Starting phenix.real_space_refine (version: dev) on Thu Dec 15 06:06:49 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qsu_4629/12_2022/6qsu_4629_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qsu_4629/12_2022/6qsu_4629.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qsu_4629/12_2022/6qsu_4629.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qsu_4629/12_2022/6qsu_4629.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qsu_4629/12_2022/6qsu_4629_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qsu_4629/12_2022/6qsu_4629_updated.pdb" } resolution = 2.4 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= 0.000 sd= 0.010 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 GLU 34": "OE1" <-> "OE2" Residue "A ARG 62": "NH1" <-> "NH2" Residue "A ARG 137": "NH1" <-> "NH2" Residue "A PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 149": "OE1" <-> "OE2" Residue "A PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 31": "OE1" <-> "OE2" Residue "B TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 41": "OE1" <-> "OE2" Residue "B GLU 65": "OE1" <-> "OE2" Residue "B GLU 187": "OE1" <-> "OE2" Residue "B GLU 222": "OE1" <-> "OE2" Residue "B GLU 254": "OE1" <-> "OE2" Residue "B GLU 276": "OE1" <-> "OE2" Residue "B PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 313": "OE1" <-> "OE2" Residue "B GLU 347": "OE1" <-> "OE2" Residue "B GLU 386": "OE1" <-> "OE2" Residue "B GLU 392": "OE1" <-> "OE2" Residue "B GLU 393": "OE1" <-> "OE2" Residue "B TYR 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 476": "NH1" <-> "NH2" Residue "B TYR 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 526": "OD1" <-> "OD2" Residue "B PHE 529": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 546": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 34": "OE1" <-> "OE2" Residue "C ARG 62": "NH1" <-> "NH2" Residue "C ARG 137": "NH1" <-> "NH2" Residue "C PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 149": "OE1" <-> "OE2" Residue "C PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 34": "OE1" <-> "OE2" Residue "E ARG 62": "NH1" <-> "NH2" Residue "E ARG 137": "NH1" <-> "NH2" Residue "E PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 149": "OE1" <-> "OE2" Residue "E PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 34": "OE1" <-> "OE2" Residue "G ARG 62": "NH1" <-> "NH2" Residue "G ARG 137": "NH1" <-> "NH2" Residue "G PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 149": "OE1" <-> "OE2" Residue "G PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 34": "OE1" <-> "OE2" Residue "I ARG 62": "NH1" <-> "NH2" Residue "I ARG 137": "NH1" <-> "NH2" Residue "I PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 149": "OE1" <-> "OE2" Residue "I PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 34": "OE1" <-> "OE2" Residue "K ARG 62": "NH1" <-> "NH2" Residue "K ARG 137": "NH1" <-> "NH2" Residue "K PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 149": "OE1" <-> "OE2" Residue "K PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 34": "OE1" <-> "OE2" Residue "M ARG 62": "NH1" <-> "NH2" Residue "M ARG 137": "NH1" <-> "NH2" Residue "M PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 149": "OE1" <-> "OE2" Residue "M PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 34": "OE1" <-> "OE2" Residue "O ARG 62": "NH1" <-> "NH2" Residue "O ARG 137": "NH1" <-> "NH2" Residue "O PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 149": "OE1" <-> "OE2" Residue "O PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 34": "OE1" <-> "OE2" Residue "Q ARG 62": "NH1" <-> "NH2" Residue "Q ARG 137": "NH1" <-> "NH2" Residue "Q PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 149": "OE1" <-> "OE2" Residue "Q PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 34": "OE1" <-> "OE2" Residue "S ARG 62": "NH1" <-> "NH2" Residue "S ARG 137": "NH1" <-> "NH2" Residue "S PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 149": "OE1" <-> "OE2" Residue "S PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 34": "OE1" <-> "OE2" Residue "U ARG 62": "NH1" <-> "NH2" Residue "U ARG 137": "NH1" <-> "NH2" Residue "U PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 149": "OE1" <-> "OE2" Residue "U PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 34": "OE1" <-> "OE2" Residue "W ARG 62": "NH1" <-> "NH2" Residue "W ARG 137": "NH1" <-> "NH2" Residue "W PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 149": "OE1" <-> "OE2" Residue "W PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 31": "OE1" <-> "OE2" Residue "J TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 41": "OE1" <-> "OE2" Residue "J GLU 65": "OE1" <-> "OE2" Residue "J GLU 187": "OE1" <-> "OE2" Residue "J GLU 222": "OE1" <-> "OE2" Residue "J GLU 254": "OE1" <-> "OE2" Residue "J GLU 276": "OE1" <-> "OE2" Residue "J PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 313": "OE1" <-> "OE2" Residue "J GLU 347": "OE1" <-> "OE2" Residue "J GLU 386": "OE1" <-> "OE2" Residue "J GLU 392": "OE1" <-> "OE2" Residue "J GLU 393": "OE1" <-> "OE2" Residue "J TYR 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 476": "NH1" <-> "NH2" Residue "J TYR 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 526": "OD1" <-> "OD2" Residue "J PHE 529": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 546": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 31": "OE1" <-> "OE2" Residue "D TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 41": "OE1" <-> "OE2" Residue "D GLU 65": "OE1" <-> "OE2" Residue "D GLU 187": "OE1" <-> "OE2" Residue "D GLU 222": "OE1" <-> "OE2" Residue "D GLU 254": "OE1" <-> "OE2" Residue "D GLU 276": "OE1" <-> "OE2" Residue "D PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 313": "OE1" <-> "OE2" Residue "D GLU 347": "OE1" <-> "OE2" Residue "D GLU 386": "OE1" <-> "OE2" Residue "D GLU 392": "OE1" <-> "OE2" Residue "D GLU 393": "OE1" <-> "OE2" Residue "D TYR 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 476": "NH1" <-> "NH2" Residue "D TYR 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 526": "OD1" <-> "OD2" Residue "D PHE 529": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 546": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 31": "OE1" <-> "OE2" Residue "F TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 41": "OE1" <-> "OE2" Residue "F GLU 65": "OE1" <-> "OE2" Residue "F GLU 187": "OE1" <-> "OE2" Residue "F GLU 222": "OE1" <-> "OE2" Residue "F GLU 254": "OE1" <-> "OE2" Residue "F GLU 276": "OE1" <-> "OE2" Residue "F PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 313": "OE1" <-> "OE2" Residue "F GLU 347": "OE1" <-> "OE2" Residue "F GLU 386": "OE1" <-> "OE2" Residue "F GLU 392": "OE1" <-> "OE2" Residue "F GLU 393": "OE1" <-> "OE2" Residue "F TYR 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 476": "NH1" <-> "NH2" Residue "F TYR 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 526": "OD1" <-> "OD2" Residue "F PHE 529": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 546": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 31": "OE1" <-> "OE2" Residue "H TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 41": "OE1" <-> "OE2" Residue "H GLU 65": "OE1" <-> "OE2" Residue "H GLU 187": "OE1" <-> "OE2" Residue "H GLU 222": "OE1" <-> "OE2" Residue "H GLU 254": "OE1" <-> "OE2" Residue "H GLU 276": "OE1" <-> "OE2" Residue "H PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 313": "OE1" <-> "OE2" Residue "H GLU 347": "OE1" <-> "OE2" Residue "H GLU 386": "OE1" <-> "OE2" Residue "H GLU 392": "OE1" <-> "OE2" Residue "H GLU 393": "OE1" <-> "OE2" Residue "H TYR 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 476": "NH1" <-> "NH2" Residue "H TYR 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 526": "OD1" <-> "OD2" Residue "H PHE 529": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 546": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 31": "OE1" <-> "OE2" Residue "L TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 41": "OE1" <-> "OE2" Residue "L GLU 65": "OE1" <-> "OE2" Residue "L GLU 187": "OE1" <-> "OE2" Residue "L GLU 222": "OE1" <-> "OE2" Residue "L GLU 254": "OE1" <-> "OE2" Residue "L GLU 276": "OE1" <-> "OE2" Residue "L PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 313": "OE1" <-> "OE2" Residue "L GLU 347": "OE1" <-> "OE2" Residue "L GLU 386": "OE1" <-> "OE2" Residue "L GLU 392": "OE1" <-> "OE2" Residue "L GLU 393": "OE1" <-> "OE2" Residue "L TYR 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 476": "NH1" <-> "NH2" Residue "L TYR 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 526": "OD1" <-> "OD2" Residue "L PHE 529": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 546": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 31": "OE1" <-> "OE2" Residue "N TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 41": "OE1" <-> "OE2" Residue "N GLU 65": "OE1" <-> "OE2" Residue "N GLU 187": "OE1" <-> "OE2" Residue "N GLU 222": "OE1" <-> "OE2" Residue "N GLU 254": "OE1" <-> "OE2" Residue "N GLU 276": "OE1" <-> "OE2" Residue "N PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 313": "OE1" <-> "OE2" Residue "N GLU 347": "OE1" <-> "OE2" Residue "N GLU 386": "OE1" <-> "OE2" Residue "N GLU 392": "OE1" <-> "OE2" Residue "N GLU 393": "OE1" <-> "OE2" Residue "N TYR 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 476": "NH1" <-> "NH2" Residue "N TYR 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 526": "OD1" <-> "OD2" Residue "N PHE 529": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 546": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 31": "OE1" <-> "OE2" Residue "P TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 41": "OE1" <-> "OE2" Residue "P GLU 65": "OE1" <-> "OE2" Residue "P GLU 187": "OE1" <-> "OE2" Residue "P GLU 222": "OE1" <-> "OE2" Residue "P GLU 254": "OE1" <-> "OE2" Residue "P GLU 276": "OE1" <-> "OE2" Residue "P PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 313": "OE1" <-> "OE2" Residue "P GLU 347": "OE1" <-> "OE2" Residue "P GLU 386": "OE1" <-> "OE2" Residue "P GLU 392": "OE1" <-> "OE2" Residue "P GLU 393": "OE1" <-> "OE2" Residue "P TYR 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 476": "NH1" <-> "NH2" Residue "P TYR 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 526": "OD1" <-> "OD2" Residue "P PHE 529": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 546": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 31": "OE1" <-> "OE2" Residue "R TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 41": "OE1" <-> "OE2" Residue "R GLU 65": "OE1" <-> "OE2" Residue "R GLU 187": "OE1" <-> "OE2" Residue "R GLU 222": "OE1" <-> "OE2" Residue "R GLU 254": "OE1" <-> "OE2" Residue "R GLU 276": "OE1" <-> "OE2" Residue "R PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 313": "OE1" <-> "OE2" Residue "R GLU 347": "OE1" <-> "OE2" Residue "R GLU 386": "OE1" <-> "OE2" Residue "R GLU 392": "OE1" <-> "OE2" Residue "R GLU 393": "OE1" <-> "OE2" Residue "R TYR 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 476": "NH1" <-> "NH2" Residue "R TYR 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 526": "OD1" <-> "OD2" Residue "R PHE 529": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 546": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 31": "OE1" <-> "OE2" Residue "T TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 41": "OE1" <-> "OE2" Residue "T GLU 65": "OE1" <-> "OE2" Residue "T GLU 187": "OE1" <-> "OE2" Residue "T GLU 222": "OE1" <-> "OE2" Residue "T GLU 254": "OE1" <-> "OE2" Residue "T GLU 276": "OE1" <-> "OE2" Residue "T PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 313": "OE1" <-> "OE2" Residue "T GLU 347": "OE1" <-> "OE2" Residue "T GLU 386": "OE1" <-> "OE2" Residue "T GLU 392": "OE1" <-> "OE2" Residue "T GLU 393": "OE1" <-> "OE2" Residue "T TYR 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 476": "NH1" <-> "NH2" Residue "T TYR 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 526": "OD1" <-> "OD2" Residue "T PHE 529": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 546": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 31": "OE1" <-> "OE2" Residue "V TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 41": "OE1" <-> "OE2" Residue "V GLU 65": "OE1" <-> "OE2" Residue "V GLU 187": "OE1" <-> "OE2" Residue "V GLU 222": "OE1" <-> "OE2" Residue "V GLU 254": "OE1" <-> "OE2" Residue "V GLU 276": "OE1" <-> "OE2" Residue "V PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 313": "OE1" <-> "OE2" Residue "V GLU 347": "OE1" <-> "OE2" Residue "V GLU 386": "OE1" <-> "OE2" Residue "V GLU 392": "OE1" <-> "OE2" Residue "V GLU 393": "OE1" <-> "OE2" Residue "V TYR 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 476": "NH1" <-> "NH2" Residue "V TYR 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 526": "OD1" <-> "OD2" Residue "V PHE 529": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 546": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 31": "OE1" <-> "OE2" Residue "X TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 41": "OE1" <-> "OE2" Residue "X GLU 65": "OE1" <-> "OE2" Residue "X GLU 187": "OE1" <-> "OE2" Residue "X GLU 222": "OE1" <-> "OE2" Residue "X GLU 254": "OE1" <-> "OE2" Residue "X GLU 276": "OE1" <-> "OE2" Residue "X PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 313": "OE1" <-> "OE2" Residue "X GLU 347": "OE1" <-> "OE2" Residue "X GLU 386": "OE1" <-> "OE2" Residue "X GLU 392": "OE1" <-> "OE2" Residue "X GLU 393": "OE1" <-> "OE2" Residue "X TYR 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 476": "NH1" <-> "NH2" Residue "X TYR 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 526": "OD1" <-> "OD2" Residue "X PHE 529": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 546": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 75758 Number of models: 1 Model: "" Number of chains: 60 Chain: "A" Number of atoms: 1869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1869 Classifications: {'peptide': 238} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 230} Chain: "B" Number of atoms: 4340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 4340 Classifications: {'peptide': 569} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 19, 'TRANS': 546} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 1869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1869 Classifications: {'peptide': 238} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 230} Chain: "E" Number of atoms: 1869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1869 Classifications: {'peptide': 238} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 230} Chain: "G" Number of atoms: 1869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1869 Classifications: {'peptide': 238} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 230} Chain: "I" Number of atoms: 1869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1869 Classifications: {'peptide': 238} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 230} Chain: "K" Number of atoms: 1869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1869 Classifications: {'peptide': 238} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 230} Chain: "M" Number of atoms: 1869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1869 Classifications: {'peptide': 238} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 230} Chain: "O" Number of atoms: 1869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1869 Classifications: {'peptide': 238} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 230} Chain: "Q" Number of atoms: 1869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1869 Classifications: {'peptide': 238} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 230} Chain: "S" Number of atoms: 1869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1869 Classifications: {'peptide': 238} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 230} Chain: "U" Number of atoms: 1869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1869 Classifications: {'peptide': 238} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 230} Chain: "W" Number of atoms: 1869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1869 Classifications: {'peptide': 238} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 230} Chain: "J" Number of atoms: 4340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 4340 Classifications: {'peptide': 569} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 19, 'TRANS': 546} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 4340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 4340 Classifications: {'peptide': 569} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 19, 'TRANS': 546} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 4340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 4340 Classifications: {'peptide': 569} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 19, 'TRANS': 546} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 4340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 4340 Classifications: {'peptide': 569} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 19, 'TRANS': 546} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 4340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 4340 Classifications: {'peptide': 569} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 19, 'TRANS': 546} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 4340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 4340 Classifications: {'peptide': 569} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 19, 'TRANS': 546} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 4340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 4340 Classifications: {'peptide': 569} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 19, 'TRANS': 546} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 4340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 4340 Classifications: {'peptide': 569} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 19, 'TRANS': 546} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "T" Number of atoms: 4340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 4340 Classifications: {'peptide': 569} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 19, 'TRANS': 546} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "V" Number of atoms: 4340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 4340 Classifications: {'peptide': 569} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 19, 'TRANS': 546} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "X" Number of atoms: 4340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 4340 Classifications: {'peptide': 569} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 19, 'TRANS': 546} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 6 Unusual residues: {' NI': 2, 'BME': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 6 Unusual residues: {' NI': 2, 'BME': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 6 Unusual residues: {' NI': 2, 'BME': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 6 Unusual residues: {' NI': 2, 'BME': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 6 Unusual residues: {' NI': 2, 'BME': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "L" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 6 Unusual residues: {' NI': 2, 'BME': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "N" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 6 Unusual residues: {' NI': 2, 'BME': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "P" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 6 Unusual residues: {' NI': 2, 'BME': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "R" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 6 Unusual residues: {' NI': 2, 'BME': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "T" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 6 Unusual residues: {' NI': 2, 'BME': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "V" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 6 Unusual residues: {' NI': 2, 'BME': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "X" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 6 Unusual residues: {' NI': 2, 'BME': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "B" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 90 Classifications: {'water': 90} Link IDs: {None: 89} Chain: "C" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "E" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "G" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "I" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "K" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "M" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "O" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "Q" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "S" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "U" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "W" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "J" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 87 Classifications: {'water': 87} Link IDs: {None: 86} Chain: "D" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 88 Classifications: {'water': 88} Link IDs: {None: 87} Chain: "F" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 85 Classifications: {'water': 85} Link IDs: {None: 84} Chain: "H" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 90 Classifications: {'water': 90} Link IDs: {None: 89} Chain: "L" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 82 Classifications: {'water': 82} Link IDs: {None: 81} Chain: "N" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 79 Classifications: {'water': 79} Link IDs: {None: 78} Chain: "P" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 79 Classifications: {'water': 79} Link IDs: {None: 78} Chain: "R" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 86 Classifications: {'water': 86} Link IDs: {None: 85} Chain: "T" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 92 Classifications: {'water': 92} Link IDs: {None: 91} Chain: "V" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 82 Classifications: {'water': 82} Link IDs: {None: 81} Chain: "X" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 83 Classifications: {'water': 83} Link IDs: {None: 82} Time building chain proxies: 31.55, per 1000 atoms: 0.42 Number of scatterers: 75758 At special positions: 0 Unit cell: (171.243, 177.705, 172.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ni 24 28.00 S 360 16.00 O 15614 8.00 N 12972 7.00 C 46788 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=0, symmetry=0 Time building additional restraints: 25.90 Conformation dependent library (CDL) restraints added in 8.6 seconds 19200 Ramachandran restraints generated. 9600 Oldfield, 0 Emsley, 9600 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 17544 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 372 helices and 144 sheets defined 31.0% alpha, 13.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.49 Creating SS restraints... Processing helix chain 'A' and resid 5 through 26 Processing helix chain 'A' and resid 32 through 49 Processing helix chain 'A' and resid 54 through 62 removed outlier: 4.395A pdb=" N ARG A 62 " --> pdb=" O MET A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 69 No H-bonds generated for 'chain 'A' and resid 67 through 69' Processing helix chain 'A' and resid 74 through 77 No H-bonds generated for 'chain 'A' and resid 74 through 77' Processing helix chain 'A' and resid 147 through 149 No H-bonds generated for 'chain 'A' and resid 147 through 149' Processing helix chain 'A' and resid 158 through 161 Processing helix chain 'A' and resid 208 through 220 removed outlier: 3.540A pdb=" N LYS A 212 " --> pdb=" O ASN A 208 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE A 213 " --> pdb=" O GLU A 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 13 Processing helix chain 'B' and resid 110 through 112 No H-bonds generated for 'chain 'B' and resid 110 through 112' Processing helix chain 'B' and resid 142 through 151 Proline residue: B 146 - end of helix Processing helix chain 'B' and resid 165 through 169 Processing helix chain 'B' and resid 175 through 188 removed outlier: 4.008A pdb=" N GLU B 187 " --> pdb=" O LEU B 183 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N GLU B 188 " --> pdb=" O ARG B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 212 Processing helix chain 'B' and resid 222 through 224 No H-bonds generated for 'chain 'B' and resid 222 through 224' Processing helix chain 'B' and resid 228 through 241 Processing helix chain 'B' and resid 258 through 265 Processing helix chain 'B' and resid 286 through 291 Processing helix chain 'B' and resid 301 through 303 No H-bonds generated for 'chain 'B' and resid 301 through 303' Processing helix chain 'B' and resid 310 through 321 Processing helix chain 'B' and resid 329 through 339 Processing helix chain 'B' and resid 341 through 353 removed outlier: 3.841A pdb=" N ASP B 348 " --> pdb=" O ILE B 344 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N THR B 349 " --> pdb=" O ALA B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 387 Processing helix chain 'B' and resid 399 through 408 removed outlier: 3.695A pdb=" N LYS B 408 " --> pdb=" O ARG B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 416 Processing helix chain 'B' and resid 439 through 441 No H-bonds generated for 'chain 'B' and resid 439 through 441' Processing helix chain 'B' and resid 479 through 481 No H-bonds generated for 'chain 'B' and resid 479 through 481' Processing helix chain 'B' and resid 485 through 489 Processing helix chain 'B' and resid 496 through 500 Processing helix chain 'B' and resid 503 through 506 No H-bonds generated for 'chain 'B' and resid 503 through 506' Processing helix chain 'B' and resid 524 through 526 No H-bonds generated for 'chain 'B' and resid 524 through 526' Processing helix chain 'C' and resid 5 through 26 Processing helix chain 'C' and resid 32 through 49 Processing helix chain 'C' and resid 54 through 62 removed outlier: 4.393A pdb=" N ARG C 62 " --> pdb=" O MET C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 69 No H-bonds generated for 'chain 'C' and resid 67 through 69' Processing helix chain 'C' and resid 74 through 77 No H-bonds generated for 'chain 'C' and resid 74 through 77' Processing helix chain 'C' and resid 147 through 149 No H-bonds generated for 'chain 'C' and resid 147 through 149' Processing helix chain 'C' and resid 158 through 161 Processing helix chain 'C' and resid 208 through 220 removed outlier: 3.540A pdb=" N LYS C 212 " --> pdb=" O ASN C 208 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE C 213 " --> pdb=" O GLU C 209 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 26 Processing helix chain 'E' and resid 32 through 49 Processing helix chain 'E' and resid 54 through 62 removed outlier: 4.394A pdb=" N ARG E 62 " --> pdb=" O MET E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 69 No H-bonds generated for 'chain 'E' and resid 67 through 69' Processing helix chain 'E' and resid 74 through 77 No H-bonds generated for 'chain 'E' and resid 74 through 77' Processing helix chain 'E' and resid 147 through 149 No H-bonds generated for 'chain 'E' and resid 147 through 149' Processing helix chain 'E' and resid 158 through 161 Processing helix chain 'E' and resid 208 through 220 removed outlier: 3.540A pdb=" N LYS E 212 " --> pdb=" O ASN E 208 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE E 213 " --> pdb=" O GLU E 209 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 26 Processing helix chain 'G' and resid 32 through 49 Processing helix chain 'G' and resid 54 through 62 removed outlier: 4.395A pdb=" N ARG G 62 " --> pdb=" O MET G 58 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 69 No H-bonds generated for 'chain 'G' and resid 67 through 69' Processing helix chain 'G' and resid 74 through 77 No H-bonds generated for 'chain 'G' and resid 74 through 77' Processing helix chain 'G' and resid 147 through 149 No H-bonds generated for 'chain 'G' and resid 147 through 149' Processing helix chain 'G' and resid 158 through 161 Processing helix chain 'G' and resid 208 through 220 removed outlier: 3.540A pdb=" N LYS G 212 " --> pdb=" O ASN G 208 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE G 213 " --> pdb=" O GLU G 209 " (cutoff:3.500A) Processing helix chain 'I' and resid 5 through 26 Processing helix chain 'I' and resid 32 through 49 Processing helix chain 'I' and resid 54 through 62 removed outlier: 4.394A pdb=" N ARG I 62 " --> pdb=" O MET I 58 " (cutoff:3.500A) Processing helix chain 'I' and resid 67 through 69 No H-bonds generated for 'chain 'I' and resid 67 through 69' Processing helix chain 'I' and resid 74 through 77 No H-bonds generated for 'chain 'I' and resid 74 through 77' Processing helix chain 'I' and resid 147 through 149 No H-bonds generated for 'chain 'I' and resid 147 through 149' Processing helix chain 'I' and resid 158 through 161 Processing helix chain 'I' and resid 208 through 220 removed outlier: 3.539A pdb=" N LYS I 212 " --> pdb=" O ASN I 208 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE I 213 " --> pdb=" O GLU I 209 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 26 Processing helix chain 'K' and resid 32 through 49 Processing helix chain 'K' and resid 54 through 62 removed outlier: 4.394A pdb=" N ARG K 62 " --> pdb=" O MET K 58 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 69 No H-bonds generated for 'chain 'K' and resid 67 through 69' Processing helix chain 'K' and resid 74 through 77 No H-bonds generated for 'chain 'K' and resid 74 through 77' Processing helix chain 'K' and resid 147 through 149 No H-bonds generated for 'chain 'K' and resid 147 through 149' Processing helix chain 'K' and resid 158 through 161 Processing helix chain 'K' and resid 208 through 220 removed outlier: 3.540A pdb=" N LYS K 212 " --> pdb=" O ASN K 208 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE K 213 " --> pdb=" O GLU K 209 " (cutoff:3.500A) Processing helix chain 'M' and resid 5 through 26 Processing helix chain 'M' and resid 32 through 49 Processing helix chain 'M' and resid 54 through 62 removed outlier: 4.395A pdb=" N ARG M 62 " --> pdb=" O MET M 58 " (cutoff:3.500A) Processing helix chain 'M' and resid 67 through 69 No H-bonds generated for 'chain 'M' and resid 67 through 69' Processing helix chain 'M' and resid 74 through 77 No H-bonds generated for 'chain 'M' and resid 74 through 77' Processing helix chain 'M' and resid 147 through 149 No H-bonds generated for 'chain 'M' and resid 147 through 149' Processing helix chain 'M' and resid 158 through 161 Processing helix chain 'M' and resid 208 through 220 removed outlier: 3.540A pdb=" N LYS M 212 " --> pdb=" O ASN M 208 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE M 213 " --> pdb=" O GLU M 209 " (cutoff:3.500A) Processing helix chain 'O' and resid 5 through 26 Processing helix chain 'O' and resid 32 through 49 Processing helix chain 'O' and resid 54 through 62 removed outlier: 4.395A pdb=" N ARG O 62 " --> pdb=" O MET O 58 " (cutoff:3.500A) Processing helix chain 'O' and resid 67 through 69 No H-bonds generated for 'chain 'O' and resid 67 through 69' Processing helix chain 'O' and resid 74 through 77 No H-bonds generated for 'chain 'O' and resid 74 through 77' Processing helix chain 'O' and resid 147 through 149 No H-bonds generated for 'chain 'O' and resid 147 through 149' Processing helix chain 'O' and resid 158 through 161 Processing helix chain 'O' and resid 208 through 220 removed outlier: 3.540A pdb=" N LYS O 212 " --> pdb=" O ASN O 208 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE O 213 " --> pdb=" O GLU O 209 " (cutoff:3.500A) Processing helix chain 'Q' and resid 5 through 26 Processing helix chain 'Q' and resid 32 through 49 Processing helix chain 'Q' and resid 54 through 62 removed outlier: 4.394A pdb=" N ARG Q 62 " --> pdb=" O MET Q 58 " (cutoff:3.500A) Processing helix chain 'Q' and resid 67 through 69 No H-bonds generated for 'chain 'Q' and resid 67 through 69' Processing helix chain 'Q' and resid 74 through 77 No H-bonds generated for 'chain 'Q' and resid 74 through 77' Processing helix chain 'Q' and resid 147 through 149 No H-bonds generated for 'chain 'Q' and resid 147 through 149' Processing helix chain 'Q' and resid 158 through 161 Processing helix chain 'Q' and resid 208 through 220 removed outlier: 3.539A pdb=" N LYS Q 212 " --> pdb=" O ASN Q 208 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE Q 213 " --> pdb=" O GLU Q 209 " (cutoff:3.500A) Processing helix chain 'S' and resid 5 through 26 Processing helix chain 'S' and resid 32 through 49 Processing helix chain 'S' and resid 54 through 62 removed outlier: 4.394A pdb=" N ARG S 62 " --> pdb=" O MET S 58 " (cutoff:3.500A) Processing helix chain 'S' and resid 67 through 69 No H-bonds generated for 'chain 'S' and resid 67 through 69' Processing helix chain 'S' and resid 74 through 77 No H-bonds generated for 'chain 'S' and resid 74 through 77' Processing helix chain 'S' and resid 147 through 149 No H-bonds generated for 'chain 'S' and resid 147 through 149' Processing helix chain 'S' and resid 158 through 161 Processing helix chain 'S' and resid 208 through 220 removed outlier: 3.540A pdb=" N LYS S 212 " --> pdb=" O ASN S 208 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE S 213 " --> pdb=" O GLU S 209 " (cutoff:3.500A) Processing helix chain 'U' and resid 5 through 26 Processing helix chain 'U' and resid 32 through 49 Processing helix chain 'U' and resid 54 through 62 removed outlier: 4.394A pdb=" N ARG U 62 " --> pdb=" O MET U 58 " (cutoff:3.500A) Processing helix chain 'U' and resid 67 through 69 No H-bonds generated for 'chain 'U' and resid 67 through 69' Processing helix chain 'U' and resid 74 through 77 No H-bonds generated for 'chain 'U' and resid 74 through 77' Processing helix chain 'U' and resid 147 through 149 No H-bonds generated for 'chain 'U' and resid 147 through 149' Processing helix chain 'U' and resid 158 through 161 Processing helix chain 'U' and resid 208 through 220 removed outlier: 3.540A pdb=" N LYS U 212 " --> pdb=" O ASN U 208 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ILE U 213 " --> pdb=" O GLU U 209 " (cutoff:3.500A) Processing helix chain 'W' and resid 5 through 26 Processing helix chain 'W' and resid 32 through 49 Processing helix chain 'W' and resid 54 through 62 removed outlier: 4.394A pdb=" N ARG W 62 " --> pdb=" O MET W 58 " (cutoff:3.500A) Processing helix chain 'W' and resid 67 through 69 No H-bonds generated for 'chain 'W' and resid 67 through 69' Processing helix chain 'W' and resid 74 through 77 No H-bonds generated for 'chain 'W' and resid 74 through 77' Processing helix chain 'W' and resid 147 through 149 No H-bonds generated for 'chain 'W' and resid 147 through 149' Processing helix chain 'W' and resid 158 through 161 Processing helix chain 'W' and resid 208 through 220 removed outlier: 3.540A pdb=" N LYS W 212 " --> pdb=" O ASN W 208 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE W 213 " --> pdb=" O GLU W 209 " (cutoff:3.500A) Processing helix chain 'J' and resid 6 through 13 Processing helix chain 'J' and resid 110 through 112 No H-bonds generated for 'chain 'J' and resid 110 through 112' Processing helix chain 'J' and resid 142 through 151 Proline residue: J 146 - end of helix Processing helix chain 'J' and resid 165 through 169 Processing helix chain 'J' and resid 175 through 188 removed outlier: 4.008A pdb=" N GLU J 187 " --> pdb=" O LEU J 183 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N GLU J 188 " --> pdb=" O ARG J 184 " (cutoff:3.500A) Processing helix chain 'J' and resid 204 through 212 Processing helix chain 'J' and resid 222 through 224 No H-bonds generated for 'chain 'J' and resid 222 through 224' Processing helix chain 'J' and resid 228 through 241 Processing helix chain 'J' and resid 258 through 265 Processing helix chain 'J' and resid 286 through 291 Processing helix chain 'J' and resid 301 through 303 No H-bonds generated for 'chain 'J' and resid 301 through 303' Processing helix chain 'J' and resid 310 through 321 Processing helix chain 'J' and resid 329 through 339 Processing helix chain 'J' and resid 341 through 353 removed outlier: 3.840A pdb=" N ASP J 348 " --> pdb=" O ILE J 344 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N THR J 349 " --> pdb=" O ALA J 345 " (cutoff:3.500A) Processing helix chain 'J' and resid 372 through 387 Processing helix chain 'J' and resid 399 through 408 removed outlier: 3.695A pdb=" N LYS J 408 " --> pdb=" O ARG J 404 " (cutoff:3.500A) Processing helix chain 'J' and resid 411 through 416 Processing helix chain 'J' and resid 439 through 441 No H-bonds generated for 'chain 'J' and resid 439 through 441' Processing helix chain 'J' and resid 479 through 481 No H-bonds generated for 'chain 'J' and resid 479 through 481' Processing helix chain 'J' and resid 485 through 489 Processing helix chain 'J' and resid 496 through 500 Processing helix chain 'J' and resid 503 through 506 No H-bonds generated for 'chain 'J' and resid 503 through 506' Processing helix chain 'J' and resid 524 through 526 No H-bonds generated for 'chain 'J' and resid 524 through 526' Processing helix chain 'D' and resid 6 through 13 Processing helix chain 'D' and resid 110 through 112 No H-bonds generated for 'chain 'D' and resid 110 through 112' Processing helix chain 'D' and resid 142 through 151 Proline residue: D 146 - end of helix Processing helix chain 'D' and resid 165 through 169 Processing helix chain 'D' and resid 175 through 188 removed outlier: 4.008A pdb=" N GLU D 187 " --> pdb=" O LEU D 183 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N GLU D 188 " --> pdb=" O ARG D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 212 Processing helix chain 'D' and resid 222 through 224 No H-bonds generated for 'chain 'D' and resid 222 through 224' Processing helix chain 'D' and resid 228 through 241 Processing helix chain 'D' and resid 258 through 265 Processing helix chain 'D' and resid 286 through 291 Processing helix chain 'D' and resid 301 through 303 No H-bonds generated for 'chain 'D' and resid 301 through 303' Processing helix chain 'D' and resid 310 through 321 Processing helix chain 'D' and resid 329 through 339 Processing helix chain 'D' and resid 341 through 353 removed outlier: 3.841A pdb=" N ASP D 348 " --> pdb=" O ILE D 344 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N THR D 349 " --> pdb=" O ALA D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 387 Processing helix chain 'D' and resid 399 through 408 removed outlier: 3.695A pdb=" N LYS D 408 " --> pdb=" O ARG D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 416 Processing helix chain 'D' and resid 439 through 441 No H-bonds generated for 'chain 'D' and resid 439 through 441' Processing helix chain 'D' and resid 479 through 481 No H-bonds generated for 'chain 'D' and resid 479 through 481' Processing helix chain 'D' and resid 485 through 489 Processing helix chain 'D' and resid 496 through 500 Processing helix chain 'D' and resid 503 through 506 No H-bonds generated for 'chain 'D' and resid 503 through 506' Processing helix chain 'D' and resid 524 through 526 No H-bonds generated for 'chain 'D' and resid 524 through 526' Processing helix chain 'F' and resid 6 through 13 Processing helix chain 'F' and resid 110 through 112 No H-bonds generated for 'chain 'F' and resid 110 through 112' Processing helix chain 'F' and resid 142 through 151 Proline residue: F 146 - end of helix Processing helix chain 'F' and resid 165 through 169 Processing helix chain 'F' and resid 175 through 188 removed outlier: 4.008A pdb=" N GLU F 187 " --> pdb=" O LEU F 183 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N GLU F 188 " --> pdb=" O ARG F 184 " (cutoff:3.500A) Processing helix chain 'F' and resid 204 through 212 Processing helix chain 'F' and resid 222 through 224 No H-bonds generated for 'chain 'F' and resid 222 through 224' Processing helix chain 'F' and resid 228 through 241 Processing helix chain 'F' and resid 258 through 265 Processing helix chain 'F' and resid 286 through 291 Processing helix chain 'F' and resid 301 through 303 No H-bonds generated for 'chain 'F' and resid 301 through 303' Processing helix chain 'F' and resid 310 through 321 Processing helix chain 'F' and resid 329 through 339 Processing helix chain 'F' and resid 341 through 353 removed outlier: 3.841A pdb=" N ASP F 348 " --> pdb=" O ILE F 344 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N THR F 349 " --> pdb=" O ALA F 345 " (cutoff:3.500A) Processing helix chain 'F' and resid 372 through 387 Processing helix chain 'F' and resid 399 through 408 removed outlier: 3.695A pdb=" N LYS F 408 " --> pdb=" O ARG F 404 " (cutoff:3.500A) Processing helix chain 'F' and resid 411 through 416 Processing helix chain 'F' and resid 439 through 441 No H-bonds generated for 'chain 'F' and resid 439 through 441' Processing helix chain 'F' and resid 479 through 481 No H-bonds generated for 'chain 'F' and resid 479 through 481' Processing helix chain 'F' and resid 485 through 489 Processing helix chain 'F' and resid 496 through 500 Processing helix chain 'F' and resid 503 through 506 No H-bonds generated for 'chain 'F' and resid 503 through 506' Processing helix chain 'F' and resid 524 through 526 No H-bonds generated for 'chain 'F' and resid 524 through 526' Processing helix chain 'H' and resid 6 through 13 Processing helix chain 'H' and resid 110 through 112 No H-bonds generated for 'chain 'H' and resid 110 through 112' Processing helix chain 'H' and resid 142 through 151 Proline residue: H 146 - end of helix Processing helix chain 'H' and resid 165 through 169 Processing helix chain 'H' and resid 175 through 188 removed outlier: 4.008A pdb=" N GLU H 187 " --> pdb=" O LEU H 183 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N GLU H 188 " --> pdb=" O ARG H 184 " (cutoff:3.500A) Processing helix chain 'H' and resid 204 through 212 Processing helix chain 'H' and resid 222 through 224 No H-bonds generated for 'chain 'H' and resid 222 through 224' Processing helix chain 'H' and resid 228 through 241 Processing helix chain 'H' and resid 258 through 265 Processing helix chain 'H' and resid 286 through 291 Processing helix chain 'H' and resid 301 through 303 No H-bonds generated for 'chain 'H' and resid 301 through 303' Processing helix chain 'H' and resid 310 through 321 