Starting phenix.real_space_refine on Sat Mar 23 04:14:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d74_30601/03_2024/7d74_30601_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d74_30601/03_2024/7d74_30601.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d74_30601/03_2024/7d74_30601.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d74_30601/03_2024/7d74_30601.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d74_30601/03_2024/7d74_30601_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d74_30601/03_2024/7d74_30601_updated.pdb" } resolution = 3.1 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 36 5.49 5 S 220 5.16 5 C 22400 2.51 5 N 6202 2.21 5 O 6495 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 16": "NH1" <-> "NH2" Residue "A PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 42": "OE1" <-> "OE2" Residue "A PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 62": "OD1" <-> "OD2" Residue "A GLU 63": "OE1" <-> "OE2" Residue "A GLU 75": "OE1" <-> "OE2" Residue "A PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 120": "OD1" <-> "OD2" Residue "A GLU 128": "OE1" <-> "OE2" Residue "A ARG 134": "NH1" <-> "NH2" Residue "A GLU 163": "OE1" <-> "OE2" Residue "A GLU 169": "OE1" <-> "OE2" Residue "A PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 195": "NH1" <-> "NH2" Residue "A ASP 225": "OD1" <-> "OD2" Residue "A TYR 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 242": "OD1" <-> "OD2" Residue "A GLU 271": "OE1" <-> "OE2" Residue "A ARG 272": "NH1" <-> "NH2" Residue "A TYR 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 321": "OE1" <-> "OE2" Residue "A GLU 332": "OE1" <-> "OE2" Residue "A PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 377": "OD1" <-> "OD2" Residue "A ARG 392": "NH1" <-> "NH2" Residue "A GLU 409": "OE1" <-> "OE2" Residue "A ARG 412": "NH1" <-> "NH2" Residue "A PHE 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 16": "NH1" <-> "NH2" Residue "D PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 42": "OE1" <-> "OE2" Residue "D PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 62": "OD1" <-> "OD2" Residue "D GLU 63": "OE1" <-> "OE2" Residue "D GLU 75": "OE1" <-> "OE2" Residue "D PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 120": "OD1" <-> "OD2" Residue "D GLU 128": "OE1" <-> "OE2" Residue "D ARG 134": "NH1" <-> "NH2" Residue "D GLU 163": "OE1" <-> "OE2" Residue "D GLU 169": "OE1" <-> "OE2" 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 ASP 225": "OD1" <-> "OD2" Residue "D TYR 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 242": "OD1" <-> "OD2" Residue "D GLU 271": "OE1" <-> "OE2" Residue "D ARG 272": "NH1" <-> "NH2" Residue "D TYR 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 321": "OE1" <-> "OE2" Residue "D GLU 332": "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 ARG 412": "NH1" <-> "NH2" Residue "D PHE 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 16": "NH1" <-> "NH2" Residue "B PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 42": "OE1" <-> "OE2" Residue "B PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 62": "OD1" <-> "OD2" Residue "B GLU 63": "OE1" <-> "OE2" 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 120": "OD1" <-> "OD2" Residue "B GLU 128": "OE1" <-> "OE2" Residue "B ARG 134": "NH1" <-> "NH2" Residue "B GLU 163": "OE1" <-> "OE2" Residue "B GLU 169": "OE1" <-> "OE2" Residue "B PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 225": "OD1" <-> "OD2" Residue "B TYR 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 242": "OD1" <-> "OD2" Residue "B GLU 271": "OE1" <-> "OE2" Residue "B ARG 272": "NH1" <-> "NH2" Residue "B TYR 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 321": "OE1" <-> "OE2" Residue "B GLU 332": "OE1" <-> "OE2" Residue "B PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 377": "OD1" <-> "OD2" Residue "B ARG 392": "NH1" <-> "NH2" Residue "B GLU 409": "OE1" <-> "OE2" Residue "B ARG 412": "NH1" <-> "NH2" Residue "B PHE 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 16": "NH1" <-> "NH2" Residue "C PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 42": "OE1" <-> "OE2" Residue "C PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 62": "OD1" <-> "OD2" Residue "C GLU 63": "OE1" <-> "OE2" Residue "C GLU 75": "OE1" <-> "OE2" Residue "C PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 120": "OD1" <-> "OD2" Residue "C GLU 128": "OE1" <-> "OE2" Residue "C ARG 134": "NH1" <-> "NH2" Residue "C GLU 163": "OE1" <-> "OE2" Residue "C GLU 169": "OE1" <-> "OE2" Residue "C PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 195": "NH1" <-> "NH2" Residue "C ASP 225": "OD1" <-> "OD2" Residue "C TYR 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 242": "OD1" <-> "OD2" Residue "C ARG 259": "NH1" <-> "NH2" Residue "C GLU 271": "OE1" <-> "OE2" Residue "C ARG 272": "NH1" <-> "NH2" Residue "C TYR 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 321": "OE1" <-> "OE2" Residue "C GLU 332": "OE1" <-> "OE2" Residue "C ASP 359": "OD1" <-> "OD2" Residue "C PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 377": "OD1" <-> "OD2" Residue "C ARG 392": "NH1" <-> "NH2" Residue "C GLU 409": "OE1" <-> "OE2" Residue "C ARG 412": "NH1" <-> "NH2" Residue "C PHE 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 39": "OE1" <-> "OE2" Residue "E ASP 47": "OD1" <-> "OD2" Residue "E TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 63": "OE1" <-> "OE2" Residue "E GLU 68": "OE1" <-> "OE2" Residue "E GLU 81": "OE1" <-> "OE2" Residue "E GLU 99": "OE1" <-> "OE2" Residue "E ASP 102": "OD1" <-> "OD2" Residue "E PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 130": "OE1" <-> "OE2" Residue "E GLU 139": "OE1" <-> "OE2" Residue "E GLU 140": "OE1" <-> "OE2" Residue "E ARG 155": "NH1" <-> "NH2" Residue "E PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 161": "OE1" <-> "OE2" Residue "E ARG 185": "NH1" <-> "NH2" Residue "E GLU 194": "OE1" <-> "OE2" Residue "E GLU 204": "OE1" <-> "OE2" Residue "E TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 211": "OE1" <-> "OE2" Residue "E PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 237": "NH1" <-> "NH2" Residue "E ARG 243": "NH1" <-> "NH2" Residue "E ASP 257": "OD1" <-> "OD2" Residue "E ARG 261": "NH1" <-> "NH2" Residue "E ASP 282": "OD1" <-> "OD2" Residue "E ARG 293": "NH1" <-> "NH2" Residue "E ARG 