Starting phenix.real_space_refine on Sat Mar 23 03:57:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d73_30600/03_2024/7d73_30600_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d73_30600/03_2024/7d73_30600.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d73_30600/03_2024/7d73_30600.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d73_30600/03_2024/7d73_30600.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d73_30600/03_2024/7d73_30600_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d73_30600/03_2024/7d73_30600_updated.pdb" } resolution = 3.0 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= 0.012 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 P 34 5.49 5 S 219 5.16 5 C 22368 2.51 5 N 6189 2.21 5 O 6482 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 23": "OE1" <-> "OE2" Residue "A PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 81": "NH1" <-> "NH2" Residue "A TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 100": "OD1" <-> "OD2" Residue "A GLU 108": "OE1" <-> "OE2" Residue "A GLU 128": "OE1" <-> "OE2" Residue "A ARG 132": "NH1" <-> "NH2" Residue "A PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 157": "OE1" <-> "OE2" Residue "A TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 177": "OD1" <-> "OD2" Residue "A TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 189": "OE1" <-> "OE2" Residue "A TYR 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 242": "OD1" <-> "OD2" Residue "A ASP 267": "OD1" <-> "OD2" Residue "A TYR 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 321": "OE1" <-> "OE2" Residue "A ASP 359": "OD1" <-> "OD2" Residue "A ASP 377": "OD1" <-> "OD2" Residue "B ARG 16": "NH1" <-> "NH2" Residue "B ARG 18": "NH1" <-> "NH2" Residue "B PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 75": "OE1" <-> "OE2" Residue "B PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 100": "OD1" <-> "OD2" Residue "B GLU 108": "OE1" <-> "OE2" Residue "B ARG 132": "NH1" <-> "NH2" Residue "B ARG 134": "NH1" <-> "NH2" Residue "B PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 177": "OD1" <-> "OD2" Residue "B TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 195": "NH1" <-> "NH2" Residue "B ASP 196": "OD1" <-> "OD2" Residue "B TYR 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 259": "NH1" <-> "NH2" Residue "B ASP 267": "OD1" <-> "OD2" Residue "B TYR 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 349": "NH1" <-> "NH2" Residue "B GLU 354": "OE1" <-> "OE2" Residue "B PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 392": "NH1" <-> "NH2" Residue "B GLU 409": "OE1" <-> "OE2" Residue "B PHE 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 13": "NH1" <-> "NH2" Residue "E ASP 27": "OD1" <-> "OD2" Residue "E ASP 47": "OD1" <-> "OD2" Residue "E GLU 61": "OE1" <-> "OE2" Residue "E ARG 74": "NH1" <-> "NH2" Residue "E GLU 81": "OE1" <-> "OE2" Residue "E ASP 95": "OD1" <-> "OD2" Residue "E GLU 99": "OE1" <-> "OE2" Residue "E ASP 102": "OD1" <-> "OD2" Residue "E ASP 110": "OD1" <-> "OD2" Residue "E PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 194": "OE1" <-> "OE2" Residue "E GLU 196": "OE1" <-> "OE2" Residue "E ASP 218": "OD1" <-> "OD2" Residue "E ASP 224": "OD1" <-> "OD2" Residue "E ASP 257": "OD1" <-> "OD2" Residue "E ASP 282": "OD1" <-> "OD2" Residue "E ARG 293": "NH1" <-> "NH2" Residue "E ARG 298": "NH1" <-> "NH2" Residue "E ARG 313": "NH1" <-> "NH2" Residue "E GLU 335": "OE1" <-> "OE2" Residue "E GLU 351": "OE1" <-> "OE2" Residue "E GLU 355": "OE1" <-> "OE2" Residue "E ARG 357": "NH1" <-> "NH2" Residue "C ARG 16": "NH1" <-> "NH2" Residue "C PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 23": "OE1" <-> "OE2" Residue "C PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 62": "OD1" <-> "OD2" Residue "C GLU 70": "OE1" <-> "OE2" Residue "C GLU 75": "OE1" <-> "OE2" Residue "C PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 85": "OE1" <-> "OE2" Residue "C TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 100": "OD1" <-> "OD2" Residue "C ARG 132": "NH1" <-> "NH2" Residue "C ARG 134": "NH1" <-> "NH2" Residue "C TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 177": "OD1" <-> "OD2" Residue "C TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 189": "OE1" <-> "OE2" Residue "C ARG 195": "NH1" <-> "NH2" Residue "C TYR 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 242": "OD1" <-> "OD2" Residue "C ARG 259": "NH1" <-> "NH2" Residue "C ASP 267": "OD1" <-> "OD2" Residue "C TYR 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 321": "OE1" <-> "OE2" Residue "C ASP 359": "OD1" <-> "OD2" Residue "C ARG 366": "NH1" <-> "NH2" Residue "C ASP 370": "OD1" <-> "OD2" Residue "C ASP 377": "OD1" <-> "OD2" Residue "C PHE 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 18": "NH1" <-> "NH2" Residue "D PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 75": "OE1" <-> "OE2" Residue "D PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 81": "NH1" <-> "NH2" Residue "D TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 100": "OD1" <-> "OD2" Residue "D ARG 132": "NH1" <-> "NH2" Residue "D ARG 134": "NH1" <-> "NH2" Residue "D ARG 146": "NH1" <-> "NH2" Residue "D PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 195": "NH1" <-> "NH2" Residue "D TYR 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 259": "NH1" <-> "NH2" Residue "D ASP 267": "OD1" <-> "OD2" Residue "D TYR 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 332": "OE1" <-> "OE2" Residue "D ARG 349": "NH1" <-> "NH2" Residue "D GLU 354": "OE1" <-> "OE2" Residue "D ASP 364": "OD1" <-> "OD2" Residue "D ARG 366": "NH1" <-> "NH2" Residue "D GLU 372": "OE1" <-> "OE2" Residue "D PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 377": "OD1" <-> "OD2" Residue "D ARG 392": "NH1" <-> "NH2" Residue "D GLU 409": "OE1" <-> "OE2" Residue "D PHE 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 13": "NH1" <-> "NH2" Residue "F ASP 27": "OD1" <-> "OD2" Residue "F ARG 74": "NH1" <-> "NH2" Residue "F GLU 82": "OE1" <-> "OE2" Residue "F ASP 102": "OD1" <-> "OD2" Residue "F ASP 110": "OD1" <-> "OD2" Residue "F ASP 114": "OD1" <-> "OD2" Residue "F PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 130": "OE1" <-> "OE2" Residue "F GLU 140": "OE1" <-> "OE2" Residue "F ARG 158": "NH1" <-> "NH2" Residue "F TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 211": "OE1" <-> "OE2" Residue "F ASP 218": "OD1" <-> "OD2" Residue "F ASP 224": "OD1" <-> "OD2" Residue "F GLU 242": "OE1" <-> "OE2" Residue "F ARG 293": "NH1" <-> "NH2" Residue "F ARG 298": "NH1" <-> "NH2" Residue "F ARG 313": "NH1" <-> "NH2" Residue "F GLU 328": "OE1" <-> "OE2" Residue "F ASP 334": "OD1" <-> "OD2" Residue "F GLU 335": "OE1" <-> "OE2" Residue "F GLU 355": "OE1" <-> "OE2" Residue "F ARG 357": "NH1" <-> "NH2" Residue "G ASP 27": "OD1" <-> "OD2" Residue "G GLU 63": "OE1" <-> "OE2" Residue "G ARG 74": "NH1" <-> "NH2" Residue "G GLU 80": "OE1" <-> "OE2" Residue "G GLU 81": "OE1" <-> "OE2" Residue "G GLU 82": "OE1" <-> "OE2" Residue "G GLU 99": "OE1" <-> "OE2" Residue "G PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 110": "OD1" <-> "OD2" Residue "G PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 139": "OE1" <-> "OE2" Residue "G TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 150": "OE1" <-> "OE2" Residue "G ASP 152": "OD1" <-> "OD2" Residue "G GLU 161": "OE1" <-> "OE2" Residue "G PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 196": "OE1" <-> "OE2" Residue "G PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 211": "OE1" <-> "OE2" Residue "G PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 237": "NH1" <-> "NH2" Residue "G ASP 257": "OD1" <-> "OD2" Residue "G ARG 293": "NH1" <-> "NH2" Residue "G ARG 298": "NH1" <-> "NH2" Residue "G ARG 313": "NH1" <-> "NH2" Residue "G GLU 321": "OE1" <-> "OE2" Residue "G GLU 328": "OE1" <-> "OE2" Residue "G ASP 334": "OD1" <-> "OD2" Residue "G GLU 335": "OE1" <-> "OE2" Residue "G GLU 355": "OE1" <-> "OE2" Residue "I ARG 13": "NH1" <-> "NH2" Residue "I GLU 39": "OE1" <-> "OE2" Residue "I ASP 47": "OD1" <-> "OD2" Residue "I GLU 63": "OE1" <-> "OE2" Residue "I GLU 68": "OE1" <-> "OE2" Residue "I ASP 102": "OD1" <-> "OD2" Residue "I ASP 110": "OD1" <-> "OD2" Residue "I ASP 114": "OD1" <-> "OD2" Residue "I PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 125": "NH1" <-> "NH2" Residue "I GLU 130": "OE1" <-> "OE2" Residue "I GLU 139": "OE1" <-> "OE2" Residue "I GLU 140": "OE1" <-> "OE2" Residue "I TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 152": "OD1" <-> "OD2" Residue "I PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 161": "OE1" <-> "OE2" Residue "I PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 196": "OE1" <-> "OE2" Residue "I GLU 204": "OE1" <-> "OE2" Residue "I GLU 211": "OE1" <-> "OE2" Residue "I ASP 218": "OD1" <-> "OD2" Residue "I GLU 242": "OE1" <-> "OE2" Residue "I ARG 261": "NH1" <-> "NH2" Residue "I ASP 282": "OD1" <-> "OD2" Residue "I ARG 293": "NH1" <-> "NH2" Residue "I ASP 294": "OD1" <-> "OD2" Residue "I ARG 313": "NH1" <-> "NH2" Residue "I GLU 328": "OE1" <-> "OE2" Residue "I ASP 334": "OD1" <-> "OD2" Residue "I GLU 351": "OE1" <-> "OE2" Residue "I ARG 357": "NH1" <-> "NH2" Residue "J ASP 27": "OD1" <-> "OD2" Residue "J ASP 47": "OD1" <-> "OD2" Residue "J ARG 74": "NH1" <-> "NH2" Residue "J GLU 82": "OE1" <-> "OE2" Residue "J GLU 99": "OE1" <-> "OE2" Residue "J ASP 102": "OD1" <-> "OD2" Residue "J PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 110": "OD1" <-> "OD2" Residue "J ASP 114": "OD1" <-> "OD2" Residue "J PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 130": "OE1" <-> "OE2" Residue "J GLU 139": "OE1" <-> "OE2" Residue "J GLU 140": "OE1" <-> "OE2" Residue "J TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 150": "OE1" <-> "OE2" Residue "J ASP 152": "OD1" <-> "OD2" Residue "J GLU 161": "OE1" <-> "OE2" Residue "J GLU 211": "OE1" <-> "OE2" Residue "J ASP 218": "OD1" <-> "OD2" Residue "J PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 257": "OD1" <-> "OD2" Residue "J ARG 293": "NH1" <-> "NH2" Residue "J ARG 298": "NH1" <-> "NH2" Residue "J ARG 313": "NH1" <-> "NH2" Residue "J GLU 321": "OE1" <-> "OE2" Residue "J ASP 329": "OD1" <-> "OD2" Residue "J GLU 355": "OE1" <-> "OE2" Residue "J ARG 357": "NH1" <-> "NH2" Residue "K TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 39": "OE1" <-> "OE2" Residue "K GLU 61": "OE1" <-> "OE2" Residue "K GLU 68": "OE1" <-> "OE2" Residue "K ARG 74": "NH1" <-> "NH2" Residue "K GLU 81": "OE1" <-> "OE2" Residue "K ASP 102": "OD1" <-> "OD2" Residue "K PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 110": "OD1" <-> "OD2" Residue "K ASP 114": "OD1" <-> "OD2" Residue "K PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 139": "OE1" <-> "OE2" Residue "K GLU 140": "OE1" <-> "OE2" Residue "K ASP 152": "OD1" <-> "OD2" Residue "K ARG 158": "NH1" <-> "NH2" Residue "K PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 194": "OE1" <-> "OE2" Residue "K GLU 196": "OE1" <-> "OE2" Residue "K TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 211": "OE1" <-> "OE2" Residue "K ASP 218": "OD1" <-> "OD2" Residue "K ASP 257": "OD1" <-> "OD2" Residue "K ASP 282": "OD1" <-> "OD2" Residue "K ARG 293": "NH1" <-> "NH2" Residue "K ARG 298": "NH1" <-> "NH2" Residue "K GLU 304": "OE1" <-> "OE2" Residue "K ARG 313": "NH1" <-> "NH2" Residue "K GLU 328": "OE1" <-> "OE2" Residue "K ASP 329": "OD1" <-> "OD2" Residue "K ASP 334": "OD1" <-> "OD2" Residue "K ARG 357": "NH1" <-> "NH2" Residue "L ASP 27": "OD1" <-> "OD2" Residue "L PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 39": "OE1" <-> "OE2" Residue "L ASP 47": "OD1" <-> "OD2" Residue "L GLU 63": "OE1" <-> "OE2" Residue "L ARG 70": "NH1" <-> "NH2" Residue "L ARG 74": "NH1" <-> "NH2" Residue "L GLU 80": "OE1" <-> "OE2" Residue "L ASP 95": "OD1" <-> "OD2" Residue "L ASP 110": "OD1" <-> "OD2" Residue "L PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 139": "OE1" <-> "OE2" Residue "L GLU 140": "OE1" <-> "OE2" Residue "L TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 152": "OD1" <-> "OD2" Residue "L TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 196": "OE1" <-> "OE2" Residue "L TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 218": "OD1" <-> "OD2" Residue "L PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 242": "OE1" <-> "OE2" Residue "L ARG 293": "NH1" <-> "NH2" Residue "L ARG 298": "NH1" <-> "NH2" Residue "L ARG 313": "NH1" <-> "NH2" Residue "L GLU 321": "OE1" <-> "OE2" Residue "L GLU 328": "OE1" <-> "OE2" Residue "L ASP 334": "OD1" <-> "OD2" Residue "L GLU 351": "OE1" <-> "OE2" Residue "L GLU 355": "OE1" <-> "OE2" Residue "L ARG 357": "NH1" <-> "NH2" Residue "H TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 63": "OE1" <-> "OE2" Residue "H GLU 68": "OE1" <-> "OE2" Residue "H GLU 80": "OE1" <-> "OE2" Residue "H GLU 82": "OE1" <-> "OE2" Residue "H GLU 99": "OE1" <-> "OE2" Residue "H PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 110": "OD1" <-> "OD2" Residue "H ASP 114": "OD1" <-> "OD2" Residue "H PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 140": "OE1" <-> "OE2" Residue "H TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 152": "OD1" <-> "OD2" Residue "H GLU 161": "OE1" <-> "OE2" Residue "H PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 196": "OE1" <-> "OE2" Residue "H TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 218": "OD1" <-> "OD2" Residue "H ASP 224": "OD1" <-> "OD2" Residue "H GLU 242": "OE1" <-> "OE2" Residue "H ASP 257": "OD1" <-> "OD2" Residue "H ARG 293": "NH1" <-> "NH2" Residue "H ARG 298": "NH1" <-> "NH2" Residue "H ARG 313": "NH1" <-> "NH2" Residue "H GLU 321": "OE1" <-> "OE2" Residue "H GLU 328": "OE1" <-> "OE2" Residue "H ASP 329": "OD1" <-> "OD2" Residue "H ASP 334": "OD1" <-> "OD2" Residue "H GLU 351": "OE1" <-> "OE2" Residue "H GLU 355": "OE1" <-> "OE2" Residue "H ARG 357": "NH1" <-> "NH2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 35292 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 3172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 3172 Classifications: {'peptide': 407} Link IDs: {'PTRANS': 31, 'TRANS': 375} Chain breaks: 1 Chain: "B" Number of atoms: 3167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3167 Classifications: {'peptide': 406} Link IDs: {'PTRANS': 31, 'TRANS': 374} Chain breaks: 1 Chain: "E" Number of atoms: 2785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2785 Classifications: {'peptide': 360} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 337} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 6 Chain: "C" Number of atoms: 3167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3167 Classifications: {'peptide': 406} Link IDs: {'PTRANS': 31, 'TRANS': 374} Chain breaks: 1 Chain: "D" Number of atoms: 3167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3167 Classifications: {'peptide': 406} Link IDs: {'PTRANS': 31, 'TRANS': 374} Chain breaks: 1 Chain: "F" Number of atoms: 2714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2714 Classifications: {'peptide': 350} Link IDs: {'PTRANS': 22, 'TRANS': 327} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 2 Chain: "G" Number of atoms: 2789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2789 Classifications: {'peptide': 360} Link IDs: {'PTRANS': 22, 'TRANS': 337} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 2 Chain: "I" Number of atoms: 2789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2789 Classifications: {'peptide': 360} Link IDs: {'PTRANS': 22, 'TRANS': 337} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 2 Chain: "J" Number of atoms: 2789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2789 Classifications: {'peptide': 360} Link IDs: {'PTRANS': 22, 'TRANS': 337} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 2 Chain: "K" Number of atoms: 2783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2783 Classifications: {'peptide': 360} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 22, 'TRANS': 337} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 2783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2783 Classifications: {'peptide': 360} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 22, 'TRANS': 337} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 2789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2789 Classifications: {'peptide': 360} Link IDs: {'PTRANS': 22, 'TRANS': 337} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 2 Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'GDD': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'GDD': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 17.39, per 1000 atoms: 0.49 Number of scatterers: 35292 At special positions: 0 Unit cell: (132.552, 194.62, 184.1, 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 219 16.00 P 34 15.00 O 6482 8.00 N 6189 7.00 C 22368 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS J 289 " - pdb=" SG CYS J 306 " distance=2.03 Simple disulfide: pdb=" SG CYS L 289 " - pdb=" SG CYS L 306 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=10, symmetry=0 Number of additional bonds: simple=10, symmetry=0 Coordination: Other bonds: Time building additional restraints: 13.01 Conformation dependent library (CDL) restraints added in 6.5 seconds 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8256 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 114 helices and 80 sheets defined 22.0% alpha, 15.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.76 Creating SS restraints... Processing helix chain 'A' and resid 26 through 28 No H-bonds generated for 'chain 'A' and resid 26 through 28' Processing helix chain 'A' and resid 36 through 45 removed outlier: 4.343A pdb=" N HIS A 40 " --> pdb=" O MET A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 90 through 97 removed outlier: 3.854A pdb=" N GLY A 94 " --> pdb=" O GLY A 90 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N LEU A 95 " --> pdb=" O THR A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 102 No H-bonds generated for 'chain 'A' and resid 99 through 102' Processing helix chain 'A' and resid 123 through 133 Processing helix chain 'A' and resid 148 through 151 removed outlier: 3.522A pdb=" N ASN A 151 " --> pdb=" O GLN A 148 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 148 through 151' Processing helix chain 'A' and resid 190 through 201 removed outlier: 3.974A pdb=" N LEU A 194 " --> pdb=" O ALA A 190 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASP A 196 " --> pdb=" O LYS A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 225 No H-bonds generated for 'chain 'A' and resid 222 through 225' Processing helix chain 'A' and resid 251 through 268 removed outlier: 4.168A pdb=" N GLN A 266 " --> pdb=" O LEU A 262 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N ASP A 267 " --> pdb=" O SER A 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 22 Proline residue: B 19 - end of helix removed outlier: 3.697A pdb=" N PHE B 22 " --> pdb=" O PRO B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 28 No H-bonds generated for 'chain 'B' and resid 26 through 28' Processing helix chain 'B' and resid 36 through 45 removed outlier: 4.275A pdb=" N HIS B 40 " --> pdb=" O MET B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 76 Processing helix chain 'B' and resid 90 through 97 removed outlier: 4.067A pdb=" N GLY B 94 " --> pdb=" O GLY B 90 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LEU B 95 " --> pdb=" O THR B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 102 No H-bonds generated for 'chain 'B' and resid 99 through 102' Processing helix chain 'B' and resid 123 through 133 Processing helix chain 'B' and resid 148 through 151 Processing helix chain 'B' and resid 188 through 202 Proline residue: B 193 - end of helix Processing helix chain 'B' and resid 222 through 225 No H-bonds generated for 'chain 'B' and resid 222 through 225' Processing helix chain 'B' and resid 253 through 266 removed outlier: 4.297A pdb=" N GLN B 266 " --> pdb=" O LEU B 262 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 18 No H-bonds generated for 'chain 'E' and resid 15 through 18' Processing helix chain 'E' and resid 33 through 40 Processing helix chain 'E' and resid 57 through 71 removed outlier: 4.287A pdb=" N GLN E 69 " --> pdb=" O LYS E 65 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ARG E 70 " --> pdb=" O ALA E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 92 Processing helix chain 'E' and resid 94 through 97 No H-bonds generated for 'chain 'E' and resid 94 through 97' Processing helix chain 'E' and resid 117 through 127 Processing helix chain 'E' and resid 180 through 183 No H-bonds generated for 'chain 'E' and resid 180 through 183' Processing helix chain 'E' and resid 197 through 203 Processing helix chain 'E' and resid 222 through 239 removed outlier: 3.724A pdb=" N GLN E 238 " --> pdb=" O GLN E 234 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS E 239 " --> pdb=" O SER E 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 28 No H-bonds generated for 'chain 'C' and resid 26 through 28' Processing helix chain 'C' and resid 38 through 45 Processing helix chain 'C' and resid 63 through 76 Processing helix chain 'C' and resid 90 through 97 removed outlier: 3.872A pdb=" N GLY C 94 " --> pdb=" O GLY C 90 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N LEU C 95 " --> pdb=" O THR C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 102 No H-bonds generated for 'chain 'C' and resid 99 through 102' Processing helix chain 'C' and resid 123 through 130 Processing helix chain 'C' and resid 149 through 151 No H-bonds generated for 'chain 'C' and resid 149 through 151' Processing helix chain 'C' and resid 188 through 202 removed outlier: 3.864A pdb=" N LEU C 191 " --> pdb=" O PRO C 188 " (cutoff:3.500A) Proline residue: C 193 - end of helix removed outlier: 4.128A pdb=" N GLN C 199 " --> pdb=" O ASP C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 225 No H-bonds generated for 'chain 'C' and resid 222 through 225' Processing helix chain 'C' and resid 251 through 267 removed outlier: 4.018A pdb=" N GLN C 266 " --> pdb=" O LEU C 262 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ASP C 267 " --> pdb=" O SER C 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 21 Proline residue: D 19 - end of helix Processing helix chain 'D' and resid 26 through 28 No H-bonds generated for 'chain 'D' and resid 26 through 28' Processing helix chain 'D' and resid 36 through 44 removed outlier: 4.353A pdb=" N HIS D 40 " --> pdb=" O MET D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 75 Processing helix chain 'D' and resid 90 through 97 removed outlier: 3.955A pdb=" N GLY D 94 " --> pdb=" O GLY D 90 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N LEU D 95 " --> pdb=" O THR D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 102 No H-bonds generated for 'chain 'D' and resid 99 through 102' Processing helix chain 'D' and resid 123 through 133 removed outlier: 3.727A pdb=" N GLN D 133 " --> pdb=" O ALA D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 151 Processing helix chain 'D' and resid 188 through 202 removed outlier: 3.919A pdb=" N LEU D 191 " --> pdb=" O PRO D 188 " (cutoff:3.500A) Proline residue: D 193 - end of helix Processing helix chain 'D' and resid 222 through 225 No H-bonds generated for 'chain 'D' and resid 222 through 225' Processing helix chain 'D' and resid 227 through 230 No H-bonds generated for 'chain 'D' and resid 227 through 230' Processing helix chain 'D' and resid 253 through 266 removed outlier: 4.157A pdb=" N GLN D 266 " --> pdb=" O LEU D 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 17 through 19 No H-bonds generated for 'chain 'F' and resid 17 through 19' Processing helix chain 'F' and resid 23 through 25 No H-bonds generated for 'chain 'F' and resid 23 through 25' Processing helix chain 