Processing helix chain 'H' and resid 329 through 339 Processing helix chain 'H' and resid 341 through 353 removed outlier: 3.841A pdb=" N ASP H 348 " --> pdb=" O ILE H 344 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N THR H 349 " --> pdb=" O ALA H 345 " (cutoff:3.500A) Processing helix chain 'H' and resid 372 through 387 Processing helix chain 'H' and resid 399 through 408 removed outlier: 3.695A pdb=" N LYS H 408 " --> pdb=" O ARG H 404 " (cutoff:3.500A) Processing helix chain 'H' and resid 411 through 416 Processing helix chain 'H' and resid 439 through 441 No H-bonds generated for 'chain 'H' and resid 439 through 441' Processing helix chain 'H' and resid 479 through 481 No H-bonds generated for 'chain 'H' and resid 479 through 481' Processing helix chain 'H' and resid 485 through 489 Processing helix chain 'H' and resid 496 through 500 Processing helix chain 'H' and resid 503 through 506 No H-bonds generated for 'chain 'H' and resid 503 through 506' Processing helix chain 'H' and resid 524 through 526 No H-bonds generated for 'chain 'H' and resid 524 through 526' Processing helix chain 'L' and resid 6 through 13 Processing helix chain 'L' and resid 110 through 112 No H-bonds generated for 'chain 'L' and resid 110 through 112' Processing helix chain 'L' and resid 142 through 151 Proline residue: L 146 - end of helix Processing helix chain 'L' and resid 165 through 169 Processing helix chain 'L' and resid 175 through 188 removed outlier: 4.008A pdb=" N GLU L 187 " --> pdb=" O LEU L 183 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N GLU L 188 " --> pdb=" O ARG L 184 " (cutoff:3.500A) Processing helix chain 'L' and resid 204 through 212 Processing helix chain 'L' and resid 222 through 224 No H-bonds generated for 'chain 'L' and resid 222 through 224' Processing helix chain 'L' and resid 228 through 241 Processing helix chain 'L' and resid 258 through 265 Processing helix chain 'L' and resid 286 through 291 Processing helix chain 'L' and resid 301 through 303 No H-bonds generated for 'chain 'L' and resid 301 through 303' Processing helix chain 'L' and resid 310 through 321 Processing helix chain 'L' and resid 329 through 339 Processing helix chain 'L' and resid 341 through 353 removed outlier: 3.841A pdb=" N ASP L 348 " --> pdb=" O ILE L 344 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N THR L 349 " --> pdb=" O ALA L 345 " (cutoff:3.500A) Processing helix chain 'L' and resid 372 through 387 Processing helix chain 'L' and resid 399 through 408 removed outlier: 3.695A pdb=" N LYS L 408 " --> pdb=" O ARG L 404 " (cutoff:3.500A) Processing helix chain 'L' and resid 411 through 416 Processing helix chain 'L' and resid 439 through 441 No H-bonds generated for 'chain 'L' and resid 439 through 441' Processing helix chain 'L' and resid 479 through 481 No H-bonds generated for 'chain 'L' and resid 479 through 481' Processing helix chain 'L' and resid 485 through 489 Processing helix chain 'L' and resid 496 through 500 Processing helix chain 'L' and resid 503 through 506 No H-bonds generated for 'chain 'L' and resid 503 through 506' Processing helix chain 'L' and resid 524 through 526 No H-bonds generated for 'chain 'L' and resid 524 through 526' Processing helix chain 'N' and resid 6 through 13 Processing helix chain 'N' and resid 110 through 112 No H-bonds generated for 'chain 'N' and resid 110 through 112' Processing helix chain 'N' and resid 142 through 151 Proline residue: N 146 - end of helix Processing helix chain 'N' and resid 165 through 169 Processing helix chain 'N' and resid 175 through 188 removed outlier: 4.008A pdb=" N GLU N 187 " --> pdb=" O LEU N 183 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N GLU N 188 " --> pdb=" O ARG N 184 " (cutoff:3.500A) Processing helix chain 'N' and resid 204 through 212 Processing helix chain 'N' and resid 222 through 224 No H-bonds generated for 'chain 'N' and resid 222 through 224' Processing helix chain 'N' and resid 228 through 241 Processing helix chain 'N' and resid 258 through 265 Processing helix chain 'N' and resid 286 through 291 Processing helix chain 'N' and resid 301 through 303 No H-bonds generated for 'chain 'N' and resid 301 through 303' Processing helix chain 'N' and resid 310 through 321 Processing helix chain 'N' and resid 329 through 339 Processing helix chain 'N' and resid 341 through 353 removed outlier: 3.841A pdb=" N ASP N 348 " --> pdb=" O ILE N 344 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N THR N 349 " --> pdb=" O ALA N 345 " (cutoff:3.500A) Processing helix chain 'N' and resid 372 through 387 Processing helix chain 'N' and resid 399 through 408 removed outlier: 3.695A pdb=" N LYS N 408 " --> pdb=" O ARG N 404 " (cutoff:3.500A) Processing helix chain 'N' and resid 411 through 416 Processing helix chain 'N' and resid 439 through 441 No H-bonds generated for 'chain 'N' and resid 439 through 441' Processing helix chain 'N' and resid 479 through 481 No H-bonds generated for 'chain 'N' and resid 479 through 481' Processing helix chain 'N' and resid 485 through 489 Processing helix chain 'N' and resid 496 through 500 Processing helix chain 'N' and resid 503 through 506 No H-bonds generated for 'chain 'N' and resid 503 through 506' Processing helix chain 'N' and resid 524 through 526 No H-bonds generated for 'chain 'N' and resid 524 through 526' Processing helix chain 'P' and resid 6 through 13 Processing helix chain 'P' and resid 110 through 112 No H-bonds generated for 'chain 'P' and resid 110 through 112' Processing helix chain 'P' and resid 142 through 151 Proline residue: P 146 - end of helix Processing helix chain 'P' and resid 165 through 169 Processing helix chain 'P' and resid 175 through 188 removed outlier: 4.009A pdb=" N GLU P 187 " --> pdb=" O LEU P 183 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N GLU P 188 " --> pdb=" O ARG P 184 " (cutoff:3.500A) Processing helix chain 'P' and resid 204 through 212 Processing helix chain 'P' and resid 222 through 224 No H-bonds generated for 'chain 'P' and resid 222 through 224' Processing helix chain 'P' and resid 228 through 241 Processing helix chain 'P' and resid 258 through 265 Processing helix chain 'P' and resid 286 through 291 Processing helix chain 'P' and resid 301 through 303 No H-bonds generated for 'chain 'P' and resid 301 through 303' Processing helix chain 'P' and resid 310 through 321 Processing helix chain 'P' and resid 329 through 339 Processing helix chain 'P' and resid 341 through 353 removed outlier: 3.841A pdb=" N ASP P 348 " --> pdb=" O ILE P 344 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N THR P 349 " --> pdb=" O ALA P 345 " (cutoff:3.500A) Processing helix chain 'P' and resid 372 through 387 Processing helix chain 'P' and resid 399 through 408 removed outlier: 3.695A pdb=" N LYS P 408 " --> pdb=" O ARG P 404 " (cutoff:3.500A) Processing helix chain 'P' and resid 411 through 416 Processing helix chain 'P' and resid 439 through 441 No H-bonds generated for 'chain 'P' and resid 439 through 441' Processing helix chain 'P' and resid 479 through 481 No H-bonds generated for 'chain 'P' and resid 479 through 481' Processing helix chain 'P' and resid 485 through 489 Processing helix chain 'P' and resid 496 through 500 Processing helix chain 'P' and resid 503 through 506 No H-bonds generated for 'chain 'P' and resid 503 through 506' Processing helix chain 'P' and resid 524 through 526 No H-bonds generated for 'chain 'P' and resid 524 through 526' Processing helix chain 'R' and resid 6 through 13 Processing helix chain 'R' and resid 110 through 112 No H-bonds generated for 'chain 'R' and resid 110 through 112' Processing helix chain 'R' and resid 142 through 151 Proline residue: R 146 - end of helix Processing helix chain 'R' and resid 165 through 169 Processing helix chain 'R' and resid 175 through 188 removed outlier: 4.008A pdb=" N GLU R 187 " --> pdb=" O LEU R 183 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N GLU R 188 " --> pdb=" O ARG R 184 " (cutoff:3.500A) Processing helix chain 'R' and resid 204 through 212 Processing helix chain 'R' and resid 222 through 224 No H-bonds generated for 'chain 'R' and resid 222 through 224' Processing helix chain 'R' and resid 228 through 241 Processing helix chain 'R' and resid 258 through 265 Processing helix chain 'R' and resid 286 through 291 Processing helix chain 'R' and resid 301 through 303 No H-bonds generated for 'chain 'R' and resid 301 through 303' Processing helix chain 'R' and resid 310 through 321 Processing helix chain 'R' and resid 329 through 339 Processing helix chain 'R' and resid 341 through 353 removed outlier: 3.841A pdb=" N ASP R 348 " --> pdb=" O ILE R 344 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N THR R 349 " --> pdb=" O ALA R 345 " (cutoff:3.500A) Processing helix chain 'R' and resid 372 through 387 Processing helix chain 'R' and resid 399 through 408 removed outlier: 3.696A pdb=" N LYS R 408 " --> pdb=" O ARG R 404 " (cutoff:3.500A) Processing helix chain 'R' and resid 411 through 416 Processing helix chain 'R' and resid 439 through 441 No H-bonds generated for 'chain 'R' and resid 439 through 441' Processing helix chain 'R' and resid 479 through 481 No H-bonds generated for 'chain 'R' and resid 479 through 481' Processing helix chain 'R' and resid 485 through 489 Processing helix chain 'R' and resid 496 through 500 Processing helix chain 'R' and resid 503 through 506 No H-bonds generated for 'chain 'R' and resid 503 through 506' Processing helix chain 'R' and resid 524 through 526 No H-bonds generated for 'chain 'R' and resid 524 through 526' Processing helix chain 'T' and resid 6 through 13 Processing helix chain 'T' and resid 110 through 112 No H-bonds generated for 'chain 'T' and resid 110 through 112' Processing helix chain 'T' and resid 142 through 151 Proline residue: T 146 - end of helix Processing helix chain 'T' and resid 165 through 169 Processing helix chain 'T' and resid 175 through 188 removed outlier: 4.008A pdb=" N GLU T 187 " --> pdb=" O LEU T 183 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N GLU T 188 " --> pdb=" O ARG T 184 " (cutoff:3.500A) Processing helix chain 'T' and resid 204 through 212 Processing helix chain 'T' and resid 222 through 224 No H-bonds generated for 'chain 'T' and resid 222 through 224' Processing helix chain 'T' and resid 228 through 241 Processing helix chain 'T' and resid 258 through 265 Processing helix chain 'T' and resid 286 through 291 Processing helix chain 'T' and resid 301 through 303 No H-bonds generated for 'chain 'T' and resid 301 through 303' Processing helix chain 'T' and resid 310 through 321 Processing helix chain 'T' and resid 329 through 339 Processing helix chain 'T' and resid 341 through 353 removed outlier: 3.841A pdb=" N ASP T 348 " --> pdb=" O ILE T 344 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N THR T 349 " --> pdb=" O ALA T 345 " (cutoff:3.500A) Processing helix chain 'T' and resid 372 through 387 Processing helix chain 'T' and resid 399 through 408 removed outlier: 3.695A pdb=" N LYS T 408 " --> pdb=" O ARG T 404 " (cutoff:3.500A) Processing helix chain 'T' and resid 411 through 416 Processing helix chain 'T' and resid 439 through 441 No H-bonds generated for 'chain 'T' and resid 439 through 441' Processing helix chain 'T' and resid 479 through 481 No H-bonds generated for 'chain 'T' and resid 479 through 481' Processing helix chain 'T' and resid 485 through 489 Processing helix chain 'T' and resid 496 through 500 Processing helix chain 'T' and resid 503 through 506 No H-bonds generated for 'chain 'T' and resid 503 through 506' Processing helix chain 'T' and resid 524 through 526 No H-bonds generated for 'chain 'T' and resid 524 through 526' Processing helix chain 'V' and resid 6 through 13 Processing helix chain 'V' and resid 110 through 112 No H-bonds generated for 'chain 'V' and resid 110 through 112' Processing helix chain 'V' and resid 142 through 151 Proline residue: V 146 - end of helix Processing helix chain 'V' and resid 165 through 169 Processing helix chain 'V' and resid 175 through 188 removed outlier: 4.008A pdb=" N GLU V 187 " --> pdb=" O LEU V 183 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N GLU V 188 " --> pdb=" O ARG V 184 " (cutoff:3.500A) Processing helix chain 'V' and resid 204 through 212 Processing helix chain 'V' and resid 222 through 224 No H-bonds generated for 'chain 'V' and resid 222 through 224' Processing helix chain 'V' and resid 228 through 241 Processing helix chain 'V' and resid 258 through 265 Processing helix chain 'V' and resid 286 through 291 Processing helix chain 'V' and resid 301 through 303 No H-bonds generated for 'chain 'V' and resid 301 through 303' Processing helix chain 'V' and resid 310 through 321 Processing helix chain 'V' and resid 329 through 339 Processing helix chain 'V' and resid 341 through 353 removed outlier: 3.841A pdb=" N ASP V 348 " --> pdb=" O ILE V 344 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N THR V 349 " --> pdb=" O ALA V 345 " (cutoff:3.500A) Processing helix chain 'V' and resid 372 through 387 Processing helix chain 'V' and resid 399 through 408 removed outlier: 3.696A pdb=" N LYS V 408 " --> pdb=" O ARG V 404 " (cutoff:3.500A) Processing helix chain 'V' and resid 411 through 416 Processing helix chain 'V' and resid 439 through 441 No H-bonds generated for 'chain 'V' and resid 439 through 441' Processing helix chain 'V' and resid 479 through 481 No H-bonds generated for 'chain 'V' and resid 479 through 481' Processing helix chain 'V' and resid 485 through 489 Processing helix chain 'V' and resid 496 through 500 Processing helix chain 'V' and resid 503 through 506 No H-bonds generated for 'chain 'V' and resid 503 through 506' Processing helix chain 'V' and resid 524 through 526 No H-bonds generated for 'chain 'V' and resid 524 through 526' Processing helix chain 'X' and resid 6 through 13 Processing helix chain 'X' and resid 110 through 112 No H-bonds generated for 'chain 'X' and resid 110 through 112' Processing helix chain 'X' and resid 142 through 151 Proline residue: X 146 - end of helix Processing helix chain 'X' and resid 165 through 169 Processing helix chain 'X' and