Starting phenix.real_space_refine on Sat Mar 16 23:29:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qsu_4629/03_2024/6qsu_4629_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qsu_4629/03_2024/6qsu_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_4629/03_2024/6qsu_4629.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qsu_4629/03_2024/6qsu_4629.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qsu_4629/03_2024/6qsu_4629_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qsu_4629/03_2024/6qsu_4629_updated.pdb" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.010 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 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. 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: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 29.10, per 1000 atoms: 0.38 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: 24.00 Conformation dependent library (CDL) restraints added in 10.2 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: 11.48 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: 36.59 Time building geometry restraints manager: 26.20 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 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: 1.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.060 Extract box with map and model: 8.520 Check model and map are aligned: 0.850 Set scattering table: 0.520 Process input model: 164.250 Find NCS groups from input model: 3.980 Set up NCS constraints: 0.600 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 190.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 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 : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.61 % Allowed : 4.84 % Favored : 94.55 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP H 377 HIS 0.008 0.002 HIS V 248 PHE 0.019 0.002 PHE A 198 TYR 0.025 0.002 TYR K 15 ARG 0.005 0.001 ARG V 401 *********************** 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 : 6.634 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 MET cc_start: 0.7810 (mtt) cc_final: 0.7429 (mtm) REVERT: A 220 GLU cc_start: 0.7930 (mt-10) cc_final: 0.7630 (mt-10) REVERT: B 104 MET cc_start: 0.8355 (mmm) cc_final: 0.8078 (mmm) REVERT: B 353 MET cc_start: 0.8528 (mtp) cc_final: 0.8148 (mtp) REVERT: E 44 MET cc_start: 0.8622 (mtm) cc_final: 0.8402 (mtm) REVERT: E 125 LYS cc_start: 0.7670 (mmmt) cc_final: 0.7428 (mmtm) REVERT: G 12 MET cc_start: 0.8397 (tmm) cc_final: 0.8154 (tmm) REVERT: G 60 GLU cc_start: 0.8133 (tt0) cc_final: 0.7917 (tt0) REVERT: K 77 MET cc_start: 0.8627 (mtp) cc_final: 0.8383 (mtp) REVERT: K 125 LYS cc_start: 0.7917 (mmmt) cc_final: 0.7651 (mmtm) REVERT: M 71 MET cc_start: 0.8882 (mtp) cc_final: 0.8298 (mtp) REVERT: Q 71 MET cc_start: 0.8819 (mtp) cc_final: 0.8438 (mtp) REVERT: Q 203 ASP cc_start: 0.8057 (m-30) cc_final: 0.7761 (m-30) REVERT: S 71 MET cc_start: 0.8828 (mtp) cc_final: 0.8574 (mtp) REVERT: U 58 MET cc_start: 0.7988 (mtt) cc_final: 0.7746 (mtm) REVERT: U 97 HIS cc_start: 0.8241 (m90) cc_final: 0.7816 (m90) REVERT: J 12 MET cc_start: 0.8506 (mtm) cc_final: 0.8250 (mtp) REVERT: J 60 ASN cc_start: 0.8147 (m110) cc_final: 0.7933 (m110) REVERT: J 92 LYS cc_start: 0.8759 (mmtt) cc_final: 0.8545 (mptt) REVERT: J 319 MET cc_start: 0.6688 (mmm) cc_final: 0.6235 (tpp) REVERT: J 540 PRO cc_start: 0.8470 (Cg_exo) cc_final: 0.8250 (Cg_endo) REVERT: D 92 LYS cc_start: 0.8547 (mmtt) cc_final: 0.8332 (mmtp) REVERT: D 333 GLN cc_start: 0.7984 (mt0) cc_final: 0.7782 (mt0) REVERT: D 478 MET cc_start: 0.8542 (mmt) cc_final: 0.7841 (mmp) REVERT: D 548 ASP cc_start: 0.8236 (m-30) cc_final: 0.8025 (m-30) REVERT: F 65 GLU cc_start: 0.7825 (tt0) cc_final: 0.7572 (tt0) REVERT: H 65 GLU cc_start: 0.7672 (tt0) cc_final: 0.7435 (tt0) REVERT: H 182 MET cc_start: 0.8760 (mmm) cc_final: 0.8472 (mmm) REVERT: H 317 MET cc_start: 0.7844 (ttm) cc_final: 0.7529 (ttp) REVERT: H 353 MET cc_start: 0.8457 (mtp) cc_final: 0.8235 (mtp) REVERT: H 478 MET cc_start: 0.8699 (mmt) cc_final: 0.8496 (mmt) REVERT: L 262 MET cc_start: 0.8548 (mmm) cc_final: 0.8236 (mmm) REVERT: L 478 MET cc_start: 0.8714 (mmt) cc_final: 0.7620 (mmt) REVERT: N 110 ASN cc_start: 0.8543 (m-40) cc_final: 0.8250 (m-40) REVERT: N 182 MET cc_start: 0.8799 (mmm) cc_final: 0.8509 (mmm) REVERT: N 191 MET cc_start: 0.8717 (tpp) cc_final: 0.8458 (tpp) REVERT: N 276 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7597 (tm-30) REVERT: N 319 MET cc_start: 0.6773 (mmm) cc_final: 0.6239 (tpp) REVERT: N 460 MET cc_start: 0.8691 (tpp) cc_final: 0.8462 (tpp) REVERT: P 105 GLN cc_start: 0.8675 (mt0) cc_final: 0.8414 (mt0) REVERT: P 182 MET cc_start: 0.8879 (mmm) cc_final: 0.8641 (mmm) REVERT: P 276 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7352 (pm20) REVERT: P 543 TYR cc_start: 0.8845 (m-10) cc_final: 0.8642 (m-10) REVERT: R 478 MET cc_start: 0.8767 (mmt) cc_final: 0.8475 (mmp) REVERT: R 533 THR cc_start: 0.8756 (p) cc_final: 0.8550 (p) REVERT: X 182 MET cc_start: 0.8581 (mmm) cc_final: 0.8191 (mmm) REVERT: X 319 MET cc_start: 0.6742 (mmm) cc_final: 0.6461 (tpp) outliers start: 48 outliers final: 2 residues processed: 1468 average time/residue: 1.7440 time to fit residues: 3307.7171 Evaluate side-chains 1035 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1031 time to evaluate : 6.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 236 ILE Chi-restraints excluded: chain O residue 236 ILE Chi-restraints excluded: chain N residue 276 GLU Chi-restraints excluded: chain P residue 276 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 948 random chunks: chunk 800 optimal weight: 4.9990 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 U 97 HIS W 208 ASN J 383 ASN D 309 ASN 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: 0.8339 moved from start: 0.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 75888 Z= 0.161 Angle : 0.509 7.896 102348 Z= 0.276 Chirality : 0.045 0.192 11400 Planarity : 0.004 0.049 13404 Dihedral : 4.950 51.386 10366 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.95 % Allowed : 9.83 % Favored : 88.23 % 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: 1.05 (0.16), residues: 1056 loop : -0.26 (0.08), residues: 5724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 377 HIS 0.006 0.001 HIS X 248 PHE 0.014 0.001 PHE U 198 TYR 0.018 0.001 TYR G 15 ARG 0.007 0.000 ARG W 21 *********************** 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 1223 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 1069 time to evaluate : 6.553 Fit side-chains revert: symmetry clash REVERT: A 58 MET cc_start: 0.7768 (mtt) cc_final: 0.7427 (mtm) REVERT: A 80 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7608 (pt0) REVERT: A 130 LYS cc_start: 0.8205 (OUTLIER) cc_final: 0.7926 (tptm) REVERT: B 353 MET cc_start: 0.8566 (mtp) cc_final: 0.8197 (mtp) REVERT: B 550 LYS cc_start: 0.8284 (mtpp) cc_final: 0.7970 (mppt) REVERT: B 565 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8350 (tt) REVERT: C 80 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7614 (pt0) REVERT: E 125 LYS