Starting phenix.real_space_refine (version: dev) on Sun Dec 18 15:29:49 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k7y_9945/12_2022/6k7y_9945_updated_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k7y_9945/12_2022/6k7y_9945.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k7y_9945/12_2022/6k7y_9945_updated_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k7y_9945/12_2022/6k7y_9945_updated_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k7y_9945/12_2022/6k7y_9945_updated_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k7y_9945/12_2022/6k7y_9945.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k7y_9945/12_2022/6k7y_9945.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k7y_9945/12_2022/6k7y_9945_updated_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k7y_9945/12_2022/6k7y_9945_updated_updated.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.103 sd= 1.837 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ARG 93": "NH1" <-> "NH2" Residue "A ARG 96": "NH1" <-> "NH2" Residue "A PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 113": "NH1" <-> "NH2" Residue "A TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 147": "OD1" <-> "OD2" Residue "A ARG 165": "NH1" <-> "NH2" Residue "A ARG 206": "NH1" <-> "NH2" Residue "A ASP 209": "OD1" <-> "OD2" Residue "A ARG 226": "NH1" <-> "NH2" Residue "A PHE 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 252": "NH1" <-> "NH2" Residue "A TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 286": "NH1" <-> "NH2" Residue "A TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 296": "OD1" <-> "OD2" Residue "A ARG 297": "NH1" <-> "NH2" Residue "A PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 313": "OD1" <-> "OD2" Residue "A TYR 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 330": "OD1" <-> "OD2" Residue "A ARG 345": "NH1" <-> "NH2" Residue "B ARG 93": "NH1" <-> "NH2" Residue "B PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 123": "OD1" <-> "OD2" Residue "B ARG 124": "NH1" <-> "NH2" Residue "B TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 252": "NH1" <-> "NH2" Residue "B TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 286": "NH1" <-> "NH2" Residue "B TYR 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 313": "OD1" <-> "OD2" Residue "C TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 89": "NH1" <-> "NH2" Residue "C ARG 93": "NH1" <-> "NH2" Residue "C PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 113": "NH1" <-> "NH2" Residue "C ASP 119": "OD1" <-> "OD2" Residue "C ARG 120": "NH1" <-> "NH2" Residue "C ARG 134": "NH1" <-> "NH2" Residue "C ASP 148": "OD1" <-> "OD2" Residue "C ARG 161": "NH1" <-> "NH2" Residue "C ARG 165": "NH1" <-> "NH2" Residue "C ASP 178": "OD1" <-> "OD2" Residue "C GLU 193": "OE1" <-> "OE2" Residue "C ARG 201": "NH1" <-> "NH2" Residue "C GLU 208": "OE1" <-> "OE2" Residue "C GLU 218": "OE1" <-> "OE2" Residue "C ARG 226": "NH1" <-> "NH2" Residue "C PHE 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 252": "NH1" <-> "NH2" Residue "C TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 286": "NH1" <-> "NH2" Residue "C PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 328": "OE1" <-> "OE2" Residue "C ARG 333": "NH1" <-> "NH2" Residue "D TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 131": "OD1" <-> "OD2" Residue "D PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 161": "NH1" <-> "NH2" Residue "D ARG 165": "NH1" <-> "NH2" Residue "D ASP 166": "OD1" <-> "OD2" Residue "D TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 193": "OE1" <-> "OE2" Residue "D GLU 205": "OE1" <-> "OE2" Residue "D GLU 212": "OE1" <-> "OE2" Residue "D ARG 221": "NH1" <-> "NH2" Residue "D ARG 226": "NH1" <-> "NH2" Residue "D PHE 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 252": "NH1" <-> "NH2" Residue "D TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 297": "NH1" <-> "NH2" Residue "D PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 335": "NH1" <-> "NH2" Residue "D ARG 345": "NH1" <-> "NH2" Residue "E ARG 52": "NH1" <-> "NH2" Residue "E PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 69": "NH1" <-> "NH2" Residue "E PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 93": "OE1" <-> "OE2" Residue "E ASP 96": "OD1" <-> "OD2" Residue "F ARG 52": "NH1" <-> "NH2" Residue "F PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 93": "OE1" <-> "OE2" Residue "F ASP 96": "OD1" <-> "OD2" Residue "G ARG 69": "NH1" <-> "NH2" Residue "G PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 93": "OE1" <-> "OE2" Residue "H PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 69": "NH1" <-> "NH2" Residue "I ARG 107": "NH1" <-> "NH2" Residue "I ASP 108": "OD1" <-> "OD2" Residue "I ARG 117": "NH1" <-> "NH2" Residue "I PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 151": "OD1" <-> "OD2" Residue "I PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 154": "NH1" <-> "NH2" Residue "I TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 208": "OD1" <-> "OD2" Residue "I PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 224": "OE1" <-> "OE2" Residue "I PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 241": "OE1" <-> "OE2" Residue "I GLU 244": "OE1" <-> "OE2" Residue "I ASP 306": "OD1" <-> "OD2" Residue "I ARG 314": "NH1" <-> "NH2" Residue "I ARG 325": "NH1" <-> "NH2" Residue "I ARG 347": "NH1" <-> "NH2" Residue "I PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 420": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 423": "OD1" <-> "OD2" Residue "I ARG 440": "NH1" <-> "NH2" Residue "I ARG 443": "NH1" <-> "NH2" Residue "J PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 101": "OE1" <-> "OE2" Residue "J TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 108": "OD1" <-> "OD2" Residue "J PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 116": "OE1" <-> "OE2" Residue "J GLU 119": "OE1" <-> "OE2" Residue "J ARG 120": "NH1" <-> "NH2" Residue "J PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 151": "OD1" <-> "OD2" Residue "J TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 185": "OD1" <-> "OD2" Residue "J ARG 195": "NH1" <-> "NH2" Residue "J PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 242": "NH1" <-> "NH2" Residue "J ARG 245": "NH1" <-> "NH2" Residue "J TYR 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 253": "NH1" <-> "NH2" Residue "J GLU 257": "OE1" <-> "OE2" Residue "J PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 279": "NH1" <-> "NH2" Residue "J GLU 281": "OE1" <-> "OE2" Residue "J PHE 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 304": "NH1" <-> "NH2" Residue "J GLU 305": "OE1" <-> "OE2" Residue "J ARG 343": "NH1" <-> "NH2" Residue "J ARG 346": "NH1" <-> "NH2" Residue "J PHE 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 352": "NH1" <-> "NH2" Residue "J GLU 380": "OE1" <-> "OE2" Residue "J ARG 394": "NH1" <-> "NH2" Residue "N ARG 93": "NH1" <-> "NH2" Residue "N ARG 96": "NH1" <-> "NH2" Residue "N PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 113": "NH1" <-> "NH2" Residue "N TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 147": "OD1" <-> "OD2" Residue "N ARG 165": "NH1" <-> "NH2" Residue "N ARG 206": "NH1" <-> "NH2" Residue "N ASP 209": "OD1" <-> "OD2" Residue "N ARG 226": "NH1" <-> "NH2" Residue "N PHE 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 252": "NH1" <-> "NH2" Residue "N TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 286": "NH1" <-> "NH2" Residue "N TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 296": "OD1" <-> "OD2" Residue "N ARG 297": "NH1" <-> "NH2" Residue "N PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 313": "OD1" <-> "OD2" Residue "N TYR 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 330": "OD1" <-> "OD2" Residue "N ARG 345": "NH1" <-> "NH2" Residue "O ARG 93": "NH1" <-> "NH2" Residue "O PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 123": "OD1" <-> "OD2" Residue "O ARG 124": "NH1" <-> "NH2" Residue "O TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 252": "NH1" <-> "NH2" Residue "O TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 286": "NH1" <-> "NH2" Residue "O ARG 297": "NH1" <-> "NH2" Residue "O