Starting phenix.real_space_refine on Sat Mar 23 04:42:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d72_30599/03_2024/7d72_30599_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d72_30599/03_2024/7d72_30599.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d72_30599/03_2024/7d72_30599.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d72_30599/03_2024/7d72_30599.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d72_30599/03_2024/7d72_30599_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d72_30599/03_2024/7d72_30599_updated.pdb" } resolution = 3.4 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= 0.006 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: 6 Type Number sf(0) Gaussians P 24 5.49 5 Mg 3 5.21 5 S 220 5.16 5 C 22479 2.51 5 N 6205 2.21 5 O 6527 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "K ARG 13": "NH1" <-> "NH2" Residue "K ASP 47": "OD1" <-> "OD2" Residue "K GLU 68": "OE1" <-> "OE2" Residue "K ARG 94": "NH1" <-> "NH2" Residue "K ASP 95": "OD1" <-> "OD2" Residue "K GLU 99": "OE1" <-> "OE2" Residue "K ASP 102": "OD1" <-> "OD2" Residue "K ASP 110": "OD1" <-> "OD2" Residue "K PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 130": "OE1" <-> "OE2" Residue "K GLU 139": "OE1" <-> "OE2" Residue "K GLU 140": "OE1" <-> "OE2" Residue "K GLU 194": "OE1" <-> "OE2" Residue "K GLU 196": "OE1" <-> "OE2" Residue "K PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 211": "OE1" <-> "OE2" Residue "K ASP 218": "OD1" <-> "OD2" Residue "K ARG 237": "NH1" <-> "NH2" Residue "K GLU 242": "OE1" <-> "OE2" Residue "K ARG 243": "NH1" <-> "NH2" Residue "K GLU 281": "OE1" <-> "OE2" Residue "K ASP 294": "OD1" <-> "OD2" Residue "K ARG 311": "NH1" <-> "NH2" Residue "K ARG 313": "NH1" <-> "NH2" Residue "K GLU 321": "OE1" <-> "OE2" Residue "K ASP 329": "OD1" <-> "OD2" Residue "K ASP 334": "OD1" <-> "OD2" Residue "K GLU 351": "OE1" <-> "OE2" Residue "K GLU 355": "OE1" <-> "OE2" Residue "I ARG 13": "NH1" <-> "NH2" Residue "I GLU 61": "OE1" <-> "OE2" Residue "I GLU 68": "OE1" <-> "OE2" Residue "I ARG 74": "NH1" <-> "NH2" Residue "I GLU 80": "OE1" <-> "OE2" Residue "I GLU 81": "OE1" <-> "OE2" Residue "I ARG 94": "NH1" <-> "NH2" Residue "I ASP 102": "OD1" <-> "OD2" Residue "I PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 110": "OD1" <-> "OD2" Residue "I PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 139": "OE1" <-> "OE2" Residue "I PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 ASP 224": "OD1" <-> "OD2" 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 ASP 294": "OD1" <-> "OD2" Residue "I GLU 321": "OE1" <-> "OE2" Residue "I ASP 329": "OD1" <-> "OD2" Residue "I GLU 351": "OE1" <-> "OE2" Residue "A PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 23": "OE1" <-> "OE2" Residue "A GLU 63": "OE1" <-> "OE2" Residue "A PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 81": "NH1" <-> "NH2" Residue "A PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 100": "OD1" <-> "OD2" Residue "A GLU 128": "OE1" <-> "OE2" Residue "A ARG 132": "NH1" <-> "NH2" Residue "A GLU 157": "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 TYR 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 315": "OE1" <-> "OE2" Residue "A GLU 321": "OE1" <-> "OE2" Residue "A ARG 349": "NH1" <-> "NH2" Residue "A PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 409": "OE1" <-> "OE2" Residue "A PHE 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 23": "OE1" <-> "OE2" Residue "B PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 81": "NH1" <-> "NH2" Residue "B GLU 85": "OE1" <-> "OE2" Residue "B TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 100": "OD1" <-> "OD2" Residue "B ARG 132": "NH1" <-> "NH2" Residue "B PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 GLU 189": "OE1" <-> "OE2" Residue "B ARG 195": "NH1" <-> "NH2" Residue "B PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 242": "OD1" <-> "OD2" Residue "B TYR 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 315": "OE1" <-> "OE2" Residue "B GLU 321": "OE1" <-> "OE2" Residue "B GLU 354": "OE1" <-> "OE2" Residue "B ASP 364": "OD1" <-> "OD2" Residue "B ASP 370": "OD1" <-> "OD2" Residue "B PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 377": "OD1" <-> "OD2" Residue "B GLU 409": "OE1" <-> "OE2" Residue "B PHE 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 16": "NH1" <-> "NH2" Residue "C PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 70": "OE1" <-> "OE2" Residue "C PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 81": "NH1" <-> "NH2" Residue "C GLU 85": "OE1" <-> "OE2" Residue "C TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 100": "OD1" <-> "OD2" Residue "C GLU 108": "OE1" <-> "OE2" Residue "C ASP 116": "OD1" <-> "OD2" Residue "C GLU 128": "OE1" <-> "OE2" Residue "C ARG 132": "NH1" <-> "NH2" 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 GLU 189": "OE1" <-> "OE2" Residue "C ARG 195": "NH1" <-> "NH2" Residue "C ASP 196": "OD1" <-> "OD2" Residue "C TYR 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 242": "OD1" <-> "OD2" Residue "C TYR 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 315": "OE1" <-> "OE2" Residue "C GLU 321": "OE1" <-> "OE2" Residue "C ASP 364": "OD1" <-> "OD2" Residue "C ARG 392": "NH1" <-> "NH2" Residue "C PHE 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 42": "OE1" <-> "OE2" Residue "D GLU 63": "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 GLU 108": "OE1" <-> "OE2" Residue "D PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 177": "OD1" <-> "OD2" 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 ASP 242": "OD1" <-> "OD2" Residue "D TYR 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 321": "OE1" <-> "OE2" Residue "D ASP 359": "OD1" <-> "OD2" Residue "D ASP 364": "OD1" <-> "OD2" Residue "D ARG 366": "NH1" <-> "NH2" Residue "D ASP 370": "OD1" <-> "OD2" Residue "D PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 377": "OD1" <-> "OD2" Residue "D GLU 409": "OE1" <-> "OE2" Residue "D ARG 412": "NH1" <-> "NH2" Residue "D PHE 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 47": "OD1" <-> "OD2" Residue "E TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 63": "OE1" <-> "OE2" Residue "E ARG 74": "NH1" <-> "NH2" Residue "E GLU 81": "OE1" <-> "OE2" Residue "E GLU 82": "OE1" <-> "OE2" Residue "E PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 110": "OD1" <-> "OD2" Residue "E PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 139": "OE1" <-> "OE2" Residue "E PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 