'F' and resid 33 through 44 Processing helix chain 'F' and resid 57 through 71 removed outlier: 5.477A pdb=" N GLN F 69 " --> pdb=" O LYS F 65 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N ARG F 70 " --> pdb=" O ALA F 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 92 Processing helix chain 'F' and resid 94 through 97 No H-bonds generated for 'chain 'F' and resid 94 through 97' Processing helix chain 'F' and resid 117 through 127 removed outlier: 3.577A pdb=" N GLN F 122 " --> pdb=" O GLN F 118 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N HIS F 126 " --> pdb=" O GLN F 122 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N HIS F 127 " --> pdb=" O PHE F 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 197 through 204 Processing helix chain 'F' and resid 222 through 239 Processing helix chain 'G' and resid 15 through 18 No H-bonds generated for 'chain 'G' and resid 15 through 18' Processing helix chain 'G' and resid 23 through 25 No H-bonds generated for 'chain 'G' and resid 23 through 25' Processing helix chain 'G' and resid 33 through 44 removed outlier: 3.607A pdb=" N GLN G 37 " --> pdb=" O ILE G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 71 removed outlier: 4.798A pdb=" N GLN G 69 " --> pdb=" O LYS G 65 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ARG G 70 " --> pdb=" O ALA G 66 " (cutoff:3.500A) Processing helix chain 'G' and resid 88 through 92 Processing helix chain 'G' and resid 94 through 97 No H-bonds generated for 'chain 'G' and resid 94 through 97' Processing helix chain 'G' and resid 117 through 127 removed outlier: 4.336A pdb=" N HIS G 126 " --> pdb=" O GLN G 122 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N HIS G 127 " --> pdb=" O PHE G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 180 through 182 No H-bonds generated for 'chain 'G' and resid 180 through 182' Processing helix chain 'G' and resid 197 through 204 removed outlier: 4.020A pdb=" N LYS G 203 " --> pdb=" O PRO G 199 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLU G 204 " --> pdb=" O ILE G 200 " (cutoff:3.500A) Processing helix chain 'G' and resid 222 through 238 Processing helix chain 'I' and resid 33 through 43 removed outlier: 3.701A pdb=" N GLN I 37 " --> pdb=" O ILE I 33 " (cutoff:3.500A) Processing helix chain 'I' and resid 58 through 71 removed outlier: 4.177A pdb=" N ALA I 66 " --> pdb=" O LYS I 62 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N GLN I 69 " --> pdb=" O LYS I 65 " (cutoff:3.500A) Processing helix chain 'I' and resid 87 through 92 removed outlier: 3.598A pdb=" N ALA I 91 " --> pdb=" O ALA I 87 " (cutoff:3.500A) Processing helix chain 'I' and resid 117 through 127 Processing helix chain 'I' and resid 197 through 202 Processing helix chain 'I' and resid 222 through 239 removed outlier: 3.600A pdb=" N LEU I 226 " --> pdb=" O PRO I 222 " (cutoff:3.500A) Processing helix chain 'J' and resid 23 through 25 No H-bonds generated for 'chain 'J' and resid 23 through 25' Processing helix chain 'J' and resid 33 through 44 removed outlier: 4.117A pdb=" N GLN J 37 " --> pdb=" O ILE J 33 " (cutoff:3.500A) Processing helix chain 'J' and resid 57 through 71 removed outlier: 4.498A pdb=" N LYS J 62 " --> pdb=" O GLN J 58 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLN J 69 " --> pdb=" O LYS J 65 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG J 70 " --> pdb=" O ALA J 66 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 92 Processing helix chain 'J' and resid 94 through 97 No H-bonds generated for 'chain 'J' and resid 94 through 97' Processing helix chain 'J' and resid 117 through 127 Processing helix chain 'J' and resid 141 through 143 No H-bonds generated for 'chain 'J' and resid 141 through 143' Processing helix chain 'J' and resid 193 through 196 No H-bonds generated for 'chain 'J' and resid 193 through 196' Processing helix chain 'J' and resid 198 through 204 Processing helix chain 'J' and resid 222 through 239 Processing helix chain 'K' and resid 17 through 20 No H-bonds generated for 'chain 'K' and resid 17 through 20' Processing helix chain 'K' and resid 23 through 25 No H-bonds generated for 'chain 'K' and resid 23 through 25' Processing helix chain 'K' and resid 33 through 44 Processing helix chain 'K' and resid 57 through 70 removed outlier: 3.976A pdb=" N GLN K 69 " --> pdb=" O LYS K 65 " (cutoff:3.500A) Processing helix chain 'K' and resid 88 through 92 Processing helix chain 'K' and resid 94 through 97 No H-bonds generated for 'chain 'K' and resid 94 through 97' Processing helix chain 'K' and resid 117 through 127 removed outlier: 3.987A pdb=" N HIS K 126 " --> pdb=" O GLN K 122 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N HIS K 127 " --> pdb=" O PHE K 123 " (cutoff:3.500A) Processing helix chain 'K' and resid 197 through 204 Processing helix chain 'K' and resid 222 through 239 Processing helix chain 'L' and resid 15 through 18 No H-bonds generated for 'chain 'L' and resid 15 through 18' Processing helix chain 'L' and resid 23 through 25 No H-bonds generated for 'chain 'L' and resid 23 through 25' Processing helix chain 'L' and resid 33 through 44 Processing helix chain 'L' and resid 57 through 71 removed outlier: 3.832A pdb=" N GLU L 63 " --> pdb=" O VAL L 59 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ALA L 66 " --> pdb=" O LYS L 62 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N GLN L 69 " --> pdb=" O LYS L 65 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ARG L 70 " --> pdb=" O ALA L 66 " (cutoff:3.500A) Processing helix chain 'L' and resid 88 through 92 Processing helix chain 'L' and resid 117 through 127 removed outlier: 4.087A pdb=" N ARG L 125 " --> pdb=" O VAL L 121 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N HIS L 126 " --> pdb=" O GLN L 122 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N HIS L 127 " --> pdb=" O PHE L 123 " (cutoff:3.500A) Processing helix chain 'L' and resid 182 through 185 Processing helix chain 'L' and resid 197 through 204 Processing helix chain 'L' and resid 222 through 238 removed outlier: 3.513A pdb=" N CYS L 230 " --> pdb=" O LEU L 226 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER L 235 " --> pdb=" O LEU L 231 " (cutoff:3.500A) Processing helix chain 'H' and resid 23 through 25 No H-bonds generated for 'chain 'H' and resid 23 through 25' Processing helix chain 'H' and resid 28 through 30 No H-bonds generated for 'chain 'H' and resid 28 through 30' Processing helix chain 'H' and resid 33 through 44 removed outlier: 3.886A pdb=" N GLN H 37 " --> pdb=" O ILE H 33 " (cutoff:3.500A) Processing helix chain 'H' and resid 58 through 71 Processing helix chain 'H' and resid 88 through 97 removed outlier: 3.923A pdb=" N ALA H 93 " --> pdb=" O PRO H 89 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG H 94 " --> pdb=" O LEU H 90 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N ASP H 95 " --> pdb=" O ALA H 91 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N LEU H 96 " --> pdb=" O LEU H 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 117 through 127 Processing helix chain 'H' and resid 182 through 185 No H-bonds generated for 'chain 'H' and resid 182 through 185' Processing helix chain 'H' and resid 197 through 203 Processing helix chain 'H' and resid 222 through 239 removed outlier: 3.651A pdb=" N LEU H 226 " --> pdb=" O PRO H 222 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 236 through 240 removed outlier: 6.479A pdb=" N PHE A 137 " --> pdb=" O TYR A 237 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N HIS A 239 " --> pdb=" O PHE A 137 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N LEU A 139 " --> pdb=" O HIS A 239 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N ILE A 183 " --> pdb=" O LEU A 140 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ALA A 4 " --> pdb=" O GLN A 51 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ILE A 53 " --> pdb=" O ALA A 4 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ILE