resid 175 through 188 removed outlier: 4.008A pdb=" N GLU X 187 " --> pdb=" O LEU X 183 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N GLU X 188 " --> pdb=" O ARG X 184 " (cutoff:3.500A) Processing helix chain 'X' and resid 204 through 212 Processing helix chain 'X' and resid 222 through 224 No H-bonds generated for 'chain 'X' and resid 222 through 224' Processing helix chain 'X' and resid 228 through 241 Processing helix chain 'X' and resid 258 through 265 Processing helix chain 'X' and resid 286 through 291 Processing helix chain 'X' and resid 301 through 303 No H-bonds generated for 'chain 'X' and resid 301 through 303' Processing helix chain 'X' and resid 310 through 321 Processing helix chain 'X' and resid 329 through 339 Processing helix chain 'X' and resid 341 through 353 removed outlier: 3.841A pdb=" N ASP X 348 " --> pdb=" O ILE X 344 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N THR X 349 " --> pdb=" O ALA X 345 " (cutoff:3.500A) Processing helix chain 'X' and resid 372 through 387 Processing helix chain 'X' and resid 399 through 408 removed outlier: 3.695A pdb=" N LYS X 408 " --> pdb=" O ARG X 404 " (cutoff:3.500A) Processing helix chain 'X' and resid 411 through 416 Processing helix chain 'X' and resid 439 through 441 No H-bonds generated for 'chain 'X' and resid 439 through 441' Processing helix chain 'X' and resid 479 through 481 No H-bonds generated for 'chain 'X' and resid 479 through 481' Processing helix chain 'X' and resid 485 through 489 Processing helix chain 'X' and resid 496 through 500 Processing helix chain 'X' and resid 503 through 506 No H-bonds generated for 'chain 'X' and resid 503 through 506' Processing helix chain 'X' and resid 524 through 526 No H-bonds generated for 'chain 'X' and resid 524 through 526' Processing sheet with id= A, first strand: chain 'A' and resid 80 through 87 Processing sheet with id= B, first strand: chain 'A' and resid 127 through 132 Processing sheet with id= C, first strand: chain 'A' and resid 139 through 142 Processing sheet with id= D, first strand: chain 'B' and resid 20 through 22 Processing sheet with id= E, first strand: chain 'B' and resid 119 through 122 removed outlier: 6.134A pdb=" N LYS B 89 " --> pdb=" O ILE B 93 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N ILE B 93 " --> pdb=" O LYS B 89 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 73 through 77 Processing sheet with id= G, first strand: chain 'B' and resid 126 through 130 removed outlier: 3.552A pdb=" N MET B 448 " --> pdb=" O LEU B 436 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU B 457 " --> pdb=" O ILE B 449 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N LYS B 451 " --> pdb=" O ILE B 455 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N ILE B 455 " --> pdb=" O LYS B 451 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 192 through 195 removed outlier: 6.817A pdb=" N GLY B 132 " --> pdb=" O THR B 154 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N MET B 156 " --> pdb=" O GLY B 132 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ASP B 134 " --> pdb=" O MET B 156 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N GLY B 158 " --> pdb=" O ASP B 134 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 270 through 272 Processing sheet with id= J, first strand: chain 'B' and resid 298 through 300 removed outlier: 6.559A pdb=" N ILE B 358 " --> pdb=" O SER B 299 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'B' and resid 491 through 494 removed outlier: 6.359A pdb=" N GLN B 512 " --> pdb=" O THR B 492 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N VAL B 494 " --> pdb=" O GLN B 512 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N LEU B 514 " --> pdb=" O VAL B 494 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'B' and resid 536 through 538 Processing sheet with id= M, first strand: chain 'C' and resid 80 through 87 Processing sheet with id= N, first strand: chain 'C' and resid 127 through 132 Processing sheet with id= O, first strand: chain 'C' and resid 139 through 142 Processing sheet with id= P, first strand: chain 'E' and resid 80 through 87 Processing sheet with id= Q, first strand: chain 'E' and resid 127 through 132 Processing sheet with id= R, first strand: chain 'E' and resid 139 through 142 Processing sheet with id= S, first strand: chain 'G' and resid 80 through 87 Processing sheet with id= T, first strand: chain 'G' and resid 127 through 132 Processing sheet with id= U, first strand: chain 'G' and resid 139 through 142 Processing sheet with id= V, first strand: chain 'I' and resid 80 through 87 Processing sheet with id= W, first strand: chain 'I' and resid 127 through 132 Processing sheet with id= X, first strand: chain 'I' and resid 139 through 142 Processing sheet with id= Y, first strand: chain 'K' and resid 80 through 87 Processing sheet with id= Z, first strand: chain 'K' and resid 127 through 132 Processing sheet with id= AA, first strand: chain 'K' and resid 139 through 142 Processing sheet with id= AB, first strand: chain 'M' and resid 80 through 87 Processing sheet with id= AC, first strand: chain 'M' and resid 127 through 132 Processing sheet with id= AD, first strand: chain 'M' and resid 139 through 142 Processing sheet with id= AE, first strand: chain 'O' and resid 80 through 87 Processing sheet with id= AF, first strand: chain 'O' and resid 127 through 132 Processing sheet with id= AG, first strand: chain 'O' and resid 139 through 142 Processing sheet with id= AH, first strand: chain 'Q' and resid 80 through 87 Processing sheet with id= AI, first strand: chain 'Q' and resid 127 through 132 Processing sheet with id= AJ, first strand: chain 'Q' and resid 139 through 142 Processing sheet with id= AK, first strand: chain 'S' and resid 80 through 87 Processing sheet with id= AL, first strand: chain 'S' and resid 127 through 132 Processing sheet with id= AM, first strand: chain 'S' and resid 139 through 142 Processing sheet with id= AN, first strand: chain 'U' and resid 80 through 87 Processing sheet with id= AO, first strand: chain 'U' and resid 127 through 132 Processing sheet with id= AP, first strand: chain 'U' and resid 139 through 142 Processing sheet with id= AQ, first strand: chain 'W' and resid 80 through 87 Processing sheet with id= AR, first strand: chain 'W' and resid 127 through 132 Processing sheet with id= AS, first strand: chain 'W' and resid 139 through 142 Processing sheet with id= AT, first strand: chain 'J' and resid 20 through 22 Processing sheet with id= AU, first strand: chain 'J' and resid 119 through 122 removed outlier: 6.134A pdb=" N LYS J 89 " --> pdb=" O ILE J 93 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N ILE J 93 " --> pdb=" O LYS J 89 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'J' and resid 73 through 77 Processing sheet with id= AW, first strand: chain 'J' and resid 126 through 130 removed outlier: 3.553A pdb=" N MET J 448 " --> pdb=" O LEU J 436 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU J 457 " --> pdb=" O ILE J 449 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N LYS J 451 " --> pdb=" O ILE J 455 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N ILE J 455 " --> pdb=" O LYS J 451 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'J' and resid 192 through 195 removed outlier: 6.818A pdb=" N GLY J 132 " --> pdb=" O THR J 154 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N MET J 156 " --> pdb=" O GLY J 132 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ASP J 134 " --> pdb=" O MET J 156 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N GLY J 158 " --> pdb=" O ASP J 134 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'J' and resid 270 through 272 Processing sheet with id= AZ, first strand: chain 'J' and resid 298 through 300 removed outlier: 6.561A pdb=" N ILE J 358 " --> pdb=" O SER J 299 " (cutoff:3.500A) No H-bonds generated for sheet with id= AZ Processing sheet with id= BA, first strand: chain 'J' and resid 491 through 494 removed outlier: 6.360A pdb=" N GLN J 512 " --> pdb=" O THR J 492 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N VAL J 494 " --> pdb=" O GLN J 512 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N LEU J 514 " --> pdb=" O VAL J 494 " (cutoff:3.500A) No H-bonds generated for sheet with id= BA Processing sheet with id= BB, first strand: chain 'J' and resid 536 through 538 Processing sheet with id= BC, first strand: chain 'D' and resid 20 through 22 Processing sheet with id= BD, first strand: chain 'D' and resid 119 through 122 removed outlier: 6.134A pdb=" N LYS D 89 " --> pdb=" O ILE D 93 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N ILE D 93 " --> pdb=" O LYS D 89 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'D' and resid 73 through 77 Processing sheet with id= BF, first strand: chain 'D' and resid 126 through 130 removed outlier: 3.553A pdb=" N MET D 448 " --> pdb=" O LEU D 436 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU D 457 " --> pdb=" O ILE D 449 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N LYS D 451 " --> pdb=" O ILE D 455 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N ILE D 455 " --> pdb=" O LYS D 451 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain 'D' and resid 192 through 195 removed outlier: 6.818A pdb=" N GLY D 132 " --> pdb=" O THR D 154 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N MET D 156 " --> pdb=" O GLY D 132 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ASP D 134 " --> pdb=" O MET D 156 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N GLY D 158 " --> pdb=" O ASP D 134 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain 'D' and resid 270 through 272 Processing sheet with id= BI, first strand: chain 'D' and resid 298 through 300 removed outlier: 6.561A pdb=" N ILE D 358 " --> pdb=" O SER D 299 " (cutoff:3.500A) No H-bonds generated for sheet with id= BI Processing sheet with id= BJ, first strand: chain 'D' and resid 491 through 494 removed outlier: 6.359A pdb=" N GLN D 512 " --> pdb=" O THR D 492 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N VAL D 494 " --> pdb=" O GLN D 512 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N LEU D 514 " --> pdb=" O VAL D 494 " (cutoff:3.500A) No H-bonds generated for sheet with id= BJ Processing sheet with id= BK, first strand: chain 'D' and resid 536 through 538 Processing sheet with id= BL, first strand: chain 'F' and resid 20 through 22 Processing sheet with id= BM, first strand: chain 'F' and resid 119 through 122 removed outlier: 6.134A pdb=" N LYS F 89 " --> pdb=" O ILE F 93 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N ILE F 93 " --> pdb=" O LYS F 89 " (cutoff:3.500A) Processing sheet with id= BN, first strand: chain 'F' and resid 73 through 77 Processing sheet with id= BO, first strand: chain 'F' and resid 126 through 130 removed outlier: 3.552A pdb=" N MET F 448 " --> pdb=" O LEU F 436 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU F 457 " --> pdb=" O ILE F 449 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N LYS F 451 " --> pdb=" O ILE F 455 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N ILE F 455 " --> pdb=" O LYS F 451 " (cutoff:3.500A) Processing sheet with id= BP, first strand: chain 'F' and resid 192 through 195 removed outlier: 6.818A pdb=" N GLY F 132 " --> pdb=" O THR F 154 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N MET F 156 " --> pdb=" O GLY F 132 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ASP F 134 " --> pdb=" O MET F 156 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N GLY F 158 " --> pdb=" O ASP F 134 " (cutoff:3.500A) Processing sheet with id= BQ, first strand: chain 'F' and resid 270 through 272 Processing sheet with id= BR, first strand: chain 'F' and resid 298 through 300 removed outlier: 6.560A pdb=" N ILE F 358 " --> pdb=" O SER F 299 " (cutoff:3.500A) No H-bonds generated for sheet with id= BR Processing sheet with id= BS, first strand: chain 'F' and resid 491 through 494 removed outlier: 6.358A pdb=" N GLN F 512 " --> pdb=" O THR F 492 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N VAL F 494 " --> pdb=" O GLN F 512 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N LEU F 514 " --> pdb=" O VAL F 494 " (cutoff:3.500A) No H-bonds generated for sheet with id= BS Processing sheet with id= BT, first strand: chain 'F' and resid 536 through 538 Processing sheet with id= BU, first strand: chain 'H' and resid 20 through 22 Processing sheet with id= BV, first strand: chain 'H' and resid 119 through 122 removed outlier: 6.134A pdb=" N LYS H 89 " --> pdb=" O ILE H 93 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N ILE H 93 " --> pdb=" O LYS H 89 " (cutoff:3.500A) Processing sheet with id= BW, first strand: chain 'H' and resid 73 through 77 Processing sheet with id= BX, first strand: chain 'H' and resid 126 through 130 removed outlier: 3.552A pdb=" N MET H 448 " --> pdb=" O LEU H 436 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU H 457 " --> pdb=" O ILE H 449 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N LYS H 451 " --> pdb=" O ILE H 455 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N ILE H 455 " --> pdb=" O LYS H 451 " (cutoff:3.500A) Processing sheet with id= BY, first strand: chain 'H' and resid 192 through 195 removed outlier: 6.818A pdb=" N GLY H 132 " --> pdb=" O THR H 154 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N MET H 156 " --> pdb=" O GLY H 132 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ASP H 134 " --> pdb=" O MET H 156 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N GLY H 158 " --> pdb=" O ASP H 134 " (cutoff:3.500A) Processing sheet with id= BZ, first strand: chain 'H' and resid 270 through 272 Processing sheet with id= CA, first strand: chain 'H' and resid 298 through 300 removed outlier: 6.560A pdb=" N ILE H 358 " --> pdb=" O SER H 299 " (cutoff:3.500A) No H-bonds generated for sheet with id= CA Processing sheet with id= CB, first strand: chain 'H' and resid 491 through 494 removed outlier: 6.360A pdb=" N GLN H 512 " --> pdb=" O THR H 492 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N VAL H 494 " --> pdb=" O GLN H 512 