194": "OE1" <-> "OE2" Residue "E GLU 196": "OE1" <-> "OE2" Residue "E PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 218": "OD1" <-> "OD2" Residue "E ARG 237": "NH1" <-> "NH2" Residue "E ARG 243": "NH1" <-> "NH2" Residue "E ASP 257": "OD1" <-> "OD2" Residue "E ASP 282": "OD1" <-> "OD2" Residue "E GLU 321": "OE1" <-> "OE2" Residue "E GLU 355": "OE1" <-> "OE2" Residue "F ASP 47": "OD1" <-> "OD2" Residue "F GLU 61": "OE1" <-> "OE2" Residue "F GLU 68": "OE1" <-> "OE2" Residue "F GLU 80": "OE1" <-> "OE2" Residue "F GLU 81": "OE1" <-> "OE2" Residue "F GLU 82": "OE1" <-> "OE2" Residue "F GLU 99": "OE1" <-> "OE2" Residue "F ASP 102": "OD1" <-> "OD2" Residue "F PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 110": "OD1" <-> "OD2" Residue "F PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 139": "OE1" <-> "OE2" Residue "F GLU 140": "OE1" <-> "OE2" Residue "F GLU 150": "OE1" <-> "OE2" Residue "F ASP 152": "OD1" <-> "OD2" Residue "F PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 194": "OE1" <-> "OE2" Residue "F GLU 204": "OE1" <-> "OE2" Residue "F ASP 218": "OD1" <-> "OD2" Residue "F ARG 237": "NH1" <-> "NH2" Residue "F ARG 243": "NH1" <-> "NH2" Residue "F ARG 261": "NH1" <-> "NH2" Residue "F ASP 294": "OD1" <-> "OD2" Residue "F ARG 311": "NH1" <-> "NH2" Residue "F GLU 321": "OE1" <-> "OE2" Residue "F GLU 328": "OE1" <-> "OE2" Residue "F GLU 355": "OE1" <-> "OE2" Residue "G ARG 15": "NH1" <-> "NH2" Residue "G ASP 27": "OD1" <-> "OD2" Residue "G GLU 39": "OE1" <-> "OE2" Residue "G GLU 61": "OE1" <-> "OE2" Residue "G ARG 74": "NH1" <-> "NH2" Residue "G GLU 81": "OE1" <-> "OE2" Residue "G GLU 82": "OE1" <-> "OE2" Residue "G ARG 94": "NH1" <-> "NH2" Residue "G GLU 99": "OE1" <-> "OE2" Residue "G ASP 102": "OD1" <-> "OD2" Residue "G PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 110": "OD1" <-> "OD2" Residue "G ASP 114": "OD1" <-> "OD2" Residue "G PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 139": "OE1" <-> "OE2" Residue "G GLU 150": "OE1" <-> "OE2" Residue "G PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 196": "OE1" <-> "OE2" Residue "G GLU 204": "OE1" <-> "OE2" Residue "G TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 218": "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 ASP 257": "OD1" <-> "OD2" Residue "G ARG 261": "NH1" <-> "NH2" Residue "G ASP 294": "OD1" <-> "OD2" Residue "G GLU 304": "OE1" <-> "OE2" Residue "G ARG 311": "NH1" <-> "NH2" Residue "G GLU 321": "OE1" <-> "OE2" Residue "G GLU 328": "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 ARG 13": "NH1" <-> "NH2" Residue "H GLU 39": "OE1" <-> "OE2" Residue "H GLU 68": "OE1" <-> "OE2" Residue "H ARG 74": "NH1" <-> "NH2" Residue "H GLU 81": "OE1" <-> "OE2" Residue "H GLU 82": "OE1" <-> "OE2" Residue "H ARG 94": "NH1" <-> "NH2" Residue "H PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 114": "OD1" <-> "OD2" Residue "H PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 130": "OE1" <-> "OE2" Residue "H GLU 161": "OE1" <-> "OE2" Residue "H PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 194": "OE1" <-> "OE2" Residue "H GLU 196": "OE1" <-> "OE2" Residue "H GLU 204": "OE1" <-> "OE2" Residue "H TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 211": "OE1" <-> "OE2" Residue "H ASP 218": "OD1" <-> "OD2" Residue "H PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 237": "NH1" <-> "NH2" Residue "H ARG 243": "NH1" <-> "NH2" Residue "H ARG 261": "NH1" <-> "NH2" Residue "H ASP 294": "OD1" <-> "OD2" Residue "H ARG 313": "NH1" <-> "NH2" Residue "H GLU 321": "OE1" <-> "OE2" Residue "H ASP 329": "OD1" <-> "OD2" Residue "H GLU 335": "OE1" <-> "OE2" Residue "H GLU 351": "OE1" <-> "OE2" Residue "H GLU 355": "OE1" <-> "OE2" Residue "J ASP 27": "OD1" <-> "OD2" Residue "J GLU 39": "OE1" <-> "OE2" Residue "J GLU 61": "OE1" <-> "OE2" Residue "J GLU 63": "OE1" <-> "OE2" Residue "J ARG 74": "NH1" <-> "NH2" 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 139": "OE1" <-> "OE2" Residue "J ASP 152": "OD1" <-> "OD2" Residue "J PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 196": "OE1" <-> "OE2" Residue "J GLU 204": "OE1" <-> "OE2" Residue "J TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 218": "OD1" <-> "OD2" Residue "J ARG 237": "NH1" <-> "NH2" Residue "J ARG 243": "NH1" <-> "NH2" Residue "J ARG 261": "NH1" <-> "NH2" Residue "J GLU 321": "OE1" <-> "OE2" Residue "L ARG 13": "NH1" <-> "NH2" Residue "L GLU 61": "OE1" <-> "OE2" Residue "L GLU 63": "OE1" <-> "OE2" Residue "L ARG 74": "NH1" <-> "NH2" Residue "L GLU 80": "OE1" <-> "OE2" Residue "L GLU 81": "OE1" <-> "OE2" Residue "L GLU 82": "OE1" <-> "OE2" Residue "L ARG 94": "NH1" <-> "NH2" Residue "L ASP 95": "OD1" <-> "OD2" Residue "L GLU 99": "OE1" <-> "OE2" Residue "L ASP 102": "OD1" <-> "OD2" Residue "L PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 130": "OE1" <-> "OE2" Residue "L GLU 139": "OE1" <-> "OE2" Residue "L ARG 155": "NH1" <-> "NH2" Residue "L ARG 158": "NH1" <-> "NH2" Residue "L PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 194": "OE1" <-> "OE2" Residue "L TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 218": "OD1" <-> "OD2" Residue "L ASP 224": "OD1" <-> "OD2" Residue "L PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 237": "NH1" <-> "NH2" Residue "L GLU 242": "OE1" <-> "OE2" Residue "L ASP 257": "OD1" <-> "OD2" Residue "L ARG 261": "NH1" <-> "NH2" Residue "L GLU 328": "OE1" <-> "OE2" Residue "L ASP 329": "OD1" <-> "OD2" Residue "L GLU 351": "OE1" <-> "OE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 35458 Number of models: 1 Model: "" Number of chains: 27 Chain: "K" Number of atoms: 2787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2787 Classifications: {'peptide': 360} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 337} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 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: "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: "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: "E" 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: "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: 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: "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: "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: "L" Number of atoms: 2787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2787 Classifications: {'peptide': 360} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 337} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'GDD': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'GDD': 1} Classifications: {'undetermined': 1} 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'GDD': 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'GDD': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 40 Unusual residues: {' MG': 1, 'GDD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 40 Unusual residues: {' MG': 1, 'GDD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 40 Unusual residues: {' MG': 1, 'GDD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'GDD': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'GDD': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'GDD': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 18.55, per 1000 atoms: 0.52 Number of scatterers: 35458 At special positions: 0 Unit cell: (135.296, 198.716, 183.918, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 220 16.00 P 24 15.00 Mg 3 11.99 O 6527 8.00 N 6205 7.00 C 22479 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS E 289 " - pdb=" SG CYS E 306 " distance=2.03 Simple disulfide: pdb=" SG CYS G 289 " - pdb=" SG CYS G 306 " distance=2.03 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 13.67 Conformation dependent library (CDL) restraints added in 6.3 seconds 8946 Ramachandran restraints generated. 4473 Oldfield, 0 Emsley, 4473 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8274 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 123 helices and 68 sheets defined 23.7% alpha, 13.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.17 Creating SS restraints... 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 28 through 30 No H-bonds generated for 'chain 'K' and resid 28 through 30' Processing helix chain 'K' and resid 33 through 44 Processing helix chain 'K' and resid 57 through 71 removed outlier: 4.355A pdb=" N ALA K 66 " --> pdb=" O LYS K 62 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARG K 70 " --> pdb=" O ALA K 66 " (cutoff:3.500A) Processing helix chain 'K' and resid 88 through 92 Processing helix chain 'K' and resid 94 through 98 Processing helix chain 'K' and resid 117 through 127 removed outlier: 3.516A pdb=" N HIS K 126 " --> pdb=" O GLN K 122 " (cutoff:3.500A) Processing helix chain 'K' and resid 180 through 183 No H-bonds generated for 'chain 'K' and resid 180 through 183' Processing helix chain 'K' and resid 193 through 204 Proline residue: K 199 - end of helix Processing helix chain 'K' and resid 222 through 239 Processing helix chain 'I' and resid 17 through 19 No H-bonds generated for 'chain 'I' and resid 17 through 19' 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 removed outlier: 3.919A pdb=" N GLN I 37 " --> pdb=" O ILE I 33 " (cutoff:3.500A) Processing helix chain 'I' and resid 58 through 71 removed outlier: 4.345A pdb=" N GLN I 69 " --> pdb=" O LYS I 65 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ARG I 70 " --> pdb=" O ALA I 66 " (cutoff:3.500A) 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 141 through 143 No H-bonds generated for 'chain 'I' and resid 141 through 143' Processing helix chain 'I' and resid 180 through 185 removed outlier: 3.838A pdb=" N GLN I 184 " --> pdb=" O PRO I 180 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ARG I 185 " --> pdb=" O ALA I 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 180 through 185' Processing helix chain 'I' and resid 193 through 196 No H-bonds generated for 'chain 'I' and resid 193 through 196' Processing helix chain 'I' and resid 198 through 204 removed outlier: 4.416A pdb=" N LYS I 203 " --> pdb=" O PRO I 199 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N GLU I 204 " --> pdb=" O ILE I 200 " (cutoff:3.500A) Processing helix chain 'I' and resid 222 through 239 removed outlier: 3.815A pdb=" N GLN I 234 " --> pdb=" O CYS I 230 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SER I 235 " --> pdb=" O LEU I 231 " (cutoff:3.500A) 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 46 Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 90 through 97 removed outlier: 4.253A 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 131 Processing helix chain 'A' and resid 188 through 202 removed outlier: 3.954A pdb=" N LEU A 191 " --> pdb=" O PRO A 188 " (cutoff:3.500A) Proline residue: A 193 - end of helix Processing helix chain 'A' and resid 222 through 229 removed outlier: 3.811A pdb=" N PHE A 227 " --> pdb=" O GLU A 223 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N SER A 228 " --> pdb=" O GLN A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 268 removed outlier: 4.522A pdb=" N GLN A 266 " --> pdb=" O LEU A 262 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N ASP A 267 " --> pdb=" O SER A 263 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N THR A 268 " --> pdb=" O ARG A 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 21 removed outlier: 4.018A pdb=" N ARG B 16 " --> pdb=" O LYS B 13 " (cutoff:3.500A) 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 removed outlier: 3.663A pdb=" N GLN B 74 " --> pdb=" O GLU B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 97 removed outlier: 4.098A pdb=" N GLY B 94 " --> pdb=" O GLY B 90 " (cutoff:3.500A) removed outlier: 4.584A 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 removed outlier: 4.003A pdb=" N ARG B 132 " --> pdb=" O GLU B 128 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLN B 133 " --> pdb=" O ALA B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 150 No H-bonds generated for 'chain 'B' and resid 148 through 150' Processing helix chain 'B' and resid 188 through 201 removed outlier: 3.696A pdb=" N LEU B 191 " --> pdb=" O PRO B 188 " (cutoff:3.500A) 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 268 removed outlier: 4.305A pdb=" N GLN B 266 " --> pdb=" O LEU B 262 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N ASP B 267 " --> pdb=" O SER B 263 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR B 268 " --> pdb=" O ARG B 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 14 No H-bonds generated for 'chain 'C' and resid 11 through 14' Processing helix chain 'C' and resid 36 through 45 removed outlier: 4.250A pdb=" N HIS C 40 " --> pdb=" O MET C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 76 removed outlier: 3.719A pdb=" N GLN C 74 " --> pdb=" O GLU C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 97 Processing helix chain 'C' and resid 99 through 103 Processing helix chain 'C' and resid 123 through 133 Processing helix chain 'C' and resid 148 through 150 No H-bonds generated for 'chain 'C' and resid 148 through 150' Processing helix chain 'C' and resid 188 through 202 removed