cc_start: 0.7708 (mmmt) cc_final: 0.7456 (mmtm) REVERT: G 12 MET cc_start: 0.8253 (tmm) cc_final: 0.7985 (tmm) REVERT: G 51 LYS cc_start: 0.8585 (OUTLIER) cc_final: 0.7681 (mptp) REVERT: G 60 GLU cc_start: 0.8110 (tt0) cc_final: 0.7862 (tt0) REVERT: G 80 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7477 (pt0) REVERT: K 77 MET cc_start: 0.8586 (mtp) cc_final: 0.8364 (mtp) REVERT: M 71 MET cc_start: 0.8964 (mtp) cc_final: 0.8337 (mtp) REVERT: M 130 LYS cc_start: 0.8070 (OUTLIER) cc_final: 0.7535 (ttmm) REVERT: O 125 LYS cc_start: 0.7914 (mmpt) cc_final: 0.7672 (mmtm) REVERT: Q 71 MET cc_start: 0.8823 (mtp) cc_final: 0.8464 (mtp) REVERT: Q 80 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.7448 (pt0) REVERT: Q 203 ASP cc_start: 0.8025 (m-30) cc_final: 0.7818 (m-30) REVERT: S 29 LYS cc_start: 0.8348 (OUTLIER) cc_final: 0.8010 (mtmt) REVERT: S 71 MET cc_start: 0.8804 (mtp) cc_final: 0.8540 (mtp) REVERT: S 80 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7571 (pt0) REVERT: U 209 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7667 (mp0) REVERT: W 60 GLU cc_start: 0.8060 (tt0) cc_final: 0.7847 (tt0) REVERT: W 220 GLU cc_start: 0.7674 (mt-10) cc_final: 0.7447 (mt-10) REVERT: J 1 MET cc_start: 0.6938 (OUTLIER) cc_final: 0.6088 (tmt) REVERT: J 4 ILE cc_start: 0.8361 (mm) cc_final: 0.8130 (mm) REVERT: J 12 MET cc_start: 0.8500 (mtm) cc_final: 0.8254 (mtp) REVERT: J 60 ASN cc_start: 0.8226 (m110) cc_final: 0.8001 (m110) REVERT: J 103 ASP cc_start: 0.8031 (m-30) cc_final: 0.7790 (m-30) REVERT: J 555 LYS cc_start: 0.7923 (ptpp) cc_final: 0.7615 (pttm) REVERT: D 396 ASP cc_start: 0.7420 (OUTLIER) cc_final: 0.7090 (t70) REVERT: D 548 ASP cc_start: 0.8258 (m-30) cc_final: 0.8027 (m-30) REVERT: D 565 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8508 (tt) REVERT: F 550 LYS cc_start: 0.8315 (mtpp) cc_final: 0.7890 (mtpt) REVERT: H 65 GLU cc_start: 0.7669 (tt0) cc_final: 0.7441 (tt0) REVERT: H 182 MET cc_start: 0.8854 (mmm) cc_final: 0.8613 (mmm) REVERT: H 353 MET cc_start: 0.8487 (mtp) cc_final: 0.8145 (mtp) REVERT: L 262 MET cc_start: 0.8549 (mmm) cc_final: 0.8175 (mmm) REVERT: L 478 MET cc_start: 0.8691 (mmt) cc_final: 0.8105 (mmt) REVERT: N 182 MET cc_start: 0.8857 (mmm) cc_final: 0.8552 (mmm) REVERT: N 191 MET cc_start: 0.8630 (tpp) cc_final: 0.8206 (tpp) REVERT: N 276 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7516 (tm-30) REVERT: N 317 MET cc_start: 0.7522 (ttm) cc_final: 0.6961 (ttp) REVERT: N 319 MET cc_start: 0.6641 (mmm) cc_final: 0.6170 (tpp) REVERT: N 396 ASP cc_start: 0.7481 (OUTLIER) cc_final: 0.7203 (t70) REVERT: N 537 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7252 (mm-30) REVERT: P 53 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7210 (tm-30) REVERT: P 276 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7367 (pm20) REVERT: P 317 MET cc_start: 0.7839 (ttm) cc_final: 0.7606 (ttm) REVERT: P 396 ASP cc_start: 0.7364 (OUTLIER) cc_final: 0.7057 (t70) REVERT: P 550 LYS cc_start: 0.8245 (mtpp) cc_final: 0.7983 (mtmt) REVERT: R 182 MET cc_start: 0.8907 (mmm) cc_final: 0.8594 (mmm) REVERT: R 340 ARG cc_start: 0.8372 (mtm-85) cc_final: 0.7928 (mtm-85) REVERT: R 478 MET cc_start: 0.8722 (mmt) cc_final: 0.8441 (mmp) REVERT: R 535 HIS cc_start: 0.8405 (t70) cc_final: 0.8050 (t-90) REVERT: R 550 LYS cc_start: 0.8287 (ttmm) cc_final: 0.7876 (mtpt) REVERT: R 555 LYS cc_start: 0.8322 (OUTLIER) cc_final: 0.7930 (ptpt) REVERT: T 396 ASP cc_start: 0.7470 (OUTLIER) cc_final: 0.7242 (t70) REVERT: T 550 LYS cc_start: 0.7970 (mtpp) cc_final: 0.7639 (mtmt) REVERT: V 104 MET cc_start: 0.8409 (mmm) cc_final: 0.8112 (mmm) REVERT: X 85 ASP cc_start: 0.8056 (m-30) cc_final: 0.7811 (m-30) REVERT: X 182 MET cc_start: 0.8813 (mmm) cc_final: 0.8330 (mmm) REVERT: X 319 MET cc_start: 0.6629 (mmm) cc_final: 0.6403 (tpp) REVERT: X 385 LYS cc_start: 0.8108 (mttp) cc_final: 0.7857 (mmtp) REVERT: X 478 MET cc_start: 0.8688 (mmt) cc_final: 0.7623 (mmt) REVERT: X 555 LYS cc_start: 0.8264 (OUTLIER) cc_final: 0.7832 (ptpt) outliers start: 154 outliers final: 44 residues processed: 1129 average time/residue: 1.7957 time to fit residues: 2612.4797 Evaluate side-chains 1073 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 1006 time to evaluate : 6.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 130 LYS Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain G residue 51 LYS Chi-restraints excluded: chain G residue 80 GLU Chi-restraints excluded: chain G residue 128 SER Chi-restraints excluded: chain I residue 128 SER Chi-restraints excluded: chain I residue 160 LYS Chi-restraints excluded: chain I residue 170 SER Chi-restraints excluded: chain M residue 130 LYS Chi-restraints excluded: chain O residue 128 SER Chi-restraints excluded: chain O residue 170 SER Chi-restraints excluded: chain Q residue 80 GLU Chi-restraints excluded: chain Q residue 128 SER Chi-restraints excluded: chain Q residue 136 ASP Chi-restraints excluded: chain Q residue 170 SER Chi-restraints excluded: chain S residue 29 LYS Chi-restraints excluded: chain S residue 80 GLU Chi-restraints excluded: chain S residue 170 SER Chi-restraints excluded: chain U residue 209 GLU Chi-restraints excluded: chain W residue 128 SER Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 27 ASP Chi-restraints excluded: chain J residue 316 ASP Chi-restraints excluded: chain J residue 366 MET Chi-restraints excluded: chain J residue 396 ASP Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain D residue 316 ASP Chi-restraints excluded: chain D residue 366 MET Chi-restraints excluded: chain D residue 396 ASP Chi-restraints excluded: chain D residue 469 THR Chi-restraints excluded: chain D residue 565 LEU Chi-restraints excluded: chain F residue 55 MET Chi-restraints excluded: chain F residue 396 ASP Chi-restraints excluded: chain H residue 319 MET Chi-restraints excluded: chain H residue 396 ASP Chi-restraints excluded: chain L residue 27 ASP Chi-restraints excluded: chain L residue 396 ASP Chi-restraints excluded: chain N residue 27 ASP Chi-restraints excluded: chain N residue 212 GLU Chi-restraints excluded: chain N residue 240 LYS Chi-restraints excluded: chain N residue 276 GLU Chi-restraints excluded: chain N residue 316 ASP Chi-restraints excluded: chain N residue 396 ASP Chi-restraints excluded: chain N residue 537 GLU Chi-restraints excluded: chain P residue 53 GLU Chi-restraints excluded: chain P residue 276 GLU Chi-restraints excluded: chain P residue 396 ASP Chi-restraints excluded: chain R residue 55 MET Chi-restraints excluded: chain R residue 212 GLU Chi-restraints excluded: chain R residue 396 ASP Chi-restraints excluded: chain R residue 555 LYS Chi-restraints excluded: chain T residue 240 LYS Chi-restraints excluded: chain T residue 396 ASP Chi-restraints excluded: chain T residue 477 GLU Chi-restraints excluded: chain V residue 38 ILE Chi-restraints excluded: chain V residue 276 GLU Chi-restraints excluded: chain V residue 396 ASP Chi-restraints excluded: chain X residue 396 ASP Chi-restraints excluded: chain X residue 555 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 948 random chunks: chunk 478 optimal weight: 8.9990 chunk 267 optimal weight: 9.9990 chunk 716 optimal weight: 8.9990 chunk 586 optimal weight: 0.8980 chunk 237 optimal weight: 10.0000 chunk 862 optimal weight: 7.9990 chunk 931 optimal weight: 5.9990 chunk 768 optimal weight: 1.9990 chunk 855 optimal weight: 6.9990 chunk 294 optimal weight: 0.8980 chunk 691 optimal weight: 4.