296": "NH1" <-> "NH2" Residue "E ARG 313": "NH1" <-> "NH2" Residue "E GLU 321": "OE1" <-> "OE2" Residue "E GLU 328": "OE1" <-> "OE2" Residue "E ASP 334": "OD1" <-> "OD2" Residue "F TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 39": "OE1" <-> "OE2" Residue "F TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 61": "OE1" <-> "OE2" Residue "F GLU 80": "OE1" <-> "OE2" Residue "F GLU 81": "OE1" <-> "OE2" Residue "F GLU 82": "OE1" <-> "OE2" Residue "F ASP 95": "OD1" <-> "OD2" Residue "F ASP 102": "OD1" <-> "OD2" Residue "F PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 130": "OE1" <-> "OE2" Residue "F GLU 150": "OE1" <-> "OE2" Residue "F ARG 155": "NH1" <-> "NH2" Residue "F PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 161": "OE1" <-> "OE2" Residue "F PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 185": "NH1" <-> "NH2" Residue "F GLU 194": "OE1" <-> "OE2" Residue "F GLU 196": "OE1" <-> "OE2" Residue "F TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 218": "OD1" <-> "OD2" Residue "F PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 237": "NH1" <-> "NH2" Residue "F GLU 242": "OE1" <-> "OE2" Residue "F ARG 243": "NH1" <-> "NH2" Residue "F ARG 261": "NH1" <-> "NH2" Residue "F ASP 282": "OD1" <-> "OD2" Residue "F ARG 293": "NH1" <-> "NH2" Residue "F ARG 296": "NH1" <-> "NH2" Residue "F ARG 313": "NH1" <-> "NH2" Residue "F GLU 321": "OE1" <-> "OE2" Residue "F GLU 351": "OE1" <-> "OE2" Residue "G TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 47": "OD1" <-> "OD2" Residue "G TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 61": "OE1" <-> "OE2" Residue "G GLU 81": "OE1" <-> "OE2" Residue "G ASP 95": "OD1" <-> "OD2" Residue "G ASP 102": "OD1" <-> "OD2" Residue "G PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 110": "OD1" <-> "OD2" Residue "G ASP 114": "OD1" <-> "OD2" Residue "G PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 130": "OE1" <-> "OE2" Residue "G GLU 139": "OE1" <-> "OE2" Residue "G GLU 150": "OE1" <-> "OE2" Residue "G ARG 155": "NH1" <-> "NH2" Residue "G PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 185": "NH1" <-> "NH2" Residue "G GLU 194": "OE1" <-> "OE2" Residue "G GLU 196": "OE1" <-> "OE2" Residue "G TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 211": "OE1" <-> "OE2" Residue "G ASP 224": "OD1" <-> "OD2" Residue "G PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 237": "NH1" <-> "NH2" Residue "G GLU 242": "OE1" <-> "OE2" Residue "G ARG 243": "NH1" <-> "NH2" Residue "G ARG 261": "NH1" <-> "NH2" Residue "G ASP 282": "OD1" <-> "OD2" Residue "G ARG 293": "NH1" <-> "NH2" Residue "G ASP 294": "OD1" <-> "OD2" Residue "G ARG 296": "NH1" <-> "NH2" Residue "G ARG 313": "NH1" <-> "NH2" Residue "G GLU 321": "OE1" <-> "OE2" Residue "G ASP 329": "OD1" <-> "OD2" Residue "G ASP 334": "OD1" <-> "OD2" Residue "G GLU 351": "OE1" <-> "OE2" Residue "H TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 61": "OE1" <-> "OE2" Residue "H GLU 63": "OE1" <-> "OE2" Residue "H GLU 80": "OE1" <-> "OE2" Residue "H GLU 81": "OE1" <-> "OE2" Residue "H GLU 82": "OE1" <-> "OE2" Residue "H ASP 95": "OD1" <-> "OD2" Residue "H PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 130": "OE1" <-> "OE2" Residue "H TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 152": "OD1" <-> "OD2" Residue "H ARG 155": "NH1" <-> "NH2" Residue "H PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 161": "OE1" <-> "OE2" Residue "H PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 185": "NH1" <-> "NH2" Residue "H GLU 204": "OE1" <-> "OE2" Residue "H TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 211": "OE1" <-> "OE2" Residue "H ARG 237": "NH1" <-> "NH2" Residue "H ARG 243": "NH1" <-> "NH2" Residue "H ASP 257": "OD1" <-> "OD2" Residue "H ARG 261": "NH1" <-> "NH2" Residue "H ASP 282": "OD1" <-> "OD2" Residue "H ARG 293": "NH1" <-> "NH2" Residue "H ASP 294": "OD1" <-> "OD2" Residue "H ARG 296": "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 "I TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 47": "OD1" <-> "OD2" Residue "I GLU 81": "OE1" <-> "OE2" Residue "I ASP 95": "OD1" <-> "OD2" Residue "I GLU 99": "OE1" <-> "OE2" Residue "I ASP 114": "OD1" <-> "OD2" Residue "I PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 130": "OE1" <-> "OE2" Residue "I GLU 139": "OE1" <-> "OE2" Residue "I GLU 140": "OE1" <-> "OE2" Residue "I GLU 150": "OE1" <-> "OE2" Residue "I ARG 155": "NH1" <-> "NH2" Residue "I PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 185": "NH1" <-> "NH2" Residue "I GLU 194": "OE1" <-> "OE2" Residue "I GLU 204": "OE1" <-> "OE2" Residue "I TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 211": "OE1" <-> "OE2" Residue "I ASP 218": "OD1" <-> "OD2" Residue "I PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 237": "NH1" <-> "NH2" Residue "I GLU 242": "OE1" <-> "OE2" Residue "I ARG 243": "NH1" <-> "NH2" Residue "I ASP 257": "OD1" <-> "OD2" Residue "I ARG 261": "NH1" <-> "NH2" Residue "I ASP 282": "OD1" <-> "OD2" Residue "I ARG 293": "NH1" <-> "NH2" Residue "I ARG 296": "NH1" <-> "NH2" Residue "I ARG 313": "NH1" <-> "NH2" Residue "I GLU 321": "OE1" <-> "OE2" Residue "I ASP 334": "OD1" <-> "OD2" Residue "I GLU 351": "OE1" <-> "OE2" Residue "I GLU 355": "OE1" <-> "OE2" Residue "J TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 39": "OE1" <-> "OE2" Residue "J TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 68": "OE1" <-> "OE2" Residue "J GLU 80": "OE1" <-> "OE2" Residue "J GLU 81": "OE1" <-> "OE2" Residue "J GLU 82": "OE1" <-> "OE2" Residue "J GLU 99": "OE1" <-> "OE2" Residue "J PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 110": "OD1" <-> "OD2" Residue "J PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 130": "OE1" <-> "OE2" Residue "J GLU 140": "OE1" <-> "OE2" Residue "J ASP 152": "OD1" <-> "OD2" Residue "J ARG 155": "NH1" <-> "NH2" Residue "J PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 161": "OE1" <-> "OE2" Residue "J PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 185": "NH1" <-> "NH2" Residue "J GLU 194": "OE1" <-> "OE2" Residue "J GLU 204": "OE1" <-> "OE2" Residue "J TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 211": "OE1" <-> "OE2" Residue "J ASP 218": "OD1" <-> "OD2" Residue "J PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 237": "NH1" <-> "NH2" Residue "J ARG 243": "NH1" <-> "NH2" Residue "J ARG 261": "NH1" <-> "NH2" Residue "J ARG 293": "NH1" <-> "NH2" Residue "J ARG 296": "NH1" <-> "NH2" Residue "J GLU 304": "OE1" <-> "OE2" Residue "J ARG 313": "NH1" <-> "NH2" Residue "J GLU 321": "OE1" <-> "OE2" Residue "J GLU 328": "OE1" <-> "OE2" Residue "J ASP 329": "OD1" <-> "OD2" Residue "K TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 47": "OD1" <-> "OD2" Residue "K TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 68": "OE1" <-> "OE2" Residue "K GLU 80": "OE1" <-> "OE2" Residue "K GLU 82": "OE1" <-> "OE2" Residue "K ASP 102": "OD1" <-> "OD2" Residue "K PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 110": "OD1" <-> "OD2" Residue "K ASP 114": "OD1" <-> "OD2" Residue "K PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 130": "OE1" <-> "OE2" Residue "K ASP 152": "OD1" <-> "OD2" Residue "K ARG 155": "NH1" <-> "NH2" Residue "K PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 161": "OE1" <-> "OE2" Residue "K ARG 185": "NH1" <-> "NH2" Residue "K GLU 194": "OE1" <-> "OE2" Residue "K GLU 196": "OE1" <-> "OE2" Residue "K GLU 204": "OE1" <-> "OE2" Residue "K TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 211": "OE1" <-> "OE2" Residue "K ASP 218": "OD1" <-> "OD2" Residue "K PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 237": "NH1" <-> "NH2" Residue "K ARG 243": "NH1" <-> "NH2" Residue "K ASP 257": "OD1" <-> "OD2" Residue "K ARG 261": "NH1" <-> "NH2" Residue "K ASP 282": "OD1" <-> "OD2" Residue "K ARG 293": "NH1" <-> "NH2" Residue "K ARG 296": "NH1" <-> "NH2" Residue "K ARG 313": "NH1" <-> "NH2" Residue "K GLU 321": "OE1" <-> "OE2" Residue "K GLU 328": "OE1" <-> "OE2" Residue "K ASP 329": "OD1" <-> "OD2" Residue "K ASP 334": "OD1" <-> "OD2" Residue "K GLU 355": "OE1" <-> "OE2" Residue "L TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 39": "OE1" <-> "OE2" Residue "L ASP 47": "OD1" <-> "OD2" Residue "L TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 61": "OE1" <-> "OE2" Residue "L GLU 63": "OE1" <-> "OE2" Residue "L GLU 68": "OE1" <-> "OE2" Residue "L GLU 81": "OE1" <-> "OE2" Residue "L ASP 95": "OD1" <-> "OD2" Residue "L ASP 114": "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 ARG 155": "NH1" <-> "NH2" Residue "L PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 185": "NH1" <-> "NH2" Residue "L GLU 196": "OE1" <-> "OE2" Residue "L GLU 204": "OE1" <-> "OE2" Residue "L TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 211": "OE1" <-> "OE2" Residue "L PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 237": "NH1" <-> "NH2" Residue "L GLU 242": "OE1" <-> "OE2" Residue "L ARG 243": "NH1" <-> "NH2" Residue "L ASP 257": "OD1" <-> "OD2" Residue "L ARG 261": "NH1" <-> "NH2" Residue "L ASP 282": "OD1" <-> "OD2" Residue "L ARG 293": "NH1" <-> "NH2" Residue "L ASP 294": "OD1" <-> "OD2" Residue "L ARG 296": "NH1" <-> "NH2" Residue "L ARG 313": "NH1" <-> "NH2" Residue "L GLU 321": "OE1" <-> "OE2" Residue "L GLU 351": "OE1" <-> "OE2" 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: 35353 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" 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: "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: "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: "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: "F" 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: "G" Number of atoms: 2782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2782 Classifications: {'peptide': 359} Link IDs: {'PTRANS': 22, 'TRANS': 336} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 2 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: "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: 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: "L" 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: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 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: "B" 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: 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: "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: "H" 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} Time building chain proxies: 18.31, per 1000 atoms: 0.52 Number of scatterers: 35353 At special positions: 0 Unit cell: (138.864, 195.672, 190.412, 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 220 16.00 P 36 15.00 O 6495 8.00 N 6202 7.00 C 22400 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS H 289 " - pdb=" SG CYS H 306 " distance=2.23 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=19, symmetry=0 Number of additional bonds: simple=19, symmetry=0 Coordination: Other bonds: Time building additional restraints: 13.19 Conformation dependent library (CDL) restraints added in 6.3 seconds 8938 Ramachandran restraints generated. 4469 Oldfield, 0 Emsley, 4469 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8270 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 125 helices and 67 sheets defined 23.6% alpha, 13.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.62 Creating SS restraints... Processing helix chain 'A' and resid 15 through 21 Proline residue: A 19 - end of helix 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 38 through 45 Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 90 through 97 removed outlier: 3.991A pdb=" N GLY A 94 " --> pdb=" O GLY A 90 " (cutoff:3.500A) removed outlier: 4.615A 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 Processing helix chain 'A' and resid 188 through 202 Proline residue: A 193 - end of helix Processing helix chain 'A' and resid 251 through 266 removed outlier: 3.664A pdb=" N ALA A 254 " --> pdb=" O ALA A 251 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU A 262 " --> pdb=" O ARG A 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 15 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 38 through 45 Processing helix chain 'D' and resid 63 through 76 Processing helix chain 'D' and resid 90 through 97 removed outlier: 3.991A pdb=" N GLY D 94 " --> pdb=" O GLY D 90 " (cutoff:3.500A) removed outlier: 4.615A 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 Processing helix chain 'D' and resid 148 through 151 Processing helix chain 'D' and resid 188 through 202 Proline residue: D 193 - end of helix Processing helix chain 'D' and resid 251 through 266 removed outlier: 3.663A pdb=" N ALA D 254 " --> pdb=" O ALA