outlier: 3.785A pdb=" N LEU C 191 " --> pdb=" O PRO C 188 " (cutoff:3.500A) Proline residue: C 193 - end of helix 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 268 removed outlier: 4.389A pdb=" N GLN C 266 " --> pdb=" O LEU C 262 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N ASP C 267 " --> pdb=" O SER C 263 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N THR C 268 " --> pdb=" O ARG C 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 15 No H-bonds generated for 'chain 'D' and resid 13 through 15' Processing helix chain 'D' and resid 18 through 22 removed outlier: 3.611A pdb=" N PHE D 22 " --> pdb=" O ARG D 18 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 18 through 22' 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 45 removed outlier: 4.178A pdb=" N HIS D 40 " --> pdb=" O MET D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 76 removed outlier: 3.793A pdb=" N GLN D 74 " --> pdb=" O GLU D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 97 removed outlier: 3.792A pdb=" N GLY D 94 " --> pdb=" O GLY D 90 " (cutoff:3.500A) removed outlier: 4.318A 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: 3.579A pdb=" N ARG D 132 " --> pdb=" O GLU D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 151 No H-bonds generated for 'chain 'D' and resid 149 through 151' Processing helix chain 'D' and resid 188 through 202 removed outlier: 3.766A 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 229 removed outlier: 3.645A pdb=" N PHE D 227 " --> pdb=" O GLU D 223 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N SER D 228 " --> pdb=" O GLN D 224 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA D 229 " --> pdb=" O ASP D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 268 removed outlier: 3.787A pdb=" N LEU D 255 " --> pdb=" O GLY D 252 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA D 257 " --> pdb=" O ALA D 254 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N TYR D 265 " --> pdb=" O LEU D 262 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLN D 266 " --> pdb=" O SER D 263 " (cutoff:3.500A) Processing helix chain 'E' and resid 12 through 18 removed outlier: 3.880A pdb=" N ARG E 15 " --> pdb=" O THR E 12 " (cutoff:3.500A) Proline residue: E 16 - end of helix No H-bonds generated for 'chain 'E' and resid 12 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 61 through 71 removed outlier: 4.059A pdb=" N GLN E 69 " --> pdb=" O LYS E 65 " (cutoff:3.500A) removed outlier: 3.831A 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 98 Processing helix chain 'E' and resid 117 through 127 Processing helix chain 'E' and resid 196 through 204 removed outlier: 3.535A pdb=" N ILE E 200 " --> pdb=" O GLU E 196 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU E 204 " --> pdb=" O ILE E 200 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 239 removed outlier: 3.701A pdb=" N LEU E 226 " --> pdb=" O PRO E 222 " (cutoff:3.500A) 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 removed outlier: 3.555A pdb=" N GLN F 37 " --> pdb=" O ILE F 33 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 66 removed outlier: 3.956A pdb=" N GLU F 63 " --> pdb=" O VAL F 59 " (cutoff:3.500A) Processing helix chain 'F' and resid 68 through 71 No H-bonds generated for 'chain 'F' and resid 68 through 71' Processing helix chain 'F' and resid 87 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 180 through 185 removed outlier: 3.625A pdb=" N GLN F 184 " --> pdb=" O ALA F 181 " (cutoff:3.500A) Processing helix chain 'F' and resid 193 through 204 removed outlier: 4.795A pdb=" N PHE F 198 " --> pdb=" O GLU F 194 " (cutoff:3.500A) Proline residue: F 199 - end of helix removed outlier: 3.514A pdb=" N LYS F 203 " --> pdb=" O PRO F 199 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU F 204 " --> pdb=" O ILE F 200 " (cutoff:3.500A) Processing helix chain 'F' and resid 222 through 239 removed outlier: 4.256A pdb=" N GLN F 234 " --> pdb=" O CYS F 230 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER F 235 " --> pdb=" O LEU F 231 " (cutoff:3.500A) 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: 3.519A pdb=" N GLN G 37 " --> pdb=" O ILE G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 58 through 71 removed outlier: 4.101A pdb=" N LYS G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N GLN G 69 " --> pdb=" O LYS G 65 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ARG G 70 " --> pdb=" O ALA G 66 " (cutoff:3.500A) Processing helix chain 'G' and resid 85 through 92 Proline residue: G 89 - end of helix Processing helix chain 'G' and resid 94 through 98 Processing helix chain 'G' and resid 117 through 127 Processing helix chain 'G' and resid 181 through 184 Processing helix chain 'G' and resid 193 through 204 removed outlier: 5.111A pdb=" N PHE G 198 " --> pdb=" O GLU G 194 " (cutoff:3.500A) Proline residue: G 199 - end of helix removed outlier: 3.601A pdb=" N GLU G 204 " --> pdb=" O ILE G 200 " (cutoff:3.500A) Processing helix chain 'G' and resid 222 through 239 removed outlier: 3.581A pdb=" N THR G 227 " --> pdb=" O LYS G 223 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN G 234 " --> pdb=" O CYS G 230 " (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 33 through 44 removed outlier: 3.866A pdb=" N GLN H 37 " --> pdb=" O ILE H 33 " (cutoff:3.500A) Processing helix chain 'H' and resid 58 through 71 removed outlier: 3.701A pdb=" N ARG H 70 " --> pdb=" O ALA H 66 " (cutoff:3.500A) 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 141 through 143 No H-bonds generated for 'chain 'H' and resid 141 through 143' Processing helix chain 'H' and resid 193 through 204 Proline residue: H 199 - end of helix Processing helix chain 'H' and resid 222 through 239 removed outlier: 3.681A pdb=" N GLN H 234 " --> pdb=" O CYS H 230 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER H 235 " --> pdb=" O LEU H 231 " (cutoff:3.500A) 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 removed outlier: 3.672A pdb=" N GLN J 37 " --> pdb=" O ILE J 33 " (cutoff:3.500A) Processing helix chain 'J' and resid 58 through 71 removed outlier: 4.107A 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 98 Processing helix chain 'J' and resid 117 through 127 removed outlier: 3.745A pdb=" N GLN J 122 " --> pdb=" O GLN J 118 " (cutoff:3.500A) Processing helix chain 'J' and resid 180 through 185 removed outlier: 3.827A pdb=" N GLN J 184 " --> pdb=" O ALA J 181 " (cutoff:3.500A) Processing helix chain 'J' and resid 197 through 204 Processing helix chain 'J' and resid 224 