TYR 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 313": "OD1" <-> "OD2" Residue "P TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 89": "NH1" <-> "NH2" Residue "P ARG 93": "NH1" <-> "NH2" Residue "P PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 113": "NH1" <-> "NH2" Residue "P ASP 119": "OD1" <-> "OD2" Residue "P ARG 120": "NH1" <-> "NH2" Residue "P ARG 134": "NH1" <-> "NH2" Residue "P ASP 148": "OD1" <-> "OD2" Residue "P ARG 161": "NH1" <-> "NH2" Residue "P ARG 165": "NH1" <-> "NH2" Residue "P ASP 178": "OD1" <-> "OD2" Residue "P GLU 193": "OE1" <-> "OE2" Residue "P ARG 201": "NH1" <-> "NH2" Residue "P GLU 208": "OE1" <-> "OE2" Residue "P GLU 218": "OE1" <-> "OE2" Residue "P ARG 226": "NH1" <-> "NH2" Residue "P PHE 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 252": "NH1" <-> "NH2" Residue "P TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 286": "NH1" <-> "NH2" Residue "P PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 328": "OE1" <-> "OE2" Residue "P ARG 333": "NH1" <-> "NH2" Residue "Q TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 131": "OD1" <-> "OD2" Residue "Q PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 161": "NH1" <-> "NH2" Residue "Q ARG 165": "NH1" <-> "NH2" Residue "Q ASP 166": "OD1" <-> "OD2" Residue "Q TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 193": "OE1" <-> "OE2" Residue "Q GLU 205": "OE1" <-> "OE2" Residue "Q GLU 212": "OE1" <-> "OE2" Residue "Q ARG 221": "NH1" <-> "NH2" Residue "Q ARG 226": "NH1" <-> "NH2" Residue "Q PHE 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 252": "NH1" <-> "NH2" Residue "Q TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 297": "NH1" <-> "NH2" Residue "Q PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 335": "NH1" <-> "NH2" Residue "Q ARG 345": "NH1" <-> "NH2" Residue "R ARG 52": "NH1" <-> "NH2" Residue "R PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 69": "NH1" <-> "NH2" Residue "R PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 93": "OE1" <-> "OE2" Residue "R ASP 96": "OD1" <-> "OD2" Residue "S ARG 52": "NH1" <-> "NH2" Residue "S PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 93": "OE1" <-> "OE2" Residue "S ASP 96": "OD1" <-> "OD2" Residue "T ARG 69": "NH1" <-> "NH2" Residue "T PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 93": "OE1" <-> "OE2" Residue "U PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 69": "NH1" <-> "NH2" Residue "V ARG 107": "NH1" <-> "NH2" Residue "V ASP 108": "OD1" <-> "OD2" Residue "V ARG 117": "NH1" <-> "NH2" Residue "V PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 151": "OD1" <-> "OD2" Residue "V PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 154": "NH1" <-> "NH2" Residue "V TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 208": "OD1" <-> "OD2" Residue "V PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 224": "OE1" <-> "OE2" Residue "V PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 241": "OE1" <-> "OE2" Residue "V GLU 244": "OE1" <-> "OE2" Residue "V ASP 306": "OD1" <-> "OD2" Residue "V ARG 314": "NH1" <-> "NH2" Residue "V ARG 325": "NH1" <-> "NH2" Residue "V ARG 347": "NH1" <-> "NH2" Residue "V PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 420": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 423": "OD1" <-> "OD2" Residue "V ARG 440": "NH1" <-> "NH2" Residue "V ARG 443": "NH1" <-> "NH2" Residue "W PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 101": "OE1" <-> "OE2" Residue "W TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 108": "OD1" <-> "OD2" Residue "W PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 116": "OE1" <-> "OE2" Residue "W GLU 119": "OE1" <-> "OE2" Residue "W ARG 120": "NH1" <-> "NH2" Residue "W PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 151": "OD1" <-> "OD2" Residue "W TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 185": "OD1" <-> "OD2" Residue "W ARG 195": "NH1" <-> "NH2" Residue "W PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 242": "NH1" <-> "NH2" Residue "W ARG 245": "NH1" <-> "NH2" Residue "W TYR 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 253": "NH1" <-> "NH2" Residue "W GLU 257": "OE1" <-> "OE2" Residue "W PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 279": "NH1" <-> "NH2" Residue "W GLU 281": "OE1" <-> "OE2" Residue "W PHE 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 304": "NH1" <-> "NH2" Residue "W GLU 305": "OE1" <-> "OE2" Residue "W ARG 343": "NH1" <-> "NH2" Residue "W ARG 346": "NH1" <-> "NH2" Residue "W PHE 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 352": "NH1" <-> "NH2" Residue "W GLU 380": "OE1" <-> "OE2" Residue "W ARG 394": "NH1" <-> "NH2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 32956 Number of models: 1 Model: "" Number of chains: 29 Chain: "A" Number of atoms: 2253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2253 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 11, 'TRANS': 261} Chain: "B" Number of atoms: 2253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2253 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 11, 'TRANS': 261} Chain: "C" Number of atoms: 2274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2274 Classifications: {'peptide': 276} Link IDs: {'PTRANS': 11, 'TRANS': 264} Chain: "D" Number of atoms: 2253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2253 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 11, 'TRANS': 261} Chain: "E" Number of atoms: 423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 423 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 4, 'TRANS': 49} Chain: "F" Number of atoms: 423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 423 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 4, 'TRANS': 49} Chain: "G" Number of atoms: 423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 423 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 4, 'TRANS': 49} Chain: "H" Number of atoms: 423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 423 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 4, 'TRANS': 49} Chain: "I" Number of atoms: 2406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2406 Classifications: {'peptide': 306} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 6, 'TRANS': 299} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 114 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'TRP:plan': 2, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 54 Chain: "J" Number of atoms: 2602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2602 Classifications: {'peptide': 319} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 4, 'TRANS': 314} Chain breaks: 1 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'TRP:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 45 Chain: "N" Number of atoms: 2253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2253 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 11, 'TRANS': 261} Chain: "O" Number of atoms: 2253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2253 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 11, 'TRANS': 261} Chain: "P" Number of atoms: 2274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2274 Classifications: {'peptide': 276} Link IDs: {'PTRANS': 11, 'TRANS': 264} Chain: "Q" Number of atoms: 2253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2253 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 11, 'TRANS': 261} Chain: "R" Number of atoms: 423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 423 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 4, 'TRANS': 49} Chain: "S" Number of atoms: 423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 423 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 4, 'TRANS': 49} Chain: "T" Number of atoms: 423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 423 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 4, 'TRANS': 49} Chain: "U" Number of atoms: 423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 423 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 4, 'TRANS': 49} Chain: "V" Number of atoms: 2406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2406 Classifications: {'peptide': 306} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 6, 'TRANS': 299} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 114 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'TRP:plan': 2, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 54 Chain: "W" Number of atoms: 2602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2602 Classifications: {'peptide': 319} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 4, 'TRANS': 314} Chain breaks: 1 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'TRP:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 45 Chain: "A" Number of atoms: 187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 187 Unusual residues: {' CA': 1, 'CDL': 1, 'PLX': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 186 Unusual residues: {'CDL': 1, 'PLX': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 220 Unusual residues: {'CDL': 1, 'PLX': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'PLX': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 100 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 187 Unusual residues: {' CA': 1, 'CDL': 1, 'PLX': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Chain: "O" Number of atoms: 186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 186 Unusual residues: {'CDL': 1, 'PLX': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Chain: "P" Number of atoms: 220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 220 Unusual residues: {'CDL': 1, 'PLX': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 152 Unusual residues: {'CDL': 1, 'PLX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 18.31, per 1000 atoms: 0.56 Number of scatterers: 32956 At special positions: 0 Unit cell: (212.745, 99.281, 184.379, 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) Ca 2 19.99 S 132 16.00 P 32 15.00 O 5950 8.00 N 5390 7.00 C 21450 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 12.21 Conformation dependent library (CDL) restraints added in 4.6 seconds 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7396 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 134 helices and 16 sheets defined 58.7% alpha, 5.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.12 Creating SS restraints... Processing helix chain 'A' and resid 108 through 119 removed outlier: 3.729A pdb=" N ASP A 119 " --> pdb=" O LEU A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 144 No H-bonds generated for 'chain 'A' and resid 141 through 144' Processing helix chain 'A' and resid 170 through 189 removed outlier: 4.596A pdb=" N LEU A 176 " --> pdb=" O ALA A 173 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N THR A 189 " --> pdb=" O LEU A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 255 removed outlier: 3.767A pdb=" N LEU A 214 " --> pdb=" O LEU A 210 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ALA A 215 " --> pdb=" O LYS A 211 " (cutoff:3.500A) Proline residue: A 216 - end of helix removed outlier: 3.859A pdb=" N VAL A 220 " --> pdb=" O PRO A 216 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLU A 223 " --> pdb=" O LYS A 219 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU A 234 " --> pdb=" O LYS A 230 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL A 235 " --> pdb=" O ARG A 231 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU A 240 " --> pdb=" O LEU A 236 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N THR A 254 " --> pdb=" O LEU A 250 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N TRP A 255 " --> pdb=" O ALA A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 285 Proline residue: A 265 - end of helix removed outlier: 3.783A pdb=" N TYR A 279 " --> pdb=" O ALA A 275 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N PHE A 282 " --> pdb=" O MET A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 310 Processing helix chain 'A' and resid 314 through 327 Processing helix chain 'A' and resid 329 through 332 No H-bonds generated for 'chain 'A' and resid 329 through 332' Processing helix chain 'B' and resid 108 through 119 Processing helix chain 'B' and resid 141 through 144 No H-bonds generated for 'chain 'B' and resid 141 through 144' Processing helix chain 'B' and resid 176 through 212 removed outlier: 4.888A pdb=" N GLU B 193 " --> pdb=" O THR B 189 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N GLN B 194 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASN B 198 " --> pdb=" O GLN B 194 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ARG B 201 " --> pdb=" O LEU B 197 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU B 205 " --> pdb=" O ARG B 201 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU B 208 " --> pdb=" O ILE B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 255 removed outlier: 4.047A pdb=" N LYS B 219 " --> pdb=" O ALA B 215 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N VAL B 220 " --> pdb=" O PRO B 216 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYS B 227 " --> pdb=" O GLU B 223 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE B 247 " --> pdb=" O MET B 243 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TRP B 255 " --> pdb=" O ALA B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 285 Proline residue: B 265 - end of helix removed outlier: 3.601A pdb=" N THR B 271 " --> pdb=" O THR B 267 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR B 279 " --> pdb=" O ALA B 275 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE B 282 " --> pdb=" O MET B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 306 Processing helix chain 'B' and resid 314 through 339 removed outlier: 3.897A pdb=" N ASP B 336 " --> pdb=" O LYS B 332 " (cutoff:3.500A) Proline residue: B 337 - end of helix Processing helix chain 'C' and resid 108 through 117 Processing helix chain 'C' and resid 141 through 144 No H-bonds generated for 'chain 'C' and resid 141 through 144' Processing helix chain 'C' and resid 172 through 190 removed outlier: 4.250A pdb=" N ASP C 178 " --> pdb=" O ALA C 174 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N VAL C 179 " --> pdb=" O THR C 175 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN C 184 " --> pdb=" O LYS C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 255 removed outlier: 3.567A pdb=" N ASP C 209 " --> pdb=" O GLU C 205 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU C 212 " --> pdb=" O GLU C 208 " (cutoff:3.500A) Proline residue: C 216 - end of helix removed outlier: 4.200A pdb=" N LYS C 219 " --> pdb=" O ALA C 215 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N VAL C 220 " --> pdb=" O PRO C 216 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LYS C 227 " --> pdb=" O GLU C 223 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG C 231 " --> pdb=" O LYS C 227 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N THR C 232 " --> pdb=" O ALA C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 285 Proline residue: C 265 - end of helix removed outlier: 3.528A pdb=" N TYR C 279 " --> pdb=" O ALA C 275 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE C 282 " --> pdb=" O MET C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 309 removed outlier: 3.902A pdb=" N LYS C 308 " --> pdb=" O HIS C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 339 removed outlier: 3.727A pdb=" N ALA C 323 " --> pdb=" O GLN C 319 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE C 324 " --> pdb=" O LEU C 320 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA C 325 " --> pdb=" O LYS C 321 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG C 335 " --> pdb=" O LEU C 331 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N ASP C 336 " --> pdb=" O LYS C 332 " (cutoff:3.500A) Proline residue: C 337 - end of helix Processing helix chain 'D' and resid 108 through 119 removed outlier: 4.557A pdb=" N ASP D 119 " --> pdb=" O LEU D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 144 No H-bonds generated for 'chain 'D' and resid 141 through 144' Processing helix chain 'D' and resid 172 through 189 Processing helix chain 'D' and resid 192 through 210 Processing helix chain 'D' and resid 215 through 253 removed outlier: 3.704A pdb=" N LYS D 219 " --> pdb=" O ALA D 215 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N VAL D 