A 6 " --> pdb=" O ILE A 53 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N LEU A 55 " --> pdb=" O ILE A 6 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N LEU A 55 " --> pdb=" O PRO A 79 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ARG A 81 " --> pdb=" O LEU A 55 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N GLY A 57 " --> pdb=" O ARG A 81 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N LEU A 83 " --> pdb=" O GLY A 57 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 117 through 119 Processing sheet with id= C, first strand: chain 'A' and resid 141 through 143 Processing sheet with id= D, first strand: chain 'A' and resid 287 through 289 removed outlier: 6.132A pdb=" N VAL A 305 " --> pdb=" O TYR A 288 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'A' and resid 318 through 320 Processing sheet with id= F, first strand: chain 'A' and resid 339 through 341 removed outlier: 6.956A pdb=" N THR A 385 " --> pdb=" O ILE A 340 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'A' and resid 154 through 158 removed outlier: 6.121A pdb=" N ASN A 158 " --> pdb=" O VAL A 164 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N VAL A 164 " --> pdb=" O ASN A 158 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 236 through 241 removed outlier: 6.400A pdb=" N PHE B 137 " --> pdb=" O TYR B 237 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N HIS B 239 " --> pdb=" O PHE B 137 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N LEU B 139 " --> pdb=" O HIS B 239 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N THR B 241 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N GLY B 141 " --> pdb=" O THR B 241 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N ILE B 183 " --> pdb=" O LEU B 140 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N LYS B 3 " --> pdb=" O PHE B 111 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N LEU B 113 " --> pdb=" O LYS B 3 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N VAL B 5 " --> pdb=" O LEU B 113 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N ALA B 4 " --> pdb=" O GLN B 51 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ILE B 53 " --> pdb=" O ALA B 4 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ILE B 6 " --> pdb=" O ILE B 53 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N LEU B 55 " --> pdb=" O ILE B 6 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N LEU B 55 " --> pdb=" O PRO B 79 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ARG B 81 " --> pdb=" O LEU B 55 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N GLY B 57 " --> pdb=" O ARG B 81 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N LEU B 83 " --> pdb=" O GLY B 57 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 117 through 119 Processing sheet with id= J, first strand: chain 'B' and resid 141 through 143 Processing sheet with id= K, first strand: chain 'B' and resid 287 through 289 removed outlier: 6.315A pdb=" N VAL B 305 " --> pdb=" O TYR B 288 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'B' and resid 318 through 320 Processing sheet with id= M, first strand: chain 'B' and resid 154 through 158 removed outlier: 6.488A pdb=" N ASN B 158 " --> pdb=" O VAL B 164 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N VAL B 164 " --> pdb=" O ASN B 158 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 175 through 178 removed outlier: 7.143A pdb=" N HIS E 48 " --> pdb=" O ALA E 3 " (cutoff:3.500A) removed outlier: 8.664A pdb=" N ILE E 5 " --> pdb=" O HIS E 48 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ILE E 50 " --> pdb=" O ILE E 5 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ARG E 74 " --> pdb=" O VAL E 49 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N LEU E 51 " --> pdb=" O ARG E 74 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N SER E 76 " --> pdb=" O LEU E 51 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N VAL E 53 " --> pdb=" O SER E 76 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N SER E 78 " --> pdb=" O VAL E 53 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 111 through 113 Processing sheet with id= P, first strand: chain 'E' and resid 207 through 211 removed outlier: 6.971A pdb=" N GLY E 131 " --> pdb=" O TYR E 208 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N MET E 210 " --> pdb=" O GLY E 131 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ILE E 133 " --> pdb=" O MET E 210 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 254 through 256 removed outlier: 6.820A pdb=" N VAL E 272 " --> pdb=" O LEU E 255 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'E' and resid 285 through 287 Processing sheet with id= S, first strand: chain 'E' and resid 319 through 321 Processing sheet with id= T, first strand: chain 'C' and resid 236 through 240 removed outlier: 6.854A pdb=" N PHE C 137 " --> pdb=" O TYR C 237 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N HIS C 239 " --> pdb=" O PHE C 137 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LEU C 139 " --> pdb=" O HIS C 239 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N ILE C 183 " --> pdb=" O LEU C 140 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS C 3 " --> pdb=" O ALA C 109 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N ALA C 4 " --> pdb=" O GLN C 51 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ILE C 53 " --> pdb=" O ALA C 4 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ILE C 6 " --> pdb=" O ILE C 53 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LEU C 55 " --> pdb=" O ILE C 6 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N LEU C 55 " --> pdb=" O PRO C 79 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ARG C 81 " --> pdb=" O LEU C 55 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N GLY C 57 " --> pdb=" O ARG C 81 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N LEU C 83 " --> pdb=" O GLY C 57 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 117 through 119 Processing sheet with id= V, first strand: chain 'C' and resid 141 through 143 Processing sheet with id= W, first strand: chain 'C' and resid 287 through 289 removed outlier: 6.290A pdb=" N VAL C 305 " --> pdb=" O TYR C 288 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain 'C' and resid 318 through 320 Processing sheet with id= Y, first strand: chain 'C' and resid 339 through 341 removed outlier: 6.573A pdb=" N THR C 385 " --> pdb=" O ILE C 340 " (cutoff:3.500A) No H-bonds generated for sheet with id= Y Processing sheet with id= Z, first strand: chain 'C' and resid 154 through 157 Processing sheet with id= AA, first strand: chain 'D' and resid 236 through 241 removed outlier: 6.523A pdb=" N PHE D 137 " --> pdb=" O TYR D 237 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N HIS D 239 " --> pdb=" O PHE D 137 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N LEU D 139 " --> pdb=" O HIS D 239 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N THR D 241 " --> pdb=" O LEU D 139 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N GLY D 141 " --> pdb=" O THR D 241 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N ILE D 183 " --> pdb=" O LEU D 140 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N ALA D 4 " --> pdb=" O GLN D 51 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ILE D 53 " --> pdb=" O ALA D 4 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ILE D 6 " --> pdb=" O ILE D 53 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LEU D 55 " --> pdb=" O ILE D 6 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N LEU D 55 " --> pdb=" O PRO D 79 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ARG D 81 " --> pdb=" O LEU D 55 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N GLY D 57 " --> pdb=" O ARG D 81 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N LEU D 83 " --> pdb=" O GLY D 57 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'D' and resid 117 through 119 Processing sheet with