D 251 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU D 262 " --> pdb=" O ARG D 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 21 Proline residue: B 19 - end of helix 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 38 through 45 Processing helix chain 'B' and resid 63 through 76 Processing helix chain 'B' and resid 90 through 97 removed outlier: 3.991A pdb=" N GLY B 94 " --> pdb=" O GLY B 90 " (cutoff:3.500A) removed outlier: 4.614A 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 251 through 266 removed outlier: 3.663A pdb=" N ALA B 254 " --> pdb=" O ALA B 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 21 Proline residue: C 19 - end of helix 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: 3.991A pdb=" N GLY C 94 " --> pdb=" O GLY C 90 " (cutoff:3.500A) removed outlier: 4.615A 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 133 Processing helix chain 'C' and resid 148 through 151 Processing helix chain 'C' and resid 188 through 202 Proline residue: C 193 - end of helix Processing helix chain 'C' and resid 251 through 266 removed outlier: 3.664A pdb=" N ALA C 254 " --> pdb=" O ALA C 251 " (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 23 through 25 No H-bonds generated for 'chain 'E' and resid 23 through 25' Processing helix chain 'E' and resid 33 through 44 Processing helix chain 'E' and resid 58 through 71 Processing helix chain 'E' and resid 88 through 92 Processing helix chain 'E' and resid 94 through 98 Processing helix chain 'E' and resid 117 through 127 Processing helix chain 'E' and resid 141 through 143 No H-bonds generated for 'chain 'E' and resid 141 through 143' Processing helix chain 'E' and resid 180 through 185 Processing helix chain 'E' and resid 193 through 203 removed outlier: 5.324A pdb=" N PHE E 198 " --> pdb=" O GLU E 194 " (cutoff:3.500A) Proline residue: E 199 - end of helix Processing helix chain 'E' and resid 222 through 239 Processing helix chain 'F' and resid 15 through 18 No H-bonds generated for 'chain 'F' and resid 15 through 18' 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 58 through 71 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 Processing helix chain 'F' and resid 141 through 143 No H-bonds generated for 'chain 'F' and resid 141 through 143' Processing helix chain 'F' and resid 180 through 185 Processing helix chain 'F' and resid 193 through 204 removed outlier: 4.786A pdb=" N PHE F 198 " --> pdb=" O GLU F 194 " (cutoff:3.500A) Proline residue: F 199 - end of helix 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 Processing helix chain 'G' and resid 58 through 71 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 Processing helix chain 'G' and resid 141 through 143 No H-bonds generated for 'chain 'G' and resid 141 through 143' Processing helix chain 'G' and resid 180 through 185 Processing helix chain 'G' and resid 193 through 203 removed outlier: 4.980A pdb=" N PHE G 198 " --> pdb=" O GLU G 194 " (cutoff:3.500A) Proline residue: G 199 - end of helix Processing helix chain 'G' and resid 222 through 239 Processing helix chain 'H' and resid 15 through 18 No H-bonds generated for 'chain 'H' and resid 15 through 18' 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 33 through 44 Processing helix chain 'H' and resid 58 through 71 Processing helix chain 'H' and resid 88 through 92 Processing helix chain 'H' and resid 94 through 97 No H-bonds generated for 'chain 'H' and resid 94 through 97' Processing helix chain 'H' and resid 117 through 127 Processing helix chain 'H' and resid 180 through 185 Processing helix chain 'H' and resid 197 through 203 Processing helix chain 'H' and resid 222 through 239 Processing helix chain 'I' and resid 15 through 18 No H-bonds generated for 'chain 'I' and resid 15 through 18' Processing helix chain 'I' and resid 23 through 25 No H-bonds generated for 'chain 'I' and resid 23 through 25' Processing helix chain 'I' and resid 33 through 44 Processing helix chain 'I' and resid 58 through 71 Processing helix chain 'I' and resid 88 through 92 Processing helix chain 'I' and resid 94 through 97 No H-bonds generated for 'chain 'I' and resid 94 through 97' Processing helix chain 'I' and resid 117 through 127 Processing helix chain 'I' and resid 180 through 185 Processing helix chain 'I' and resid 197 through 203 Processing helix chain 'I' and resid 222 through 237 Processing helix chain 'J' and resid 15 through 18 No H-bonds generated for 'chain 'J' and resid 15 through 18' 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 Processing helix chain 'J' and resid 58 through 71 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 180 through 185 Processing helix chain 'J' and resid 197 through 204 removed outlier: 3.813A pdb=" N LYS J 203 " --> pdb=" O PRO J 199 " (cutoff:3.500A) Processing helix chain 'J' and resid 222 through 239 Processing helix chain 'K' and resid 15 through 18 No H-bonds generated for 'chain 'K' and resid 15 through 18' 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 58 through 71 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 Processing helix chain 'K' and resid 141 through 143 No H-bonds generated for 'chain 'K' and resid 141 through 143' Processing helix chain 'K' and resid 180 through 185 Processing helix chain 'K' and resid 193 through 203 removed outlier: 5.583A pdb=" N PHE K 198 " --> pdb=" O GLU K 194 " (cutoff:3.500A) Proline residue: K 199 - end of helix 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 58 through 71 Processing helix chain 'L' and resid 88 through 92 Processing helix chain 'L' and resid 94 through 97 No H-bonds generated for 'chain 'L' and resid 94 through 97' Processing helix chain 'L' and resid 117 through 127 Processing helix chain 'L' and resid 180 through 185 Processing helix chain 'L' and resid 197 through 203 Processing helix chain 'L' and resid 222 through 239 Processing sheet with id= A, first strand: chain 'A' and resid 236 through 240 removed outlier: 6.499A pdb=" N PHE A 137 " --> pdb=" O TYR A 237 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N HIS A 239 " --> pdb=" O PHE A 137 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N LEU A 139 " --> pdb=" O HIS A 239 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N ILE A 183 " --> pdb=" O LEU A 140 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N ALA A 4 " --> pdb=" O GLN A 51 