220 " --> pdb=" O PRO D 216 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLU D 223 " --> pdb=" O LYS D 219 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ARG D 231 " --> pdb=" O LYS D 227 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU D 234 " --> pdb=" O LYS D 230 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LEU D 253 " --> pdb=" O ILE D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 285 Proline residue: D 265 - end of helix removed outlier: 3.628A pdb=" N PHE D 282 " --> pdb=" O MET D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 309 removed outlier: 3.642A pdb=" N LYS D 308 " --> pdb=" O HIS D 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 334 removed outlier: 3.647A pdb=" N ALA D 325 " --> pdb=" O LYS D 321 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 94 removed outlier: 3.899A pdb=" N ILE E 73 " --> pdb=" O ARG E 69 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ILE E 75 " --> pdb=" O PHE E 71 " (cutoff:3.500A) Proline residue: E 76 - end of helix Processing helix chain 'F' and resid 66 through 94 removed outlier: 4.109A pdb=" N ILE F 73 " --> pdb=" O ARG F 69 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE F 75 " --> pdb=" O PHE F 71 " (cutoff:3.500A) Proline residue: F 76 - end of helix Processing helix chain 'G' and resid 66 through 94 removed outlier: 4.042A pdb=" N ILE G 73 " --> pdb=" O ARG G 69 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ILE G 75 " --> pdb=" O PHE G 71 " (cutoff:3.500A) Proline residue: G 76 - end of helix Processing helix chain 'H' and resid 66 through 94 removed outlier: 3.832A pdb=" N PHE H 71 " --> pdb=" O LEU H 67 " (cutoff:3.500A) Proline residue: H 76 - end of helix Processing helix chain 'I' and resid 107 through 120 Processing helix chain 'I' and resid 124 through 130 removed outlier: 4.065A pdb=" N PHE I 128 " --> pdb=" O PRO I 124 " (cutoff:3.500A) Processing helix chain 'I' and resid 149 through 156 Processing helix chain 'I' and resid 194 through 200 Processing helix chain 'I' and resid 206 through 217 Processing helix chain 'I' and resid 220 through 230 Processing helix chain 'I' and resid 240 through 250 removed outlier: 4.880A pdb=" N ILE I 250 " --> pdb=" O VAL I 246 " (cutoff:3.500A) Processing helix chain 'I' and resid 278 through 282 Processing helix chain 'I' and resid 293 through 314 Processing helix chain 'I' and resid 324 through 334 Processing helix chain 'I' and resid 342 through 352 removed outlier: 4.250A pdb=" N LYS I 350 " --> pdb=" O GLN I 346 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N LYS I 351 " --> pdb=" O ARG I 347 " (cutoff:3.500A) Processing helix chain 'I' and resid 361 through 380 removed outlier: 3.595A pdb=" N ILE I 374 " --> pdb=" O PHE I 370 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N ASN I 375 " --> pdb=" O LEU I 371 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ASP I 376 " --> pdb=" O LYS I 372 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N VAL I 377 " --> pdb=" O ASN I 373 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N THR I 379 " --> pdb=" O ASN I 375 " (cutoff:3.500A) Processing helix chain 'I' and resid 393 through 402 Processing helix chain 'I' and resid 410 through 420 Processing helix chain 'I' and resid 434 through 442 removed outlier: 3.920A pdb=" N MET I 442 " --> pdb=" O LYS I 438 " (cutoff:3.500A) Processing helix chain 'I' and resid 457 through 472 Processing helix chain 'J' and resid 85 through 93 Processing helix chain 'J' and resid 106 through 114 Processing helix chain 'J' and resid 129 through 141 removed outlier: 5.056A pdb=" N GLY J 138 " --> pdb=" O ASP J 134 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N ILE J 139 " --> pdb=" O THR J 135 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N GLN J 140 " --> pdb=" O LEU J 136 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N THR J 141 " --> pdb=" O SER J 137 " (cutoff:3.500A) Processing helix chain 'J' and resid 149 through 152 No H-bonds generated for 'chain 'J' and resid 149 through 152' Processing helix chain 'J' and resid 160 through 170 Processing helix chain 'J' and resid 177 through 183 Processing helix chain 'J' and resid 194 through 209 Processing helix chain 'J' and resid 233 through 238 Processing helix chain 'J' and resid 249 through 271 Processing helix chain 'J' and resid 280 through 290 removed outlier: 4.351A pdb=" N PHE J 290 " --> pdb=" O TRP J 286 " (cutoff:3.500A) Processing helix chain 'J' and resid 297 through 305 Processing helix chain 'J' and resid 315 through 326 Processing helix chain 'J' and resid 328 through 339 removed outlier: 4.573A pdb=" N MET J 337 " --> pdb=" O ILE J 333 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N PHE J 338 " --> pdb=" O ALA J 334 " (cutoff:3.500A) Processing helix chain 'J' and resid 347 through 358 Processing helix chain 'J' and resid 364 through 374 Processing helix chain 'J' and resid 384 through 390 Processing helix chain 'J' and resid 405 through 416 Processing helix chain 'N' and resid 108 through 119 removed outlier: 3.729A pdb=" N ASP N 119 " --> pdb=" O LEU N 115 " (cutoff:3.500A) Processing helix chain 'N' and resid 141 through 144 No H-bonds generated for 'chain 'N' and resid 141 through 144' Processing helix chain 'N' and resid 170 through 189 removed outlier: 4.597A pdb=" N LEU N 176 " --> pdb=" O ALA N 173 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N THR N 189 " --> pdb=" O LEU N 186 " (cutoff:3.500A) Processing helix chain 'N' and resid 192 through 255 removed outlier: 3.767A pdb=" N LEU N 214 " --> pdb=" O LEU N 210 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ALA N 215 " --> pdb=" O LYS N 211 " (cutoff:3.500A) Proline residue: N 216 - end of helix removed outlier: 3.859A pdb=" N VAL N 220 " --> pdb=" O PRO N 216 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLU N 223 " --> pdb=" O LYS N 219 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU N 234 " --> pdb=" O LYS N 230 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL N 235 " --> pdb=" O ARG N 231 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU N 240 " --> pdb=" O LEU N 236 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N THR N 254 " --> pdb=" O LEU N 250 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N TRP N 255 " --> pdb=" O ALA N 251 " (cutoff:3.500A) Processing helix chain 'N' and resid 260 through 285 Proline residue: N 265 - end of helix removed outlier: 3.784A pdb=" N TYR N 279 " --> pdb=" O ALA N 275 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N PHE N 282 " --> pdb=" O MET N 278 " (cutoff:3.500A) Processing helix chain 'N' and resid 291 through 310 Processing helix chain 'N' and resid 314 through 327 Processing helix chain 'N' and resid 329 through 332 No H-bonds generated for 'chain 'N' and resid 329 through 332' Processing helix chain 'O' and resid 108 through 119 Processing helix chain 'O' and resid 141 through 144 No H-bonds generated for 'chain 'O' and resid 141 through 144' Processing helix chain 'O' and resid 176 through 212 removed outlier: 4.888A pdb=" N GLU O 193 " --> pdb=" O THR O 189 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N GLN O 194 " --> pdb=" O LEU O 190 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASN O 198 " --> pdb=" O GLN O 194 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ARG O 201 " --> pdb=" O LEU O 197 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU O 205 " --> pdb=" O ARG O 201 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU O 208 " --> pdb=" O ILE O 204 " (cutoff:3.500A) Processing helix chain 'O' and resid 215 through 255 removed outlier: 4.047A pdb=" N LYS O 219 " --> pdb=" O ALA O 215 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N VAL O 220 " --> pdb=" O PRO O 216 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYS O 227 " --> pdb=" O GLU O 223 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE O 247 " --> pdb=" O MET O 243 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TRP O 255 " --> pdb=" O ALA O 251 " (cutoff:3.500A) Processing helix chain 'O' and resid 260 through 285 Proline residue: O 265 - end of helix removed outlier: 3.601A pdb=" N THR O 271 " --> pdb=" O THR O 267 