65 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA2P 74 " --> pdb=" O ASP2P 70 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE2P 75 " --> pdb=" O ILE2P 71 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLN2P 77 " --> pdb=" O ALA2P 73 " (cutoff:3.500A) Processing helix chain '2Q' and resid 7 through 16 removed outlier: 3.564A pdb=" N PHE2Q 16 " --> pdb=" O VAL2Q 12 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '1F' and resid 164 through 165 1744 hydrogen bonds defined for protein. 5214 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: 18.16 Time building geometry restraints manager: 41.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.02: 24072 1.02 - 1.22: 20 1.22 - 1.42: 9864 1.42 - 1.61: 14052 1.61 - 1.81: 161 Bond restraints: 48169 Sorted by residual: bond pdb=" N GLY1A 2 " pdb=" CA GLY1A 2 " ideal model delta sigma weight residual 1.451 1.493 -0.042 1.60e-02 3.91e+03 6.84e+00 bond pdb=" N GLY1E 2 " pdb=" CA GLY1E 2 " ideal model delta sigma weight residual 1.451 1.492 -0.041 1.60e-02 3.91e+03 6.43e+00 bond pdb=" N GLY1C 2 " pdb=" CA GLY1C 2 " ideal model delta sigma weight residual 1.451 1.487 -0.036 1.60e-02 3.91e+03 5.02e+00 bond pdb=" N GLY1B 2 " pdb=" CA GLY1B 2 " ideal model delta sigma weight residual 1.451 1.487 -0.036 1.60e-02 3.91e+03 4.99e+00 bond pdb=" CB GLU2G 53 " pdb=" CG GLU2G 53 " ideal model delta sigma weight residual 1.520 1.464 0.056 3.00e-02 1.11e+03 3.45e+00 ... (remaining 48164 not shown) Histogram of bond angle deviations from ideal: 98.07 - 105.38: 396 105.38 - 112.68: 56922 112.68 - 119.98: 14513 119.98 - 127.29: 15238 127.29 - 134.59: 170 Bond angle restraints: 87239 Sorted by residual: angle pdb=" N THR1F 109 " pdb=" CA THR1F 109 " pdb=" C THR1F 109 " ideal model delta sigma weight residual 108.90 101.62 7.28 1.63e+00 3.76e-01 1.99e+01 angle pdb=" CA TYR1C 72 " pdb=" CB TYR1C 72 " pdb=" CG TYR1C 72 " ideal model delta sigma weight residual 113.90 120.56 -6.66 1.80e+00 3.09e-01 1.37e+01 angle pdb=" C GLY1F 107 " pdb=" N ALA1F 108 " pdb=" CA ALA1F 108 " ideal model delta sigma weight residual 122.37 116.16 6.21 1.72e+00 3.38e-01 1.31e+01 angle pdb=" N GLU1H 44 " pdb=" CA GLU1H 44 " pdb=" C GLU1H 44 " ideal model delta sigma weight residual 108.48 101.98 6.50 1.80e+00 3.09e-01 1.30e+01 angle pdb=" N GLN1H 43 " pdb=" CA GLN1H 43 " pdb=" C GLN1H 43 " ideal model delta sigma weight residual 108.75 114.86 -6.11 1.71e+00 3.42e-01 1.28e+01 ... (remaining 87234 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 20626 17.95 - 35.90: 1076 35.90 - 53.86: 374 53.86 - 71.81: 529 71.81 - 89.76: 51 Dihedral angle restraints: 22656 sinusoidal: 12218 harmonic: 10438 Sorted by residual: dihedral pdb=" CA ALA1F 108 " pdb=" C ALA1F 108 " pdb=" N THR1F 109 " pdb=" CA THR1F 109 " ideal model delta harmonic sigma weight residual 180.00 150.53 29.47 0 5.00e+00 4.00e-02 3.47e+01 dihedral pdb=" CA THR1F 122 " pdb=" C THR1F 122 " pdb=" N SER1F 123 " pdb=" CA SER1F 123 " ideal model delta harmonic sigma weight residual -180.00 -151.45 -28.55 0 5.00e+00 4.00e-02 3.26e+01 dihedral pdb=" CA ARG1F 106 " pdb=" C ARG1F 106 " pdb=" N GLY1F 107 " pdb=" CA GLY1F 107 " ideal model delta harmonic sigma weight residual 180.00 -151.46 -28.54 0 5.00e+00 4.00e-02 3.26e+01 ... (remaining 22653 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 2465 0.041 - 0.081: 1165 0.081 - 0.122: 233 0.122 - 0.162: 53 0.162 - 0.203: 8 Chirality restraints: 3924 Sorted by residual: chirality pdb=" CA PRO1F 56 " pdb=" N PRO1F 56 " pdb=" C PRO1F 56 " pdb=" CB PRO1F 56 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CA MET1A 187 " pdb=" N MET1A 187 " pdb=" C MET1A 187 " pdb=" CB MET1A 187 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.19 2.00e-01 2.50e+01 8.57e-01 chirality pdb=" CA ILE1A 46 " pdb=" N ILE1A 46 " pdb=" C ILE1A 46 " pdb=" CB ILE1A 46 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.18 2.00e-01 2.50e+01 8.44e-01 ... (remaining 3921 not shown) Planarity restraints: 6966 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN2K 61 " 0.061 2.00e-02 2.50e+03 7.56e-02 8.58e+01 pdb=" CD GLN2K 61 " -0.051 2.00e-02 2.50e+03 pdb=" OE1 GLN2K 61 " -0.000 2.00e-02 2.50e+03 pdb=" NE2 GLN2K 61 " -0.118 2.00e-02 2.50e+03 pdb="HE21 GLN2K 61 " -0.009 2.00e-02 2.50e+03 pdb="HE22 GLN2K 61 " 0.118 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR2I 57 " -0.008 2.00e-02 2.50e+03 4.91e-02 7.23e+01 pdb=" CG TYR2I 57 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TYR2I 57 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TYR2I 57 " -0.027 2.00e-02 2.50e+03 pdb=" CE1 TYR2I 57 " 0.064 2.00e-02 2.50e+03 pdb=" CE2 TYR2I 57 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR2I 57 " 0.064 2.00e-02 2.50e+03 pdb=" OH TYR2I 57 " -0.063 2.00e-02 2.50e+03 pdb=" HD1 TYR2I 57 " 0.022 2.00e-02 2.50e+03 pdb=" HD2 TYR2I 57 " -0.067 2.00e-02 2.50e+03 pdb=" HE1 TYR2I 57 " -0.066 2.00e-02 2.50e+03 pdb=" HE2 TYR2I 57 " 0.061 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR2H 57 " -0.003 2.00e-02 2.50e+03 3.73e-02 4.18e+01 pdb=" CG TYR2H 57 " 0.051 2.00e-02 2.50e+03 pdb=" CD1 TYR2H 57 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 TYR2H 57 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR2H 57 " -0.024 2.00e-02 2.50e+03 pdb=" CE2 TYR2H 57 " 0.048 2.00e-02 2.50e+03 pdb=" CZ TYR2H 57 " 0.027 2.00e-02 2.50e+03 pdb=" OH TYR2H 57 " -0.024 2.00e-02 2.50e+03 pdb=" HD1 TYR2H 57 " -0.065 2.00e-02 2.50e+03 pdb=" HD2 TYR2H 57 " 0.002 2.00e-02 2.50e+03 pdb=" HE1 TYR2H 57 " 0.051 2.00e-02 2.50e+03 pdb=" HE2 TYR2H 57 " -0.054 2.00e-02 2.50e+03 ... (remaining 6963 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.13: 1252 2.13 - 2.75: 87965 2.75 - 3.36: 131215 3.36 - 3.98: 160614 3.98 - 4.60: 264047 Nonbonded interactions: 645093 Sorted by model distance: nonbonded pdb=" O VAL2O 20 " pdb=" H GLN2O 24 " model vdw 1.508 1.850 nonbonded pdb=" OE1 GLN2E 77 " pdb="HH21 ARG2E 80 " model vdw 1.511 1.850 nonbonded pdb=" O ASP2B 21 " pdb=" HG1 THR2B 25 " model vdw 1.534 1.850 nonbonded pdb=" HG SER2I 13 " pdb=" OE1 GLN2I 61 " model vdw 1.545 1.850 nonbonded pdb=" O SER1B 107 " pdb="HH11 ARG1B 109 " model vdw 1.549 1.850 ... (remaining 645088 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 '1A' and (resid 3 through 75 or resid 85 through 114 or resid 116 or resi \ d 141 through 220)) selection = (chain '1B' and (resid 3 through 75 or resid 85 through 114 or resid 116 or resi \ d 141 through 220)) selection = (chain '1C' and (resid 3 through 75 or resid 85 through 114 or resid 116 or resi \ d 141 through 220)) selection = (chain '1D' and (resid 3 through 75 or resid 85 through 137 or resid 141 through \ 220)) selection = (chain '1E' and (resid 3 through 75 or resid 85 through 114 or resid 116 or resi \ d 141 through 220)) } ncs_group { reference = chain '1G' selection = (chain '1H' and (resid 2 through 36 or resid 47 through 84)) selection = (chain '1I' and (resid 2 through 36 or resid 47 through 84)) selection = (chain '1J' and (resid 2 through 36 or resid 47 through 84)) } ncs_group { reference = (chain '1K' and resid 29 through 100) selection = (chain '1L' and (resid 29 through 50 or resid 60 through 100)) selection = (chain '1M' and (resid 29 through 50 or resid 60 through 100)) selection = (chain '1N' and (resid 29 through 50 or resid 60 through 100)) selection = (chain '1O' and (resid 29 through 50 or resid 60 through 100)) selection = (chain '1P' and (resid 29 through 50 or resid 60 through 100)) } ncs_group { reference = (chain '2A' and (resid 22 through 79 or (resid 80 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 \ or name NH2 or name H or name HA or name HB2 or name HB3 or name HG2 or name HG3 \ or name HD2 or name HD3 or name HE or name HH11 or name HH12 or name HH21 or na \ me HH22)))) selection = (chain '2B' and resid 22 through 80) selection = (chain '2C' and (resid 22 through 79 or (resid 80 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 \ or name NH2 or name H or name HA or name HB2 or name HB3 or name HG2 or name HG3 \ or name HD2 or name HD3 or name HE or name HH11 or name HH12 or name HH21 or na \ me HH22)))) selection = (chain '2D' and (resid 22 through 79 or (resid 80 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 \ or name NH2 or name H or name HA or name HB2 or name HB3 or name HG2 or name HG3 \ or name HD2 or name HD3 or name HE or name HH11 or name HH12 or name HH21 or na \ me HH22)))) selection = (chain '2E' and (resid 22 through 79 or (resid 80 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 \ or name NH2 or name H or name HA or name HB2 or name HB3 or name HG2 or name HG3 \ or name HD2 or name HD3 or name HE or name HH11 or name HH12 or name HH21 or na \ me HH22)))) } ncs_group { reference = (chain '2F' and (resid 9 through 79 or (resid 80 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 o \ r name NH2 or name H or name HA or name HB2 or name HB3 or name HG2 or name HG3 \ or name HD2 or name HD3 or name HE or name HH11 or name HH12 or name HH21 or nam \ e HH22)))) selection = (chain '2G' and resid 9 through 80) selection = (chain '2H' and (resid 9 through 79 or (resid 80 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 o \ r name NH2 or name H or name HA or name HB2 or name HB3 or name HG2 or name HG3 \ or name HD2 or name HD3 or name HE or name HH11 or name HH12 or name HH21 or nam \ e HH22)))) selection = (chain '2I' and (resid 9 through 79 or (resid 80 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 o \ r name NH2 or name H or name HA or name HB2 or name HB3 or name HG2 or name HG3 \ or name HD2 or name HD3 or name HE or name HH11 or name HH12 or name HH21 or nam \ e HH22)))) selection = (chain '2J' and (resid 9 through 79 or (resid 80 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 o \ r name NH2 or name H or name HA or name HB2 or name HB3 or name HG2 or name HG3 \ or name HD2 or name HD3 or name HE or name HH11 or name HH12 or name HH21 or nam \ e HH22)))) selection = (chain '2K' and resid 9 through 80) } ncs_group { reference = (chain '2L' and (resid 4 through 28 or resid 49 through 80)) selection = (chain '2M' and (resid 4 through 28 or resid 49 through 80)) selection = (chain '2N' and (resid 4 through 79 or (resid 80 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 o \ r name NH2 or name H or name HA or name HB2 or name HB3 or name HG2 or name HG3 \ or name HD2 or name HD3 or name HE or name HH11 or name HH12 or name HH21 or nam \ e HH22)))) } ncs_group { reference = (chain '2O' and (resid 4 through 20 or resid 54 through 80)) selection = chain '2P' } 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: 4.020 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: 0.710 Extract box with map and model: 20.840 Check model and map are aligned: 0.720 Set scattering table: 0.400 Process input model: 144.500 Find NCS groups from input model: 2.240 Set up NCS constraints: 0.210 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 176.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 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 : 0.007 0.065 24080 Z= 0.449 Angle : 0.803 7.589 32694 Z= 0.476 Chirality : 0.047 0.203 3924 Planarity : 0.006 0.079 4080 Dihedral : 12.338 89.573 8630 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 0.08 % Allowed : 1.11 % Favored : 98.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.48 (0.13), residues: 2933 helix: -1.47 (0.09), residues: 2476 sheet: None (None), residues: 0 loop : -1.29 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.005 TRP1A 65 HIS 0.006 0.003 HIS1A 69 PHE 0.049 0.003 PHE1A 30 TYR 0.064 0.007 TYR2I 57 ARG 0.095 0.012 ARG1P 89 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5866 Ramachandran restraints generated. 2933 Oldfield, 0 Emsley, 2933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5866 Ramachandran restraints generated. 2933 Oldfield, 0 Emsley, 2933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 661 residues out of total 2611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 659 time to evaluate : 3.890 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: 1A 186 MET cc_start: 0.7005 (tpt) cc_final: 0.6625 (tpt) REVERT: 1B 108 ASP cc_start: 0.6880 (t70) cc_final: 0.6538 (t0) REVERT: 1B 186 MET cc_start: 0.6401 (mtm) cc_final: 0.6136 (mtm) REVERT: 1B 187 MET cc_start: 0.5934 (mtp) cc_final: 0.5629 (mmm) REVERT: 1B 188 MET cc_start: 0.6098 (tpt) cc_final: 0.5138 (tpt) REVERT: 1C 97 ASP cc_start: 0.6429 (t70) cc_final: 0.6079 (t0) REVERT: 1E 64 MET cc_start: 0.7569 (mmm) cc_final: 0.6720 (mmp) REVERT: 1F 209 MET cc_start: 0.7117 (ttm) cc_final: 0.6712 (ttm) REVERT: 1F 256 ARG cc_start: 0.7585 (mtt180) cc_final: 0.6673 (tpp80) REVERT: 1K 35 GLN cc_start: 0.7401 (pt0) cc_final: 0.7104 (pt0) REVERT: 1L 35 GLN cc_start: 0.7922 (mm110) cc_final: 0.7645 (tt0) REVERT: 1L 57 ASP cc_start: 0.8028 (t0) cc_final: 0.7755 (t0) REVERT: 2A 22 ASN cc_start: 0.7483 (m-40) cc_final: 0.7224 (p0) REVERT: 2A 53 GLU cc_start: 0.8637 (mt-10) cc_final: 0.8073 (mt-10) REVERT: 2B 25 THR cc_start: 0.6824 (p) cc_final: 0.5651 (t) REVERT: 2F 53 GLU cc_start: 0.7882 (mt-10) cc_final: 0.7633 (mt-10) REVERT: 2G 25 THR cc_start: 0.8580 (m) cc_final: 0.8321 (m) REVERT: 2K 53 GLU cc_start: 0.7553 (mm-30) cc_final: 0.7337 (mm-30) REVERT: 2M 24 GLN cc_start: 0.8319 (tp40) cc_final: 0.8105 (tp-100) REVERT: 2O 10 ASP cc_start: 0.6545 (m-30) cc_final: 0.6331 (m-30) outliers start: 2 outliers final: 1 residues processed: 661 average time/residue: 0.9207 time to fit residues: 923.3087 Evaluate side-chains 387 residues out of total 2611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 386 time to evaluate : 3.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1F residue 57 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 244 optimal weight: 8.9990 chunk 219 optimal weight: 5.9990 chunk 121 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 148 optimal weight: 10.0000 chunk 117 optimal weight: 10.0000 chunk 227 optimal weight: 3.9990 chunk 87 optimal weight: 6.9990 chunk 138 optimal weight: 0.8980 chunk 169 optimal weight: 5.9990 chunk 263 optimal weight: 7.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1A 44 GLN 1F 127 ASN ** 1F 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1G 9 ASN 2E 59 ASN 2G 78 ASN 2K 78 ASN 2P 61 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.3410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 24080 Z= 0.234 Angle : 0.652 8.556 32694 Z= 0.355 Chirality : 0.037 0.163 3924 Planarity : 0.004 0.053 4080 Dihedral : 4.813 87.122 3208 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 1.30 % Allowed : 7.35 % Favored : 91.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.15), residues: 2933 helix: 0.81 (0.10), residues: 2509 sheet: None (None), residues: 0 loop : -1.23 (0.28), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP1A 65 HIS 0.006 0.001 HIS1C 91 PHE 0.020 0.002 PHE1G 61 TYR 0.026 0.002 TYR1E 72 ARG 0.005 0.001 ARG1L 89 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5866 Ramachandran restraints generated. 