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 33 through 44 removed outlier: 3.698A pdb=" N GLN L 37 " --> pdb=" O ILE L 33 " (cutoff:3.500A) Processing helix chain 'L' and resid 57 through 71 removed outlier: 4.482A pdb=" N LYS L 62 " --> pdb=" O VAL L 59 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLU L 68 " --> pdb=" O LYS L 65 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLN L 69 " --> pdb=" O ALA L 66 " (cutoff:3.500A) Processing helix chain 'L' and resid 88 through 92 Processing helix chain 'L' and resid 94 through 98 Processing helix chain 'L' and resid 117 through 127 Processing helix chain 'L' and resid 180 through 185 removed outlier: 3.876A pdb=" N GLN L 184 " --> pdb=" O PRO L 180 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ARG L 185 " --> pdb=" O ALA L 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 180 through 185' Processing helix chain 'L' and resid 196 through 204 removed outlier: 3.590A pdb=" N ILE L 200 " --> pdb=" O GLU L 196 " (cutoff:3.500A) Processing helix chain 'L' and resid 222 through 239 removed outlier: 4.278A pdb=" N GLN L 234 " --> pdb=" O CYS L 230 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N SER L 235 " --> pdb=" O LEU L 231 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'K' and resid 207 through 211 removed outlier: 7.256A pdb=" N GLY K 131 " --> pdb=" O TYR K 208 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N MET K 210 " --> pdb=" O GLY K 131 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ILE K 133 " --> pdb=" O MET K 210 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N MET K 175 " --> pdb=" O LEU K 134 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N HIS K 48 " --> pdb=" O ALA K 3 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N ILE K 5 " --> pdb=" O HIS K 48 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ILE K 50 " --> pdb=" O ILE K 5 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ARG K 74 " --> pdb=" O VAL K 49 " (cutoff:3.500A) removed outlier: 8.408A pdb=" N LEU K 51 " --> pdb=" O ARG K 74 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N SER K 76 " --> pdb=" O LEU K 51 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N VAL K 53 " --> pdb=" O SER K 76 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N SER K 78 " --> pdb=" O VAL K 53 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'K' and resid 135 through 137 Processing sheet with id= C, first strand: chain 'K' and resid 254 through 256 removed outlier: 6.240A pdb=" N VAL K 272 " --> pdb=" O LEU K 255 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'K' and resid 285 through 287 Processing sheet with id= E, first strand: chain 'K' and resid 319 through 321 Processing sheet with id= F, first strand: chain 'I' and resid 175 through 178 removed outlier: 6.772A pdb=" N HIS I 48 " --> pdb=" O ALA I 3 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N ILE I 5 " --> pdb=" O HIS I 48 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ILE I 50 " --> pdb=" O ILE I 5 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ARG I 74 " --> pdb=" O VAL I 49 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N LEU I 51 " --> pdb=" O ARG I 74 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N SER I 76 " --> pdb=" O LEU I 51 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N VAL I 53 " --> pdb=" O SER I 76 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N SER I 78 " --> pdb=" O VAL I 53 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'I' and resid 208 through 211 Processing sheet with id= H, first strand: chain 'I' and resid 254 through 256 removed outlier: 6.080A pdb=" N VAL I 272 " --> pdb=" O LEU I 255 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'I' and resid 285 through 287 Processing sheet with id= J, first strand: chain 'I' and resid 319 through 321 Processing sheet with id= K, first strand: chain 'A' and resid 236 through 240 removed outlier: 6.416A pdb=" N PHE A 137 " --> pdb=" O TYR A 237 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N HIS A 239 " --> pdb=" O PHE A 137 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N LEU A 139 " --> pdb=" O HIS A 239 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N ILE A 183 " --> pdb=" O LEU A 140 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LYS A 3 " --> pdb=" O ALA A 109 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N ALA A 4 " --> pdb=" O GLN A 51 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ILE A 53 " --> pdb=" O ALA A 4 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ILE A 6 " --> pdb=" O ILE A 53 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N LEU A 55 " --> pdb=" O ILE A 6 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N LEU A 55 " --> pdb=" O PRO A 79 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ARG A 81 " --> pdb=" O LEU A 55 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 117 through 119 Processing sheet with id= M, first strand: chain 'A' and resid 141 through 143 Processing sheet with id= N, first strand: chain 'A' and resid 287 through 289 removed outlier: 6.260A pdb=" N VAL A 305 " --> pdb=" O TYR A 288 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'A' and resid 318 through 320 Processing sheet with id= P, first strand: chain 'A' and resid 339 through 341 removed outlier: 6.453A pdb=" N THR A 385 " --> pdb=" O ILE A 340 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'A' and resid 154 through 157 removed outlier: 3.690A pdb=" N HIS A 166 " --> pdb=" O VAL A 156 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'B' and resid 236 through 240 removed outlier: 6.470A pdb=" N PHE B 137 " --> pdb=" O TYR B 237 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N HIS B 239 " --> pdb=" O PHE B 137 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N LEU B 139 " --> pdb=" O HIS B 239 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N ILE B 183 " --> pdb=" O LEU B 140 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N ALA B 4 " --> pdb=" O GLN B 51 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ILE B 53 " --> pdb=" O ALA B 4 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ILE B 6 " --> pdb=" O ILE B 53 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N LEU B 55 " --> pdb=" O ILE B 6 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N LEU B 55 " --> pdb=" O PRO B 79 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ARG B 81 " --> pdb=" O LEU B 55 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N GLY B 57 " --> pdb=" O ARG B 81 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N LEU B 