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- 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 309 ASN B 539 ASN I 208 ASN W 208 ASN J 309 ASN J 383 ASN J 512 GLN D 168 ASN D 309 ASN F 34 HIS F 333 GLN F 383 ASN H 34 HIS H 309 ASN L 309 ASN L 314 HIS N 34 HIS N 168 ASN N 314 HIS P 60 ASN P 314 HIS P 333 GLN R 34 HIS R 60 ASN R 309 ASN R 383 ASN T 34 HIS T 60 ASN T 168 ASN T 309 ASN T 314 HIS V 34 HIS V 333 GLN X 309 ASN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 75888 Z= 0.286 Angle : 0.575 8.802 102348 Z= 0.311 Chirality : 0.048 0.200 11400 Planarity : 0.005 0.048 13404 Dihedral : 5.148 44.785 10362 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.12 % Allowed : 10.57 % Favored : 87.30 % 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: 0.33 (0.08), residues: 9600 helix: 1.04 (0.09), residues: 2904 sheet: 0.89 (0.16), residues: 1068 loop : -0.31 (0.08), residues: 5628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP F 377 HIS 0.008 0.001 HIS X 248 PHE 0.021 0.002 PHE A 198 TYR 0.025 0.002 TYR M 15 ARG 0.006 0.001 ARG W 21 *********************** 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 1208 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 1040 time to evaluate : 6.744 Fit side-chains REVERT: A 58 MET cc_start: 0.7816 (mtt) cc_final: 0.7361 (mtm) REVERT: A 80 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7738 (pt0) REVERT: A 130 LYS cc_start: 0.8218 (OUTLIER) cc_final: 0.7931 (tptm) REVERT: C 80 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7710 (pt0) REVERT: E 125 LYS cc_start: 0.7882 (mmmt) cc_final: 0.7637 (mmtm) REVERT: G 12 MET cc_start: 0.8201 (tmm) cc_final: 0.7950 (tmm) REVERT: G 51 LYS cc_start: 0.8637 (OUTLIER) cc_final: 0.7707 (mptp) REVERT: G 60 GLU cc_start: 0.8110 (tt0) cc_final: 0.7875 (tt0) REVERT: G 80 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7538 (pt0) REVERT: K 77 MET cc_start: 0.8550 (mtp) cc_final: 0.8324 (mtp) REVERT: K 80 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7620 (pt0) REVERT: K 125 LYS cc_start: 0.8169 (OUTLIER) cc_final: 0.7770 (mmmt) REVERT: M 71 MET cc_start: 0.8870 (mtp) cc_final: 0.8275 (mtp) REVERT: M 130 LYS cc_start: 0.8283 (OUTLIER) cc_final: 0.7797 (ttmm) REVERT: Q 60 GLU cc_start: 0.7855 (tt0) cc_final: 0.7645 (tt0) REVERT: Q 71 MET cc_start: 0.8817 (mtp) cc_final: 0.8581 (mtp) REVERT: Q 80 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.7511 (pt0) REVERT: S 29 LYS cc_start: 0.8274 (OUTLIER) cc_final: 0.7929 (mtmt) REVERT: S 71 MET cc_start: 0.8719 (mtp) cc_final: 0.8487 (mtp) REVERT: S 80 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7619 (pt0) REVERT: U 209 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7746 (tp30) REVERT: W 116 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.7179 (mm-30) REVERT: J 8 GLU cc_start: 0.7455 (OUTLIER) cc_final: 0.7230 (pt0) REVERT: J 60 ASN cc_start: 0.8297 (m110) cc_final: 0.8064 (m110) REVERT: J 103 ASP cc_start: 0.8023 (m-30) cc_final: 0.7785 (m-30) REVERT: J 254 GLU cc_start: 0.7783 (tt0) cc_final: 0.7550 (tt0) REVERT: D 537 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.7359 (mt-10) REVERT: H 65 GLU cc_start: 0.7780 (tt0) cc_final: 0.7564 (tt0) REVERT: H 182 MET cc_start: 0.8888 (mmm) cc_final: 0.8539 (mmm) REVERT: H 212 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7392 (mt-10) REVERT: H 353 MET cc_start: 0.8487 (mtp) cc_final: 0.8175 (mtp) REVERT: H 537 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.7323 (mm-30) REVERT: L 262 MET cc_start: 0.8523 (mmm) cc_final: 0.8192 (mmm) REVERT: L 366 MET cc_start: 0.7244 (ptp) cc_final: 0.6876 (ptp) REVERT: L 550 LYS cc_start: 0.8310 (mtpp) cc_final: 0.7936 (mtmt) REVERT: N 182 MET cc_start: 0.8819 (mmm) cc_final: 0.8579 (mmm) REVERT: N 276 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7543 (tm-30) REVERT: N 319 MET cc_start: 0.6715 (mmm) cc_final: 0.6190 (tpp) REVERT: N 396 ASP cc_start: 0.7592 (OUTLIER) cc_final: 0.7278 (t70) REVERT: N 537 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.7219 (mm-30) REVERT: P 276 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7305 (pm20) REVERT: P 317 MET cc_start: 0.7897 (ttm) cc_final: 0.7641 (ttm) REVERT: P 396 ASP cc_start: 0.7441 (OUTLIER) cc_final: 0.7117 (t70) REVERT: P 421 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.7246 (pt0) REVERT: P 537 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7465 (mm-30) REVERT: P 550 LYS cc_start: 0.8197 (mtpp) cc_final: 0.7923 (mtmt) REVERT: R 182 MET cc_start: 0.8861 (mmm) cc_final: 0.8546 (mmm) REVERT: R 319 MET cc_start: 0.6469 (OUTLIER) cc_final: 0.5895 (tpp) REVERT: R 340 ARG cc_start: 0.8354 (mtm-85) cc_final: 0.7988 (mtm-85) REVERT: R 478 MET cc_start: 0.8787 (mmt) cc_final: 0.8531 (mmp) REVERT: R 555 LYS cc_start: 0.8359 (OUTLIER) cc_final: 0.7945 (ptpt) REVERT: T 1 MET cc_start: 0.6730 (tmm) cc_final: 0.6494 (tmm) REVERT: T 396 ASP cc_start: 0.7540 (OUTLIER) cc_final: 0.7305 (t70) REVERT: T 550 LYS cc_start: 0.7971 (mtpp) cc_final: 0.7656 (mtmt) REVERT: T 551 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7720 (tm-30) REVERT: T 559 LYS cc_start: 0.8390 (OUTLIER) cc_final: 0.8109 (tttm) REVERT: V 537 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.7328 (mt-10) REVERT: X 319 MET cc_start: 0.6861 (mmm) cc_final: 0.6618 (tpp) REVERT: X 385 LYS cc_start: 0.8091 (mttp) cc_final: 0.7851 (mmtp) REVERT: X 555 LYS cc_start: 0.8325 (OUTLIER) cc_final: 0.7826 (ptpt) outliers start: 168 outliers final: 67 residues processed: 1113 average time/residue: 1.8125 time to fit residues: 2587.7655 Evaluate side-chains 1099 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 1001 time to evaluate : 6.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 130 LYS Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 160 LYS Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain G residue 51 LYS Chi-restraints excluded: chain G residue 80 GLU Chi-restraints excluded: chain G residue 128 SER Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain I residue 128 SER Chi-restraints excluded: chain I residue 170 SER Chi-restraints excluded: chain K residue 80 GLU Chi-restraints excluded: chain K residue 125 LYS Chi-restraints excluded: chain M residue 80 GLU Chi-restraints excluded: chain M residue 130 LYS Chi-restraints excluded: chain O residue 105 LYS Chi-restraints excluded: chain O residue 128 SER Chi-restraints excluded: chain O residue 170 SER Chi-restraints excluded: chain Q residue 80 GLU Chi-restraints excluded: chain Q residue 128 SER Chi-restraints excluded: chain Q residue 136 ASP Chi-restraints excluded: chain Q residue 170 SER Chi-restraints excluded: chain S residue 29 LYS Chi-restraints excluded: chain S residue 80 GLU Chi-restraints excluded: chain S residue 170 SER Chi-restraints excluded: chain S residue 183 SER Chi-restraints excluded: chain U residue 44 MET Chi-restraints excluded: chain U residue 183 SER Chi-restraints excluded: chain U residue 209 GLU Chi-restraints excluded: chain W residue 116 GLU Chi-restraints excluded: chain J residue 8 GLU Chi-restraints excluded: chain J residue 27 ASP Chi-restraints excluded: chain J residue 316 ASP Chi-restraints excluded: chain J residue 366 MET Chi-restraints excluded: chain J residue 396 ASP Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 396 ASP Chi-restraints excluded: chain D residue 421 GLU Chi-restraints excluded: chain D residue 469 THR Chi-restraints excluded: chain D residue 537 GLU Chi-restraints excluded: chain F residue 276 GLU Chi-restraints excluded: chain F residue 396 ASP Chi-restraints excluded: chain H residue 212 GLU Chi-restraints excluded: chain H residue 319 MET Chi-restraints excluded: chain H residue 391 LYS Chi-restraints excluded: chain H residue 396 ASP Chi-restraints excluded: chain H residue 537 GLU Chi-restraints excluded: chain L residue 27 ASP Chi-restraints excluded: chain L residue 276 GLU Chi-restraints excluded: chain L residue 316 ASP Chi-restraints excluded: chain L residue 396 ASP Chi-restraints excluded: chain N residue 27 ASP Chi-restraints excluded: chain N residue 212 GLU Chi-restraints excluded: chain N residue 240 LYS Chi-restraints excluded: chain N residue 276 GLU Chi-restraints excluded: chain N residue 316 ASP Chi-restraints excluded: chain N residue 396 ASP Chi-restraints excluded: chain N residue 421 GLU Chi-restraints excluded: chain N residue 469 THR Chi-restraints excluded: chain N residue 537 GLU Chi-restraints excluded: chain P residue 276 GLU Chi-restraints excluded: chain P residue 396 ASP Chi-restraints excluded: chain P residue 421 GLU Chi-restraints excluded: chain P residue 537 GLU Chi-restraints excluded: chain P residue 565 LEU Chi-restraints excluded: chain P residue 567 SER Chi-restraints excluded: chain R residue 55 MET Chi-restraints excluded: chain R residue 212 GLU Chi-restraints excluded: chain R residue 319 MET Chi-restraints excluded: chain R residue 391 LYS Chi-restraints excluded: chain R residue 396 ASP Chi-restraints excluded: chain R residue 517 LYS Chi-restraints excluded: chain R residue 555 LYS Chi-restraints excluded: chain R residue 565 LEU Chi-restraints excluded: chain T residue 240 LYS Chi-restraints excluded: chain T residue 396 ASP Chi-restraints excluded: chain T residue 551 GLU Chi-restraints excluded: chain T residue 559 LYS Chi-restraints excluded: chain V residue 276 GLU Chi-restraints excluded: chain V residue 338 ARG Chi-restraints excluded: chain V residue 396 ASP Chi-restraints excluded: chain V residue 421 GLU Chi-restraints excluded: chain V residue 537 GLU Chi-restraints excluded: chain V residue 565 LEU Chi-restraints excluded: chain X residue 8 GLU Chi-restraints excluded: chain X residue 236 ASP Chi-restraints excluded: chain X residue 396 ASP Chi-restraints excluded: chain X residue 555 LYS Chi-restraints excluded: chain X residue 565 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 948 random chunks: chunk 852 optimal weight: 6.9990 chunk 648 optimal weight: 9.9990 chunk 447 optimal weight: 10.0000 chunk 95 optimal weight: 7.9990 chunk 411 optimal weight: 5.9990 chunk 579 optimal weight: 2.9990 chunk 865 optimal weight: 5.9990 chunk 916 optimal weight: 7.9990 chunk 452 optimal weight: 10.0000 chunk 820 optimal weight: 0.8980 chunk 246 optimal weight: 0.7980 overall best weight: 3.3386 ------------------------------------------------------------------------------- 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 168 ASN J 309 ASN D 309 ASN F 34 HIS F 314 HIS F 333 GLN H 34 HIS H 168 ASN H 309 ASN H 539 ASN L 34 HIS L 168 ASN L 309 ASN L 314 HIS L 333 GLN N 34 HIS P 333 GLN R 34 HIS R 60 ASN T 34 HIS T 60 ASN T 314 HIS T 496 GLN V 34 HIS V 314 HIS V 333 GLN V 539 ASN X 309 ASN X 333 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1954 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= 0.308 Angle : 0.581 9.352 102348 Z= 0.315 Chirality : 0.049 0.213 11400 Planarity : 0.005 0.050 13404 Dihedral : 5.235 49.725 10362 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.35 % Allowed : 11.19 % Favored : 86.46 % 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: 0.20 (0.08), residues: 9600 helix: 0.88 (0.09), residues: 2904 sheet: 0.83 (0.16), residues: 1068 loop : -0.37 (0.08), residues: 5628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP F 377 HIS 0.008 0.001 HIS X 248 PHE 0.021 0.002 PHE A 198 TYR 0.026 0.002 TYR C 15 ARG 0.008 0.001 ARG W 21 *********************** 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 1222 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 1036 time to evaluate : 6.567 Fit side-chains REVERT: A 58 MET cc_start: 0.7803 (mtt) cc_final: 0.7372 (mtm) REVERT: A 66 LYS cc_start: 0.8196 (OUTLIER) cc_final: 0.7877 (mttm) REVERT: A 80 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7792 (pt0) REVERT: A 122 GLU cc_start: 0.7016 (OUTLIER) cc_final: 0.6774 (pm20) REVERT: A 130 LYS cc_start: 0.8186 (OUTLIER) cc_final: 0.7883 (tptm) REVERT: A 219 LYS cc_start: 0.8569 (OUTLIER) cc_final: 0.8151 (tppt) REVERT: B 537 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7380 (mt-10) REVERT: B 550 LYS cc_start: 0.8286 (mtpp) cc_final: 0.8014 (mtmt) REVERT: C 80 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7707 (pt0) REVERT: C 110 GLU cc_start: 0.8000 (tt0) cc_final: 0.7696 (tt0) REVERT: C 155 ASP cc_start: 0.8317 (t0) cc_final: 0.8107 (t0) REVERT: E 125 LYS cc_start: 0.7983 (mmmt) cc_final: 0.7758 (mmtm) REVERT: G 12 MET cc_start: 0.8201 (tmm) cc_final: 0.7968 (tmm) REVERT: G 51 LYS cc_start: 0.8650 (OUTLIER) cc_final: 0.7761 (mptp) REVERT: G 80 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7521 (pt0) REVERT: I 21 ARG cc_start: 0.7351 (OUTLIER) cc_final: 0.6895 (ttp-170) REVERT: K 77 MET cc_start: 0.8537 (mtp) cc_final: 0.8236 (mtp) REVERT: K 80 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7624 (pt0) REVERT: K 125 LYS cc_start: 0.8188 (OUTLIER) cc_final: 0.7800 (mmmt) REVERT: M 71 MET cc_start: 0.8829 (mtp) cc_final: 0.8252 (mtp) REVERT: M 130 LYS cc_start: 0.8370 (OUTLIER) cc_final: 0.7901 (ttmm) REVERT: O 72 ASP cc_start: 0.8308 (t0) cc_final: 0.7992 (t0) REVERT: Q 60 GLU cc_start: 0.7865 (tt0) cc_final: 0.7654 (tt0) REVERT: Q 71 MET cc_start: 0.8809 (mtp) cc_final: 0.8568 (mtp) REVERT: Q 80 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7568 (pt0) REVERT: S 29 LYS cc_start: 0.8282 (OUTLIER) cc_final: 0.7930 (mtmt) REVERT: S 71 MET cc_start: 0.8691 (mtp) cc_final: 0.8449 (mtp) REVERT: S 80 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7679 (pt0) REVERT: U 116 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.7119 (mm-30) REVERT: U 130 LYS cc_start: 0.8447 (OUTLIER) cc_final: 0.8206 (tmmm) REVERT: U 209 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7737 (tp30) REVERT: J 1 MET cc_start: 0.6945 (OUTLIER) cc_final: 0.6119 (tmt) REVERT: J 8 GLU cc_start: 0.7498 (OUTLIER) cc_final: 0.7273 (pt0) REVERT: J 60 ASN cc_start: 0.8322 (m110) cc_final: 0.8087 (m110) REVERT: J 103 ASP cc_start: 0.8018 (m-30) cc_final: 0.7790 (m-30) REVERT: J 254 GLU cc_start: 0.7785 (tt0) cc_final: 0.7569 (tt0) REVERT: D 1 MET cc_start: 0.6706 (tmm) cc_final: 0.6290 (tmm) REVERT: D 537 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.7365 (mt-10) REVERT: D 565 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8631 (tt) REVERT: F 550 LYS cc_start: 0.8263 (mtpp) cc_final: 0.7898 (mtpt) REVERT: H 65 GLU cc_start: 0.7742 (tt0) cc_final: 0.7528 (tt0) REVERT: H 98 LYS cc_start: 0.8004 (OUTLIER) cc_final: 0.6962 (tttm) REVERT: H 182 MET cc_start: 0.8893 (mmm) cc_final: 0.8508 (mmm) REVERT: H 319 MET cc_start: 0.6991 (OUTLIER) cc_final: 0.6755 (mpt) REVERT: H 353 MET cc_start: 0.8485 (mtp) cc_final: 0.8209 (mtp) REVERT: H 537 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.7327 (mm-30) REVERT: L 262 MET cc_start: 0.8490 (mmm) cc_final: 0.8288 (mmm) REVERT: L 340 ARG cc_start: 0.8398 (mtm-85) cc_final: 0.8119 (mtm180) REVERT: L 366 MET cc_start: 0.7182 (ptp) cc_final: 0.6778 (ptp) REVERT: L 478 MET cc_start: 0.8704 (mmt) cc_final: 0.8026 (mmt) REVERT: L 550 LYS cc_start: 0.8271 (mtpp) cc_final: 0.7909 (mtmt) REVERT: N 182 MET cc_start: 0.8802 (mmm) cc_final: 0.8544 (mmm) REVERT: N 276 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7593 (tm-30) REVERT: N 319 MET cc_start: 0.6668 (mmm) cc_final: 0.6084 (tpp) REVERT: N 396 ASP cc_start: 0.7585 (OUTLIER) cc_final: 0.7252 (t70) REVERT: N 537 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.7100 (mm-30) REVERT: P 98 LYS cc_start: 0.7957 (OUTLIER) cc_final: 0.6751 (tmtm) REVERT: P 276 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7276 (pm20) REVERT: P 396 ASP cc_start: 0.7484 (OUTLIER) cc_final: 0.7158 (t70) REVERT: P 421 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7259 (pt0) REVERT: P 537 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7429 (mm-30) REVERT: P 550 LYS cc_start: 0.8210 (mtpp) cc_final: 0.7960 (mtmt) REVERT: R 98 LYS cc_start: 0.7944 (OUTLIER) cc_final: 0.7516 (tptp) REVERT: R 182 MET cc_start: 0.8861 (mmm) cc_final: 0.8533 (mmm) REVERT: R 319 MET cc_start: 0.6619 (OUTLIER) cc_final: 0.6053 (tpp) REVERT: R 478 MET cc_start: 0.8776 (mmt) cc_final: 0.8497 (mmp) REVERT: R 537 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7308 (mt-10) REVERT: R 555 LYS cc_start: 0.8337 (OUTLIER) cc_final: 0.7936 (ptpt) REVERT: T 1 MET cc_start: 0.6779 (tmm) cc_final: 0.6482 (tmm) REVERT: T 396 ASP cc_start: 0.7554 (OUTLIER) cc_final: 0.7291 (t70) REVERT: T 551 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7749 (tm-30) REVERT: T 559 LYS cc_start: 0.8353 (OUTLIER) cc_final: 0.8060 (tttm) REVERT: V 537 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7336 (mt-10) REVERT: X 385 LYS cc_start: 0.8096 (mttp) cc_final: 0.7837 (mmtp) REVERT: X 555 LYS cc_start: 0.8374 (OUTLIER) cc_final: 0.7828 (ptpt) REVERT: X 559 LYS cc_start: 0.8309 (OUTLIER) cc_final: 0.8017 (tttp) outliers start: 186 outliers final: 85 residues processed: 1113 average time/residue: 1.7930 time to fit residues: 2566.4290 Evaluate side-chains 1130 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 1001 time to evaluate : 6.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ARG Chi-restraints excluded: chain A residue 66 LYS Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 130 LYS Chi-restraints excluded: chain A residue 219 LYS Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 503 ILE Chi-restraints excluded: chain B residue 537 GLU Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain G residue 51 LYS Chi-restraints excluded: chain G residue 80 GLU Chi-restraints excluded: chain G residue 128 SER Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 183 SER Chi-restraints excluded: chain I residue 21 ARG Chi-restraints excluded: chain I residue 128 SER Chi-restraints excluded: chain I residue 160 LYS Chi-restraints excluded: chain I residue 170 SER Chi-restraints excluded: chain K residue 80 GLU Chi-restraints excluded: chain K residue 125 LYS Chi-restraints excluded: chain M residue 80 GLU Chi-restraints excluded: chain M residue 130 LYS Chi-restraints excluded: chain O residue 128 SER Chi-restraints excluded: chain O residue 132 LYS Chi-restraints excluded: chain O residue 170 SER Chi-restraints excluded: chain Q residue 68 ASP Chi-restraints excluded: chain Q residue 80 GLU Chi-restraints excluded: chain Q residue 128 SER Chi-restraints excluded: chain Q residue 136 ASP Chi-restraints excluded: chain Q residue 170 SER Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 29 LYS Chi-restraints excluded: chain S residue 80 GLU Chi-restraints excluded: chain S residue 128 SER Chi-restraints excluded: chain S residue 170 SER Chi-restraints excluded: chain S residue 183 SER Chi-restraints excluded: chain U residue 44 MET Chi-restraints excluded: chain U residue 116 GLU Chi-restraints excluded: chain U residue 130 LYS Chi-restraints excluded: chain U residue 183 SER Chi-restraints excluded: chain U residue 209 GLU Chi-restraints excluded: chain W residue 128 SER Chi-restraints excluded: chain W residue 183 SER Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 8 GLU Chi-restraints excluded: chain J residue 27 ASP Chi-restraints excluded: chain J residue 316 ASP Chi-restraints excluded: chain J residue 319 MET Chi-restraints excluded: chain J residue 396 ASP Chi-restraints excluded: chain J residue 433 ASP Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain D residue 316 ASP Chi-restraints excluded: chain D residue 396 ASP Chi-restraints excluded: chain D residue 421 GLU Chi-restraints excluded: chain D residue 469 THR Chi-restraints excluded: chain D residue 537 GLU Chi-restraints excluded: chain D residue 565 LEU Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 276 GLU Chi-restraints excluded: chain F residue 316 ASP Chi-restraints excluded: chain F residue 396 ASP Chi-restraints excluded: chain H residue 27 ASP Chi-restraints excluded: chain H residue 98 LYS Chi-restraints excluded: chain H residue 319 MET Chi-restraints excluded: chain H residue 391 LYS Chi-restraints excluded: chain H residue 396 ASP Chi-restraints excluded: chain H residue 537 GLU Chi-restraints excluded: chain L residue 27 ASP Chi-restraints excluded: chain L residue 60 ASN Chi-restraints excluded: chain L residue 276 GLU Chi-restraints excluded: chain L residue 316 ASP Chi-restraints excluded: chain L residue 396 ASP Chi-restraints excluded: chain N residue 27 ASP Chi-restraints excluded: chain N residue 212 GLU Chi-restraints excluded: chain N residue 240 LYS Chi-restraints excluded: chain N residue 276 GLU Chi-restraints excluded: chain N residue 316 ASP Chi-restraints excluded: chain N residue 396 ASP Chi-restraints excluded: chain N residue 421 GLU Chi-restraints excluded: chain N residue 444 VAL Chi-restraints excluded: chain N residue 469 THR Chi-restraints excluded: chain N residue 537 GLU Chi-restraints excluded: chain P residue 51 LEU Chi-restraints excluded: chain P residue 98 LYS Chi-restraints excluded: chain P residue 276 GLU Chi-restraints excluded: chain P residue 366 MET Chi-restraints excluded: chain P residue 396 ASP Chi-restraints excluded: chain P residue 421 GLU Chi-restraints excluded: chain P residue 537 GLU Chi-restraints excluded: chain P residue 559 LYS Chi-restraints excluded: chain P residue 565 LEU Chi-restraints excluded: chain R residue 8 GLU Chi-restraints excluded: chain R residue 55 MET Chi-restraints excluded: chain R residue 98 LYS Chi-restraints excluded: chain R residue 212 GLU Chi-restraints excluded: chain R residue 319 MET Chi-restraints excluded: chain R residue 391 LYS Chi-restraints excluded: chain R residue 396 ASP Chi-restraints excluded: chain R residue 517 LYS Chi-restraints excluded: chain R residue 537 GLU Chi-restraints excluded: chain R residue 555 LYS Chi-restraints excluded: chain R residue 565 LEU Chi-restraints excluded: chain T residue 240 LYS Chi-restraints excluded: chain T residue 396 ASP Chi-restraints excluded: chain T residue 421 GLU Chi-restraints excluded: chain T residue 477 GLU Chi-restraints excluded: chain T residue 551 GLU Chi-restraints excluded: chain T residue 559 LYS Chi-restraints excluded: chain V residue 38 ILE Chi-restraints excluded: chain V residue 276 GLU Chi-restraints excluded: chain V residue 319 MET Chi-restraints excluded: chain V residue 396 ASP Chi-restraints excluded: chain V residue 537 GLU Chi-restraints excluded: chain V residue 565 LEU Chi-restraints excluded: chain X residue 8 GLU Chi-restraints excluded: chain X residue 236 ASP Chi-restraints excluded: chain X residue 396 ASP Chi-restraints excluded: chain X residue 555 LYS Chi-restraints excluded: chain X residue 559 LYS Chi-restraints excluded: chain X residue 565 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 948 random chunks: chunk 763 optimal weight: 3.9990 chunk 520 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 682 optimal weight: 1.9990 chunk 378 optimal weight: 9.9990 chunk 781 optimal weight: 0.7980 chunk 633 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 467 optimal weight: 1.9990 chunk 822 optimal weight: 0.9990 chunk 231 optimal weight: 7.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 HIS B 512 GLN B 539 ASN W 208 ASN J 309 ASN D 309 ASN D 512 GLN F 34 HIS F 314 HIS F 333 GLN F 383 ASN F 512 GLN H 34 HIS H 309 ASN H 512 GLN L 34 HIS L 309 ASN L 314 HIS L 333 GLN L 512 GLN N 34 HIS N 512 GLN P 333 GLN R 34 HIS R 60 ASN T 34 HIS T 60 ASN T 314 HIS V 34 HIS V 168 ASN V 314 HIS V 333 GLN V 544 HIS X 309 ASN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.2066 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 : 0.511 8.409 102348 Z= 0.277 Chirality : 0.045 0.208 11400 Planarity : 0.004 0.049 13404 Dihedral : 4.992 53.298 10362 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.01 % Allowed : 12.11 % Favored : 85.88 % 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: 0.33 (0.08), residues: 9600 helix: 1.14 (0.10), residues: 2892 sheet: 0.70 (0.16), residues: 972 loop : -0.31 (0.08), residues: 5736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP P 181 HIS 0.006 0.001 HIS X 248 PHE 0.019 0.001 PHE O 198 TYR 0.022 0.002 TYR G 15 ARG 0.008 0.000 ARG W 21 *********************** 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 1193 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 1034 time to evaluate : 6.790 Fit side-chains REVERT: A 58 MET cc_start: 0.7733 (mtt) cc_final: 0.7311 (mtm) REVERT: A 66 LYS cc_start: 0.8197 (OUTLIER) cc_final: 0.7873 (mttm) REVERT: A 80 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7760 (pt0) REVERT: A 130 LYS cc_start: 0.8154 (OUTLIER) cc_final: 0.7851 (tptm) REVERT: B 550 LYS cc_start: 0.8255 (mtpp) cc_final: 0.8017 (mtmt) REVERT: C 80 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.7722 (pt0) REVERT: C 110 GLU cc_start: 0.7968 (tt0) cc_final: 0.7666 (tt0) REVERT: C 155 ASP cc_start: 0.8306 (t0) cc_final: 0.8077 (t0) REVERT: E 125 LYS cc_start: 0.7903 (mmmt) cc_final: 0.7682 (mmtm) REVERT: G 51 LYS cc_start: 0.8639 (OUTLIER) cc_final: 0.7755 (mptp) REVERT: G 80 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7495 (pt0) REVERT: I 21 ARG cc_start: 0.7330 (OUTLIER) cc_final: 0.6968 (ttp-170) REVERT: K 77 MET cc_start: 0.8531 (mtp) cc_final: 0.8254 (mtp) REVERT: K 80 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7611 (pt0) REVERT: K 125 LYS cc_start: 0.8222 (OUTLIER) cc_final: 0.7809 (mmmt) REVERT: M 71 MET cc_start: 0.8831 (mtp) cc_final: 0.8142 (mtp) REVERT: M 80 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7609 (pt0) REVERT: M 130 LYS cc_start: 0.8331 (OUTLIER) cc_final: 0.7852 (ttmm) REVERT: O 72 ASP cc_start: 0.8247 (t0) cc_final: 0.7912 (t0) REVERT: Q 60 GLU cc_start: 0.7873 (tt0) cc_final: 0.7635 (tt0) REVERT: Q 71 MET cc_start: 0.8817 (mtp) cc_final: 0.8542 (mtp) REVERT: Q 80 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7549 (pt0) REVERT: S 21 ARG cc_start: 0.7764 (ttp80) cc_final: 0.7474 (tmm160) REVERT: S 29 LYS cc_start: 0.8237 (OUTLIER) cc_final: 0.7899 (mtmt) REVERT: U 58 MET cc_start: 0.7923 (mtt) cc_final: 0.7696 (mtm) REVERT: U 116 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7110 (mm-30) REVERT: U 209 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7777 (tp30) REVERT: J 1 MET cc_start: 0.6905 (OUTLIER) cc_final: 0.6081 (tmt) REVERT: J 8 GLU cc_start: 0.7421 (OUTLIER) cc_final: 0.7213 (pt0) REVERT: J 60 ASN cc_start: 0.8313 (m110) cc_final: 0.8084 (m110) REVERT: J 85 ASP cc_start: 0.7598 (m-30) cc_final: 0.7324 (m-30) REVERT: J 103 ASP cc_start: 0.7962 (m-30) cc_final: 0.7738 (m-30) REVERT: J 254 GLU cc_start: 0.7746 (tt0) cc_final: 0.7529 (tt0) REVERT: D 565 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8537 (tt) REVERT: F 1 MET cc_start: 0.6807 (OUTLIER) cc_final: 0.6187 (tmt) REVERT: F 550 LYS cc_start: 0.8230 (mtpp) cc_final: 0.7856 (mtpt) REVERT: H 65 GLU cc_start: 0.7736 (tt0) cc_final: 0.7516 (tt0) REVERT: H 182 MET cc_start: 0.8898 (mmm) cc_final: 0.8583 (mmm) REVERT: H 311 GLU cc_start: 0.7519 (OUTLIER) cc_final: 0.6817 (tt0) REVERT: H 319 MET cc_start: 0.6934 (OUTLIER) cc_final: 0.6708 (mpt) REVERT: H 353 MET cc_start: 0.8466 (mtp) cc_final: 0.8152 (mtp) REVERT: H 537 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7319 (mm-30) REVERT: L 262 MET cc_start: 0.8495 (mmm) cc_final: 0.8190 (mmm) REVERT: L 340 ARG cc_start: 0.8339 (mtm-85) cc_final: 0.8083 (mtm180) REVERT: L 366 MET cc_start: 0.7070 (ptp) cc_final: 0.6587 (ptp) REVERT: L 478 MET cc_start: 0.8645 (mmt) cc_final: 0.8353 (mmt) REVERT: L 550 LYS cc_start: 0.8237 (mtpp) cc_final: 0.7910 (mtmt) REVERT: L 555 LYS cc_start: 0.8268 (ptpt) cc_final: 0.7874 (mttt) REVERT: N 182 MET cc_start: 0.8820 (mmm) cc_final: 0.8505 (mmm) REVERT: N 319 MET cc_start: 0.6635 (mmm) cc_final: 0.6081 (tpp) REVERT: N 396 ASP cc_start: 0.7550 (OUTLIER) cc_final: 0.7252 (t70) REVERT: N 537 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.7167 (mm-30) REVERT: P 276 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7243 (pm20) REVERT: P 396 ASP cc_start: 0.7461 (OUTLIER) cc_final: 0.7142 (t70) REVERT: P 421 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.7235 (pt0) REVERT: P 550 LYS cc_start: 0.8144 (mtpp) cc_final: 0.7913 (mtmt) REVERT: R 27 ASP cc_start: 0.7838 (OUTLIER) cc_final: 0.7618 (m-30) REVERT: R 182 MET cc_start: 0.8862 (mmm) cc_final: 0.8581 (mmm) REVERT: R 319 MET cc_start: 0.6557 (OUTLIER) cc_final: 0.6020 (tpp) REVERT: R 478 MET cc_start: 0.8713 (mmt) cc_final: 0.8335 (mmp) REVERT: R 537 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.7225 (mt-10) REVERT: R 555 LYS cc_start: 0.8332 (OUTLIER) cc_final: 0.7957 (ptpt) REVERT: T 1 MET cc_start: 0.6665 (tmm) cc_final: 0.6344 (tmm) REVERT: T 396 ASP cc_start: 0.7547 (OUTLIER) cc_final: 0.7288 (t70) REVERT: X 478 MET cc_start: 0.8731 (mmt) cc_final: 0.7855 (mmt) REVERT: X 555 LYS cc_start: 0.8264 (OUTLIER) cc_final: 0.7742 (ptpt) outliers start: 159 outliers final: 75 residues processed: 1098 average time/residue: 1.8508 time to fit residues: 2629.3001 Evaluate side-chains 1127 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 1019 time to evaluate : 6.