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR O 279 " --> pdb=" O ALA O 275 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE O 282 " --> pdb=" O MET O 278 " (cutoff:3.500A) Processing helix chain 'O' and resid 291 through 306 Processing helix chain 'O' and resid 314 through 339 removed outlier: 3.897A pdb=" N ASP O 336 " --> pdb=" O LYS O 332 " (cutoff:3.500A) Proline residue: O 337 - end of helix Processing helix chain 'P' and resid 108 through 117 Processing helix chain 'P' and resid 141 through 144 No H-bonds generated for 'chain 'P' and resid 141 through 144' Processing helix chain 'P' and resid 172 through 190 removed outlier: 4.250A pdb=" N ASP P 178 " --> pdb=" O ALA P 174 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N VAL P 179 " --> pdb=" O THR P 175 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN P 184 " --> pdb=" O LYS P 180 " (cutoff:3.500A) Processing helix chain 'P' and resid 193 through 255 removed outlier: 3.567A pdb=" N ASP P 209 " --> pdb=" O GLU P 205 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU P 212 " --> pdb=" O GLU P 208 " (cutoff:3.500A) Proline residue: P 216 - end of helix removed outlier: 4.200A pdb=" N LYS P 219 " --> pdb=" O ALA P 215 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N VAL P 220 " --> pdb=" O PRO P 216 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LYS P 227 " --> pdb=" O GLU P 223 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG P 231 " --> pdb=" O LYS P 227 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N THR P 232 " --> pdb=" O ALA P 228 " (cutoff:3.500A) Processing helix chain 'P' and resid 260 through 285 Proline residue: P 265 - end of helix removed outlier: 3.529A pdb=" N TYR P 279 " --> pdb=" O ALA P 275 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE P 282 " --> pdb=" O MET P 278 " (cutoff:3.500A) Processing helix chain 'P' and resid 291 through 309 removed outlier: 3.903A pdb=" N LYS P 308 " --> pdb=" O HIS P 304 " (cutoff:3.500A) Processing helix chain 'P' and resid 314 through 339 removed outlier: 3.727A pdb=" N ALA P 323 " --> pdb=" O GLN P 319 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE P 324 " --> pdb=" O LEU P 320 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA P 325 " --> pdb=" O LYS P 321 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG P 335 " --> pdb=" O LEU P 331 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N ASP P 336 " --> pdb=" O LYS P 332 " (cutoff:3.500A) Proline residue: P 337 - end of helix Processing helix chain 'Q' and resid 108 through 119 removed outlier: 4.558A pdb=" N ASP Q 119 " --> pdb=" O LEU Q 115 " (cutoff:3.500A) Processing helix chain 'Q' and resid 141 through 144 No H-bonds generated for 'chain 'Q' and resid 141 through 144' Processing helix chain 'Q' and resid 172 through 189 Processing helix chain 'Q' and resid 192 through 210 Processing helix chain 'Q' and resid 215 through 253 removed outlier: 3.703A pdb=" N LYS Q 219 " --> pdb=" O ALA Q 215 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N VAL Q 220 " --> pdb=" O PRO Q 216 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLU Q 223 " --> pdb=" O LYS Q 219 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ARG Q 231 " --> pdb=" O LYS Q 227 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU Q 234 " --> pdb=" O LYS Q 230 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LEU Q 253 " --> pdb=" O ILE Q 249 " (cutoff:3.500A) Processing helix chain 'Q' and resid 260 through 285 Proline residue: Q 265 - end of helix removed outlier: 3.628A pdb=" N PHE Q 282 " --> pdb=" O MET Q 278 " (cutoff:3.500A) Processing helix chain 'Q' and resid 291 through 309 removed outlier: 3.642A pdb=" N LYS Q 308 " --> pdb=" O HIS Q 304 " (cutoff:3.500A) Processing helix chain 'Q' and resid 314 through 334 removed outlier: 3.647A pdb=" N ALA Q 325 " --> pdb=" O LYS Q 321 " (cutoff:3.500A) Processing helix chain 'R' and resid 66 through 94 removed outlier: 3.898A pdb=" N ILE R 73 " --> pdb=" O ARG R 69 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ILE R 75 " --> pdb=" O PHE R 71 " (cutoff:3.500A) Proline residue: R 76 - end of helix Processing helix chain 'S' and resid 66 through 94 removed outlier: 4.109A pdb=" N ILE S 73 " --> pdb=" O ARG S 69 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE S 75 " --> pdb=" O PHE S 71 " (cutoff:3.500A) Proline residue: S 76 - end of helix Processing helix chain 'T' and resid 66 through 94 removed outlier: 4.041A pdb=" N ILE T 73 " --> pdb=" O ARG T 69 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ILE T 75 " --> pdb=" O PHE T 71 " (cutoff:3.500A) Proline residue: T 76 - end of helix Processing helix chain 'U' and resid 66 through 94 removed outlier: 3.832A pdb=" N PHE U 71 " --> pdb=" O LEU U 67 " (cutoff:3.500A) Proline residue: U 76 - end of helix Processing helix chain 'V' and resid 107 through 120 Processing helix chain 'V' and resid 124 through 130 removed outlier: 4.064A pdb=" N PHE V 128 " --> pdb=" O PRO V 124 " (cutoff:3.500A) Processing helix chain 'V' and resid 149 through 156 Processing helix chain 'V' and resid 194 through 200 Processing helix chain 'V' and resid 206 through 217 Processing helix chain 'V' and resid 220 through 230 Processing helix chain 'V' and resid 240 through 250 removed outlier: 4.880A pdb=" N ILE V 250 " --> pdb=" O VAL V 246 " (cutoff:3.500A) Processing helix chain 'V' and resid 278 through 282 Processing helix chain 'V' and resid 293 through 314 Processing helix chain 'V' and resid 324 through 334 Processing helix chain 'V' and resid 342 through 352 removed outlier: 4.250A pdb=" N LYS V 350 " --> pdb=" O GLN V 346 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N LYS V 351 " --> pdb=" O ARG V 347 " (cutoff:3.500A) Processing helix chain 'V' and resid 361 through 380 removed outlier: 3.594A pdb=" N ILE V 374 " --> pdb=" O PHE V 370 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N ASN V 375 " --> pdb=" O LEU V 371 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ASP V 376 " --> pdb=" O LYS V 372 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N VAL V 377 " --> pdb=" O ASN V 373 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N THR V 379 " --> pdb=" O ASN V 375 " (cutoff:3.500A) Processing helix chain 'V' and resid 393 through 402 Processing helix chain 'V' and resid 410 through 420 Processing helix chain 'V' and resid 434 through 442 removed outlier: 3.920A pdb=" N MET V 442 " --> pdb=" O LYS V 438 " (cutoff:3.500A) Processing helix chain 'V' and resid 457 through 472 Processing helix chain 'W' and resid 85 through 93 Processing helix chain 'W' and resid 106 through 114 Processing helix chain 'W' and resid 129 through 141 removed outlier: 5.056A pdb=" N GLY W 138 " --> pdb=" O ASP W 134 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N ILE W 139 " --> pdb=" O THR W 135 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N GLN W 140 " --> pdb=" O LEU W 136 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N THR W 141 " --> pdb=" O SER W 137 " (cutoff:3.500A) Processing helix chain 'W' and resid 149 through 152 No H-bonds generated for 'chain 'W' and resid 149 through 152' Processing helix chain 'W' and resid 160 through 170 Processing helix chain 'W' and resid 177 through 183 Processing helix chain 'W' and resid 194 through 209 Processing helix chain 'W' and resid 233 through 238 Processing helix chain 'W' and resid 249 through 271 Processing helix chain 'W' and resid 280 through 290 removed outlier: 4.351A pdb=" N PHE W 290 " --> pdb=" O TRP W 286 " (cutoff:3.500A) Processing helix chain 'W' and resid 297 through 305 Processing helix chain 'W' and resid 315 through 326 Processing helix chain 'W' and resid 328 through 339 removed outlier: 4.573A pdb=" N MET W 337 " --> pdb=" O ILE W 333 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N PHE W 338 " --> pdb=" O ALA W 334 " (cutoff:3.500A) Processing helix chain 'W' and resid 347 through 358 Processing helix chain 'W' and resid 364 through 374 Processing helix chain 'W' and resid 384 through 390 Processing helix chain 'W' and resid 405 through 416 Processing sheet with id= A, first strand: chain 'A' and resid 76 through 80 removed outlier: 3.704A pdb=" N GLU A 95 " --> pdb=" O LEU A 90 