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N LEU H 514 " --> pdb=" O VAL H 494 " (cutoff:3.500A) No H-bonds generated for sheet with id= CB Processing sheet with id= CC, first strand: chain 'H' and resid 536 through 538 Processing sheet with id= CD, first strand: chain 'L' and resid 20 through 22 Processing sheet with id= CE, first strand: chain 'L' and resid 119 through 122 removed outlier: 6.133A pdb=" N LYS L 89 " --> pdb=" O ILE L 93 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N ILE L 93 " --> pdb=" O LYS L 89 " (cutoff:3.500A) Processing sheet with id= CF, first strand: chain 'L' and resid 73 through 77 Processing sheet with id= CG, first strand: chain 'L' and resid 126 through 130 removed outlier: 3.551A pdb=" N MET L 448 " --> pdb=" O LEU L 436 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU L 457 " --> pdb=" O ILE L 449 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N LYS L 451 " --> pdb=" O ILE L 455 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N ILE L 455 " --> pdb=" O LYS L 451 " (cutoff:3.500A) Processing sheet with id= CH, first strand: chain 'L' and resid 192 through 195 removed outlier: 6.817A pdb=" N GLY L 132 " --> pdb=" O THR L 154 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N MET L 156 " --> pdb=" O GLY L 132 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ASP L 134 " --> pdb=" O MET L 156 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N GLY L 158 " --> pdb=" O ASP L 134 " (cutoff:3.500A) Processing sheet with id= CI, first strand: chain 'L' and resid 270 through 272 Processing sheet with id= CJ, first strand: chain 'L' and resid 298 through 300 removed outlier: 6.560A pdb=" N ILE L 358 " --> pdb=" O SER L 299 " (cutoff:3.500A) No H-bonds generated for sheet with id= CJ Processing sheet with id= CK, first strand: chain 'L' and resid 491 through 494 removed outlier: 6.360A pdb=" N GLN L 512 " --> pdb=" O THR L 492 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N VAL L 494 " --> pdb=" O GLN L 512 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N LEU L 514 " --> pdb=" O VAL L 494 " (cutoff:3.500A) No H-bonds generated for sheet with id= CK Processing sheet with id= CL, first strand: chain 'L' and resid 536 through 538 Processing sheet with id= CM, first strand: chain 'N' and resid 20 through 22 Processing sheet with id= CN, first strand: chain 'N' and resid 119 through 122 removed outlier: 6.134A pdb=" N LYS N 89 " --> pdb=" O ILE N 93 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N ILE N 93 " --> pdb=" O LYS N 89 " (cutoff:3.500A) Processing sheet with id= CO, first strand: chain 'N' and resid 73 through 77 Processing sheet with id= CP, first strand: chain 'N' and resid 126 through 130 removed outlier: 3.552A pdb=" N MET N 448 " --> pdb=" O LEU N 436 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU N 457 " --> pdb=" O ILE N 449 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N LYS N 451 " --> pdb=" O ILE N 455 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N ILE N 455 " --> pdb=" O LYS N 451 " (cutoff:3.500A) Processing sheet with id= CQ, first strand: chain 'N' and resid 192 through 195 removed outlier: 6.817A pdb=" N GLY N 132 " --> pdb=" O THR N 154 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N MET N 156 " --> pdb=" O GLY N 132 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ASP N 134 " --> pdb=" O MET N 156 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N GLY N 158 " --> pdb=" O ASP N 134 " (cutoff:3.500A) Processing sheet with id= CR, first strand: chain 'N' and resid 270 through 272 Processing sheet with id= CS, first strand: chain 'N' and resid 298 through 300 removed outlier: 6.560A pdb=" N ILE N 358 " --> pdb=" O SER N 299 " (cutoff:3.500A) No H-bonds generated for sheet with id= CS Processing sheet with id= CT, first strand: chain 'N' and resid 491 through 494 removed outlier: 6.359A pdb=" N GLN N 512 " --> pdb=" O THR N 492 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N VAL N 494 " --> pdb=" O GLN N 512 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N LEU N 514 " --> pdb=" O VAL N 494 " (cutoff:3.500A) No H-bonds generated for sheet with id= CT Processing sheet with id= CU, first strand: chain 'N' and resid 536 through 538 Processing sheet with id= CV, first strand: chain 'P' and resid 20 through 22 Processing sheet with id= CW, first strand: chain 'P' and resid 119 through 122 removed outlier: 6.133A pdb=" N LYS P 89 " --> pdb=" O ILE P 93 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N ILE P 93 " --> pdb=" O LYS P 89 " (cutoff:3.500A) Processing sheet with id= CX, first strand: chain 'P' and resid 73 through 77 Processing sheet with id= CY, first strand: chain 'P' and resid 126 through 130 removed outlier: 3.552A pdb=" N MET P 448 " --> pdb=" O LEU P 436 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU P 457 " --> pdb=" O ILE P 449 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N LYS P 451 " --> pdb=" O ILE P 455 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N ILE P 455 " --> pdb=" O LYS P 451 " (cutoff:3.500A) Processing sheet with id= CZ, first strand: chain 'P' and resid 192 through 195 removed outlier: 6.818A pdb=" N GLY P 132 " --> pdb=" O THR P 154 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N MET P 156 " --> pdb=" O GLY P 132 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ASP P 134 " --> pdb=" O MET P 156 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N GLY P 158 " --> pdb=" O ASP P 134 " (cutoff:3.500A) Processing sheet with id= DA, first strand: chain 'P' and resid 270 through 272 Processing sheet with id= DB, first strand: chain 'P' and resid 298 through 300 removed outlier: 6.560A pdb=" N ILE P 358 " --> pdb=" O SER P 299 " (cutoff:3.500A) No H-bonds generated for sheet with id= DB Processing sheet with id= DC, first strand: chain 'P' and resid 491 through 494 removed outlier: 6.359A pdb=" N GLN P 512 " --> pdb=" O THR P 492 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N VAL P 494 " --> pdb=" O GLN P 512 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N LEU P 514 " --> pdb=" O VAL P 494 " (cutoff:3.500A) No H-bonds generated for sheet with id= DC Processing sheet with id= DD, first strand: chain 'P' and resid 536 through 538 Processing sheet with id= DE, first strand: chain 'R' and resid 20 through 22 Processing sheet with id= DF, first strand: chain 'R' and resid 119 through 122 removed outlier: 6.134A pdb=" N LYS R 89 " --> pdb=" O ILE R 93 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N ILE R 93 " --> pdb=" O LYS R 89 " (cutoff:3.500A) Processing sheet with id= DG, first strand: chain 'R' and resid 73 through 77 Processing sheet with id= DH, first strand: chain 'R' and resid 126 through 130 removed outlier: 3.552A pdb=" N MET R 448 " --> pdb=" O LEU R 436 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU R 457 " --> pdb=" O ILE R 449 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N LYS R 451 " --> pdb=" O ILE R 455 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N ILE R 455 " --> pdb=" O LYS R 451 " (cutoff:3.500A) Processing sheet with id= DI, first strand: chain 'R' and resid 192 through 195 removed outlier: 6.819A pdb=" N GLY R 132 " --> pdb=" O THR R 154 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N MET R 156 " --> pdb=" O GLY R 132 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ASP R 134 " --> pdb=" O MET R 156 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N GLY R 158 " --> pdb=" O ASP R 134 " (cutoff:3.500A) Processing sheet with id= DJ, first strand: chain 'R' and resid 270 through 272 Processing sheet with id= DK, first strand: chain 'R' and resid 298 through 300 removed outlier: 6.560A pdb=" N ILE R 358 " --> pdb=" O SER R 299 " (cutoff:3.500A) No H-bonds generated for sheet with id= DK Processing sheet with id= DL, first strand: chain 'R' and resid 491 through 494 removed outlier: 6.359A pdb=" N GLN R 512 " --> pdb=" O THR R 492 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N VAL R 494 " --> pdb=" O GLN R 512 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N LEU R 514 " --> pdb=" O VAL R 494 " (cutoff:3.500A) No H-bonds generated for sheet with id= DL Processing sheet with id= DM, first strand: chain 'R' and resid 536 through 538 Processing sheet with id= DN, first strand: chain 'T' and resid 20 through 22 Processing sheet with id= DO, first strand: chain 'T' and resid 119 through 122 removed outlier: 6.133A pdb=" N LYS T 89 " --> pdb=" O ILE T 93 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N ILE T 93 " --> pdb=" O LYS T 89 " (cutoff:3.500A) Processing sheet with id= DP, first strand: chain 'T' and resid 73 through 77 Processing sheet with id= DQ, first strand: chain 'T' and resid 126 through 130 removed outlier: 3.552A pdb=" N MET T 448 " --> pdb=" O LEU T 436 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU T 457 " --> pdb=" O ILE T 449 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N LYS T 451 " --> pdb=" O ILE T 455 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N ILE T 455 " --> pdb=" O LYS T 451 " (cutoff:3.500A) Processing sheet with id= DR, first strand: chain 'T' and resid 192 through 195 removed outlier: 6.818A pdb=" N GLY T 132 " --> pdb=" O THR T 154 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N MET T 156 " --> pdb=" O GLY T 132 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ASP T 134 " --> pdb=" O MET T 156 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N GLY T 158 " --> pdb=" O ASP T 134 " (cutoff:3.500A) Processing sheet with id= DS, first strand: chain 'T' and resid 270 through 272 Processing sheet with id= DT, first strand: chain 'T' and resid 298 through 300 removed outlier: 6.559A pdb=" N ILE T 358 " --> pdb=" O SER T 299 " (cutoff:3.500A) No H-bonds generated for sheet with id= DT Processing sheet with id= DU, first strand: chain 'T' and resid 491 through 494 removed outlier: 6.359A pdb=" N GLN T 512 " --> pdb=" O THR T 492 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N VAL T 494 " --> pdb=" O GLN T 512 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N LEU T 514 " --> pdb=" O VAL T 494 " (cutoff:3.500A) No H-bonds generated for sheet with id= DU Processing sheet with id= DV, first strand: chain 'T' and resid 536 through 538 Processing sheet with id= DW, first strand: chain 'V' and resid 20 through 22 Processing sheet with id= DX, first strand: chain 'V' and resid 119 through 122 removed outlier: 6.134A pdb=" N LYS V 89 " --> pdb=" O ILE V 93 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N ILE V 93 " --> pdb=" O LYS V 89 " (cutoff:3.500A) Processing sheet with id= DY, first strand: chain 'V' and resid 73 through 77 Processing sheet with id= DZ, first strand: chain 'V' and resid 126 through 130 removed outlier: 3.552A pdb=" N MET V 448 " --> pdb=" O LEU V 436 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU V 457 " --> pdb=" O ILE V 449 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N LYS V 451 " --> pdb=" O ILE V 455 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N ILE V 455 " --> pdb=" O LYS V 451 " (cutoff:3.500A) Processing sheet with id= EA, first strand: chain 'V' and resid 192 through 195 removed outlier: 6.818A pdb=" N GLY V 132 " --> pdb=" O THR V 154 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N MET V 156 " --> pdb=" O GLY V 132 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ASP V 134 " --> pdb=" O MET V 156 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N GLY V 158 " --> pdb=" O ASP V 134 " (cutoff:3.500A) Processing sheet with id= EB, first strand: chain 'V' and resid 270 through 272 Processing sheet with id= EC, first strand: chain 'V' and resid 298 through 300 removed outlier: 6.561A pdb=" N ILE V 358 " --> pdb=" O SER V 299 " (cutoff:3.500A) No H-bonds generated for sheet with id= EC Processing sheet with id= ED, first strand: chain 'V' and resid 491 through 494 removed outlier: 6.359A pdb=" N GLN V 512 " --> pdb=" O THR V 492 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N VAL V 494 " --> pdb=" O GLN V 512 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N LEU V 514 " --> pdb=" O VAL V 494 " (cutoff:3.500A) No H-bonds generated for sheet with id= ED Processing sheet with id= EE, first strand: chain 'V' and resid 536 through 538 Processing sheet with id= 0, first strand: chain 'X' and resid 20 through 22 Processing sheet with id= 1, first strand: chain 'X' and resid 119 through 122 removed outlier: 6.134A pdb=" N LYS X 89 " --> pdb=" O ILE X 93 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N ILE X 93 " --> pdb=" O LYS X 89 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'X' and resid 73 through 77 Processing sheet with id= 3, first strand: chain 'X' and resid 126 through 130 removed outlier: 3.552A pdb=" N MET X 448 " --> pdb=" O LEU X 436 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU X 457 " --> pdb=" O ILE X 449 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N LYS X 451 " --> pdb=" O ILE X 455 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N ILE X 455 " --> pdb=" O LYS X 451 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'X' and resid 192 through 195 removed outlier: 6.818A pdb=" N GLY X 132 " --> pdb=" O THR X 154 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N MET X 156 " --> pdb=" O GLY X 132 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ASP X 134 " --> pdb=" O MET X 156 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N GLY X 158 " --> pdb=" O ASP X 134 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'X' and resid 270 through 272 Processing sheet with id= 6, first strand: chain 'X' and resid 298 through 300 removed outlier: 6.560A pdb=" N ILE X 358 " --> pdb=" O SER X 299 " (cutoff:3.500A) No H-bonds generated for sheet with id= 6 Processing sheet with id= 7, first strand: chain 'X' and resid 491 through 494 removed outlier: 6.359A pdb=" N GLN X 512 " --> pdb=" O THR X 492 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N VAL X 494 " --> pdb=" O GLN X 512 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N LEU X 514 " --> pdb=" O VAL X 494 " (cutoff:3.500A) No H-bonds generated for sheet with id= 7 Processing sheet with id= 8, first strand: chain 'X' and resid 536 through 538 2220 hydrogen bonds defined for protein. 