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ILE A 53 " --> pdb=" O ALA A 4 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ILE A 6 " --> pdb=" O ILE A 53 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LEU A 55 " --> pdb=" O ILE A 6 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N LEU A 55 " --> pdb=" O PRO A 79 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ARG A 81 " --> pdb=" O LEU A 55 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N GLY A 57 " --> pdb=" O ARG A 81 " (cutoff:3.500A) removed outlier: 6.024A 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: 6.204A 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 154 through 158 removed outlier: 6.195A pdb=" N ASN A 158 " --> pdb=" O VAL A 164 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N VAL A 164 " --> pdb=" O ASN A 158 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 236 through 240 removed outlier: 6.500A pdb=" N PHE D 137 " --> pdb=" O TYR D 237 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N HIS D 239 " --> pdb=" O PHE D 137 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N LEU D 139 " --> pdb=" O HIS D 239 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N ILE D 183 " --> pdb=" O LEU D 140 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N ALA D 4 " --> pdb=" O GLN D 51 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ILE D 53 " --> pdb=" O ALA D 4 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ILE D 6 " --> pdb=" O ILE D 53 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N LEU D 55 " --> pdb=" O ILE D 6 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N LEU D 55 " --> pdb=" O PRO D 79 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ARG D 81 " --> pdb=" O LEU D 55 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N GLY D 57 " --> pdb=" O ARG D 81 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N LEU D 83 " --> pdb=" O GLY D 57 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 117 through 119 Processing sheet with id= I, first strand: chain 'D' and resid 141 through 143 Processing sheet with id= J, first strand: chain 'D' and resid 287 through 289 removed outlier: 6.205A pdb=" N VAL D 305 " --> pdb=" O TYR D 288 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'D' and resid 318 through 320 Processing sheet with id= L, first strand: chain 'D' and resid 154 through 158 removed outlier: 6.195A pdb=" N ASN D 158 " --> pdb=" O VAL D 164 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N VAL D 164 " --> pdb=" O ASN D 158 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 236 through 240 removed outlier: 6.500A pdb=" N PHE B 137 " --> pdb=" O TYR B 237 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N HIS B 239 " --> pdb=" O PHE B 137 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N LEU B 139 " --> pdb=" O HIS B 239 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N ILE B 183 " --> pdb=" O LEU B 140 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N ALA B 4 " --> pdb=" O GLN B 51 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ILE B 53 " --> pdb=" O ALA B 4 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ILE B 6 " --> pdb=" O ILE B 53 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N LEU B 55 " --> pdb=" O ILE B 6 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N LEU B 55 " --> pdb=" O PRO B 79 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ARG B 81 " --> pdb=" O LEU B 55 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N GLY B 57 " --> pdb=" O ARG B 81 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N LEU B 83 " --> pdb=" O GLY B 57 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 117 through 119 Processing sheet with id= O, first strand: chain 'B' and resid 141 through 143 Processing sheet with id= P, first strand: chain 'B' and resid 287 through 289 removed outlier: 6.204A pdb=" N VAL B 305 " --> pdb=" O TYR B 288 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'B' and resid 318 through 320 Processing sheet with id= R, first strand: chain 'B' and resid 154 through 158 removed outlier: 6.195A pdb=" N ASN B 158 " --> pdb=" O VAL B 164 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N VAL B 164 " --> pdb=" O ASN B 158 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 236 through 240 removed outlier: 6.500A pdb=" N PHE C 137 " --> pdb=" O TYR C 237 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N HIS C 239 " --> pdb=" O PHE C 137 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N LEU C 139 " --> pdb=" O HIS C 239 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N ILE C 183 " --> pdb=" O LEU C 140 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N ALA C 4 " --> pdb=" O GLN C 51 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ILE C 53 " --> pdb=" O ALA C 4 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ILE C 6 " --> pdb=" O ILE C 53 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N LEU C 55 " --> pdb=" O ILE C 6 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N LEU C 55 " --> pdb=" O PRO C 79 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ARG C 81 " --> pdb=" O LEU C 55 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N GLY C 57 " --> pdb=" O ARG C 81 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N LEU C 83 " --> pdb=" O GLY C 57 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 117 through 119 Processing sheet with id= U, first strand: chain 'C' and resid 141 through 143 Processing sheet with id= V, first strand: chain 'C' and resid 287 through 289 removed outlier: 6.204A pdb=" N VAL C 305 " --> pdb=" O TYR C 288 " (cutoff:3.500A) No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain 'C' and resid 318 through 320 Processing sheet with id= X, first strand: chain 'C' and resid 154 through 158 removed outlier: 6.194A pdb=" N ASN C 158 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N VAL C 164 " --> pdb=" O ASN C 158 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 207 through 211 removed outlier: 6.680A pdb=" N GLY E 131 " --> pdb=" O TYR E 208 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N MET E 210 " --> pdb=" O GLY E 131 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ILE E 133 " --> pdb=" O MET E 210 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N MET E 175 " --> pdb=" O LEU E 134 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA E 3 " --> pdb=" O HIS E 48 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ARG E 74 " --> pdb=" O VAL E 49 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N LEU E 51 " --> pdb=" O ARG E 74 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N SER E 76 " --> pdb=" O LEU E 51 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N VAL E 53 " --> pdb=" O SER E 76 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N SER E 78 " --> pdb=" O VAL E 53 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'E' and resid 111 through 113 Processing sheet with id= AA, first strand: chain 'E' and resid 254 through 256 removed outlier: 6.200A pdb=" N VAL E 272 " --> pdb=" O LEU E 255 " (cutoff:3.500A) No H-bonds generated for sheet with id= AA Processing sheet with id= AB, first strand: chain 'E' and resid 285 through 287 Processing sheet with id= AC, first strand: chain 'E' and resid 319 through 321 Processing sheet with id= AD, first strand: chain 'F' and resid 175 through 178 removed outlier: 3.714A pdb=" N ALA F 3 " --> pdb=" O HIS F 48 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N ARG F 74 " --> pdb=" O VAL F 49 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N LEU F 51 " --> pdb=" O ARG F 74 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N SER F 76 " --> pdb=" O LEU F 51 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N VAL F 53 " --> pdb=" O SER F 76 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N SER F 78 " --> pdb=" O VAL F 53 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'F' and resid 111 through 113 Processing sheet with id= AF, first strand: chain 'F' and resid 131 through 135 Processing sheet with id= AG, first strand: chain 'F' and resid 254 through 256 removed outlier: 6.377A pdb=" N VAL F 272 " --> pdb=" O LEU F 255 " (cutoff:3.500A) No H-bonds generated for sheet with id= AG Processing sheet with id= AH, first strand: chain 'F' and resid 285 through 287 Processing sheet with id= AI, first strand: chain 'F' and resid 319 through 321 Processing sheet with id= AJ, first strand: chain 'G' and resid 207 through 211 removed outlier: 7.013A pdb=" N GLY G 131 " --> pdb=" O TYR G 208 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N MET G 210 " --> pdb=" O GLY G 131 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ILE G 133 " --> pdb=" O MET G 210 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N MET G 175 " --> pdb=" O LEU G 134 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N HIS G 48 " --> pdb=" O ALA G 3 " (cutoff:3.500A) removed outlier: 8.486A pdb=" N ILE G 5 " --> pdb=" O HIS G 48 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ILE G 50 " --> pdb=" O ILE G 5 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ARG G 74 " --> pdb=" O VAL G 49 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N LEU G 51 " --> pdb=" O ARG G 74 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N SER G 76 " --> pdb=" O LEU G 51 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'G' and resid 111 through 113 Processing sheet with id= AL, first strand: chain 'G' and resid 254 through 256 removed outlier: 6.469A pdb=" N VAL G 272 " --> pdb=" O LEU G 255 " (cutoff:3.500A) No H-bonds generated for sheet with id= AL Processing sheet with id= AM, first strand: chain 'G' and resid 285 through 287 Processing sheet with id= AN, first strand: chain 'G' and resid 319 through 321 Processing sheet with id= AO, first strand: chain 'H' and resid 175 through 178 removed outlier: 7.119A pdb=" N HIS H 48 " --> pdb=" O ALA H 3 " (cutoff:3.500A) removed outlier: 8.386A pdb=" N ILE H 5 " --> pdb=" O HIS H 48 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ILE H 50 " --> pdb=" O ILE H 5 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ARG H 74 " --> pdb=" O VAL H 49 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N LEU H 51 " --> pdb=" O ARG H 74 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N SER H 76 " --> pdb=" O LEU H 51 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N VAL H 53 " --> pdb=" O SER H 76 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N SER H 78 " --> pdb=" O VAL H 53 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'H' and resid 111 through 113 Processing sheet with id= AQ, first strand: chain 'H' and resid 207 through 211 removed outlier: 7.026A pdb=" N GLY H 131 " --> pdb=" O TYR H 208 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N MET H 210 " --> pdb=" O GLY H 131 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ILE H 133 " --> pdb=" O MET H 210 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'H' and resid 254 through 256 removed outlier: 6.355A pdb=" N VAL H 272 " --> pdb=" O LEU H 255 " (cutoff:3.500A) No H-bonds generated for sheet with id= AR Processing sheet with id= AS, first strand: chain 'H' and resid 285 through 287 Processing sheet with id= AT, first strand: chain 'H' and resid 319 through 321 Processing sheet with id= AU, first strand: chain 'I' and resid 207 through 211 removed outlier: 6.829A pdb=" N GLY I 131 " --> pdb=" O TYR I 208 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N MET I 210 " --> pdb=" O GLY I 131 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ILE I 133 " --> pdb=" O MET I 210 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N MET I 175 " --> pdb=" O LEU I 134 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N HIS I 48 " --> pdb=" O ALA I 3 " (cutoff:3.500A) removed outlier: 8.405A pdb=" N ILE I 5 " --> pdb=" O HIS I 48 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ILE I 50 " --> pdb=" O ILE I 5 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ARG I 74 " --> pdb=" O VAL I 49 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N LEU I 51 " --> pdb=" O ARG I 74 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N SER I 76 " --> pdb=" O LEU I 51 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N VAL I 53 " --> pdb=" O SER I 76 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N SER I 78 " --> pdb=" O VAL I 53 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'I' and resid 111 through 113 Processing sheet with id= AW, first strand: chain 'I' and resid 135 through 137 Processing sheet with id= AX, first strand: chain 'I' and resid 254 through 256 removed outlier: 6.418A pdb=" N VAL I 272 " --> pdb=" O LEU I 255 " (cutoff:3.500A) No H-bonds generated for