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 126 through 129 Processing sheet with id= C, first strand: chain 'B' and resid 76 through 80 removed outlier: 3.577A pdb=" N THR B 76 " --> pdb=" O SER B 87 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 125 through 129 Processing sheet with id= E, first strand: chain 'C' and resid 76 through 80 removed outlier: 3.686A pdb=" N GLU C 95 " --> pdb=" O LEU C 90 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 126 through 129 Processing sheet with id= G, first strand: chain 'D' and resid 76 through 80 Processing sheet with id= H, first strand: chain 'D' and resid 126 through 129 Processing sheet with id= I, first strand: chain 'N' and resid 76 through 80 removed outlier: 3.705A pdb=" N GLU N 95 " --> pdb=" O LEU N 90 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'N' and resid 126 through 129 Processing sheet with id= K, first strand: chain 'O' and resid 76 through 80 removed outlier: 3.577A pdb=" N THR O 76 " --> pdb=" O SER O 87 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'O' and resid 125 through 129 Processing sheet with id= M, first strand: chain 'P' and resid 76 through 80 removed outlier: 3.686A pdb=" N GLU P 95 " --> pdb=" O LEU P 90 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'P' and resid 126 through 129 Processing sheet with id= O, first strand: chain 'Q' and resid 76 through 80 Processing sheet with id= P, first strand: chain 'Q' and resid 126 through 129 1662 hydrogen bonds defined for protein. 4794 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: 9.51 Time building geometry restraints manager: 13.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 5361 1.32 - 1.44: 8482 1.44 - 1.57: 19423 1.57 - 1.69: 64 1.69 - 1.81: 236 Bond restraints: 33566 Sorted by residual: bond pdb=" C ASP B 296 " pdb=" N ARG B 297 " ideal model delta sigma weight residual 1.335 1.402 -0.067 1.31e-02 5.83e+03 2.59e+01 bond pdb=" O2 PLX O 402 " pdb=" P1 PLX O 402 " ideal model delta sigma weight residual 1.513 1.449 0.064 2.00e-02 2.50e+03 1.01e+01 bond pdb=" O2 PLX N 403 " pdb=" P1 PLX N 403 " ideal model delta sigma weight residual 1.513 1.450 0.063 2.00e-02 2.50e+03 1.01e+01 bond pdb=" O2 PLX A 403 " pdb=" P1 PLX A 403 " ideal model delta sigma weight residual 1.513 1.450 0.063 2.00e-02 2.50e+03 9.99e+00 bond pdb=" O2 PLX B 402 " pdb=" P1 PLX B 402 " ideal model delta sigma weight residual 1.513 1.450 0.063 2.00e-02 2.50e+03 9.95e+00 ... (remaining 33561 not shown) Histogram of bond angle deviations from ideal: 94.74 - 102.61: 167 102.61 - 110.47: 9205 110.47 - 118.34: 16789 118.34 - 126.20: 18497 126.20 - 134.06: 364 Bond angle restraints: 45022 Sorted by residual: angle pdb=" CA2 CDL P 401 " pdb=" OA2 CDL P 401 " pdb=" PA1 CDL P 401 " ideal model delta sigma weight residual 121.27 114.00 7.27 1.00e+00 1.00e+00 5.28e+01 angle pdb=" CA2 CDL C 401 " pdb=" OA2 CDL C 401 " pdb=" PA1 CDL C 401 " ideal model delta sigma weight residual 121.27 114.06 7.21 1.00e+00 1.00e+00 5.20e+01 angle pdb=" CB2 CDL C 401 " pdb=" OB2 CDL C 401 " pdb=" PB2 CDL C 401 " ideal model delta sigma weight residual 121.27 115.62 5.65 1.00e+00 1.00e+00 3.19e+01 angle pdb=" CB2 CDL P 401 " pdb=" OB2 CDL P 401 " pdb=" PB2 CDL P 401 " ideal model delta sigma weight residual 121.27 115.63 5.64 1.00e+00 1.00e+00 3.18e+01 angle pdb=" C51 CDL Q 401 " pdb=" CB5 CDL Q 401 " pdb=" OB6 CDL Q 401 " ideal model delta sigma weight residual 111.33 118.25 -6.92 1.32e+00 5.72e-01 2.74e+01 ... (remaining 45017 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 18046 17.97 - 35.94: 1764 35.94 - 53.91: 472 53.91 - 71.88: 144 71.88 - 89.85: 26 Dihedral angle restraints: 20452 sinusoidal: 9066 harmonic: 11386 Sorted by residual: dihedral pdb=" CA THR V 123 " pdb=" C THR V 123 " pdb=" N PRO V 124 " pdb=" CA PRO V 124 " ideal model delta harmonic sigma weight residual 180.00 -153.90 -26.10 0 5.00e+00 4.00e-02 2.72e+01 dihedral pdb=" CA THR I 123 " pdb=" C THR I 123 " pdb=" N PRO I 124 " pdb=" CA PRO I 124 " ideal model delta harmonic sigma weight residual -180.00 -153.91 -26.09 0 5.00e+00 4.00e-02 2.72e+01 dihedral pdb=" CA ILE D 153 " pdb=" C ILE D 153 " pdb=" N ASN D 154 " pdb=" CA ASN D 154 " ideal model delta harmonic sigma weight residual 180.00 -158.16 -21.84 0 5.00e+00 4.00e-02 1.91e+01 ... (remaining 20449 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.114: 4850 0.114 - 0.228: 68 0.228 - 0.343: 6 0.343 - 0.457: 0 0.457 - 0.571: 2 Chirality restraints: 4926 Sorted by residual: chirality pdb=" CB4 CDL N 402 " pdb=" CB3 CDL N 402 " pdb=" CB6 CDL N 402 " pdb=" OB6 CDL N 402 " both_signs ideal model delta sigma weight residual False -2.57 -2.00 -0.57 2.00e-01 2.50e+01 8.15e+00 chirality pdb=" CB4 CDL A 402 " pdb=" CB3 CDL A 402 " pdb=" CB6 CDL A 402 " pdb=" OB6 CDL A 402 " both_signs ideal model delta sigma weight residual False -2.57 -2.01 -0.57 2.00e-01 2.50e+01 8.03e+00 chirality pdb=" CB4 CDL H 201 " pdb=" CB3 CDL H 201 " pdb=" CB6 CDL H 201 " pdb=" OB6 CDL H 201 " both_signs ideal model delta sigma weight residual False -2.57 -2.24 -0.34 2.00e-01 2.50e+01 2.84e+00 ... (remaining 4923 not shown) Planarity restraints: 5546 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO B 292 " -0.017 2.00e-02 2.50e+03 3.29e-02 1.08e+01 pdb=" C PRO B 292 " 0.057 2.00e-02 2.50e+03 pdb=" O PRO B 292 " -0.021 2.00e-02 2.50e+03 pdb=" N GLU B 293 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO O 292 " 0.016 2.00e-02 2.50e+03 3.28e-02 1.07e+01 pdb=" C PRO O 292 " -0.057 2.00e-02 2.50e+03 pdb=" O PRO O 292 " 0.021 2.00e-02 2.50e+03 pdb=" N GLU O 293 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 297 " 0.197 9.50e-02 1.11e+02 9.10e-02 1.05e+01 pdb=" NE ARG A 297 " 0.002 2.00e-02 2.50e+03 pdb=" CZ ARG A 297 " -0.044 2.00e-02 2.50e+03 pdb=" NH1 ARG A 297 " 0.012 2.00e-02 2.50e+03 pdb=" NH2 ARG A 297 " 0.021 2.00e-02 2.50e+03 ... (remaining 5543 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 2747 2.73 - 3.27: 32544 3.27 - 3.82: 51539 3.82 - 4.36: 60127 4.36 - 4.90: 104428 Nonbonded interactions: 251385 Sorted by model distance: nonbonded pdb=" OG SER A 92 " pdb=" OD1 ASP A 119 " model vdw 2.190 2.440 nonbonded pdb=" OG SER N 92 " pdb=" OD1 ASP N 119 " model vdw 2.190 2.440 nonbonded pdb=" NH1 ARG J 343 " pdb=" O PRO J 344 " model vdw 2.217 2.520 nonbonded pdb=" NH1 ARG W 343 " pdb=" O PRO W 344 " model vdw 2.217 2.520 nonbonded pdb=" NH1 ARG Q 297 " pdb=" OA4 CDL Q 401 " model vdw 2.220 2.520 ... (remaining 251380 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 73 through 345) selection = (chain 'B' and resid 73 through 345) selection = (chain 'C' and resid 73 through 345) selection = (chain 'D' and resid 73 through 345) selection = (chain 'N' and resid 73 through 345) selection = (chain 'O' and resid 73 through 345) selection = (chain 'P' and resid 73 through 345) selection = (chain 'Q' and resid 73 through 345) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = (chain 'H' and resid 48 through 101) selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' } ncs_group { reference = chain 'I' selection = chain 'V' } ncs_group { reference = chain 'J' selection = chain 'W' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 2 9.91 5 P 32 5.49 5 S 132 5.16 5 C 21450 2.51 5 N 5390 2.21 5 O 5950 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.620 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: 13.080 Check model and map are aligned: 0.460 Convert atoms to be neutral: 0.270 Process input model: 76.160 Find NCS groups from input model: 2.680 Set up NCS constraints: 0.210 Set refine NCS operators: 0.000 Set scattering table: 0.020 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 97.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 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 : 0.006 0.067 33566 Z= 0.375 Angle : 0.712 14.185 45022 Z= 0.371 Chirality : 0.045 0.571 4926 Planarity : 0.004 0.106 5546 Dihedral : 15.909 89.847 13056 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.70 % Favored : 95.20 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % 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: -1.75 (0.13), residues: 3812 helix: -0.43 (0.10), residues: 2404 sheet: -1.16 (0.30), residues: 232 loop : -2.55 (0.16), residues: 1176 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 3474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 439 time to evaluate : 4.