2933 Oldfield, 0 Emsley, 2933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5866 Ramachandran restraints generated. 2933 Oldfield, 0 Emsley, 2933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 2611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 477 time to evaluate : 3.925 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: 1A 186 MET cc_start: 0.6564 (tpt) cc_final: 0.6219 (tpt) REVERT: 1B 76 GLU cc_start: 0.6831 (mm-30) cc_final: 0.6357 (tp30) REVERT: 1B 186 MET cc_start: 0.5941 (mtm) cc_final: 0.5718 (mtm) REVERT: 1C 97 ASP cc_start: 0.5936 (t70) cc_final: 0.5708 (t0) REVERT: 1C 205 LEU cc_start: 0.8254 (mt) cc_final: 0.8028 (mt) REVERT: 1E 90 LYS cc_start: 0.8373 (ttmt) cc_final: 0.8135 (tttt) REVERT: 1F 209 MET cc_start: 0.6897 (ttm) cc_final: 0.6592 (ttm) REVERT: 1F 256 ARG cc_start: 0.7531 (mtt180) cc_final: 0.6422 (tpp80) REVERT: 1I 64 SER cc_start: 0.6776 (OUTLIER) cc_final: 0.6478 (m) REVERT: 1L 57 ASP cc_start: 0.7662 (t0) cc_final: 0.7299 (t0) REVERT: 1L 100 ARG cc_start: 0.7690 (ptm160) cc_final: 0.7428 (ptm160) REVERT: 2A 22 ASN cc_start: 0.7555 (m-40) cc_final: 0.7126 (p0) REVERT: 2F 53 GLU cc_start: 0.7506 (mt-10) cc_final: 0.7023 (mt-10) REVERT: 2G 25 THR cc_start: 0.8641 (m) cc_final: 0.8407 (m) REVERT: 2G 53 GLU cc_start: 0.7809 (tt0) cc_final: 0.7322 (tt0) REVERT: 2K 53 GLU cc_start: 0.7423 (mm-30) cc_final: 0.7211 (mm-30) REVERT: 2K 76 ILE cc_start: 0.9416 (pt) cc_final: 0.9179 (mt) REVERT: 2M 24 GLN cc_start: 0.8100 (tp40) cc_final: 0.7842 (tp-100) outliers start: 34 outliers final: 18 residues processed: 496 average time/residue: 0.7943 time to fit residues: 616.4785 Evaluate side-chains 407 residues out of total 2611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 388 time to evaluate : 3.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1A residue 86 SER Chi-restraints excluded: chain 1A residue 174 LEU Chi-restraints excluded: chain 1A residue 216 ILE Chi-restraints excluded: chain 1B residue 180 LEU Chi-restraints excluded: chain 1C residue 191 VAL Chi-restraints excluded: chain 1C residue 212 SER Chi-restraints excluded: chain 1E residue 68 MET Chi-restraints excluded: chain 1G residue 17 ILE Chi-restraints excluded: chain 1G residue 59 CYS Chi-restraints excluded: chain 1I residue 37 GLN Chi-restraints excluded: chain 1I residue 64 SER Chi-restraints excluded: chain 1K residue 63 ASP Chi-restraints excluded: chain 1M residue 96 GLU Chi-restraints excluded: chain 1N residue 42 ILE Chi-restraints excluded: chain 1O residue 31 ASP Chi-restraints excluded: chain 2B residue 29 GLU Chi-restraints excluded: chain 2K residue 22 ASN Chi-restraints excluded: chain 2K residue 43 LEU Chi-restraints excluded: chain 2P residue 6 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 146 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 219 optimal weight: 6.9990 chunk 179 optimal weight: 9.9990 chunk 72 optimal weight: 6.9990 chunk 263 optimal weight: 9.9990 chunk 285 optimal weight: 9.9990 chunk 234 optimal weight: 6.9990 chunk 261 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 chunk 211 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1A 44 GLN ** 1F 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2A 24 GLN 2B 59 ASN ** 2C 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2J 77 GLN ** 2L 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.3997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 24080 Z= 0.292 Angle : 0.585 7.294 32694 Z= 0.324 Chirality : 0.036 0.146 3924 Planarity : 0.004 0.042 4080 Dihedral : 4.674 86.033 3206 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.65 % Allowed : 8.96 % Favored : 89.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.15), residues: 2933 helix: 1.29 (0.10), residues: 2495 sheet: None (None), residues: 0 loop : -1.29 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP1E 208 HIS 0.006 0.001 HIS1C 91 PHE 0.018 0.002 PHE1C 163 TYR 0.020 0.002 TYR1E 72 ARG 0.003 0.000 ARG1N 89 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5866 Ramachandran restraints generated. 2933 Oldfield, 0 Emsley, 2933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5866 Ramachandran restraints generated. 2933 Oldfield, 0 Emsley, 2933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 2611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 394 time to evaluate : 4.229 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: 1A 186 MET cc_start: 0.6666 (tpt) cc_final: 0.6425 (tpt) REVERT: 1A 187 MET cc_start: 0.7393 (mmt) cc_final: 0.6758 (tpp) REVERT: 1B 76 GLU cc_start: 0.6753 (mm-30) cc_final: 0.6404 (tp30) REVERT: 1B 186 MET cc_start: 0.6028 (mtm) cc_final: 0.5795 (mtm) REVERT: 1C 205 LEU cc_start: 0.8367 (mt) cc_final: 0.7928 (mt) REVERT: 1F 209 MET cc_start: 0.6828 (ttm) cc_final: 0.6617 (ttm) REVERT: 1F 230 TYR cc_start: 0.6101 (m-80) cc_final: 0.5795 (m-80) REVERT: 1F 256 ARG cc_start: 0.7710 (mtt180) cc_final: 0.6708 (tpp80) REVERT: 1K 80 TYR cc_start: 0.8929 (t80) cc_final: 0.8696 (t80) REVERT: 1L 57 ASP cc_start: 0.7675 (t0) cc_final: 0.7472 (t0) REVERT: 2A 22 ASN cc_start: 0.7563 (m-40) cc_final: 0.7190 (p0) REVERT: 2F 53 GLU cc_start: 0.7544 (mt-10) cc_final: 0.7078 (mt-10) REVERT: 2G 25 THR cc_start: 0.8583 (m) cc_final: 0.8354 (m) REVERT: 2K 53 GLU cc_start: 0.7414 (mm-30) cc_final: 0.7193 (mm-30) REVERT: 2K 76 ILE cc_start: 0.9406 (pt) cc_final: 0.9114 (mt) REVERT: 2M 24 GLN cc_start: 0.8188 (tp40) cc_final: 0.7915 (tp-100) outliers start: 43 outliers final: 29 residues processed: 420 average time/residue: 0.8142 time to fit residues: 536.8048 Evaluate side-chains 396 residues out of total 2611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 367 time to evaluate : 3.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1A residue 43 LEU Chi-restraints excluded: chain 1A residue 86 SER Chi-restraints excluded: chain 1A residue 216 ILE Chi-restraints excluded: chain 1B residue 179 VAL Chi-restraints excluded: chain 1C residue 212 SER Chi-restraints excluded: chain 1C residue 221 ASP Chi-restraints excluded: chain 1D residue 50 MET Chi-restraints excluded: chain 1D residue 86 SER Chi-restraints excluded: chain 1E residue 20 ILE Chi-restraints excluded: chain 1E residue 68 MET Chi-restraints excluded: chain 1E residue 165 LEU Chi-restraints excluded: chain 1G residue 59 CYS Chi-restraints excluded: chain 1I residue 19 SER Chi-restraints excluded: chain 1J residue 32 LEU Chi-restraints excluded: chain 1K residue 63 ASP Chi-restraints excluded: chain 1L residue 31 ASP Chi-restraints excluded: chain 1L residue 48 LYS Chi-restraints excluded: chain 1M residue 31 ASP Chi-restraints excluded: chain 1M residue 96 GLU Chi-restraints excluded: chain 1O residue 31 ASP Chi-restraints excluded: chain 1O residue 97 THR Chi-restraints excluded: chain 2B residue 29 GLU Chi-restraints excluded: chain 2H residue 25 THR Chi-restraints excluded: chain 2H residue 57 TYR Chi-restraints excluded: chain 2K residue 22 ASN Chi-restraints excluded: chain 2K residue 43 LEU Chi-restraints excluded: chain 2M residue 17 ASP Chi-restraints excluded: chain 2O residue 77 GLN Chi-restraints excluded: chain 2P residue 6 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 260 optimal weight: 9.9990 chunk 198 optimal weight: 2.9990 chunk 136 optimal weight: 9.9990 chunk 29 optimal weight: 6.9990 chunk 125 optimal weight: 10.0000 chunk 177 optimal weight: 7.9990 chunk 264 optimal weight: 3.9990 chunk 280 optimal weight: 9.9990 chunk 138 optimal weight: 0.9990 chunk 250 optimal weight: 9.9990 chunk 75 optimal weight: 8.