id= AC, first strand: chain 'D' and resid 141 through 143 Processing sheet with id= AD, first strand: chain 'D' and resid 287 through 289 removed outlier: 6.263A pdb=" N VAL D 305 " --> pdb=" O TYR D 288 " (cutoff:3.500A) No H-bonds generated for sheet with id= AD Processing sheet with id= AE, first strand: chain 'D' and resid 318 through 320 Processing sheet with id= AF, first strand: chain 'D' and resid 339 through 341 removed outlier: 6.515A pdb=" N THR D 385 " --> pdb=" O ILE D 340 " (cutoff:3.500A) No H-bonds generated for sheet with id= AF Processing sheet with id= AG, first strand: chain 'D' and resid 154 through 158 removed outlier: 6.213A pdb=" N ASN D 158 " --> pdb=" O VAL D 164 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N VAL D 164 " --> pdb=" O ASN D 158 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'F' and resid 207 through 211 removed outlier: 7.358A pdb=" N GLY F 131 " --> pdb=" O TYR F 208 " (cutoff:3.500A) removed outlier: 8.244A pdb=" N MET F 210 " --> pdb=" O GLY F 131 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ILE F 133 " --> pdb=" O MET F 210 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N MET F 175 " --> pdb=" O LEU F 134 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N HIS F 48 " --> pdb=" O ALA F 3 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N ILE F 5 " --> pdb=" O HIS F 48 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ILE F 50 " --> pdb=" O ILE F 5 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N VAL F 7 " --> pdb=" O ILE F 50 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N ALA F 52 " --> pdb=" O VAL F 7 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ARG F 74 " --> pdb=" O VAL F 49 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N LEU F 51 " --> pdb=" O ARG F 74 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N SER F 76 " --> pdb=" O LEU F 51 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N VAL F 53 " --> pdb=" O SER F 76 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N SER F 78 " --> pdb=" O VAL F 53 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'F' and resid 111 through 113 Processing sheet with id= AJ, first strand: chain 'F' and resid 135 through 137 Processing sheet with id= AK, first strand: chain 'F' and resid 254 through 256 removed outlier: 6.955A pdb=" N VAL F 272 " --> pdb=" O LEU F 255 " (cutoff:3.500A) No H-bonds generated for sheet with id= AK Processing sheet with id= AL, first strand: chain 'F' and resid 285 through 287 Processing sheet with id= AM, first strand: chain 'F' and resid 319 through 321 Processing sheet with id= AN, first strand: chain 'F' and resid 341 through 343 removed outlier: 7.074A pdb=" N ARG F 357 " --> pdb=" O SER F 342 " (cutoff:3.500A) No H-bonds generated for sheet with id= AN Processing sheet with id= AO, first strand: chain 'G' and resid 207 through 211 removed outlier: 7.017A pdb=" N GLY G 131 " --> pdb=" O TYR G 208 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N MET G 210 " --> pdb=" O GLY G 131 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ILE G 133 " --> pdb=" O MET G 210 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N MET G 175 " --> pdb=" O LEU G 134 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N LYS G 2 " --> pdb=" O PHE G 105 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N LEU G 107 " --> pdb=" O LYS G 2 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LEU G 4 " --> pdb=" O LEU G 107 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N HIS G 48 " --> pdb=" O ALA G 3 " (cutoff:3.500A) removed outlier: 8.838A pdb=" N ILE G 5 " --> pdb=" O HIS G 48 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ILE G 50 " --> pdb=" O ILE G 5 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N SER G 76 " --> pdb=" O LEU G 51 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'G' and resid 111 through 113 removed outlier: 3.570A pdb=" N MET G 217 " --> pdb=" O ILE G 112 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'G' and resid 135 through 137 Processing sheet with id= AR, first strand: chain 'G' and resid 254 through 256 removed outlier: 6.791A pdb=" N VAL G 272 " --> pdb=" O LEU G 255 " (cutoff:3.500A) No H-bonds generated for sheet with id= AR Processing sheet with id= AS, first strand: chain 'G' and resid 285 through 287 Processing sheet with id= AT, first strand: chain 'G' and resid 306 through 308 removed outlier: 6.268A pdb=" N THR G 324 " --> pdb=" O ILE G 307 " (cutoff:3.500A) No H-bonds generated for sheet with id= AT Processing sheet with id= AU, first strand: chain 'G' and resid 319 through 321 Processing sheet with id= AV, first strand: chain 'I' and resid 208 through 211 removed outlier: 4.943A pdb=" N MET I 175 " --> pdb=" O LEU I 134 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N HIS I 48 " --> pdb=" O ALA I 3 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N ILE I 5 " --> pdb=" O HIS I 48 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ILE I 50 " --> pdb=" O ILE I 5 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N VAL I 7 " --> pdb=" O ILE I 50 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N ALA I 52 " --> pdb=" O VAL I 7 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'I' and resid 111 through 113 Processing sheet with id= AX, first strand: chain 'I' and resid 135 through 137 Processing sheet with id= AY, first strand: chain 'I' and resid 285 through 287 Processing sheet with id= AZ, first strand: chain 'I' and resid 341 through 343 removed outlier: 6.652A pdb=" N ARG I 357 " --> pdb=" O SER I 342 " (cutoff:3.500A) No H-bonds generated for sheet with id= AZ Processing sheet with id= BA, first strand: chain 'J' and resid 207 through 211 removed outlier: 7.091A pdb=" N GLY J 131 " --> pdb=" O TYR J 208 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N MET J 210 " --> pdb=" O GLY J 131 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ILE J 133 " --> pdb=" O MET J 210 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N MET J 175 " --> pdb=" O LEU J 134 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N LYS J 2 " --> pdb=" O PHE J 105 " (cutoff:3.500A) removed outlier: 8.346A pdb=" N LEU J 107 " --> pdb=" O LYS J 2 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N LEU J 4 " --> pdb=" O LEU J 107 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N HIS J 48 " --> pdb=" O ALA J 3 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N ILE J 5 " --> pdb=" O HIS J 48 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ILE J 50 " --> pdb=" O ILE J 5 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ARG J 74 " --> pdb=" O VAL J 49 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N LEU J 51 " --> pdb=" O ARG J 74 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N SER J 76 " --> pdb=" O LEU J 51 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N VAL J 53 " --> pdb=" O SER J 76 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N SER J 78 " --> pdb=" O VAL J 53 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'J' and resid 135 through 137 Processing sheet with id= BC, first strand: chain 'J' and resid 254 through 256 removed outlier: 6.428A pdb=" N VAL J 272 " --> pdb=" O LEU J 255 " (cutoff:3.500A) No H-bonds generated for sheet with id= BC Processing sheet with id= BD, first strand: chain 'J' and resid 285 through 287 Processing sheet with id= BE, first strand: chain 'J' and resid 319 through 321 Processing sheet with id= BF, first strand: chain 'J' and resid 330 through 332 removed outlier: 6.447A pdb=" N LYS J 347 " --> pdb=" O ILE J 331 " (cutoff:3.500A) No H-bonds generated for sheet with id= BF Processing sheet with id= BG, first strand: chain 'J' and resid 341 through 343 removed outlier: 6.664A pdb=" N ARG J 357 " --> pdb=" O SER J 342 " (cutoff:3.500A) No H-bonds generated for sheet with id= BG Processing sheet with id= BH, first strand: chain 'J' and resid 146 through 149 removed outlier: 3.731A pdb=" N ARG J 158 " --> pdb=" O VAL