6012 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: 37.51 Time building geometry restraints manager: 28.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 22441 1.33 - 1.45: 10750 1.45 - 1.57: 42037 1.57 - 1.69: 0 1.69 - 1.81: 660 Bond restraints: 75888 Sorted by residual: bond pdb=" NZ KCX D 219 " pdb=" CX KCX D 219 " ideal model delta sigma weight residual 1.411 1.325 0.086 2.00e-02 2.50e+03 1.86e+01 bond pdb=" NZ KCX J 219 " pdb=" CX KCX J 219 " ideal model delta sigma weight residual 1.411 1.325 0.086 2.00e-02 2.50e+03 1.86e+01 bond pdb=" NZ KCX X 219 " pdb=" CX KCX X 219 " ideal model delta sigma weight residual 1.411 1.325 0.086 2.00e-02 2.50e+03 1.85e+01 bond pdb=" NZ KCX F 219 " pdb=" CX KCX F 219 " ideal model delta sigma weight residual 1.411 1.325 0.086 2.00e-02 2.50e+03 1.85e+01 bond pdb=" NZ KCX V 219 " pdb=" CX KCX V 219 " ideal model delta sigma weight residual 1.411 1.325 0.086 2.00e-02 2.50e+03 1.84e+01 ... (remaining 75883 not shown) Histogram of bond angle deviations from ideal: 99.98 - 106.80: 1973 106.80 - 113.63: 42695 113.63 - 120.45: 27669 120.45 - 127.27: 29315 127.27 - 134.09: 696 Bond angle restraints: 102348 Sorted by residual: angle pdb=" C GLY U 197 " pdb=" N PHE U 198 " pdb=" CA PHE U 198 " ideal model delta sigma weight residual 121.54 130.06 -8.52 1.91e+00 2.74e-01 1.99e+01 angle pdb=" C GLY G 197 " pdb=" N PHE G 198 " pdb=" CA PHE G 198 " ideal model delta sigma weight residual 121.54 130.06 -8.52 1.91e+00 2.74e-01 1.99e+01 angle pdb=" C GLY C 197 " pdb=" N PHE C 198 " pdb=" CA PHE C 198 " ideal model delta sigma weight residual 121.54 130.05 -8.51 1.91e+00 2.74e-01 1.98e+01 angle pdb=" C GLY O 197 " pdb=" N PHE O 198 " pdb=" CA PHE O 198 " ideal model delta sigma weight residual 121.54 130.03 -8.49 1.91e+00 2.74e-01 1.98e+01 angle pdb=" C GLY I 197 " pdb=" N PHE I 198 " pdb=" CA PHE I 198 " ideal model delta sigma weight residual 121.54 130.03 -8.49 1.91e+00 2.74e-01 1.97e+01 ... (remaining 102343 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.84: 42263 16.84 - 33.69: 2701 33.69 - 50.53: 456 50.53 - 67.37: 252 67.37 - 84.22: 144 Dihedral angle restraints: 45816 sinusoidal: 18384 harmonic: 27432 Sorted by residual: dihedral pdb=" CA GLU D 188 " pdb=" C GLU D 188 " pdb=" N TYR D 189 " pdb=" CA TYR D 189 " ideal model delta harmonic sigma weight residual -180.00 -152.89 -27.11 0 5.00e+00 4.00e-02 2.94e+01 dihedral pdb=" CA GLU R 188 " pdb=" C GLU R 188 " pdb=" N TYR R 189 " pdb=" CA TYR R 189 " ideal model delta harmonic sigma weight residual -180.00 -152.91 -27.09 0 5.00e+00 4.00e-02 2.94e+01 dihedral pdb=" CA GLU J 188 " pdb=" C GLU J 188 " pdb=" N TYR J 189 " pdb=" CA TYR J 189 " ideal model delta harmonic sigma weight residual -180.00 -152.91 -27.09 0 5.00e+00 4.00e-02 2.94e+01 ... (remaining 45813 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 6100 0.035 - 0.070: 3521 0.070 - 0.105: 1295 0.105 - 0.140: 436 0.140 - 0.174: 48 Chirality restraints: 11400 Sorted by residual: chirality pdb=" CA ASN L 301 " pdb=" N ASN L 301 " pdb=" C ASN L 301 " pdb=" CB ASN L 301 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.60e-01 chirality pdb=" CA THR D 469 " pdb=" N THR D 469 " pdb=" C THR D 469 " pdb=" CB THR D 469 " both_signs ideal model delta sigma weight residual False 2.53 2.35 0.17 2.00e-01 2.50e+01 7.58e-01 chirality pdb=" CA ASN T 301 " pdb=" N ASN T 301 " pdb=" C ASN T 301 " pdb=" CB ASN T 301 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.55e-01 ... (remaining 11397 not shown) Planarity restraints: 13404 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA L 283 " -0.032 5.00e-02 4.00e+02 4.84e-02 3.75e+00 pdb=" N PRO L 284 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO L 284 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO L 284 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA P 283 " 0.032 5.00e-02 4.00e+02 4.82e-02 3.72e+00 pdb=" N PRO P 284 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO P 284 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO P 284 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA X 283 " -0.032 5.00e-02 4.00e+02 4.82e-02 3.71e+00 pdb=" N PRO X 284 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO X 284 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO X 284 " -0.025 5.00e-02 4.00e+02 ... (remaining 13401 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.51: 505 2.51 - 3.11: 58261 3.11 - 3.71: 130611 3.71 - 4.30: 205242 4.30 - 4.90: 314879 Nonbonded interactions: 709498 Sorted by model distance: nonbonded pdb=" NE2 HIS J 274 " pdb="NI NI J 601 " model vdw 1.918 2.260 nonbonded pdb=" NE2 HIS T 274 " pdb="NI NI T 601 " model vdw 1.919 2.260 nonbonded pdb=" NE2 HIS V 274 " pdb="NI NI V 601 " model vdw 1.919 2.260 nonbonded pdb=" NE2 HIS R 274 " pdb="NI NI R 601 " model vdw 1.919 2.260 nonbonded pdb=" NE2 HIS L 274 " pdb="NI NI L 601 " model vdw 1.919 2.260 ... (remaining 709493 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'U' selection = chain 'W' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'V' selection = chain 'X' } 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: 5 Type Number sf(0) Gaussians Ni 24 6.56 5 S 360 5.16 5 C 46788 2.51 5 N 12972 2.21 5 O 15614 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.290 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: 0.090 Extract box with map and model: 11.200 Check model and map are aligned: 0.850 Convert atoms to be neutral: 0.500 Process input model: 167.280 Find NCS groups from input model: 4.750 Set up NCS constraints: 0.630 Set refine NCS operators: 0.000 Set scattering table: 0.040 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:12.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 198.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 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 0.086 75888 Z= 0.381 Angle : 0.652 8.517 102348 Z= 0.362 Chirality : 0.050 0.174 11400 Planarity : 0.005 0.048 13404 Dihedral : 13.440 84.218 28272 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer Outliers : 0.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: 0.27 (0.08), residues: 9600 helix: 0.88 (0.09), residues: 2856 sheet: 1.18 (0.15), residues: 1020 loop : -0.34 (0.08), residues: 5724 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19200 Ramachandran restraints generated. 9600 Oldfield, 0 Emsley, 9600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19200 Ramachandran restraints generated. 9600 Oldfield, 0 Emsley, 9600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1483 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 1435 time to evaluate : 6.825 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 48 outliers final: 2 residues processed: 1468 average time/residue: 1.6769 time to fit residues: 3189.9449 Evaluate side-chains 1026 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1024 time to evaluate : 6.744 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 9.0504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 948 random chunks: chunk 800 optimal weight: 9.9990 chunk 718 optimal weight: 0.9990 chunk 398 optimal weight: 0.7980 chunk 245 optimal weight: 3.9990 chunk 484 optimal weight: 1.9990 chunk 383 optimal weight: 3.9990 chunk 743 optimal weight: 1.9990 chunk 287 optimal weight: 0.7980 chunk 451 optimal weight: 0.8980 chunk 553 optimal weight: 9.9990 chunk 860 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 HIS B 34 HIS B 309 ASN B 539 ASN C 97 HIS E 97 HIS G 97 HIS I 31 ASN I 97 HIS I 133 ASN I 208 ASN K 151 ASN O 97 HIS Q 97 HIS S 97 HIS W 208 ASN J 383 ASN D 309 ASN D 333 GLN F 60 ASN F 333 GLN F 383 ASN H 309 ASN H 333 GLN L 309 ASN N 34 HIS N 314 HIS N 333 GLN P 60 ASN P 333 GLN R 34 HIS R 60 ASN R 309 ASN R 314 HIS R 333 GLN R 383 ASN T 60 ASN T 309 ASN T 314 HIS T 535 HIS V 309 ASN V 333 GLN V 512 GLN X 309 ASN Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.1427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.050 75888 Z= 0.158 Angle : 0.507 7.929 102348 Z= 0.275 Chirality : 0.045 0.194 11400 Planarity : 0.004 0.049 13404 Dihedral : 4.852 31.420 10356 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer Outliers : 2.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: 0.54 (0.08), residues: 9600 helix: 1.38 (0.10), residues: 2820 sheet: 1.06 (0.16), residues: 1056 loop : -0.26 (0.08), residues: 5724 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19200 Ramachandran restraints generated. 9600 Oldfield, 0 Emsley, 9600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19200 Ramachandran restraints generated. 9600 Oldfield, 0 Emsley, 9600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1224 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 1066 time to evaluate : 6.934 Fit side-chains revert: symmetry clash outliers start: 158 outliers final: 47 residues processed: 1128 average time/residue: 1.7185 time to fit residues: 2517.7123 Evaluate side-chains 1067 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 1020 time to evaluate : 6.752 Switching outliers to nearest non-outliers outliers start: 47 outliers final: 12 residues processed: 35 average time/residue: 0.9860 time to fit residues: 61.2472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 948 random chunks: chunk 478 optimal weight: 7.9990 chunk 267 optimal weight: 10.0000 chunk 716 optimal weight: 0.7980 chunk 586 optimal weight: 0.7980 chunk 237 optimal weight: 0.9990 chunk 862 optimal weight: 8.9990 chunk 931 optimal weight: 0.0270 chunk 768 optimal weight: 0.8980 chunk 855 optimal weight: 2.9990 chunk 294 optimal weight: 0.9980 chunk 691 optimal weight: 4.9990 overall best weight: 0.7038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 HIS ** B 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 309 ASN B 539 ASN I 208 ASN W 208 ASN J 309 ASN J 383 ASN ** J 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 309 ASN D 383 ASN F 34 HIS F 60 ASN F 333 GLN F 383 ASN H 34 HIS ** H 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 309 ASN H 539 ASN L 309 ASN L 314 HIS N 34 HIS N 168 ASN ** N 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 314 HIS P 60 ASN P 333 GLN R 34 HIS R 60 ASN R 309 ASN R 383 ASN T 34 HIS T 60 ASN T 309 ASN T 314 HIS T 535 HIS V 34 HIS V 168 ASN V 333 GLN X 309 ASN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 75888 Z= 0.125 Angle : 0.466 7.727 102348 Z= 0.251 Chirality : 0.044 0.187 11400 Planarity : 0.004 0.049 13404 Dihedral : 4.512 27.493 10356 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer Outliers : 1.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: 0.67 (0.09), residues: 9600 helix: 1.52 (0.10), residues: 2892 sheet: 0.76 (0.15), residues: 1164 loop : -0.16 (0.08), residues: 5544 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19200 Ramachandran restraints generated. 9600 Oldfield, 0 Emsley, 9600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19200 Ramachandran restraints generated. 9600 Oldfield, 0 Emsley, 9600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1193 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 1062 time to evaluate : 6.845 Fit side-chains revert: symmetry clash outliers start: 131 outliers final: 45 residues processed: 1127 average time/residue: 1.7268 time to fit residues: 2528.9785 Evaluate side-chains 1047 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 1002 time to evaluate : 6.700 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 22 residues processed: 23 average time/residue: 1.0033 time to fit residues: 43.6914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 948 random chunks: chunk 852 optimal weight: 4.9990 chunk 648 optimal weight: 0.8980 chunk 447 optimal weight: 9.9990 chunk 95 optimal weight: 0.0980 chunk 411 optimal weight: 1.9990 chunk 579 optimal weight: 0.9980 chunk 865 optimal weight: 8.9990 chunk 916 optimal weight: 8.9990 chunk 452 optimal weight: 10.0000 chunk 820 optimal weight: 9.9990 chunk 246 optimal weight: 6.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 HIS B 168 ASN ** B 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 539 ASN I 208 ASN K 151 ASN W 208 ASN J 168 ASN J 309 ASN J 383 ASN J 512 GLN D 168 ASN D 383 ASN F 34 HIS F 60 ASN F 309 ASN F 333 GLN F 383 ASN H 34 HIS H 168 ASN ** H 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 309 ASN H 512 GLN L 34 HIS L 168 ASN L 309 ASN L 314 HIS N 34 HIS N 301 ASN N 314 HIS P 309 ASN P 333 GLN R 34 HIS R 60 ASN R 535 HIS T 34 HIS T 60 ASN T 168 ASN T 309 ASN T 314 HIS V 34 HIS V 309 ASN V 314 HIS V 333 GLN X 309 ASN X 383 ASN Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 75888 Z= 0.192 Angle : 0.506 8.809 102348 Z= 0.273 Chirality : 0.045 0.193 11400 Planarity : 0.004 0.048 13404 Dihedral : 4.648 28.534 10356 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer Outliers : 1.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: 0.56 (0.08), residues: 9600 helix: 1.35 (0.10), residues: 2904 sheet: 0.73 (0.15), residues: 1164 loop : -0.19 (0.08), residues: 5532 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19200 Ramachandran restraints generated. 9600 Oldfield, 0 Emsley, 9600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19200 Ramachandran restraints generated. 9600 Oldfield, 0 Emsley, 9600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1185 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 1032 time to evaluate : 7.644 Fit side-chains revert: symmetry clash outliers start: 153 outliers final: 61 residues processed: 1102 average time/residue: 1.7059 time to fit residues: 2451.3044 Evaluate side-chains 1074 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 1013 time to evaluate : 6.773 Switching outliers to nearest non-outliers outliers start: 61 outliers final: 25 residues processed: 36 average time/residue: 1.0503 time to fit residues: 65.2318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 948 random chunks: chunk 763 optimal weight: 1.9990 chunk 520 optimal weight: 9.9990 chunk 13 optimal weight: 5.9990 chunk 682 optimal weight: 3.9990 chunk 378 optimal weight: 9.9990 chunk 781 optimal weight: 3.9990 chunk 633 optimal weight: 4.9990 chunk 1 optimal weight: 7.9990 chunk 467 optimal weight: 6.9990 chunk 822 optimal weight: 3.9990 chunk 231 optimal weight: 10.