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1E 91 HIS ** 1F 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2A 24 GLN 2C 77 GLN ** 2D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2J 61 GLN 2J 77 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.4371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 24080 Z= 0.257 Angle : 0.558 6.876 32694 Z= 0.305 Chirality : 0.035 0.173 3924 Planarity : 0.003 0.041 4080 Dihedral : 4.604 84.972 3206 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.80 % Allowed : 9.88 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.15), residues: 2933 helix: 1.50 (0.10), residues: 2505 sheet: None (None), residues: 0 loop : -1.44 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP1E 208 HIS 0.005 0.001 HIS1C 91 PHE 0.013 0.001 PHE1E 62 TYR 0.020 0.001 TYR1E 72 ARG 0.003 0.000 ARG1L 100 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5866 Ramachandran restraints generated. 2933 Oldfield, 0 Emsley, 2933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5866 Ramachandran restraints generated. 2933 Oldfield, 0 Emsley, 2933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 2611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 395 time to evaluate : 3.782 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: 1A 50 MET cc_start: 0.7229 (tpp) cc_final: 0.6912 (mmt) REVERT: 1A 83 ASN cc_start: 0.7677 (t0) cc_final: 0.7455 (t0) REVERT: 1A 186 MET cc_start: 0.6843 (tpt) cc_final: 0.6599 (tpt) REVERT: 1A 187 MET cc_start: 0.7413 (mmt) cc_final: 0.6910 (tpp) REVERT: 1B 76 GLU cc_start: 0.6692 (mm-30) cc_final: 0.6321 (tp30) REVERT: 1C 205 LEU cc_start: 0.8392 (mt) cc_final: 0.7929 (mt) REVERT: 1D 166 TYR cc_start: 0.8017 (OUTLIER) cc_final: 0.7788 (m-80) REVERT: 1F 256 ARG cc_start: 0.7686 (mtt180) cc_final: 0.6712 (tpp80) REVERT: 1G 69 GLU cc_start: 0.5253 (tp30) cc_final: 0.5050 (tp30) REVERT: 1K 80 TYR cc_start: 0.8902 (t80) cc_final: 0.8413 (t80) REVERT: 2A 22 ASN cc_start: 0.7629 (m-40) cc_final: 0.7263 (p0) REVERT: 2F 53 GLU cc_start: 0.7524 (mt-10) cc_final: 0.7052 (mt-10) REVERT: 2G 25 THR cc_start: 0.8627 (m) cc_final: 0.8384 (m) REVERT: 2K 53 GLU cc_start: 0.7359 (mm-30) cc_final: 0.7139 (mm-30) REVERT: 2K 76 ILE cc_start: 0.9355 (pt) cc_final: 0.9144 (mt) REVERT: 2L 21 ASP cc_start: 0.5970 (p0) cc_final: 0.5550 (p0) REVERT: 2M 24 GLN cc_start: 0.8080 (tp40) cc_final: 0.7783 (tp-100) outliers start: 47 outliers final: 32 residues processed: 420 average time/residue: 0.8002 time to fit residues: 537.4737 Evaluate side-chains 406 residues out of total 2611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 373 time to evaluate : 3.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1A residue 43 LEU Chi-restraints excluded: chain 1A residue 86 SER Chi-restraints excluded: chain 1A residue 174 LEU Chi-restraints excluded: chain 1A residue 216 ILE Chi-restraints excluded: chain 1B residue 179 VAL Chi-restraints excluded: chain 1C residue 23 SER Chi-restraints excluded: chain 1C residue 188 MET Chi-restraints excluded: chain 1C residue 212 SER Chi-restraints excluded: chain 1C residue 221 ASP Chi-restraints excluded: chain 1D residue 61 MET Chi-restraints excluded: chain 1D residue 86 SER Chi-restraints excluded: chain 1D residue 166 TYR Chi-restraints excluded: chain 1E residue 20 ILE Chi-restraints excluded: chain 1E residue 68 MET Chi-restraints excluded: chain 1G residue 2 ASP Chi-restraints excluded: chain 1G residue 59 CYS Chi-restraints excluded: chain 1I residue 19 SER Chi-restraints excluded: chain 1K residue 63 ASP Chi-restraints excluded: chain 1L residue 31 ASP Chi-restraints excluded: chain 1M residue 40 SER Chi-restraints excluded: chain 1M residue 96 GLU Chi-restraints excluded: chain 1O residue 31 ASP Chi-restraints excluded: chain 1O residue 97 THR Chi-restraints excluded: chain 2B residue 29 GLU Chi-restraints excluded: chain 2C residue 29 GLU Chi-restraints excluded: chain 2H residue 25 THR Chi-restraints excluded: chain 2H residue 57 TYR Chi-restraints excluded: chain 2K residue 22 ASN Chi-restraints excluded: chain 2K residue 43 LEU Chi-restraints excluded: chain 2K residue 57 TYR Chi-restraints excluded: chain 2M residue 17 ASP Chi-restraints excluded: chain 2O residue 77 GLN Chi-restraints excluded: chain 2P residue 6 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 233 optimal weight: 10.0000 chunk 159 optimal weight: 6.9990 chunk 4 optimal weight: 9.9990 chunk 208 optimal weight: 7.9990 chunk 115 optimal weight: 6.9990 chunk 239 optimal weight: 9.9990 chunk 193 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 143 optimal weight: 3.9990 chunk 251 optimal weight: 10.0000 chunk 70 optimal weight: 8.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1F 175 ASN 2A 24 GLN 2B 24 GLN ** 2D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2J 77 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.4555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 24080 Z= 0.317 Angle : 0.580 7.069 32694 Z= 0.319 Chirality : 0.036 0.143 3924 Planarity : 0.004 0.039 4080 Dihedral : 4.688 85.201 3206 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.41 % Allowed : 10.61 % Favored : 86.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.15), residues: 2933 helix: 1.40 (0.10), residues: 2511 sheet: None (None), residues: 0 loop : -1.61 (0.28), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP1E 208 HIS 0.007 0.002 HIS1D 91 PHE 0.015 0.002 PHE1E 62 TYR 0.025 0.002 TYR1C 72 ARG 0.004 0.000 ARG1J 76 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5866 Ramachandran restraints generated. 2933 Oldfield, 0 Emsley, 2933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5866 Ramachandran restraints generated. 2933 Oldfield, 0 Emsley, 2933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 2611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 369 time to evaluate : 3.751 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: 1A 50 MET cc_start: 0.7237 (tpp) cc_final: 0.6933 (mmt) REVERT: 1A 83 ASN cc_start: 0.7718 (t0) cc_final: 0.7492 (t0) REVERT: 1A 186 MET cc_start: 0.6776 (tpt) cc_final: 0.6565 (tpt) REVERT: 1A 187 MET cc_start: 0.7544 (mmt) cc_final: 0.7175 (tpp) REVERT: 1B 76 GLU cc_start: 0.6870 (mm-30) cc_final: 0.6417 (tp30) REVERT: 1C 205 LEU cc_start: 0.8433 (mt) cc_final: 0.7964 (mt) REVERT: 1D 137 GLU cc_start: 0.7077 (mm-30) cc_final: 0.6484 (mm-30) REVERT: 1E 122 ARG cc_start: 0.7976 (mtm-85) cc_final: 0.7766 (mtm-85) REVERT: 1F 256 ARG cc_start: 0.7740 (mtt180) cc_final: 0.6741 (tpp80) REVERT: 1I 64 SER cc_start: 0.6336 (OUTLIER) cc_final: 0.6091 (m) REVERT: 1K 80 TYR cc_start: 0.8912 (t80) cc_final: 0.8528 (t80) REVERT: 2C 80 ARG cc_start: 0.7436 (ttp80) cc_final: 0.7134 (ttp80) REVERT: 2F 53 GLU cc_start: 0.7560 (mt-10) cc_final: 0.7104 (mt-10) REVERT: 2K 53 GLU cc_start: 0.7303 (mm-30) cc_final: 0.7084 (mm-30) REVERT: 2K 76 ILE cc_start: 0.9360 (pt) cc_final: 0.9094 (mt) REVERT: 2L 21 ASP cc_start: 0.6081 (p0) cc_final: 0.5705 (p0) REVERT: 2M 24 GLN cc_start: 0.8236 (tp40) cc_final: 0.7976 (tp-100) outliers start: 63 outliers final: 50 residues processed: 407 average time/residue: 0.8139 time to fit residues: 530.5099 Evaluate side-chains 412 residues out of total 2611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 361 time to evaluate : 3.