J 148 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain 'K' and resid 207 through 211 removed outlier: 6.977A pdb=" N GLY K 131 " --> pdb=" O TYR K 208 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N MET K 210 " --> pdb=" O GLY K 131 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ILE K 133 " --> pdb=" O MET K 210 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N MET K 175 " --> pdb=" O LEU K 134 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N THR K 136 " --> pdb=" O ALA K 173 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N ALA K 173 " --> pdb=" O THR K 136 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE K 105 " --> pdb=" O LYS K 2 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N HIS K 48 " --> pdb=" O ALA K 3 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N ILE K 5 " --> pdb=" O HIS K 48 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ILE K 50 " --> pdb=" O ILE K 5 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N SER K 76 " --> pdb=" O LEU K 51 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N VAL K 53 " --> pdb=" O SER K 76 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N SER K 78 " --> pdb=" O VAL K 53 " (cutoff:3.500A) Processing sheet with id= BJ, first strand: chain 'K' and resid 111 through 113 Processing sheet with id= BK, first strand: chain 'K' and resid 285 through 287 Processing sheet with id= BL, first strand: chain 'K' and resid 319 through 321 Processing sheet with id= BM, first strand: chain 'K' and resid 341 through 343 removed outlier: 6.634A pdb=" N ARG K 357 " --> pdb=" O SER K 342 " (cutoff:3.500A) No H-bonds generated for sheet with id= BM Processing sheet with id= BN, first strand: chain 'K' and resid 147 through 149 removed outlier: 3.569A pdb=" N ARG K 158 " --> pdb=" O VAL K 148 " (cutoff:3.500A) Processing sheet with id= BO, first strand: chain 'L' and resid 207 through 211 removed outlier: 7.187A pdb=" N GLY L 131 " --> pdb=" O TYR L 208 " (cutoff:3.500A) removed outlier: 8.763A pdb=" N MET L 210 " --> pdb=" O GLY L 131 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ILE L 133 " --> pdb=" O MET L 210 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N MET L 175 " --> pdb=" O LEU L 134 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N THR L 136 " --> pdb=" O ALA L 173 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ALA L 173 " --> pdb=" O THR L 136 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N HIS L 48 " --> pdb=" O ALA L 3 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N ILE L 5 " --> pdb=" O HIS L 48 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ILE L 50 " --> pdb=" O ILE L 5 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N ARG L 74 " --> pdb=" O VAL L 49 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N LEU L 51 " --> pdb=" O ARG L 74 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N SER L 76 " --> pdb=" O LEU L 51 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N VAL L 53 " --> pdb=" O SER L 76 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N SER L 78 " --> pdb=" O VAL L 53 " (cutoff:3.500A) Processing sheet with id= BP, first strand: chain 'L' and resid 111 through 113 Processing sheet with id= BQ, first strand: chain 'L' and resid 254 through 256 removed outlier: 6.184A pdb=" N VAL L 272 " --> pdb=" O LEU L 255 " (cutoff:3.500A) No H-bonds generated for sheet with id= BQ Processing sheet with id= BR, first strand: chain 'L' and resid 285 through 287 Processing sheet with id= BS, first strand: chain 'L' and resid 289 through 291 removed outlier: 6.318A pdb=" N CYS L 306 " --> pdb=" O THR L 290 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N THR L 324 " --> pdb=" O ILE L 307 " (cutoff:3.500A) No H-bonds generated for sheet with id= BS Processing sheet with id= BT, first strand: chain 'L' and resid 330 through 332 removed outlier: 6.644A pdb=" N LYS L 347 " --> pdb=" O ILE L 331 " (cutoff:3.500A) No H-bonds generated for sheet with id= BT Processing sheet with id= BU, first strand: chain 'L' and resid 341 through 343 removed outlier: 6.591A pdb=" N ARG L 357 " --> pdb=" O SER L 342 " (cutoff:3.500A) No H-bonds generated for sheet with id= BU Processing sheet with id= BV, first strand: chain 'H' and resid 175 through 178 removed outlier: 6.657A pdb=" N HIS H 48 " --> pdb=" O ALA H 3 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N ILE H 5 " --> pdb=" O HIS H 48 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ILE H 50 " --> pdb=" O ILE H 5 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N VAL H 7 " --> pdb=" O ILE H 50 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N ALA H 52 " --> pdb=" O VAL H 7 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ARG H 74 " --> pdb=" O VAL H 49 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N LEU H 51 " --> pdb=" O ARG H 74 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N SER H 76 " --> pdb=" O LEU H 51 " (cutoff:3.500A) removed outlier: 8.534A pdb=" N VAL H 53 " --> pdb=" O SER H 76 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N SER H 78 " --> pdb=" O VAL H 53 " (cutoff:3.500A) Processing sheet with id= BW, first strand: chain 'H' and resid 111 through 113 Processing sheet with id= BX, first strand: chain 'H' and resid 207 through 211 removed outlier: 6.630A pdb=" N GLY H 131 " --> pdb=" O TYR H 208 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N MET H 210 " --> pdb=" O GLY H 131 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N ILE H 133 " --> pdb=" O MET H 210 " (cutoff:3.500A) Processing sheet with id= BY, first strand: chain 'H' and resid 254 through 256 removed outlier: 6.830A pdb=" N VAL H 272 " --> pdb=" O LEU H 255 " (cutoff:3.500A) No H-bonds generated for sheet with id= BY Processing sheet with id= BZ, first strand: chain 'H' and resid 285 through 287 Processing sheet with id= CA, first strand: chain 'H' and resid 319 through 321 Processing sheet with id= CB, first strand: chain 'H' and resid 146 through 149 removed outlier: 3.671A pdb=" N ARG H 158 " --> pdb=" O VAL H 148 " (cutoff:3.500A) 720 hydrogen bonds defined for protein. 2025 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: 11.76 Time building geometry restraints manager: 13.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 8433 1.33 - 1.45: 7263 1.45 - 1.57: 19957 1.57 - 1.70: 92 1.70 - 1.82: 335 Bond restraints: 36080 Sorted by residual: bond pdb=" O2A GDD A 501 " pdb=" PA GDD A 501 " ideal model delta sigma weight residual 1.496 1.606 -0.110 2.00e-02 2.50e+03 3.03e+01 bond pdb=" O2B GDD C 501 " pdb=" PB GDD C 501 " ideal model delta sigma weight residual 1.496 1.605 -0.109 2.00e-02 2.50e+03 2.98e+01 bond pdb=" O2A GDD C 501 " pdb=" PA GDD C 501 " ideal model delta sigma weight residual 1.496 1.604 -0.108 2.00e-02 2.50e+03 2.91e+01 bond pdb=" O2G GTP B 501 " pdb=" PG GTP B 501 " ideal model delta sigma weight residual 1.510 1.616 -0.106 2.00e-02 2.50e+03 2.81e+01 bond pdb=" O2A GTP H 401 " pdb=" PA GTP H 401 " ideal model delta sigma weight residual 1.510 1.616 -0.106 2.00e-02 2.50e+03 2.81e+01 ... (remaining 36075 not shown) Histogram of bond angle deviations from ideal: 91.35 - 100.65: 58 100.65 - 109.95: 7602 109.95 - 119.25: 23069 119.25 - 128.56: 17970 128.56 - 137.86: 364 Bond angle restraints: 49063 Sorted by residual: angle pdb=" N VAL E 160 " pdb=" CA VAL E 160 " pdb=" C VAL E 160 " ideal model delta sigma weight residual 108.84 124.50 -15.66 1.32e+00 5.74e-01 1.41e+02 angle pdb=" C LYS L 31 " pdb=" N PRO L 32 " pdb=" CA PRO L 32 " ideal model delta sigma weight residual 119.78 108.27 11.51 1.03e+00 9.43e-01 1.25e+02 angle pdb=" N ARG C 16 " pdb=" CA ARG C 16 " pdb=" C ARG C 16 " ideal model delta sigma weight residual 111.36 123.45 -12.09 1.09e+00 8.42e-01 1.23e+02 angle pdb=" N GLN K 164 " pdb=" CA GLN K 164 " pdb=" C GLN K 164 " ideal model delta sigma weight residual 110.80 91.35 19.45 2.13e+00 2.20e-01 8.34e+01 angle pdb=" N ARG B 18 " pdb=" CA ARG B 18 " pdb=" C ARG B 