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ARG Chi-restraints excluded: chain A residue 66 LYS Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 130 LYS Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 503 ILE Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain G residue 51 LYS Chi-restraints excluded: chain G residue 80 GLU Chi-restraints excluded: chain G residue 128 SER Chi-restraints excluded: chain I residue 21 ARG Chi-restraints excluded: chain I residue 128 SER Chi-restraints excluded: chain I residue 170 SER Chi-restraints excluded: chain K residue 80 GLU Chi-restraints excluded: chain K residue 125 LYS Chi-restraints excluded: chain M residue 80 GLU Chi-restraints excluded: chain M residue 130 LYS Chi-restraints excluded: chain O residue 125 LYS Chi-restraints excluded: chain O residue 128 SER Chi-restraints excluded: chain O residue 170 SER Chi-restraints excluded: chain Q residue 68 ASP Chi-restraints excluded: chain Q residue 80 GLU Chi-restraints excluded: chain Q residue 128 SER Chi-restraints excluded: chain Q residue 170 SER Chi-restraints excluded: chain S residue 29 LYS Chi-restraints excluded: chain S residue 128 SER Chi-restraints excluded: chain S residue 170 SER Chi-restraints excluded: chain U residue 44 MET Chi-restraints excluded: chain U residue 116 GLU Chi-restraints excluded: chain U residue 183 SER Chi-restraints excluded: chain U residue 209 GLU Chi-restraints excluded: chain W residue 128 SER Chi-restraints excluded: chain W residue 183 SER Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 8 GLU Chi-restraints excluded: chain J residue 27 ASP Chi-restraints excluded: chain J residue 316 ASP Chi-restraints excluded: chain J residue 366 MET Chi-restraints excluded: chain J residue 396 ASP Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 316 ASP Chi-restraints excluded: chain D residue 396 ASP Chi-restraints excluded: chain D residue 421 GLU Chi-restraints excluded: chain D residue 469 THR Chi-restraints excluded: chain D residue 565 LEU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 55 MET Chi-restraints excluded: chain F residue 316 ASP Chi-restraints excluded: chain F residue 396 ASP Chi-restraints excluded: chain H residue 27 ASP Chi-restraints excluded: chain H residue 311 GLU Chi-restraints excluded: chain H residue 319 MET Chi-restraints excluded: chain H residue 391 LYS Chi-restraints excluded: chain H residue 396 ASP Chi-restraints excluded: chain H residue 421 GLU Chi-restraints excluded: chain H residue 537 GLU Chi-restraints excluded: chain L residue 27 ASP Chi-restraints excluded: chain L residue 60 ASN Chi-restraints excluded: chain L residue 276 GLU Chi-restraints excluded: chain L residue 316 ASP Chi-restraints excluded: chain L residue 396 ASP Chi-restraints excluded: chain N residue 27 ASP Chi-restraints excluded: chain N residue 212 GLU Chi-restraints excluded: chain N residue 240 LYS Chi-restraints excluded: chain N residue 316 ASP Chi-restraints excluded: chain N residue 396 ASP Chi-restraints excluded: chain N residue 421 GLU Chi-restraints excluded: chain N residue 444 VAL Chi-restraints excluded: chain N residue 469 THR Chi-restraints excluded: chain N residue 537 GLU Chi-restraints excluded: chain P residue 51 LEU Chi-restraints excluded: chain P residue 276 GLU Chi-restraints excluded: chain P residue 366 MET Chi-restraints excluded: chain P residue 396 ASP Chi-restraints excluded: chain P residue 421 GLU Chi-restraints excluded: chain P residue 477 GLU Chi-restraints excluded: chain P residue 565 LEU Chi-restraints excluded: chain R residue 27 ASP Chi-restraints excluded: chain R residue 212 GLU Chi-restraints excluded: chain R residue 319 MET Chi-restraints excluded: chain R residue 396 ASP Chi-restraints excluded: chain R residue 517 LYS Chi-restraints excluded: chain R residue 537 GLU Chi-restraints excluded: chain R residue 555 LYS Chi-restraints excluded: chain R residue 565 LEU Chi-restraints excluded: chain T residue 240 LYS Chi-restraints excluded: chain T residue 396 ASP Chi-restraints excluded: chain T residue 421 GLU Chi-restraints excluded: chain T residue 477 GLU Chi-restraints excluded: chain V residue 51 LEU Chi-restraints excluded: chain V residue 314 HIS Chi-restraints excluded: chain V residue 338 ARG Chi-restraints excluded: chain V residue 396 ASP Chi-restraints excluded: chain V residue 421 GLU Chi-restraints excluded: chain V residue 444 VAL Chi-restraints excluded: chain V residue 565 LEU Chi-restraints excluded: chain X residue 8 GLU Chi-restraints excluded: chain X residue 236 ASP Chi-restraints excluded: chain X residue 396 ASP Chi-restraints excluded: chain X residue 555 LYS Chi-restraints excluded: chain X residue 565 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 948 random chunks: chunk 308 optimal weight: 0.0060 chunk 825 optimal weight: 4.9990 chunk 181 optimal weight: 10.0000 chunk 538 optimal weight: 5.9990 chunk 226 optimal weight: 5.9990 chunk 917 optimal weight: 1.9990 chunk 761 optimal weight: 1.9990 chunk 424 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 303 optimal weight: 6.9990 chunk 481 optimal weight: 2.9990 overall best weight: 2.0004 ------------------------------------------------------------------------------- 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 314 HIS F 333 GLN F 383 ASN H 34 HIS H 136 HIS 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 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 314 HIS V 333 GLN V 544 HIS X 168 ASN X 309 ASN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 75888 Z= 0.211 Angle : 0.521 8.784 102348 Z= 0.282 Chirality : 0.046 0.213 11400 Planarity : 0.004 0.048 13404 Dihedral : 4.930 44.637 10359 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.23 % Allowed : 12.47 % Favored : 85.31 % 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: 0.35 (0.08), residues: 9600 helix: 1.15 (0.10), residues: 2892 sheet: 0.80 (0.15), residues: 1140 loop : -0.35 (0.08), residues: 5568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP P 181 HIS 0.006 0.001 HIS X 248 PHE 0.019 