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1A residue 43 LEU Chi-restraints excluded: chain 1A residue 86 SER Chi-restraints excluded: chain 1A residue 174 LEU Chi-restraints excluded: chain 1A residue 216 ILE Chi-restraints excluded: chain 1B residue 179 VAL Chi-restraints excluded: chain 1C residue 23 SER Chi-restraints excluded: chain 1C residue 188 MET Chi-restraints excluded: chain 1C residue 212 SER Chi-restraints excluded: chain 1C residue 221 ASP Chi-restraints excluded: chain 1D residue 50 MET Chi-restraints excluded: chain 1D residue 61 MET Chi-restraints excluded: chain 1D residue 86 SER Chi-restraints excluded: chain 1D residue 97 ASP Chi-restraints excluded: chain 1D residue 165 LEU Chi-restraints excluded: chain 1D residue 194 SER Chi-restraints excluded: chain 1E residue 20 ILE Chi-restraints excluded: chain 1E residue 44 GLN Chi-restraints excluded: chain 1E residue 68 MET Chi-restraints excluded: chain 1E residue 91 HIS Chi-restraints excluded: chain 1E residue 165 LEU Chi-restraints excluded: chain 1E residue 199 LEU Chi-restraints excluded: chain 1F residue 175 ASN Chi-restraints excluded: chain 1G residue 2 ASP Chi-restraints excluded: chain 1G residue 17 ILE Chi-restraints excluded: chain 1G residue 59 CYS Chi-restraints excluded: chain 1I residue 19 SER Chi-restraints excluded: chain 1I residue 64 SER Chi-restraints excluded: chain 1J residue 32 LEU Chi-restraints excluded: chain 1K residue 63 ASP Chi-restraints excluded: chain 1L residue 31 ASP Chi-restraints excluded: chain 1L residue 48 LYS Chi-restraints excluded: chain 1M residue 31 ASP Chi-restraints excluded: chain 1M residue 40 SER Chi-restraints excluded: chain 1M residue 96 GLU Chi-restraints excluded: chain 1O residue 31 ASP Chi-restraints excluded: chain 1O residue 97 THR Chi-restraints excluded: chain 2A residue 43 LEU Chi-restraints excluded: chain 2B residue 29 GLU Chi-restraints excluded: chain 2C residue 29 GLU Chi-restraints excluded: chain 2F residue 57 TYR Chi-restraints excluded: chain 2G residue 53 GLU Chi-restraints excluded: chain 2H residue 17 ASP Chi-restraints excluded: chain 2H residue 25 THR Chi-restraints excluded: chain 2H residue 57 TYR Chi-restraints excluded: chain 2K residue 22 ASN Chi-restraints excluded: chain 2K residue 43 LEU Chi-restraints excluded: chain 2K residue 57 TYR Chi-restraints excluded: chain 2M residue 17 ASP Chi-restraints excluded: chain 2M residue 57 TYR Chi-restraints excluded: chain 2O residue 77 GLN Chi-restraints excluded: chain 2P residue 6 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 94 optimal weight: 0.9980 chunk 252 optimal weight: 0.7980 chunk 55 optimal weight: 6.9990 chunk 164 optimal weight: 9.9990 chunk 69 optimal weight: 6.9990 chunk 280 optimal weight: 10.0000 chunk 232 optimal weight: 8.9990 chunk 129 optimal weight: 10.0000 chunk 23 optimal weight: 8.9990 chunk 92 optimal weight: 0.7980 chunk 147 optimal weight: 5.9990 overall best weight: 3.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1F 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2D 24 GLN 2J 77 GLN ** 2L 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.4767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 24080 Z= 0.198 Angle : 0.517 6.692 32694 Z= 0.281 Chirality : 0.034 0.140 3924 Planarity : 0.003 0.040 4080 Dihedral : 4.453 81.499 3206 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.03 % Allowed : 11.30 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.16), residues: 2933 helix: 1.78 (0.10), residues: 2505 sheet: None (None), residues: 0 loop : -1.61 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP1E 208 HIS 0.004 0.001 HIS1D 91 PHE 0.013 0.001 PHE1C 163 TYR 0.017 0.001 TYR1C 72 ARG 0.004 0.000 ARG1J 76 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5866 Ramachandran restraints generated. 2933 Oldfield, 0 Emsley, 2933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5866 Ramachandran restraints generated. 2933 Oldfield, 0 Emsley, 2933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 2611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 379 time to evaluate : 3.797 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: 1A 50 MET cc_start: 0.7186 (tpp) cc_final: 0.6896 (mmt) REVERT: 1A 83 ASN cc_start: 0.7741 (t0) cc_final: 0.7530 (t0) REVERT: 1A 187 MET cc_start: 0.7583 (mmt) cc_final: 0.7295 (tpp) REVERT: 1B 76 GLU cc_start: 0.6932 (mm-30) cc_final: 0.6502 (tp30) REVERT: 1C 205 LEU cc_start: 0.8404 (mt) cc_final: 0.7951 (mt) REVERT: 1D 137 GLU cc_start: 0.6929 (mm-30) cc_final: 0.6457 (mm-30) REVERT: 1E 94 GLU cc_start: 0.6858 (mm-30) cc_final: 0.6647 (mm-30) REVERT: 1F 256 ARG cc_start: 0.7681 (mtt180) cc_final: 0.6706 (tpp80) REVERT: 1K 80 TYR cc_start: 0.8894 (t80) cc_final: 0.8480 (t80) REVERT: 2F 53 GLU cc_start: 0.7520 (mt-10) cc_final: 0.7058 (mt-10) REVERT: 2K 53 GLU cc_start: 0.7240 (mm-30) cc_final: 0.7027 (mm-30) REVERT: 2K 76 ILE cc_start: 0.9300 (pt) cc_final: 0.9095 (mt) REVERT: 2L 21 ASP cc_start: 0.5937 (p0) cc_final: 0.5600 (p0) REVERT: 2M 24 GLN cc_start: 0.8167 (tp40) cc_final: 0.7877 (tp-100) outliers start: 53 outliers final: 44 residues processed: 408 average time/residue: 0.7893 time to fit residues: 510.9250 Evaluate side-chains 408 residues out of total 2611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 364 time to evaluate : 3.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1A residue 43 LEU Chi-restraints excluded: chain 1A residue 86 SER Chi-restraints excluded: chain 1A residue 174 LEU Chi-restraints excluded: chain 1A residue 211 LEU Chi-restraints excluded: chain 1A residue 216 ILE Chi-restraints excluded: chain 1B residue 179 VAL Chi-restraints excluded: chain 1C residue 23 SER Chi-restraints excluded: chain 1C residue 97 ASP Chi-restraints excluded: chain 1C residue 188 MET Chi-restraints excluded: chain 1C residue 212 SER Chi-restraints excluded: chain 1C residue 221 ASP Chi-restraints excluded: chain 1D residue 50 MET Chi-restraints excluded: chain 1D residue 61 MET Chi-restraints excluded: chain 1D residue 97 ASP Chi-restraints excluded: chain 1D residue 194 SER Chi-restraints excluded: chain 1E residue 20 ILE Chi-restraints excluded: chain 1E residue 68 MET Chi-restraints excluded: chain 1E residue 199 LEU Chi-restraints excluded: chain 1F residue 157 CYS Chi-restraints excluded: chain 1G residue 2 ASP Chi-restraints excluded: chain 1G residue 17 ILE Chi-restraints excluded: chain 1G residue 59 CYS Chi-restraints excluded: chain 1I residue 19 SER Chi-restraints excluded: chain 1J residue 32 LEU Chi-restraints excluded: chain 1J residue 39 VAL Chi-restraints excluded: chain 1J residue 63 LEU Chi-restraints excluded: chain 1K residue 63 ASP Chi-restraints excluded: chain 1M residue 40 SER Chi-restraints excluded: chain 1M residue 96 GLU Chi-restraints excluded: chain 1O residue 31 ASP Chi-restraints excluded: chain 1O residue 97 THR Chi-restraints excluded: chain 2B residue 29 GLU Chi-restraints excluded: chain 2C residue 29 GLU Chi-restraints excluded: chain 2G residue 10 ASP Chi-restraints excluded: chain 2H residue 25 THR Chi-restraints excluded: chain 2H residue 57 TYR Chi-restraints excluded: chain 2K residue 22 ASN Chi-restraints excluded: chain 2K residue 43 LEU Chi-restraints excluded: chain 2K residue 57 TYR Chi-restraints excluded: chain 2K residue 69 LYS Chi-restraints excluded: chain 2M residue 17 ASP Chi-restraints excluded: chain 2M residue 57 TYR Chi-restraints excluded: chain 2O residue 77 GLN Chi-restraints excluded: chain 2P residue 6 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 270 optimal weight: 9.9990 chunk 31 optimal weight: 0.2980 chunk 159 optimal weight: 7.9990 chunk 204 optimal weight: 7.9990 chunk 158 optimal weight: 2.9990 chunk 236 optimal weight: 9.9990 chunk 156 optimal weight: 5.9990 chunk 279 optimal weight: 6.9990 chunk 174 optimal weight: 6.9990 chunk 170 optimal weight: 7.9990 chunk 129 optimal weight: 10.0000 overall best weight: 4.