18 " ideal model delta sigma weight residual 113.16 125.74 -12.58 1.42e+00 4.96e-01 7.85e+01 ... (remaining 49058 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.89: 20739 35.89 - 71.77: 1010 71.77 - 107.66: 82 107.66 - 143.54: 9 143.54 - 179.43: 7 Dihedral angle restraints: 21847 sinusoidal: 9021 harmonic: 12826 Sorted by residual: dihedral pdb=" C8 GTP D 501 " pdb=" C1' GTP D 501 " pdb=" N9 GTP D 501 " pdb=" O4' GTP D 501 " ideal model delta sinusoidal sigma weight residual 104.59 -74.83 179.43 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C4' GTP H 401 " pdb=" C5' GTP H 401 " pdb=" O5' GTP H 401 " pdb=" PA GTP H 401 " ideal model delta sinusoidal sigma weight residual 260.87 88.81 172.06 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" C8 GTP B 501 " pdb=" C1' GTP B 501 " pdb=" N9 GTP B 501 " pdb=" O4' GTP B 501 " ideal model delta sinusoidal sigma weight residual 104.59 -54.13 158.73 1 2.00e+01 2.50e-03 4.64e+01 ... (remaining 21844 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 4791 0.106 - 0.211: 685 0.211 - 0.317: 56 0.317 - 0.422: 12 0.422 - 0.528: 5 Chirality restraints: 5549 Sorted by residual: chirality pdb=" CA ASN D 361 " pdb=" N ASN D 361 " pdb=" C ASN D 361 " pdb=" CB ASN D 361 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 6.97e+00 chirality pdb=" CA ARG B 18 " pdb=" N ARG B 18 " pdb=" C ARG B 18 " pdb=" CB ARG B 18 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.59e+00 chirality pdb=" CA ARG C 16 " pdb=" N ARG C 16 " pdb=" C ARG C 16 " pdb=" CB ARG C 16 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.00e+00 ... (remaining 5546 not shown) Planarity restraints: 6308 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TRP D 282 " -0.022 2.00e-02 2.50e+03 4.67e-02 2.18e+01 pdb=" C TRP D 282 " 0.081 2.00e-02 2.50e+03 pdb=" O TRP D 282 " -0.032 2.00e-02 2.50e+03 pdb=" N ILE D 283 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL I 165 " 0.020 2.00e-02 2.50e+03 4.00e-02 1.60e+01 pdb=" C VAL I 165 " -0.069 2.00e-02 2.50e+03 pdb=" O VAL I 165 " 0.026 2.00e-02 2.50e+03 pdb=" N PHE I 166 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY K 88 " 0.061 5.00e-02 4.00e+02 9.10e-02 1.33e+01 pdb=" N PRO K 89 " -0.157 5.00e-02 4.00e+02 pdb=" CA PRO K 89 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO K 89 " 0.050 5.00e-02 4.00e+02 ... (remaining 6305 not shown) Histogram of nonbonded interaction distances: 1.30 - 2.02: 5 2.02 - 2.74: 3360 2.74 - 3.46: 48001 3.46 - 4.18: 90518 4.18 - 4.90: 157394 Nonbonded interactions: 299278 Sorted by model distance: nonbonded pdb=" O VAL H 146 " pdb=" CG1 VAL H 160 " model vdw 1.302 3.460 nonbonded pdb=" O PRO C 406 " pdb=" NH2 ARG D 18 " model vdw 1.659 2.520 nonbonded pdb=" CG1 VAL I 146 " pdb=" O SER I 168 " model vdw 1.880 3.460 nonbonded pdb=" OE2 GLU I 80 " pdb=" CB PRO I 89 " model vdw 1.945 3.440 nonbonded pdb=" NH2 ARG B 16 " pdb=" O ASP B 370 " model vdw 1.971 2.520 ... (remaining 299273 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 203 or resid 218 through 420)) selection = (chain 'B' and resid 1 through 420) selection = (chain 'C' and resid 1 through 420) selection = (chain 'D' and resid 1 through 420) } ncs_group { reference = (chain 'E' and (resid 1 through 147 or resid 158 through 160 or (resid 161 throu \ gh 162 and (name N or name CA or name C or name O or name CB )) or resid 163 thr \ ough 166 or (resid 167 and (name N or name CA or name C or name O or name CB )) \ or resid 168 through 360 or resid 401)) selection = (chain 'F' and (resid 1 through 160 or (resid 161 through 162 and (name N or nam \ e CA or name C or name O or name CB )) or resid 163 through 166 or (resid 167 an \ d (name N or name CA or name C or name O or name CB )) or resid 168 through 360 \ or resid 401)) selection = (chain 'G' and (resid 1 through 147 or resid 158 through 160 or (resid 161 throu \ gh 162 and (name N or name CA or name C or name O or name CB )) or resid 163 thr \ ough 166 or (resid 167 and (name N or name CA or name C or name O or name CB )) \ or resid 168 through 360 or resid 401)) selection = (chain 'H' and (resid 1 through 147 or resid 158 through 160 or (resid 161 throu \ gh 162 and (name N or name CA or name C or name O or name CB )) or resid 163 thr \ ough 166 or (resid 167 and (name N or name CA or name C or name O or name CB )) \ or resid 168 through 360 or resid 401)) selection = (chain 'I' and (resid 1 through 147 or resid 158 through 160 or (resid 161 throu \ gh 162 and (name N or name CA or name C or name O or name CB )) or resid 163 thr \ ough 166 or (resid 167 and (name N or name CA or name C or name O or name CB )) \ or resid 168 through 360 or resid 401)) selection = (chain 'J' and (resid 1 through 147 or resid 158 through 160 or (resid 161 throu \ gh 162 and (name N or name CA or name C or name O or name CB )) or resid 163 thr \ ough 166 or (resid 167 and (name N or name CA or name C or name O or name CB )) \ or resid 168 through 360 or resid 401)) selection = (chain 'K' and (resid 1 through 147 or resid 158 through 161 or (resid 162 and ( \ name N or name CA or name C or name O or name CB )) or resid 163 through 360 or \ resid 401)) selection = (chain 'L' and (resid 1 through 147 or resid 158 through 161 or (resid 162 and ( \ name N or name CA or name C or name O or name CB )) or resid 163 through 360 or \ resid 401)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.30 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.160 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: 0.020 Extract box with map and model: 5.370 Check model and map are aligned: 0.540 Set scattering table: 0.330 Process input model: 89.470 Find NCS groups from input model: 2.930 Set up NCS constraints: 0.140 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: 0.000 Load rotamer database and sin/cos tables:12.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 112.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6838 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 : 0.011 0.110 36080 Z= 0.708 Angle : 1.232 19.454 49063 Z= 0.661 Chirality : 0.074 0.528 5549 Planarity : 0.009 0.091 6308 Dihedral : 19.931 179.427 13585 Min Nonbonded Distance : 1.302 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.30 % Favored : 93.43 % Rotamer: Outliers : 10.36 % Allowed : 22.30 % Favored : 67.34 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.01 (0.11), residues: 4461 helix: -2.87 (0.12), residues: 970 sheet: -1.43 (0.19), residues: 609 loop : -1.87 (0.10), residues: 2882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.004 TRP D 282 HIS 0.015 0.002 HIS J 48 PHE 0.036 0.004 PHE K 225 TYR 0.023 0.003 TYR G 55 ARG 0.023 0.001 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 961 residues out of total 3856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 405 poor density : 556 time to evaluate : 3.947 Fit side-chains revert: symmetry clash revert: symmetry clash Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 303, in __init__ self.caller(self.optimize_sidechains) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 609, in optimize_sidechains log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 83, in __init__ rotatable_hd = self.rotatable_hd) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 189, in run_one pdb_hierarchy = self.run_one_one(args=args) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 133, in run_one_one log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 108, in __init__ self.loop(function = self.one_residue_iteration) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 284, in loop function(residue = residue) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 271, in one_residue_iteration log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residue.py", line 172, in __init__ self.fit_proline() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residue.py", line 217, in fit_proline for rotamer, sites_cart in rotamer_iterator: TypeError: 'NoneType' object is not iterable