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 HIS B 314 HIS B 539 ASN I 208 ASN W 208 ASN J 309 ASN J 383 ASN F 34 HIS F 309 ASN F 314 HIS F 333 GLN F 383 ASN H 34 HIS H 309 ASN L 34 HIS L 309 ASN L 314 HIS N 34 HIS N 309 ASN P 314 HIS P 333 GLN R 34 HIS R 60 ASN ** R 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 34 HIS T 60 ASN T 314 HIS T 496 GLN V 34 HIS V 168 ASN V 309 ASN V 333 GLN X 309 ASN X 383 ASN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.057 75888 Z= 0.345 Angle : 0.607 9.799 102348 Z= 0.328 Chirality : 0.050 0.223 11400 Planarity : 0.005 0.049 13404 Dihedral : 5.129 32.478 10356 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer Outliers : 1.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: 0.26 (0.08), residues: 9600 helix: 0.94 (0.09), residues: 2904 sheet: 0.85 (0.16), residues: 1068 loop : -0.33 (0.08), residues: 5628 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19200 Ramachandran restraints generated. 9600 Oldfield, 0 Emsley, 9600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19200 Ramachandran restraints generated. 9600 Oldfield, 0 Emsley, 9600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1184 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 1044 time to evaluate : 6.898 Fit side-chains outliers start: 140 outliers final: 70 residues processed: 1108 average time/residue: 1.7652 time to fit residues: 2545.5292 Evaluate side-chains 1088 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 1018 time to evaluate : 6.756 Switching outliers to nearest non-outliers outliers start: 70 outliers final: 33 residues processed: 38 average time/residue: 0.9750 time to fit residues: 65.7797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 948 random chunks: chunk 308 optimal weight: 8.9990 chunk 825 optimal weight: 10.0000 chunk 181 optimal weight: 6.9990 chunk 538 optimal weight: 5.9990 chunk 226 optimal weight: 3.9990 chunk 917 optimal weight: 0.7980 chunk 761 optimal weight: 0.8980 chunk 424 optimal weight: 10.0000 chunk 76 optimal weight: 9.9990 chunk 303 optimal weight: 6.9990 chunk 481 optimal weight: 1.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 HIS B 309 ASN B 539 ASN W 208 ASN J 309 ASN J 383 ASN D 309 ASN D 512 GLN F 34 HIS F 309 ASN F 314 HIS F 333 GLN F 383 ASN H 34 HIS H 301 ASN H 309 ASN L 34 HIS L 309 ASN L 314 HIS L 333 GLN N 34 HIS N 314 HIS N 512 GLN P 333 GLN R 34 HIS R 60 ASN R 535 HIS T 34 HIS T 60 ASN T 309 ASN T 314 HIS V 34 HIS V 333 GLN V 539 ASN X 309 ASN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 75888 Z= 0.262 Angle : 0.550 9.769 102348 Z= 0.298 Chirality : 0.047 0.211 11400 Planarity : 0.004 0.048 13404 Dihedral : 5.035 33.279 10356 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer Outliers : 1.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: 0.26 (0.08), residues: 9600 helix: 0.96 (0.09), residues: 2904 sheet: 0.86 (0.16), residues: 1068 loop : -0.35 (0.08), residues: 5628 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19200 Ramachandran restraints generated. 9600 Oldfield, 0 Emsley, 9600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19200 Ramachandran restraints generated. 9600 Oldfield, 0 Emsley, 9600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1168 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 1030 time to evaluate : 6.830 Fit side-chains outliers start: 138 outliers final: 73 residues processed: 1092 average time/residue: 1.7335 time to fit residues: 2461.6380 Evaluate side-chains 1094 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 1021 time to evaluate : 6.716 Switching outliers to nearest non-outliers outliers start: 73 outliers final: 36 residues processed: 37 average time/residue: 1.1366 time to fit residues: 70.2460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 948 random chunks: chunk 884 optimal weight: 0.0870 chunk 103 optimal weight: 4.9990 chunk 522 optimal weight: 3.9990 chunk 669 optimal weight: 10.0000 chunk 518 optimal weight: 3.9990 chunk 772 optimal weight: 6.9990 chunk 512 optimal weight: 10.0000 chunk 913 optimal weight: 0.9990 chunk 571 optimal weight: 9.9990 chunk 557 optimal weight: 7.9990 chunk 421 optimal weight: 5.9990 overall best weight: 2.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 HIS B 309 ASN B 539 ASN S 31 ASN W 208 ASN J 309 ASN J 383 ASN D 309 ASN F 34 HIS F 309 ASN F 314 HIS F 333 GLN F 383 ASN H 34 HIS ** H 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 309 ASN L 34 HIS L 309 ASN L 314 HIS L 333 GLN N 34 HIS P 333 GLN R 34 HIS R 60 ASN R 535 HIS T 34 HIS T 60 ASN T 314 HIS V 34 HIS V 333 GLN V 539 ASN V 544 HIS X 309 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 75888 Z= 0.271 Angle : 0.560 9.713 102348 Z= 0.303 Chirality : 0.047 0.219 11400 Planarity : 0.004 0.048 13404 Dihedral : 5.062 35.714 10356 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer Outliers : 1.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: 0.23 (0.08), residues: 9600 helix: 0.94 (0.09), residues: 2904 sheet: 0.84 (0.16), residues: 1068 loop : -0.37 (0.08), residues: 5628 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19200 Ramachandran restraints generated. 9600 Oldfield, 0 Emsley, 9600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19200 Ramachandran restraints generated. 9600 Oldfield, 0 Emsley, 9600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1150 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 1033 time to evaluate : 6.878 Fit side-chains outliers start: 117 outliers final: 73 residues processed: 1090 average time/residue: 1.7668 time to fit residues: 2502.6920 Evaluate side-chains 1091 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 1018 time to evaluate : 6.914 Switching outliers to nearest non-outliers outliers start: 73 outliers final: 37 residues processed: 37 average time/residue: 1.0233 time to fit residues: 66.2018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 948 random chunks: chunk 565 optimal weight: 5.9990 chunk 364 optimal weight: 3.9990 chunk 545 optimal weight: 5.9990 chunk 275 optimal weight: 3.9990 chunk 179 optimal weight: 0.0670 chunk 177 optimal weight: 5.9990 chunk 580 optimal weight: 3.9990 chunk 622 optimal weight: 5.9990 chunk 451 optimal weight: 4.9990 chunk 85 optimal weight: 8.9990 chunk 718 optimal weight: 5.9990 overall best weight: 3.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 ASN B 34 HIS B 309 ASN B 512 GLN B 539 ASN W 208 ASN J 309 ASN D 309 ASN F 34 HIS F 309 ASN F 333 GLN H 34 HIS H 136 HIS ** H 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 309 ASN L 34 HIS L 309 ASN L 314 HIS L 333 GLN N 34 HIS P 333 GLN R 34 HIS R 60 ASN R 535 HIS T 34 HIS T 60 ASN T 314 HIS V 34 HIS V 333 GLN V 539 ASN V 544 HIS X 168 ASN X 309 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.058 75888 Z= 0.317 Angle : 0.588 10.356 102348 Z= 0.318 Chirality : 0.049 0.221 11400 Planarity : 0.005 0.049 13404 Dihedral : 5.174 36.816 10356 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer Outliers : 1.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: 0.14 (0.08), residues: 9600 helix: 0.86 (0.09), residues: 2892 sheet: 0.80 (0.16), residues: 1068 loop : -0.42 (0.08), residues: 5640 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19200 Ramachandran restraints generated. 9600 Oldfield, 0 Emsley, 9600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19200 Ramachandran restraints generated. 9600 Oldfield, 0 Emsley, 9600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1137 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 1025 time to evaluate : 6.929 Fit side-chains revert: symmetry clash outliers start: 112 outliers final: 73 residues processed: 1084 average time/residue: 1.7597 time to fit residues: 2483.3714 Evaluate side-chains 1091 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 1018 time to evaluate : 6.950 Switching outliers to nearest non-outliers outliers start: 73 outliers final: 42 residues processed: 32 average time/residue: 1.0501 time to fit residues: 59.2795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 948 random chunks: chunk 831 optimal weight: 0.9980 chunk 875 optimal weight: 0.4980 chunk 798 optimal weight: 0.6980 chunk 851 optimal weight: 10.0000 chunk 512 optimal weight: 10.0000 chunk 370 optimal weight: 5.9990 chunk 668 optimal weight: 6.9990 chunk 261 optimal weight: 7.9990 chunk 769 optimal weight: 1.9990 chunk 805 optimal weight: 0.9990 chunk 848 optimal weight: 8.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 ASN B 309 ASN B 539 ASN S 31 ASN W 208 ASN J 309 ASN J 383 ASN D 309 ASN F 34 HIS F 309 ASN F 333 GLN F 383 ASN F 512 GLN H 34 HIS H 309 ASN L 34 HIS L 309 ASN L 314 HIS L 512 GLN N 34 HIS N 314 HIS N 333 GLN P 333 GLN R 34 HIS R 333 GLN R 535 HIS T 34 HIS T 309 ASN T 314 HIS V 34 HIS V 168 ASN V 333 GLN V 539 ASN V 544 HIS X 309 ASN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.043 75888 Z= 0.149 Angle : 0.487 8.890 102348 Z= 0.263 Chirality : 0.044 0.224 11400 Planarity : 0.004 0.049 13404 Dihedral : 4.785 33.739 10356 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer Outliers : 1.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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 (0.08), residues: 9600 helix: 1.27 (0.10), residues: 2880 sheet: 0.74 (0.15), residues: 1032 loop : -0.31 (0.08), residues: 5688 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19200 Ramachandran restraints generated. 9600 Oldfield, 0 Emsley, 9600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19200 Ramachandran restraints generated. 9600 Oldfield, 0 Emsley, 9600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1140 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 1061 time to evaluate : 6.854 Fit side-chains revert: symmetry clash outliers start: 79 outliers final: 48 residues processed: 1108 average time/residue: 1.7317 time to fit residues: 2498.8549 Evaluate side-chains 1081 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 1033 time to evaluate : 6.767 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 31 residues processed: 18 average time/residue: 1.2161 time to fit residues: 40.3349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 948 random chunks: chunk 559 optimal weight: 0.6980 chunk 900 optimal weight: 8.9990 chunk 549 optimal weight: 0.4980 chunk 427 optimal weight: 0.6980 chunk 625 optimal weight: 8.9990 chunk 944 optimal weight: 6.9990 chunk 869 optimal weight: 9.9990 chunk 752 optimal weight: 10.0000 chunk 78 optimal weight: 20.0000 chunk 580 optimal weight: 4.9990 chunk 461 optimal weight: 8.9990 overall best weight: 2.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 ASN B 309 ASN B 539 ASN W 208 ASN J 309 ASN J 383 ASN D 309 ASN F 34 HIS F 309 ASN F 333 GLN F 383 ASN H 34 HIS ** H 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 309 ASN L 34 HIS L 309 ASN L 314 HIS N 34 HIS R 34 HIS R 60 ASN ** R 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 34 HIS T 314 HIS V 34 HIS V 333 GLN V 539 ASN V 544 HIS X 309 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 75888 Z= 0.268 Angle : 0.554 9.961 102348 Z= 0.299 Chirality : 0.047 0.224 11400 Planarity : 0.004 0.048 13404 Dihedral : 4.975 35.958 10356 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer Outliers : 0.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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 (0.08), residues: 9600 helix: 1.07 (0.10), residues: 2892 sheet: 0.67 (0.16), residues: 972 loop : -0.32 (0.08), residues: 5736 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19200 Ramachandran restraints generated. 9600 Oldfield, 0 Emsley, 9600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19200 Ramachandran restraints generated. 9600 Oldfield, 0 Emsley, 9600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1091 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 1028 time to evaluate : 6.879 Fit side-chains outliers start: 63 outliers final: 48 residues processed: 1067 average time/residue: 1.7719 time to fit residues: 2458.0202 Evaluate side-chains 1060 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 1012 time to evaluate : 6.798 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 36 residues processed: 13 average time/residue: 0.7990 time to fit residues: 26.3795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 948 random chunks: chunk 597 optimal weight: 0.9980 chunk 801 optimal weight: 5.9990 chunk 230 optimal weight: 0.4980 chunk 693 optimal weight: 0.1980 chunk 111 optimal weight: 8.9990 chunk 208 optimal weight: 7.9990 chunk 753 optimal weight: 7.9990 chunk 315 optimal weight: 8.9990 chunk 773 optimal weight: 3.9990 chunk 95 optimal weight: 9.9990 chunk 138 optimal weight: 3.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 ASN B 309 ASN B 539 ASN W 208 ASN J 309 ASN J 383 ASN D 309 ASN F 34 HIS F 309 ASN F 333 GLN F 383 ASN H 34 HIS ** H 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 309 ASN L 34 HIS L 309 ASN L 314 HIS N 34 HIS N 314 HIS R 34 HIS ** R 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 34 HIS T 314 HIS V 34 HIS V 333 GLN V 539 ASN V 544 HIS X 309 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.125347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.099971 restraints weight = 76231.108| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 1.42 r_work: 0.3099 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 75888 Z= 0.207 Angle : 0.522 9.736 102348 Z= 0.282 Chirality : 0.046 0.230 11400 Planarity : 0.004 0.048 13404 Dihedral : 4.898 35.782 10356 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer Outliers : 0.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: 0.34 (0.08), residues: 9600 helix: 1.14 (0.10), residues: 2892 sheet: 0.64 (0.15), residues: 1164 loop : -0.32 (0.08), residues: 5544 =============================================================================== Job complete usr+sys time: 32440.02 seconds wall clock time: 563 minutes 2.34 seconds (33782.34 seconds total)