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1F 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1F 175 ASN 2J 77 GLN 2N 61 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.4880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 24080 Z= 0.262 Angle : 0.540 6.899 32694 Z= 0.295 Chirality : 0.035 0.140 3924 Planarity : 0.004 0.039 4080 Dihedral : 4.467 76.803 3206 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.37 % Allowed : 11.45 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.15), residues: 2933 helix: 1.74 (0.10), residues: 2505 sheet: None (None), residues: 0 loop : -1.76 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP1E 208 HIS 0.006 0.001 HIS1D 91 PHE 0.014 0.001 PHE1C 163 TYR 0.022 0.001 TYR1C 72 ARG 0.004 0.000 ARG1J 76 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5866 Ramachandran restraints generated. 2933 Oldfield, 0 Emsley, 2933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5866 Ramachandran restraints generated. 2933 Oldfield, 0 Emsley, 2933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 2611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 372 time to evaluate : 4.294 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: 1A 50 MET cc_start: 0.7188 (tpp) cc_final: 0.6911 (mmt) REVERT: 1B 76 GLU cc_start: 0.7032 (mm-30) cc_final: 0.6535 (tp30) REVERT: 1C 164 TYR cc_start: 0.7978 (m-80) cc_final: 0.7740 (m-80) REVERT: 1C 205 LEU cc_start: 0.8466 (mt) cc_final: 0.8022 (mt) REVERT: 1D 165 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8725 (mm) REVERT: 1F 256 ARG cc_start: 0.7672 (mtt180) cc_final: 0.6753 (tpp80) REVERT: 1I 64 SER cc_start: 0.6185 (OUTLIER) cc_final: 0.5963 (m) REVERT: 1K 80 TYR cc_start: 0.8944 (t80) cc_final: 0.8564 (t80) REVERT: 2F 53 GLU cc_start: 0.7557 (mt-10) cc_final: 0.7095 (mt-10) REVERT: 2K 76 ILE cc_start: 0.9304 (pt) cc_final: 0.9049 (mt) REVERT: 2L 21 ASP cc_start: 0.5996 (p0) cc_final: 0.5649 (p0) REVERT: 2M 24 GLN cc_start: 0.8253 (tp40) cc_final: 0.7969 (tp-100) outliers start: 62 outliers final: 51 residues processed: 409 average time/residue: 0.7845 time to fit residues: 508.4129 Evaluate side-chains 418 residues out of total 2611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 365 time to evaluate : 4.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1A residue 43 LEU Chi-restraints excluded: chain 1A residue 86 SER Chi-restraints excluded: chain 1A residue 174 LEU Chi-restraints excluded: chain 1A residue 211 LEU Chi-restraints excluded: chain 1A residue 216 ILE Chi-restraints excluded: chain 1B residue 179 VAL Chi-restraints excluded: chain 1C residue 23 SER Chi-restraints excluded: chain 1C residue 97 ASP Chi-restraints excluded: chain 1C residue 188 MET Chi-restraints excluded: chain 1C residue 212 SER Chi-restraints excluded: chain 1C residue 221 ASP Chi-restraints excluded: chain 1D residue 20 ILE Chi-restraints excluded: chain 1D residue 50 MET Chi-restraints excluded: chain 1D residue 61 MET Chi-restraints excluded: chain 1D residue 97 ASP Chi-restraints excluded: chain 1D residue 165 LEU Chi-restraints excluded: chain 1D residue 194 SER Chi-restraints excluded: chain 1E residue 20 ILE Chi-restraints excluded: chain 1E residue 44 GLN Chi-restraints excluded: chain 1E residue 68 MET Chi-restraints excluded: chain 1E residue 91 HIS Chi-restraints excluded: chain 1E residue 165 LEU Chi-restraints excluded: chain 1E residue 199 LEU Chi-restraints excluded: chain 1E residue 206 ASP Chi-restraints excluded: chain 1F residue 157 CYS Chi-restraints excluded: chain 1F residue 175 ASN Chi-restraints excluded: chain 1G residue 2 ASP Chi-restraints excluded: chain 1G residue 17 ILE Chi-restraints excluded: chain 1G residue 59 CYS Chi-restraints excluded: chain 1I residue 19 SER Chi-restraints excluded: chain 1I residue 64 SER Chi-restraints excluded: chain 1J residue 32 LEU Chi-restraints excluded: chain 1J residue 39 VAL Chi-restraints excluded: chain 1J residue 63 LEU Chi-restraints excluded: chain 1K residue 63 ASP Chi-restraints excluded: chain 1L residue 31 ASP Chi-restraints excluded: chain 1M residue 40 SER Chi-restraints excluded: chain 1M residue 96 GLU Chi-restraints excluded: chain 1N residue 59 ASN Chi-restraints excluded: chain 1O residue 31 ASP Chi-restraints excluded: chain 1O residue 97 THR Chi-restraints excluded: chain 2B residue 29 GLU Chi-restraints excluded: chain 2C residue 29 GLU Chi-restraints excluded: chain 2E residue 59 ASN Chi-restraints excluded: chain 2H residue 17 ASP Chi-restraints excluded: chain 2H residue 25 THR Chi-restraints excluded: chain 2H residue 57 TYR Chi-restraints excluded: chain 2K residue 43 LEU Chi-restraints excluded: chain 2K residue 57 TYR Chi-restraints excluded: chain 2M residue 17 ASP Chi-restraints excluded: chain 2M residue 57 TYR Chi-restraints excluded: chain 2O residue 77 GLN Chi-restraints excluded: chain 2P residue 6 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 172 optimal weight: 5.9990 chunk 111 optimal weight: 5.9990 chunk 166 optimal weight: 7.9990 chunk 84 optimal weight: 9.9990 chunk 54 optimal weight: 8.9990 chunk 177 optimal weight: 0.9990 chunk 190 optimal weight: 7.9990 chunk 138 optimal weight: 0.9980 chunk 26 optimal weight: 6.9990 chunk 219 optimal weight: 4.9990 chunk 254 optimal weight: 9.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1F 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2J 77 GLN ** 2L 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.4981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24080 Z= 0.222 Angle : 0.522 6.761 32694 Z= 0.284 Chirality : 0.034 0.142 3924 Planarity : 0.003 0.039 4080 Dihedral : 4.389 74.245 3206 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.26 % Allowed : 11.83 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.16), residues: 2933 helix: 1.86 (0.10), residues: 2506 sheet: None (None), residues: 0 loop : -1.76 (0.28), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP1E 208 HIS 0.005 0.001 HIS1D 91 PHE 0.013 0.001 PHE1C 163 TYR 0.019 0.001 TYR1C 72 ARG 0.004 0.000 ARG1J 76 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5866 Ramachandran restraints generated. 2933 Oldfield, 0 Emsley, 2933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5866 Ramachandran restraints generated. 2933 Oldfield, 0 Emsley, 2933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 2611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 377 time to evaluate : 4.203 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: 1A 50 MET cc_start: 0.7217 (tpp) cc_final: 0.7014 (mmt) REVERT: 1B 76 GLU cc_start: 0.7022 (mm-30) cc_final: 0.6542 (tp30) REVERT: 1C 164 TYR cc_start: 0.7969 (m-80) cc_final: 0.7726 (m-80) REVERT: 1C 205 LEU cc_start: 0.8459 (mt) cc_final: 0.7993 (mt) REVERT: 1D 165 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8728 (mm) REVERT: 1F 256 ARG cc_start: 0.7630 (mtt180) cc_final: 0.6724 (tpp80) REVERT: 1I 64 SER cc_start: 0.6200 (OUTLIER) cc_final: 0.5962 (m) REVERT: 1K 80 TYR cc_start: 0.8909 (t80) cc_final: 0.8559 (t80) REVERT: 2F 53 GLU cc_start: 0.7539 (mt-10) cc_final: 0.7080 (mt-10) REVERT: 2K 76 ILE cc_start: 0.9284 (pt) cc_final: 0.9051 (mt) REVERT: 2L 21 ASP cc_start: 0.5967 (p0) cc_final: 0.5640 (p0) REVERT: 2O 72 ASP cc_start: 0.7576 (m-30) cc_final: 0.7351 (m-30) outliers start: 59 outliers final: 52 residues processed: 414 average time/residue: 0.8086 time to fit residues: 531.8324 Evaluate side-chains 423 residues out of total 2611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 369 time to evaluate : 3.