83 " --> pdb=" O GLY B 57 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'B' and resid 117 through 119 Processing sheet with id= T, first strand: chain 'B' and resid 141 through 143 Processing sheet with id= U, first strand: chain 'B' and resid 287 through 289 removed outlier: 6.372A pdb=" N VAL B 305 " --> pdb=" O TYR B 288 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'B' and resid 318 through 320 Processing sheet with id= W, first strand: chain 'B' and resid 154 through 158 removed outlier: 6.583A pdb=" N ASN B 158 " --> pdb=" O VAL B 164 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N VAL B 164 " --> pdb=" O ASN B 158 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'C' and resid 236 through 240 removed outlier: 6.350A pdb=" N PHE C 137 " --> pdb=" O TYR C 237 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N HIS C 239 " --> pdb=" O PHE C 137 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N LEU C 139 " --> pdb=" O HIS C 239 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N ILE C 183 " --> pdb=" O LEU C 140 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LYS C 3 " --> pdb=" O ALA C 109 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N ALA C 4 " --> pdb=" O GLN C 51 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ILE C 53 " --> pdb=" O ALA C 4 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ILE C 6 " --> pdb=" O ILE C 53 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N LEU C 55 " --> pdb=" O ILE C 6 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N LEU C 55 " --> pdb=" O PRO C 79 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ARG C 81 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'C' and resid 117 through 119 Processing sheet with id= Z, first strand: chain 'C' and resid 141 through 143 Processing sheet with id= AA, first strand: chain 'C' and resid 318 through 320 Processing sheet with id= AB, first strand: chain 'C' and resid 339 through 341 removed outlier: 6.343A pdb=" N THR C 385 " --> pdb=" O ILE C 340 " (cutoff:3.500A) No H-bonds generated for sheet with id= AB Processing sheet with id= AC, first strand: chain 'C' and resid 153 through 158 removed outlier: 5.935A pdb=" N ASN C 158 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N VAL C 164 " --> pdb=" O ASN C 158 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'D' and resid 236 through 240 removed outlier: 6.373A pdb=" N PHE D 137 " --> pdb=" O TYR D 237 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N HIS D 239 " --> pdb=" O PHE D 137 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N LEU D 139 " --> pdb=" O HIS D 239 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N ILE D 183 " --> pdb=" O LEU D 140 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS D 3 " --> pdb=" O ALA D 109 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N ALA D 4 " --> pdb=" O GLN D 51 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ILE D 53 " --> pdb=" O ALA D 4 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ILE D 6 " --> pdb=" O ILE D 53 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N LEU D 55 " --> pdb=" O ILE D 6 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N LEU D 55 " --> pdb=" O PRO D 79 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ARG D 81 " --> pdb=" O LEU D 55 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N GLY D 57 " --> pdb=" O ARG D 81 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N LEU D 83 " --> pdb=" O GLY D 57 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'D' and resid 117 through 119 Processing sheet with id= AF, first strand: chain 'D' and resid 141 through 143 Processing sheet with id= AG, first strand: chain 'D' and resid 287 through 289 removed outlier: 6.257A pdb=" N VAL D 305 " --> pdb=" O TYR D 288 " (cutoff:3.500A) No H-bonds generated for sheet with id= AG Processing sheet with id= AH, first strand: chain 'D' and resid 318 through 320 Processing sheet with id= AI, first strand: chain 'D' and resid 339 through 341 removed outlier: 7.065A pdb=" N THR D 385 " --> pdb=" O ILE D 340 " (cutoff:3.500A) No H-bonds generated for sheet with id= AI Processing sheet with id= AJ, first strand: chain 'D' and resid 154 through 158 removed outlier: 6.482A pdb=" N ASN D 158 " --> pdb=" O VAL D 164 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N VAL D 164 " --> pdb=" O ASN D 158 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'E' and resid 207 through 211 removed outlier: 7.085A pdb=" N GLY E 131 " --> pdb=" O TYR E 208 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N MET E 210 " --> pdb=" O GLY E 131 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ILE E 133 " --> pdb=" O MET E 210 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N MET E 175 " --> pdb=" O LEU E 134 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE E 105 " --> pdb=" O LYS E 2 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N HIS E 48 " --> pdb=" O ALA E 3 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N ILE E 5 " --> pdb=" O HIS E 48 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE E 50 " --> pdb=" O ILE E 5 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N ARG E 74 " --> pdb=" O VAL E 49 " (cutoff:3.500A) removed outlier: 8.381A pdb=" N LEU E 51 " --> pdb=" O ARG E 74 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N SER E 76 " --> pdb=" O LEU E 51 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'E' and resid 135 through 137 Processing sheet with id= AM, first strand: chain 'E' and resid 254 through 256 removed outlier: 6.500A pdb=" N VAL E 272 " --> pdb=" O LEU E 255 " (cutoff:3.500A) No H-bonds generated for sheet with id= AM Processing sheet with id= AN, first strand: chain 'E' and resid 285 through 287 Processing sheet with id= AO, first strand: chain 'F' and resid 207 through 211 removed outlier: 7.102A pdb=" N GLY F 131 " --> pdb=" O TYR F 208 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N MET F 210 " --> pdb=" O GLY F 131 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ILE F 133 " --> pdb=" O MET F 210 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N MET F 175 " --> pdb=" O LEU F 134 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N LYS F 2 " --> pdb=" O PHE F 105 " (cutoff:3.500A) removed outlier: 8.501A pdb=" N LEU F 107 " --> pdb=" O LYS F 2 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N LEU F 4 " --> pdb=" O LEU F 107 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N HIS F 48 " --> pdb=" O ALA F 3 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N ILE F 5 " --> pdb=" O HIS F 48 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ILE F 50 " --> pdb=" O ILE F 5 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ARG F 74 " --> pdb=" O VAL F 49 " (cutoff:3.500A) removed outlier: 7.564A 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: 7.437A pdb=" N VAL F 53 " --> pdb=" O SER F 76 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N SER F 78 " --> pdb=" O VAL F 53 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'F' and resid 135 through 137 Processing sheet with id= AQ, first strand: chain 'F' and resid 254 through 256 removed outlier: 6.579A pdb=" N VAL F 272 " --> pdb=" O LEU F 255 " (cutoff:3.500A) No H-bonds generated for sheet with id= AQ Processing sheet with id= AR, first strand: chain 'F' and resid 319 through 321 removed outlier: 3.550A pdb=" N GLU F 321 " --> pdb=" O LEU F 338 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'F' and resid 146 through 149 removed outlier: 3.722A pdb=" N ARG F 158 " --> pdb=" O VAL F 148 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'G' and resid 207 through 211 removed outlier: 7.039A pdb=" N GLY G 131 " --> pdb=" O TYR G 208 " (cutoff:3.500A) removed outlier: 8.364A pdb=" N MET G 210 " --> pdb=" O GLY G 131 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ILE G 133 " --> pdb=" O MET G 210 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N MET G 175 " --> pdb=" O LEU G 134 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N HIS G 48 " --> pdb=" O ALA G 3 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N ILE G 5 " --> pdb=" O HIS G 48 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ILE G 50 " --> pdb=" O ILE G 5 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ARG G 74 " --> pdb=" O VAL G 49 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N LEU G 51 " --> pdb=" O ARG G 74 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N SER G 76 " --> pdb=" O LEU G 51 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'G' and resid 135 through 137 Processing sheet with id= AV, first strand: chain 'G' and resid 254 through 256 removed outlier: 6.478A pdb=" N VAL G 272 " --> pdb=" O LEU G 255 " (cutoff:3.500A) No H-bonds generated for sheet with id= AV Processing sheet with id= AW, first strand: chain 'G' and resid 285 through 287 Processing sheet with id= AX, first strand: chain 'G' and resid 319 through 321 Processing sheet with id= AY, first strand: chain 'G' and resid 146 through 149 removed outlier: 4.249A pdb=" N ARG G 158 " --> pdb=" O VAL G 148 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'H' and resid 207 through 210 removed outlier: 7.200A pdb=" N GLY H 131 " --> pdb=" O TYR H 208 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N MET H 210 " --> pdb=" O GLY H 131 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ILE H 133 " --> pdb=" O MET H 210 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N MET H 175 " --> pdb=" O LEU H 134 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N HIS H 48 " --> pdb=" O ALA H 3 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N ILE H 5 " --> pdb=" O HIS H 48 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ILE H 50 " --> pdb=" O ILE H 5 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N ARG H 74 " --> pdb=" O VAL H 49 " (cutoff:3.500A) removed outlier: 8.493A pdb=" N LEU H 51 " --> pdb=" O ARG H 74 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N SER H 76 " --> pdb=" O LEU H 51 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N VAL H 53 " --> pdb=" O SER H 76 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N SER H 78 " --> pdb=" O VAL H 53 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'H' and resid 135 through 137 Processing sheet with id= BB, first strand: chain 'H' and resid 254 through 256 removed outlier: 6.513A pdb=" N VAL H 272 " --> pdb=" O LEU H 255 " (cutoff:3.500A) No H-bonds generated for sheet with id= BB Processing sheet with id= BC, first strand: chain 'H' and resid 285 through 287 Processing sheet with id= BD, first strand: chain 'H' and resid 319 through 321 Processing sheet with id= BE, first strand: chain 'H' and resid 146 through 149 removed outlier: 3.717A pdb=" N ARG H 158 " --> pdb=" O VAL H 148 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 'J' and resid 175 through 178 removed outlier: 6.760A pdb=" N HIS J 48 " --> pdb=" O ALA J 3 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N ILE J 5 " --> pdb=" O HIS J 48 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ILE J 50 " --> pdb=" O ILE J 5 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain 'J' and resid 207 through 211 removed outlier: 6.872A pdb=" N GLY J 131 " --> pdb=" O TYR J 208 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N MET J 210 " --> pdb=" O GLY J 131 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ILE J 133 " --> pdb=" O MET J 210 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain 'J' and resid 146 through 148 removed outlier: 4.042A pdb=" N ARG J 158 " --> pdb=" O VAL J 148 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain 'J' and resid 254 through 256 removed outlier: 6.708A pdb=" N VAL J 272 " --> pdb=" O LEU J 255 " (cutoff:3.500A) No H-bonds generated for sheet with id= BI Processing sheet with id= BJ, first strand: chain 'J' and resid 285 through 287 Processing sheet with id= BK, first strand: chain 'J' and resid 319 through 321 Processing sheet with id= BL, first strand: chain 'L' and resid 48 through 51 removed outlier: 5.808A pdb=" N PHE L 105 " --> pdb=" O LEU L 4 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N LEU L 6 " --> pdb=" O PHE L 105 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N LEU L 107 " --> pdb=" O LEU L 6 " (cutoff:3.500A) Processing sheet with id= BM, first strand: chain 'L' and resid 135 through 137 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 Processing sheet with id= BP, first strand: chain 'L' and resid 146 through 149 737 hydrogen bonds defined for protein. 1986 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: 14.