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 441 average time/residue: 0.4887 time to fit residues: 334.5621 Evaluate side-chains 320 residues out of total 3474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 320 time to evaluate : 3.795 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.1798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 319 optimal weight: 0.3980 chunk 286 optimal weight: 1.9990 chunk 158 optimal weight: 0.0170 chunk 97 optimal weight: 1.9990 chunk 193 optimal weight: 0.8980 chunk 153 optimal weight: 3.9990 chunk 296 optimal weight: 1.9990 chunk 114 optimal weight: 0.5980 chunk 180 optimal weight: 3.9990 chunk 220 optimal weight: 6.9990 chunk 343 optimal weight: 7.9990 overall best weight: 0.7820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN A 185 GLN A 196 GLN A 298 GLN B 195 HIS B 213 GLN B 318 ASN C 80 GLN C 172 ASN C 185 GLN C 196 GLN C 213 GLN D 80 GLN D 114 GLN D 196 GLN D 213 GLN D 246 GLN H 95 HIS I 159 ASN I 245 GLN ** I 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 348 GLN I 352 HIS ** I 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 397 GLN I 398 GLN I 411 HIS J 98 HIS J 117 GLN J 235 GLN J 260 GLN N 80 GLN N 185 GLN N 196 GLN N 319 GLN O 195 HIS O 213 GLN O 318 ASN P 80 GLN P 172 ASN P 185 GLN P 196 GLN P 213 GLN Q 80 GLN Q 114 GLN Q 196 GLN Q 213 GLN Q 246 GLN U 95 HIS V 159 ASN V 245 GLN ** V 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 348 GLN V 352 HIS ** V 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 397 GLN V 398 GLN V 411 HIS W 98 HIS W 117 GLN W 235 GLN W 260 GLN Total number of N/Q/H flips: 58 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.1007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 33566 Z= 0.169 Angle : 0.504 7.224 45022 Z= 0.252 Chirality : 0.039 0.187 4926 Planarity : 0.003 0.043 5546 Dihedral : 12.963 59.932 5258 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer Outliers : 1.03 % Cbeta Deviations : 0.00 % 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: -0.37 (0.14), residues: 3812 helix: 0.68 (0.11), residues: 2418 sheet: -0.57 (0.31), residues: 232 loop : -2.11 (0.17), residues: 1162 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 3474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 352 time to evaluate : 4.001 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 18 residues processed: 367 average time/residue: 0.4362 time to fit residues: 258.8003 Evaluate side-chains 329 residues out of total 3474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 311 time to evaluate : 3.801 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.3013 time to fit residues: 15.4990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 190 optimal weight: 0.0970 chunk 106 optimal weight: 3.9990 chunk 285 optimal weight: 2.9990 chunk 233 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 343 optimal weight: 5.9990 chunk 371 optimal weight: 8.9990 chunk 306 optimal weight: 4.9990 chunk 341 optimal weight: 3.9990 chunk 117 optimal weight: 4.9990 chunk 275 optimal weight: 2.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 159 ASN ** I 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 300 GLN ** I 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 300 GLN ** V 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.1327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.045 33566 Z= 0.409 Angle : 0.605 6.786 45022 Z= 0.306 Chirality : 0.044 0.177 4926 Planarity : 0.004 0.045 5546 Dihedral : 12.371 59.916 5258 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer Outliers : 1.29 % Cbeta Deviations : 0.00 % 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: -0.04 (0.14), residues: 3812 helix: 0.91 (0.11), residues: 2424 sheet: -0.37 (0.32), residues: 232 loop : -1.94 (0.17), residues: 1156 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 3474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 308 time to evaluate : 3.914 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 22 residues processed: 336 average time/residue: 0.4354 time to fit residues: 241.1569 Evaluate side-chains 317 residues out of total 3474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 295 time to evaluate : 3.479 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.3007 time to fit residues: 17.9786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 339 optimal weight: 3.9990 chunk 258 optimal weight: 0.6980 chunk 178 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 chunk 164 optimal weight: 4.9990 chunk 230 optimal weight: 2.9990 chunk 345 optimal weight: 9.9990 chunk 365 optimal weight: 2.9990 chunk 180 optimal weight: 1.9990 chunk 327 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 95 HIS ** I 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 248 HIS ** V 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 248 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.041 33566 Z= 0.292 Angle : 0.541 6.550 45022 Z= 0.274 Chirality : 0.041 0.169 4926 Planarity : 0.004 0.045 5546 Dihedral : 11.740 59.900 5258 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer Outliers : 1.35 % Cbeta Deviations : 0.00 % 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: 0.28 (0.14), residues: 3812 helix: 1.16 (0.11), residues: 2418 sheet: -0.17 (0.33), residues: 232 loop : -1.81 (0.18), residues: 1162 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 3474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 309 time to evaluate : 3.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 24 residues processed: 336 average time/residue: 0.4387 time to fit residues: 240.7570 Evaluate side-chains 309 residues out of total 3474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 285 time to evaluate : 3.514 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.2920 time to fit residues: 18.8209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 304 optimal weight: 0.6980 chunk 207 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 272 optimal weight: 0.6980 chunk 150 optimal weight: 3.9990 chunk 311 optimal weight: 2.9990 chunk 252 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 186 optimal weight: 2.9990 chunk 327 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 385 HIS S 95 HIS ** V 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 352 HIS V 385 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 33566 Z= 0.260 Angle : 0.534 9.724 45022 Z= 0.268 Chirality : 0.041 0.168 4926 Planarity : 0.003 0.046 5546 Dihedral : 11.379 59.781 5258 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer Outliers : 1.06 % Cbeta Deviations : 0.00 % 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: 0.49 (0.14), residues: 3812 helix: 1.30 (0.11), residues: 2418 sheet: -0.03 (0.33), residues: 232 loop : -1.71 (0.18), residues: 1162 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 3474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 302 time to evaluate : 3.985 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 16 residues processed: 329 average time/residue: 0.4448 time to fit residues: 240.8947 Evaluate side-chains 300 residues out of total 3474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 284 time to evaluate : 4.080 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.2877 time to fit residues: 14.0593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 122 optimal weight: 7.9990 chunk 329 optimal weight: 7.9990 chunk 72 optimal weight: 3.9990 chunk 214 optimal weight: 0.0870 chunk 90 optimal weight: 3.9990 chunk 365 optimal weight: 3.9990 chunk 303 optimal weight: 3.9990 chunk 169 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 120 optimal weight: 0.9980 chunk 192 optimal weight: 2.9990 overall best weight: 2.