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1A residue 43 LEU Chi-restraints excluded: chain 1A residue 86 SER Chi-restraints excluded: chain 1A residue 174 LEU Chi-restraints excluded: chain 1A residue 211 LEU Chi-restraints excluded: chain 1A residue 216 ILE Chi-restraints excluded: chain 1B residue 109 ARG Chi-restraints excluded: chain 1B residue 179 VAL Chi-restraints excluded: chain 1C residue 23 SER Chi-restraints excluded: chain 1C residue 97 ASP Chi-restraints excluded: chain 1C residue 188 MET Chi-restraints excluded: chain 1C residue 212 SER Chi-restraints excluded: chain 1C residue 221 ASP Chi-restraints excluded: chain 1D residue 20 ILE Chi-restraints excluded: chain 1D residue 50 MET Chi-restraints excluded: chain 1D residue 61 MET Chi-restraints excluded: chain 1D residue 97 ASP Chi-restraints excluded: chain 1D residue 165 LEU Chi-restraints excluded: chain 1D residue 194 SER Chi-restraints excluded: chain 1E residue 20 ILE Chi-restraints excluded: chain 1E residue 44 GLN Chi-restraints excluded: chain 1E residue 68 MET Chi-restraints excluded: chain 1E residue 91 HIS Chi-restraints excluded: chain 1E residue 165 LEU Chi-restraints excluded: chain 1E residue 199 LEU Chi-restraints excluded: chain 1E residue 206 ASP Chi-restraints excluded: chain 1F residue 157 CYS Chi-restraints excluded: chain 1G residue 2 ASP Chi-restraints excluded: chain 1G residue 17 ILE Chi-restraints excluded: chain 1G residue 59 CYS Chi-restraints excluded: chain 1H residue 28 ILE Chi-restraints excluded: chain 1I residue 19 SER Chi-restraints excluded: chain 1I residue 64 SER Chi-restraints excluded: chain 1J residue 32 LEU Chi-restraints excluded: chain 1J residue 39 VAL Chi-restraints excluded: chain 1J residue 63 LEU Chi-restraints excluded: chain 1K residue 63 ASP Chi-restraints excluded: chain 1M residue 40 SER Chi-restraints excluded: chain 1M residue 96 GLU Chi-restraints excluded: chain 1O residue 31 ASP Chi-restraints excluded: chain 1O residue 97 THR Chi-restraints excluded: chain 2A residue 79 PHE Chi-restraints excluded: chain 2B residue 29 GLU Chi-restraints excluded: chain 2C residue 29 GLU Chi-restraints excluded: chain 2H residue 17 ASP Chi-restraints excluded: chain 2H residue 25 THR Chi-restraints excluded: chain 2H residue 57 TYR Chi-restraints excluded: chain 2K residue 6 SER Chi-restraints excluded: chain 2K residue 43 LEU Chi-restraints excluded: chain 2K residue 57 TYR Chi-restraints excluded: chain 2K residue 69 LYS Chi-restraints excluded: chain 2M residue 17 ASP Chi-restraints excluded: chain 2M residue 57 TYR Chi-restraints excluded: chain 2O residue 77 GLN Chi-restraints excluded: chain 2P residue 6 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 267 optimal weight: 8.9990 chunk 244 optimal weight: 9.9990 chunk 260 optimal weight: 9.9990 chunk 156 optimal weight: 7.9990 chunk 113 optimal weight: 6.9990 chunk 204 optimal weight: 6.9990 chunk 79 optimal weight: 5.9990 chunk 235 optimal weight: 7.9990 chunk 246 optimal weight: 5.9990 chunk 259 optimal weight: 2.9990 chunk 171 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1F 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1F 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1F 175 ASN 2J 77 GLN ** 2L 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.4997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 24080 Z= 0.314 Angle : 0.566 7.024 32694 Z= 0.310 Chirality : 0.036 0.141 3924 Planarity : 0.004 0.043 4080 Dihedral : 4.520 72.127 3206 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.45 % Allowed : 11.83 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.15), residues: 2933 helix: 1.65 (0.10), residues: 2503 sheet: None (None), residues: 0 loop : -1.92 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP1E 208 HIS 0.006 0.002 HIS1D 91 PHE 0.021 0.002 PHE1A 163 TYR 0.025 0.002 TYR1C 72 ARG 0.004 0.000 ARG1J 76 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5866 Ramachandran restraints generated. 2933 Oldfield, 0 Emsley, 2933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5866 Ramachandran restraints generated. 2933 Oldfield, 0 Emsley, 2933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 2611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 365 time to evaluate : 3.775 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: 1A 50 MET cc_start: 0.7191 (tpp) cc_final: 0.6913 (mmt) REVERT: 1A 187 MET cc_start: 0.7220 (mmt) cc_final: 0.6977 (tpp) REVERT: 1C 164 TYR cc_start: 0.8020 (m-80) cc_final: 0.7794 (m-80) REVERT: 1C 205 LEU cc_start: 0.8446 (mt) cc_final: 0.8163 (mt) REVERT: 1D 165 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8728 (mm) REVERT: 1I 64 SER cc_start: 0.6279 (OUTLIER) cc_final: 0.6057 (m) REVERT: 1K 80 TYR cc_start: 0.8933 (t80) cc_final: 0.8606 (t80) REVERT: 2F 53 GLU cc_start: 0.7586 (mt-10) cc_final: 0.7128 (mt-10) REVERT: 2K 76 ILE cc_start: 0.9327 (pt) cc_final: 0.9003 (mt) REVERT: 2L 21 ASP cc_start: 0.6048 (p0) cc_final: 0.5693 (p0) outliers start: 64 outliers final: 54 residues processed: 403 average time/residue: 0.7976 time to fit residues: 513.6885 Evaluate side-chains 413 residues out of total 2611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 357 time to evaluate : 3.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1A residue 43 LEU Chi-restraints excluded: chain 1A residue 86 SER Chi-restraints excluded: chain 1A residue 174 LEU Chi-restraints excluded: chain 1A residue 216 ILE Chi-restraints excluded: chain 1B residue 61 MET Chi-restraints excluded: chain 1B residue 109 ARG Chi-restraints excluded: chain 1B residue 179 VAL Chi-restraints excluded: chain 1C residue 23 SER Chi-restraints excluded: chain 1C residue 97 ASP Chi-restraints excluded: chain 1C residue 188 MET Chi-restraints excluded: chain 1C residue 212 SER Chi-restraints excluded: chain 1C residue 221 ASP Chi-restraints excluded: chain 1D residue 20 ILE Chi-restraints excluded: chain 1D residue 50 MET Chi-restraints excluded: chain 1D residue 61 MET Chi-restraints excluded: chain 1D residue 97 ASP Chi-restraints excluded: chain 1D residue 165 LEU Chi-restraints excluded: chain 1D residue 194 SER Chi-restraints excluded: chain 1E residue 20 ILE Chi-restraints excluded: chain 1E residue 44 GLN Chi-restraints excluded: chain 1E residue 68 MET Chi-restraints excluded: chain 1E residue 91 HIS Chi-restraints excluded: chain 1E residue 199 LEU Chi-restraints excluded: chain 1E residue 206 ASP Chi-restraints excluded: chain 1F residue 157 CYS Chi-restraints excluded: chain 1G residue 2 ASP Chi-restraints excluded: chain 1G residue 17 ILE Chi-restraints excluded: chain 1G residue 59 CYS Chi-restraints excluded: chain 1H residue 28 ILE Chi-restraints excluded: chain 1H residue 59 CYS Chi-restraints excluded: chain 1I residue 19 SER Chi-restraints excluded: chain 1I residue 64 SER Chi-restraints excluded: chain 1J residue 39 VAL Chi-restraints excluded: chain 1J residue 63 LEU Chi-restraints excluded: chain 1K residue 63 ASP Chi-restraints