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8917 1.33 - 1.45: 6764 1.45 - 1.57: 20159 1.57 - 1.70: 73 1.70 - 1.82: 336 Bond restraints: 36249 Sorted by residual: bond pdb=" O2A GDD J 401 " pdb=" PA GDD J 401 " ideal model delta sigma weight residual 1.496 1.609 -0.113 2.00e-02 2.50e+03 3.20e+01 bond pdb=" O2A GDD F 401 " pdb=" PA GDD F 401 " ideal model delta sigma weight residual 1.496 1.609 -0.113 2.00e-02 2.50e+03 3.17e+01 bond pdb=" O2B GDD I 401 " pdb=" PB GDD I 401 " ideal model delta sigma weight residual 1.496 1.608 -0.112 2.00e-02 2.50e+03 3.15e+01 bond pdb=" O2A GDD I 401 " pdb=" PA GDD I 401 " ideal model delta sigma weight residual 1.496 1.608 -0.112 2.00e-02 2.50e+03 3.13e+01 bond pdb=" O2A GDD L 401 " pdb=" PA GDD L 401 " ideal model delta sigma weight residual 1.496 1.606 -0.110 2.00e-02 2.50e+03 3.04e+01 ... (remaining 36244 not shown) Histogram of bond angle deviations from ideal: 97.18 - 105.45: 1105 105.45 - 113.73: 20790 113.73 - 122.00: 19666 122.00 - 130.27: 7473 130.27 - 138.54: 259 Bond angle restraints: 49293 Sorted by residual: angle pdb=" N SER L 57 " pdb=" CA SER L 57 " pdb=" C SER L 57 " ideal model delta sigma weight residual 111.28 119.85 -8.57 1.09e+00 8.42e-01 6.18e+01 angle pdb=" N ARG D 18 " pdb=" CA ARG D 18 " pdb=" C ARG D 18 " ideal model delta sigma weight residual 113.16 123.56 -10.40 1.42e+00 4.96e-01 5.36e+01 angle pdb=" C ARG K 15 " pdb=" N PRO K 16 " pdb=" CA PRO K 16 " ideal model delta sigma weight residual 119.19 112.02 7.17 1.06e+00 8.90e-01 4.58e+01 angle pdb=" N LEU E 60 " pdb=" CA LEU E 60 " pdb=" C LEU E 60 " ideal model delta sigma weight residual 114.04 105.66 8.38 1.24e+00 6.50e-01 4.57e+01 angle pdb=" C ASP C 359 " pdb=" N PRO C 360 " pdb=" CA PRO C 360 " ideal model delta sigma weight residual 119.84 128.19 -8.35 1.25e+00 6.40e-01 4.46e+01 ... (remaining 49288 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 19167 18.00 - 36.00: 2296 36.00 - 54.00: 651 54.00 - 71.99: 149 71.99 - 89.99: 46 Dihedral angle restraints: 22309 sinusoidal: 9454 harmonic: 12855 Sorted by residual: dihedral pdb=" C VAL K 165 " pdb=" N VAL K 165 " pdb=" CA VAL K 165 " pdb=" CB VAL K 165 " ideal model delta harmonic sigma weight residual -122.00 -138.65 16.65 0 2.50e+00 1.60e-01 4.43e+01 dihedral pdb=" CA ASP F 95 " pdb=" C ASP F 95 " pdb=" N LEU F 96 " pdb=" CA LEU F 96 " ideal model delta harmonic sigma weight residual 180.00 151.81 28.19 0 5.00e+00 4.00e-02 3.18e+01 dihedral pdb=" N PHE K 166 " pdb=" C PHE K 166 " pdb=" CA PHE K 166 " pdb=" CB PHE K 166 " ideal model delta harmonic sigma weight residual 122.80 136.82 -14.02 0 2.50e+00 1.60e-01 3.15e+01 ... (remaining 22306 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.113: 5067 0.113 - 0.226: 492 0.226 - 0.340: 42 0.340 - 0.453: 8 0.453 - 0.566: 2 Chirality restraints: 5611 Sorted by residual: chirality pdb=" CA PHE K 166 " pdb=" N PHE K 166 " pdb=" C PHE K 166 " pdb=" CB PHE K 166 " both_signs ideal model delta sigma weight residual False 2.51 1.94 0.57 2.00e-01 2.50e+01 8.00e+00 chirality pdb=" CB VAL K 165 " pdb=" CA VAL K 165 " pdb=" CG1 VAL K 165 " pdb=" CG2 VAL K 165 " both_signs ideal model delta sigma weight residual False -2.63 -2.15 -0.48 2.00e-01 2.50e+01 5.79e+00 chirality pdb=" CA VAL K 165 " pdb=" N VAL K 165 " pdb=" C VAL K 165 " pdb=" CB VAL K 165 " both_signs ideal model delta sigma weight residual False 2.44 2.03 0.41 2.00e-01 2.50e+01 4.21e+00 ... (remaining 5608 not shown) Planarity restraints: 6325 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS E 79 " -0.043 2.00e-02 2.50e+03 3.81e-02 2.17e+01 pdb=" CG HIS E 79 " 0.080 2.00e-02 2.50e+03 pdb=" ND1 HIS E 79 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 HIS E 79 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 HIS E 79 " -0.017 2.00e-02 2.50e+03 pdb=" NE2 HIS E 79 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY G 88 " -0.061 5.00e-02 4.00e+02 9.19e-02 1.35e+01 pdb=" N PRO G 89 " 0.159 5.00e-02 4.00e+02 pdb=" CA PRO G 89 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO G 89 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY I 88 " -0.056 5.00e-02 4.00e+02 8.50e-02 1.15e+01 pdb=" N PRO I 89 " 0.147 5.00e-02 4.00e+02 pdb=" CA PRO I 89 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO I 89 " -0.047 5.00e-02 4.00e+02 ... (remaining 6322 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.29: 38 2.29 - 2.94: 15079 2.94 - 3.60: 50888 3.60 - 4.25: 83000 4.25 - 4.90: 141917 Nonbonded interactions: 290922 Sorted by model distance: nonbonded pdb=" OD1 ASP I 110 " pdb=" O3' GDD I 401 " model vdw 1.640 2.440 nonbonded pdb=" CB LEU H 344 " pdb=" O MET H 360 " model vdw 1.695 3.440 nonbonded pdb=" NH2 ARG K 15 " pdb=" O PRO L 345 " model vdw 1.900 2.520 nonbonded pdb=" O PRO A 406 " pdb=" NH2 ARG B 18 " model vdw 1.990 2.520 nonbonded pdb=" O3B GDD F 401 " pdb="MG MG F 402 " model vdw 2.002 2.170 ... (remaining 290917 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 or resid 501)) selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = (chain 'E' and (resid 1 through 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 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 'G' and (resid 1 through 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 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 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 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' selection = chain 'L' } 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: 0.840 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: 0.030 Extract box with map and model: 5.520 Check model and map are aligned: 0.540 Set scattering table: 0.320 Process input model: 90.590 Find NCS groups from input model: 2.670 Set up NCS constraints: 0.340 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 103.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 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 0.113 36249 Z= 0.634 Angle : 1.230 18.325 49293 Z= 0.641 Chirality : 0.071 0.566 5611 Planarity : 0.009 0.092 6325 Dihedral : 17.319 89.993 14023 Min Nonbonded Distance : 1.640 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.92 % Favored : 94.84 % Rotamer: Outliers : 8.56 % Allowed : 16.76 % Favored : 74.68 % Cbeta Deviations : 0.10 % 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: -2.44 (0.11), residues: 4473 helix: -2.88 (0.12), residues: 955 sheet: -1.05 (0.17), residues: 803 loop : -1.29 (0.11), residues: 2715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 343 HIS 0.031 0.002 HIS E 79 PHE 0.039 0.003 PHE G 215 TYR 0.018 0.002 TYR A 167 ARG 0.007 0.001 ARG B 264 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8946 Ramachandran restraints generated. 4473 Oldfield, 0 Emsley, 4473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8946 Ramachandran restraints generated. 4473 Oldfield, 0 Emsley, 4473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1192 residues out of total 3864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 336 poor density : 856 time to evaluate : 4.214 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