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 305 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.050 33566 Z= 0.401 Angle : 0.610 14.786 45022 Z= 0.306 Chirality : 0.044 0.219 4926 Planarity : 0.004 0.046 5546 Dihedral : 11.565 59.996 5258 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer Outliers : 1.35 % Cbeta Deviations : 0.00 % 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: 0.40 (0.14), residues: 3812 helix: 1.23 (0.11), residues: 2418 sheet: -0.09 (0.33), residues: 232 loop : -1.71 (0.18), residues: 1162 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 3474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 304 time to evaluate : 4.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 29 residues processed: 336 average time/residue: 0.4257 time to fit residues: 236.6319 Evaluate side-chains 327 residues out of total 3474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 298 time to evaluate : 4.217 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.2810 time to fit residues: 20.5725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 352 optimal weight: 0.0370 chunk 41 optimal weight: 2.9990 chunk 208 optimal weight: 1.9990 chunk 267 optimal weight: 0.8980 chunk 206 optimal weight: 0.8980 chunk 307 optimal weight: 2.9990 chunk 204 optimal weight: 1.9990 chunk 364 optimal weight: 6.9990 chunk 228 optimal weight: 0.9990 chunk 222 optimal weight: 3.9990 chunk 168 optimal weight: 3.9990 overall best weight: 0.9662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 305 HIS S 95 HIS ** V 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 352 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 33566 Z= 0.188 Angle : 0.516 11.746 45022 Z= 0.258 Chirality : 0.040 0.249 4926 Planarity : 0.003 0.047 5546 Dihedral : 11.020 59.891 5258 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer Outliers : 0.68 % Cbeta Deviations : 0.00 % 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: 0.73 (0.14), residues: 3812 helix: 1.48 (0.11), residues: 2412 sheet: 0.16 (0.33), residues: 232 loop : -1.57 (0.18), residues: 1168 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 3474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 316 time to evaluate : 3.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 7 residues processed: 331 average time/residue: 0.4378 time to fit residues: 236.9635 Evaluate side-chains 308 residues out of total 3474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 301 time to evaluate : 3.869 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2746 time to fit residues: 8.7983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 225 optimal weight: 3.9990 chunk 145 optimal weight: 10.0000 chunk 217 optimal weight: 0.5980 chunk 109 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 231 optimal weight: 3.9990 chunk 248 optimal weight: 0.6980 chunk 180 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 286 optimal weight: 3.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 33566 Z= 0.284 Angle : 0.555 11.663 45022 Z= 0.278 Chirality : 0.042 0.233 4926 Planarity : 0.004 0.057 5546 Dihedral : 11.008 59.924 5258 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer Outliers : 0.79 % Cbeta Deviations : 0.00 % 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: 0.78 (0.14), residues: 3812 helix: 1.50 (0.11), residues: 2416 sheet: 0.21 (0.33), residues: 232 loop : -1.54 (0.18), residues: 1164 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 3474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 306 time to evaluate : 3.861 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 13 residues processed: 320 average time/residue: 0.4390 time to fit residues: 231.1865 Evaluate side-chains 313 residues out of total 3474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 300 time to evaluate : 3.834 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.3045 time to fit residues: 12.7889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 331 optimal weight: 5.9990 chunk 349 optimal weight: 0.9990 chunk 318 optimal weight: 10.0000 chunk 339 optimal weight: 2.9990 chunk 348 optimal weight: 0.8980 chunk 204 optimal weight: 2.9990 chunk 147 optimal weight: 4.9990 chunk 266 optimal weight: 0.9990 chunk 104 optimal weight: 3.9990 chunk 306 optimal weight: 4.9990 chunk 321 optimal weight: 6.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 95 HIS ** I 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 352 HIS ** V 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 352 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.038 33566 Z= 0.303 Angle : 0.560 11.511 45022 Z= 0.280 Chirality : 0.042 0.233 4926 Planarity : 0.004 0.049 5546 Dihedral : 10.959 59.979 5258 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer Outliers : 0.18 % Cbeta Deviations : 0.00 % 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: 0.77 (0.14), residues: 3812 helix: 1.49 (0.11), residues: 2416 sheet: 0.21 (0.33), residues: 232 loop : -1.53 (0.18), residues: 1164 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 3474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 299 time to evaluate : 3.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 304 average time/residue: 0.4496 time to fit residues: 223.7705 Evaluate side-chains 299 residues out of total 3474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 296 time to evaluate : 3.817 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.3268 time to fit residues: 7.0846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 338 optimal weight: 2.9990 chunk 222 optimal weight: 3.9990 chunk 359 optimal weight: 1.9990 chunk 219 optimal weight: 3.9990 chunk 170 optimal weight: 4.9990 chunk 249 optimal weight: 0.9980 chunk 376 optimal weight: 0.0470 chunk 346 optimal weight: 30.0000 chunk 299 optimal weight: 0.0010 chunk 31 optimal weight: 5.9990 chunk 231 optimal weight: 0.7980 overall best weight: 0.7686 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 159 HIS ** I 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 352 HIS J 404 HIS O 159 HIS ** V 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 404 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 33566 Z= 0.162 Angle : 0.508 10.409 45022 Z= 0.253 Chirality : 0.040 0.238 4926 Planarity : 0.003 0.055 5546 Dihedral : 10.419 59.649 5258 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % 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: 1.04 (0.14), residues: 3812 helix: 1.69 (0.11), residues: 2408 sheet: 0.44 (0.34), residues: 232 loop : -1.41 (0.18), residues: 1172 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 3474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 308 time to evaluate : 3.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 308 average time/residue: 0.4380 time to fit residues: 220.8432 Evaluate side-chains 297 residues out of total 3474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 295 time to evaluate : 3.839 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2801 time to fit residues: 6.3649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 183 optimal weight: 0.8980 chunk 238 optimal weight: 0.9990 chunk 319 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 chunk 276 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 chunk 300 optimal weight: 0.7980 chunk 125 optimal weight: 0.9980 chunk 308 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 159 ASN ** V 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.112112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.089465 restraints weight = 57001.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.091468 restraints weight = 35578.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.093031 restraints weight = 26006.198| |-----------------------------------------------------------------------------| r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 33566 Z= 0.176 Angle : 0.514 10.624 45022 Z= 0.255 Chirality : 0.040 0.239 4926 Planarity : 0.003 0.048 5546 Dihedral : 10.167 59.682 5258 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer Outliers : 0.18 % Cbeta Deviations : 0.00 % 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: 1.16 (0.14), residues: 3812 helix: 1.79 (0.11), residues: 2396 sheet: 0.48 (0.34), residues: 236 loop : -1.36 (0.18), residues: 1180 =============================================================================== Job complete usr+sys time: 5245.48 seconds wall clock time: 96 minutes 46.86 seconds (5806.86 seconds total)