excluded: chain 1M residue 40 SER Chi-restraints excluded: chain 1M residue 96 GLU Chi-restraints excluded: chain 1N residue 59 ASN Chi-restraints excluded: chain 1O residue 31 ASP Chi-restraints excluded: chain 1O residue 97 THR Chi-restraints excluded: chain 2A residue 79 PHE Chi-restraints excluded: chain 2B residue 29 GLU Chi-restraints excluded: chain 2C residue 29 GLU Chi-restraints excluded: chain 2G residue 57 TYR Chi-restraints excluded: chain 2H residue 17 ASP Chi-restraints excluded: chain 2H residue 25 THR Chi-restraints excluded: chain 2H residue 57 TYR Chi-restraints excluded: chain 2H residue 72 ASP Chi-restraints excluded: chain 2K residue 40 ASP Chi-restraints excluded: chain 2K residue 43 LEU Chi-restraints excluded: chain 2K residue 57 TYR Chi-restraints excluded: chain 2K residue 69 LYS Chi-restraints excluded: chain 2M residue 17 ASP Chi-restraints excluded: chain 2M residue 57 TYR Chi-restraints excluded: chain 2O residue 77 GLN Chi-restraints excluded: chain 2P residue 6 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 275 optimal weight: 10.0000 chunk 168 optimal weight: 5.9990 chunk 130 optimal weight: 6.9990 chunk 191 optimal weight: 0.8980 chunk 288 optimal weight: 4.9990 chunk 265 optimal weight: 4.9990 chunk 230 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 chunk 177 optimal weight: 2.9990 chunk 141 optimal weight: 7.9990 chunk 182 optimal weight: 5.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1A 44 GLN 1A 91 HIS ** 1F 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1F 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2L 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.5138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 24080 Z= 0.205 Angle : 0.518 6.930 32694 Z= 0.280 Chirality : 0.034 0.136 3924 Planarity : 0.003 0.045 4080 Dihedral : 4.328 68.501 3206 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.99 % Allowed : 12.33 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.16), residues: 2933 helix: 1.93 (0.10), residues: 2503 sheet: None (None), residues: 0 loop : -1.85 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP1E 208 HIS 0.004 0.001 HIS1D 91 PHE 0.017 0.001 PHE1A 163 TYR 0.018 0.001 TYR1C 72 ARG 0.004 0.000 ARG1J 76 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5866 Ramachandran restraints generated. 2933 Oldfield, 0 Emsley, 2933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5866 Ramachandran restraints generated. 2933 Oldfield, 0 Emsley, 2933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 2611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 369 time to evaluate : 3.774 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: 1C 164 TYR cc_start: 0.7985 (m-80) cc_final: 0.7746 (m-80) REVERT: 1K 80 TYR cc_start: 0.8911 (t80) cc_final: 0.8585 (t80) REVERT: 2A 79 PHE cc_start: 0.8769 (OUTLIER) cc_final: 0.8340 (t80) REVERT: 2F 53 GLU cc_start: 0.7532 (mt-10) cc_final: 0.7068 (mt-10) REVERT: 2K 76 ILE cc_start: 0.9265 (pt) cc_final: 0.8995 (mt) REVERT: 2L 21 ASP cc_start: 0.6016 (p0) cc_final: 0.5678 (p0) REVERT: 2O 72 ASP cc_start: 0.7441 (m-30) cc_final: 0.7186 (m-30) outliers start: 52 outliers final: 46 residues processed: 399 average time/residue: 0.7979 time to fit residues: 508.1240 Evaluate side-chains 408 residues out of total 2611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 361 time to evaluate : 3.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1A residue 43 LEU Chi-restraints excluded: chain 1A residue 86 SER Chi-restraints excluded: chain 1A residue 174 LEU Chi-restraints excluded: chain 1A residue 216 ILE Chi-restraints excluded: chain 1B residue 109 ARG Chi-restraints excluded: chain 1B residue 179 VAL Chi-restraints excluded: chain 1C residue 23 SER Chi-restraints excluded: chain 1C residue 188 MET Chi-restraints excluded: chain 1C residue 212 SER Chi-restraints excluded: chain 1C residue 221 ASP Chi-restraints excluded: chain 1D residue 20 ILE Chi-restraints excluded: chain 1D residue 50 MET Chi-restraints excluded: chain 1D residue 61 MET Chi-restraints excluded: chain 1D residue 97 ASP Chi-restraints excluded: chain 1D residue 194 SER Chi-restraints excluded: chain 1E residue 20 ILE Chi-restraints excluded: chain 1E residue 44 GLN Chi-restraints excluded: chain 1E residue 68 MET Chi-restraints excluded: chain 1E residue 165 LEU Chi-restraints excluded: chain 1E residue 206 ASP Chi-restraints excluded: chain 1F residue 157 CYS Chi-restraints excluded: chain 1G residue 2 ASP Chi-restraints excluded: chain 1G residue 17 ILE Chi-restraints excluded: chain 1G residue 59 CYS Chi-restraints excluded: chain 1H residue 28 ILE Chi-restraints excluded: chain 1H residue 59 CYS Chi-restraints excluded: chain 1I residue 19 SER Chi-restraints excluded: chain 1J residue 39 VAL Chi-restraints excluded: chain 1J residue 63 LEU Chi-restraints excluded: chain 1K residue 63 ASP Chi-restraints excluded: chain 1M residue 40 SER Chi-restraints excluded: chain 1M residue 96 GLU Chi-restraints excluded: chain 1O residue 31 ASP Chi-restraints excluded: chain 1O residue 97 THR Chi-restraints excluded: chain 2A residue 79 PHE Chi-restraints excluded: chain 2B residue 29 GLU Chi-restraints excluded: chain 2C residue 29 GLU Chi-restraints excluded: chain 2G residue 57 TYR Chi-restraints excluded: chain 2H residue 17 ASP Chi-restraints excluded: chain 2H residue 25 THR Chi-restraints excluded: chain 2H residue 57 TYR Chi-restraints excluded: chain 2K residue 43 LEU Chi-restraints excluded: chain 2K residue 57 TYR Chi-restraints excluded: chain 2M residue 17 ASP Chi-restraints excluded: chain 2M residue 57 TYR Chi-restraints excluded: chain 2O residue 77 GLN Chi-restraints excluded: chain 2P residue 6 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 245 optimal weight: 0.9990 chunk 70 optimal weight: 9.9990 chunk 212 optimal weight: 7.9990 chunk 33 optimal weight: 5.9990 chunk 63 optimal weight: 10.0000 chunk 230 optimal weight: 3.9990 chunk 96 optimal weight: 6.9990 chunk 236 optimal weight: 8.9990 chunk 29 optimal weight: 8.9990 chunk 42 optimal weight: 1.9990 chunk 202 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: ** 1F 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1F 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2J 77 GLN ** 2L 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.121241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.112524 restraints weight = 137262.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.114678 restraints weight = 65404.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.116002 restraints weight = 38067.207| |-----------------------------------------------------------------------------| r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.5200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 24080 Z= 0.226 Angle : 0.522 7.026 32694 Z= 0.283 Chirality : 0.035 0.136 3924 Planarity : 0.003 0.046 4080 Dihedral : 4.293 66.933 3206 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.95 % Allowed : 12.72 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.14 (0.16), residues: 2933 helix: 1.96 (0.10), residues: 2503 sheet: None (None), residues: 0 loop : -1.88 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP1E 208 HIS 0.005 0.001 HIS1D 91 PHE 0.017 0.001 PHE1A 163 TYR 0.020 0.001 TYR1C 72 ARG 0.004 0.000 ARG1J 76 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10077.36 seconds wall clock time: 179 minutes 30.59 seconds (10770.59 seconds total)