sheet with id= AX 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 319 through 321 Processing sheet with id= BA, first strand: chain 'J' and resid 208 through 211 removed outlier: 4.950A pdb=" N MET J 175 " --> pdb=" O LEU J 134 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N HIS J 48 " --> pdb=" O ALA J 3 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N ILE J 5 " --> pdb=" O HIS J 48 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ILE J 50 " --> pdb=" O ILE J 5 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ARG J 74 " --> pdb=" O VAL J 49 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N LEU J 51 " --> pdb=" O ARG J 74 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N SER J 76 " --> pdb=" O LEU J 51 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N VAL J 53 " --> pdb=" O SER J 76 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N SER J 78 " --> pdb=" O VAL J 53 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'J' and resid 111 through 113 Processing sheet with id= BC, first strand: chain 'J' and resid 254 through 256 removed outlier: 6.262A 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 'K' and resid 207 through 211 removed outlier: 6.794A pdb=" N GLY K 131 " --> pdb=" O TYR K 208 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N MET K 210 " --> pdb=" O GLY K 131 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ILE K 133 " --> pdb=" O MET K 210 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N MET K 175 " --> pdb=" O LEU K 134 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N HIS K 48 " --> pdb=" O ALA K 3 " (cutoff:3.500A) removed outlier: 8.285A pdb=" N ILE K 5 " --> pdb=" O HIS K 48 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE K 50 " --> pdb=" O ILE K 5 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ARG K 74 " --> pdb=" O VAL K 49 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N LEU K 51 " --> pdb=" O ARG K 74 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N SER K 76 " --> pdb=" O LEU K 51 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N VAL K 53 " --> pdb=" O SER K 76 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N SER K 78 " --> pdb=" O VAL K 53 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain 'K' and resid 111 through 113 Processing sheet with id= BH, first strand: chain 'K' and resid 254 through 256 removed outlier: 6.281A pdb=" N VAL K 272 " --> pdb=" O LEU K 255 " (cutoff:3.500A) No H-bonds generated for sheet with id= BH Processing sheet with id= BI, first strand: chain 'K' and resid 285 through 287 Processing sheet with id= BJ, first strand: chain 'K' and resid 319 through 321 Processing sheet with id= BK, first strand: chain 'L' and resid 207 through 211 removed outlier: 6.785A pdb=" N GLY L 131 " --> pdb=" O TYR L 208 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N MET L 210 " --> pdb=" O GLY L 131 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ILE L 133 " --> pdb=" O MET L 210 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N MET L 175 " --> pdb=" O LEU L 134 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N HIS L 48 " --> pdb=" O ALA L 3 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N ILE L 5 " --> pdb=" O HIS L 48 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ILE L 50 " --> pdb=" O ILE L 5 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ARG L 74 " --> pdb=" O VAL L 49 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N LEU L 51 " --> pdb=" O ARG L 74 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N SER L 76 " --> pdb=" O LEU L 51 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N VAL L 53 " --> pdb=" O SER L 76 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N SER L 78 " --> pdb=" O VAL L 53 " (cutoff:3.500A) Processing sheet with id= BL, first strand: chain 'L' and resid 111 through 113 Processing sheet with id= BM, first strand: chain 'L' and resid 254 through 256 removed outlier: 6.380A pdb=" N VAL L 272 " --> pdb=" O LEU L 255 " (cutoff:3.500A) No H-bonds generated for sheet with id= BM Processing sheet with id= BN, first strand: chain 'L' and resid 285 through 287 Processing sheet with id= BO, first strand: chain 'L' and resid 319 through 321 795 hydrogen bonds defined for protein. 2076 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: 12.57 Time building geometry restraints manager: 13.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 8783 1.33 - 1.47: 10554 1.47 - 1.60: 16415 1.60 - 1.74: 53 1.74 - 1.88: 335 Bond restraints: 36140 Sorted by residual: bond pdb=" O2G GTP G 401 " pdb=" PG GTP G 401 " ideal model delta sigma weight residual 1.510 1.620 -0.110 2.00e-02 2.50e+03 3.05e+01 bond pdb=" O2G GTP H 401 " pdb=" PG GTP H 401 " ideal model delta sigma weight residual 1.510 1.620 -0.110 2.00e-02 2.50e+03 3.05e+01 bond pdb=" O2G GTP F 401 " pdb=" PG GTP F 401 " ideal model delta sigma weight residual 1.510 1.620 -0.110 2.00e-02 2.50e+03 3.04e+01 bond pdb=" O2G GTP K 401 " pdb=" PG GTP K 401 " ideal model delta sigma weight residual 1.510 1.620 -0.110 2.00e-02 2.50e+03 3.02e+01 bond pdb=" O2G GTP E 401 " pdb=" PG GTP E 401 " ideal model delta sigma weight residual 1.510 1.620 -0.110 2.00e-02 2.50e+03 3.02e+01 ... (remaining 36135 not shown) Histogram of bond angle deviations from ideal: 92.17 - 100.96: 70 100.96 - 109.76: 6430 109.76 - 118.56: 22634 118.56 - 127.35: 19485 127.35 - 136.15: 524 Bond angle restraints: 49143 Sorted by residual: angle pdb=" N GLY F 9 " pdb=" CA GLY F 9 " pdb=" C GLY F 9 " ideal model delta sigma weight residual 110.56 127.47 -16.91 1.66e+00 3.63e-01 1.04e+02 angle pdb=" N2 GTP F 401 " pdb=" C2 GTP F 401 " pdb=" N3 GTP F 401 " ideal model delta sigma weight residual 120.00 96.32 23.68 3.00e+00 1.11e-01 6.23e+01 angle pdb=" N2 GTP E 401 " pdb=" C2 GTP E 401 " pdb=" N3 GTP E 401 " ideal model delta sigma weight residual 120.00 96.35 23.65 3.00e+00 1.11e-01 6.22e+01 angle pdb=" N2 GTP I 401 " pdb=" C2 GTP I 401 " pdb=" N3 GTP I 401 " ideal model delta sigma weight residual 120.00 96.36 23.64 3.00e+00 1.11e-01 6.21e+01 angle pdb=" N2 GTP J 401 " pdb=" C2 GTP J 401 " pdb=" N3 GTP J 401 " ideal model delta sigma weight residual 120.00 96.37 23.63 3.00e+00 1.11e-01 6.20e+01 ... (remaining 49138 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.35: 20636 35.35 - 70.71: 1084 70.71 - 106.06: 70 106.06 - 141.41: 8 141.41 - 176.77: 12 Dihedral angle restraints: 21810 sinusoidal: 8962 harmonic: 12848 Sorted by residual: dihedral pdb=" C8 GTP A 501 " pdb=" C1' GTP A 501 " pdb=" N9 GTP A 501 " pdb=" O4' GTP A 501 " ideal model delta sinusoidal sigma weight residual 104.59 -72.18 176.77 1 2.00e+01 2.50e-03 4.80e+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 -72.17 176.77 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C8 GTP C 501 " pdb=" C1' GTP C 501 " pdb=" N9 GTP C 501 " pdb=" O4' GTP C 501 " ideal model delta sinusoidal sigma weight residual 104.59 -72.15 176.74 1 2.00e+01 2.50e-03 4.80e+01 ... (remaining 21807 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.114: 4922 0.114 - 0.228: 522 0.228 - 0.341: 87 0.341 - 0.455: 17 0.455 - 0.569: 2 Chirality restraints: 5550 Sorted by residual: chirality pdb=" CG LEU F 84 " pdb=" CB LEU F 84 " pdb=" CD1 LEU F 84 " pdb=" CD2 LEU F 84 " both_signs ideal model delta sigma weight residual False -2.59 -2.02 -0.57 2.00e-01 2.50e+01 8.09e+00 chirality pdb=" CB VAL H 46 " pdb=" CA VAL H 46 " pdb=" CG1 VAL H 46 " pdb=" CG2 VAL H 46 " both_signs ideal model delta sigma weight residual False -2.63 -2.16 -0.47 2.00e-01 2.50e+01 5.51e+00 chirality pdb=" CB ILE F 200 " pdb=" CA ILE F 200 " pdb=" CG1 ILE F 200 " pdb=" CG2 ILE F 200 " both_signs ideal model delta sigma weight residual False 2.64 2.21 0.43 2.00e-01 2.50e+01 4.63e+00 ... (remaining 5547 not shown) Planarity restraints: 6322 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' GTP L 401 " 0.020 2.00e-02 2.50e+03 3.89e-02 4.54e+01 pdb=" C2 GTP L 401 " 0.113 2.00e-02 2.50e+03 pdb=" C4 GTP L 401 " 0.002 2.00e-02 2.50e+03 pdb=" C5 GTP L 401 " -0.004 2.00e-02 2.50e+03 pdb=" C6 GTP L 401 " -0.001 2.00e-02 2.50e+03 pdb=" C8 GTP L 401 " 0.000 2.00e-02 2.50e+03 pdb=" N1 GTP L 401 " -0.019 2.00e-02 2.50e+03 pdb=" N2 GTP L 401 " -0.037 2.00e-02 2.50e+03 pdb=" N3 GTP L 401 " -0.056 2.00e-02 2.50e+03 pdb=" N7 GTP L 401 " -0.003 2.00e-02 2.50e+03 pdb=" N9 GTP L 401 " -0.011 2.00e-02 2.50e+03 pdb=" O6 GTP L 401 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' GTP F 401 " 0.020 2.00e-02 2.50e+03 3.89e-02 4.54e+01 pdb=" C2 GTP F 401 " 0.113 2.00e-02 2.50e+03 pdb=" C4 GTP F 401 " 0.002 2.00e-02 2.50e+03 pdb=" C5 GTP F 401 " -0.004 2.00e-02 2.50e+03 pdb=" C6 GTP F 401 " -0.001 2.00e-02 2.50e+03 pdb=" C8 GTP F 401 " 0.001 2.00e-02 2.50e+03 pdb=" N1 GTP F 401 " -0.018 2.00e-02 2.50e+03 pdb=" N2 GTP F 401 " -0.037 2.00e-02 2.50e+03 pdb=" N3 GTP F 401 " -0.057 2.00e-02 2.50e+03 pdb=" N7 GTP F 401 " -0.003 2.00e-02 2.50e+03 pdb=" N9 GTP F 401 " -0.011 2.00e-02 2.50e+03 pdb=" O6 GTP F 401 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' GTP E 401 " -0.020 2.00e-02 2.50e+03 3.89e-02 4.54e+01 pdb=" C2 GTP E 401 " -0.113 2.00e-02 2.50e+03 pdb=" C4 GTP E 401 " -0.002 2.00e-02 2.50e+03 pdb=" C5 GTP E 401 " 0.004 2.00e-02 2.50e+03 pdb=" C6 GTP E 401 " 0.001 2.00e-02 2.50e+03 pdb=" C8 GTP E 401 " -0.000 2.00e-02 2.50e+03 pdb=" N1 GTP E 401 " 0.019 2.00e-02 2.50e+03 pdb=" N2 GTP E 401 " 0.037 2.00e-02 2.50e+03 pdb=" N3 GTP E 401 " 0.057 2.00e-02 2.50e+03 pdb=" N7 GTP E 401 " 0.003 2.00e-02 2.50e+03 pdb=" N9 GTP E 401 " 0.011 2.00e-02 2.50e+03 pdb=" O6 GTP E 401 " 0.003 2.00e-02 2.50e+03 ... (remaining 6319 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 170 2.52 - 3.11: 22911 3.11 - 3.71: 55685 3.71 - 4.30: 80779 4.30 - 4.90: 134933 Nonbonded interactions: 294478 Sorted by model distance: nonbonded pdb=" NH1 ARG D 259 " pdb=" OE1 GLU D 321 " model vdw 1.922 2.520 nonbonded pdb=" CG HIS I 346 " pdb=" CE2 TYR J 10 " model vdw 2.132 3.560 nonbonded pdb=" CA GLY E 8 " pdb=" N2 GTP E 401 " model vdw 2.158 2.816 nonbonded pdb=" OE2 GLU L 321 " pdb=" CE1 TYR L 337 " model vdw 2.201 3.340 nonbonded pdb=" N GLY F 9 " pdb=" O2' GTP F 401 " model vdw 2.231 2.520 ... (remaining 294473 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = (chain 'E' and (resid 1 through 6 or resid 8 through 360 or resid 401)) selection = (chain 'F' and (resid 1 through 6 or resid 8 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 resi \ d 401)) selection = (chain 'G' and (resid 1 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 'H' and (resid 1 through 6 or resid 8 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 resi \ d 401)) selection = (chain 'I' and (resid 1 through 6 or resid 8 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 resi \ d 401)) selection = (chain 'J' and (resid 1 through 6 or resid 8 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 resi \ d 401)) selection = (chain 'K' and (resid 1 through 6 or resid 8 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 resi \ d 401)) selection = (chain 'L' and (resid 1 through 6 or resid 8 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 resi \ d 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: 1.280 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: 5.260 Check model and map are aligned: 0.510 Set scattering table: 0.280 Process input model: 91.860 Find NCS groups from input model: 2.760 Set up NCS constraints: 0.310 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 105.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6293 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.128 36140 Z= 0.627 Angle : 1.382 23.680 49143 Z= 0.728 Chirality : 0.079 0.569 5550 Planarity : 0.010 0.080 6322 Dihedral : 19.734 176.768 13537 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.36 % Allowed : 4.83 % Favored : 94.81 % Rotamer: Outliers : 8.87 % Allowed : 17.88 % Favored : 73.25 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.46 (0.11), residues: 4469 helix: -2.85 (0.12), residues: 1015 sheet: -0.97 (0.19), residues: 668 loop : -1.32 (0.10), residues: 2786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP F 302 HIS 0.022 0.003 HIS I 79 PHE 0.066 0.004 PHE K 166 TYR 0.038 0.003 TYR E 144 ARG 0.019 0.001 ARG I 158 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8938 Ramachandran restraints generated. 4469 Oldfield, 0 Emsley, 4469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8938 Ramachandran restraints generated. 4469 Oldfield, 0 Emsley, 4469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 984 residues out of total 3863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 350 poor density : 634 time to evaluate : 3.908 Fit side-chains 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