0.001 PHE A 198 TYR 0.023 0.002 TYR I 15 ARG 0.008 0.000 ARG O 21 *********************** 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 1206 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 1030 time to evaluate : 6.701 Fit side-chains REVERT: A 58 MET cc_start: 0.7785 (mtt) cc_final: 0.7362 (mtm) REVERT: A 66 LYS cc_start: 0.8236 (OUTLIER) cc_final: 0.7914 (mttm) REVERT: A 80 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7756 (pt0) REVERT: A 130 LYS cc_start: 0.8155 (OUTLIER) cc_final: 0.7851 (tptm) REVERT: A 219 LYS cc_start: 0.8553 (OUTLIER) cc_final: 0.8134 (tppt) REVERT: B 550 LYS cc_start: 0.8245 (mtpp) cc_final: 0.8029 (mtmt) REVERT: C 80 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7711 (pt0) REVERT: C 110 GLU cc_start: 0.7956 (tt0) cc_final: 0.7639 (tt0) REVERT: C 155 ASP cc_start: 0.8314 (t0) cc_final: 0.8088 (t0) REVERT: E 125 LYS cc_start: 0.7924 (mmmt) cc_final: 0.7641 (mmtm) REVERT: G 51 LYS cc_start: 0.8636 (OUTLIER) cc_final: 0.7754 (mptp) REVERT: G 80 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7498 (pt0) REVERT: I 21 ARG cc_start: 0.7414 (OUTLIER) cc_final: 0.7008 (ttp-170) REVERT: I 58 MET cc_start: 0.7966 (mtm) cc_final: 0.7716 (mtm) REVERT: K 77 MET cc_start: 0.8521 (mtp) cc_final: 0.8237 (mtp) REVERT: K 80 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.7621 (pt0) REVERT: K 125 LYS cc_start: 0.8265 (OUTLIER) cc_final: 0.7842 (mmmt) REVERT: M 21 ARG cc_start: 0.7462 (OUTLIER) cc_final: 0.7241 (tmm160) REVERT: M 71 MET cc_start: 0.8808 (mtp) cc_final: 0.8112 (mtp) REVERT: M 80 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7612 (pt0) REVERT: M 130 LYS cc_start: 0.8336 (OUTLIER) cc_final: 0.7861 (ttmm) REVERT: Q 58 MET cc_start: 0.7980 (mtm) cc_final: 0.7768 (mtt) REVERT: Q 60 GLU cc_start: 0.7876 (tt0) cc_final: 0.7640 (tt0) REVERT: Q 71 MET cc_start: 0.8810 (mtp) cc_final: 0.8538 (mtp) REVERT: Q 80 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.7551 (pt0) REVERT: Q 134 VAL cc_start: 0.8097 (OUTLIER) cc_final: 0.7886 (t) REVERT: S 21 ARG cc_start: 0.7764 (ttp80) cc_final: 0.7496 (tmm160) REVERT: S 29 LYS cc_start: 0.8240 (OUTLIER) cc_final: 0.7892 (mtmt) REVERT: U 116 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.7113 (mm-30) REVERT: U 209 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7877 (tp30) REVERT: J 1 MET cc_start: 0.6904 (OUTLIER) cc_final: 0.6085 (tmt) REVERT: J 8 GLU cc_start: 0.7453 (OUTLIER) cc_final: 0.7236 (pt0) REVERT: J 51 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8109 (tt) REVERT: J 60 ASN cc_start: 0.8290 (m110) cc_final: 0.8052 (m110) REVERT: J 85 ASP cc_start: 0.7707 (m-30) cc_final: 0.7411 (m-30) REVERT: J 98 LYS cc_start: 0.8040 (OUTLIER) cc_final: 0.7818 (tmtt) REVERT: J 103 ASP cc_start: 0.7956 (m-30) cc_final: 0.7729 (m-30) REVERT: J 550 LYS cc_start: 0.8244 (mtpp) cc_final: 0.7879 (mtpt) REVERT: D 565 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8554 (tt) REVERT: F 550 LYS cc_start: 0.8225 (mtpp) cc_final: 0.7863 (mtpt) REVERT: H 65 GLU cc_start: 0.7734 (tt0) cc_final: 0.7512 (tt0) REVERT: H 98 LYS cc_start: 0.7973 (OUTLIER) cc_final: 0.6924 (tttm) REVERT: H 182 MET cc_start: 0.8897 (mmm) cc_final: 0.8574 (mmm) REVERT: H 311 GLU cc_start: 0.7526 (OUTLIER) cc_final: 0.6833 (tt0) REVERT: H 319 MET cc_start: 0.6932 (OUTLIER) cc_final: 0.6710 (mpt) REVERT: H 353 MET cc_start: 0.8455 (mtp) cc_final: 0.8132 (mtp) REVERT: H 537 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.7326 (mm-30) REVERT: L 262 MET cc_start: 0.8505 (mmm) cc_final: 0.8212 (mmm) REVERT: L 340 ARG cc_start: 0.8328 (mtm-85) cc_final: 0.8083 (mtm180) REVERT: L 366 MET cc_start: 0.7076 (ptp) cc_final: 0.6567 (ptp) REVERT: L 478 MET cc_start: 0.8658 (mmt) cc_final: 0.8291 (mmt) REVERT: L 550 LYS cc_start: 0.8260 (mtpp) cc_final: 0.7940 (mtmt) REVERT: L 555 LYS cc_start: 0.8263 (ptpt) cc_final: 0.7883 (mttt) REVERT: N 182 MET cc_start: 0.8808 (mmm) cc_final: 0.8509 (mmm) REVERT: N 319 MET cc_start: 0.6649 (mmm) cc_final: 0.6088 (tpp) REVERT: N 396 ASP cc_start: 0.7517 (OUTLIER) cc_final: 0.7206 (t70) REVERT: N 537 GLU cc_start: 0.7539 (OUTLIER) cc_final: 0.7108 (mm-30) REVERT: P 276 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7234 (pm20) REVERT: P 319 MET cc_start: 0.6953 (OUTLIER) cc_final: 0.6665 (mpp) REVERT: P 396 ASP cc_start: 0.7463 (OUTLIER) cc_final: 0.7141 (t70) REVERT: P 421 GLU cc_start: 0.7590 (OUTLIER) cc_final: 0.7234 (pt0) REVERT: P 550 LYS cc_start: 0.8141 (mtpp) cc_final: 0.7932 (mtmt) REVERT: R 182 MET cc_start: 0.8853 (mmm) cc_final: 0.8575 (mmm) REVERT: R 319 MET cc_start: 0.6655 (OUTLIER) cc_final: 0.6090 (tpp) REVERT: R 478 MET cc_start: 0.8711 (mmt) cc_final: 0.8343 (mmp) REVERT: R 537 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.7231 (mt-10) REVERT: T 1 MET cc_start: 0.6667 (tmm) cc_final: 0.6338 (tmm) REVERT: T 98 LYS cc_start: 0.8124 (OUTLIER) cc_final: 0.7765 (tmtm) REVERT: T 396 ASP cc_start: 0.7552 (OUTLIER) cc_final: 0.7289 (t70) REVERT: X 385 LYS cc_start: 0.8011 (mttp) cc_final: 0.7808 (mmtp) REVERT: X 555 LYS cc_start: 0.8292 (OUTLIER) cc_final: 0.7766 (ptpt) outliers start: 176 outliers final: 88 residues processed: 1106 average time/residue: 1.7711 time to fit residues: 2526.8761 Evaluate side-chains 1144 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 1018 time to evaluate : 6.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 62 ARG Chi-restraints excluded: chain A residue 66 LYS Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 130 LYS Chi-restraints excluded: chain A residue 219 LYS Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 503 ILE Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain G residue 51 LYS Chi-restraints excluded: chain G residue 80 GLU Chi-restraints excluded: chain G residue 128 SER Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 183 SER Chi-restraints excluded: chain I residue 21 ARG Chi-restraints excluded: chain I residue 128 SER Chi-restraints excluded: chain I residue 170 SER Chi-restraints excluded: chain I residue 183 SER Chi-restraints excluded: chain K residue 80 GLU Chi-restraints excluded: chain K residue 125 LYS Chi-restraints excluded: chain M residue 21 ARG Chi-restraints excluded: chain M residue 80 GLU Chi-restraints excluded: chain M residue 130 LYS Chi-restraints excluded: chain O residue 44 MET Chi-restraints excluded: chain O residue 128 SER Chi-restraints excluded: chain O residue 170 SER Chi-restraints excluded: chain Q residue 68 ASP Chi-restraints excluded: chain Q residue 80 GLU Chi-restraints excluded: chain Q residue 128 SER Chi-restraints excluded: chain Q residue 134 VAL Chi-restraints excluded: chain Q residue 136 ASP Chi-restraints excluded: chain Q residue 170 SER Chi-restraints excluded: chain S residue 29 LYS Chi-restraints excluded: chain S residue 128 SER Chi-restraints excluded: chain S residue 170 SER Chi-restraints excluded: chain U residue 44 MET Chi-restraints excluded: chain U residue 116 GLU Chi-restraints excluded: chain U residue 183 SER Chi-restraints excluded: chain U residue 209 GLU Chi-restraints excluded: chain W residue 128 SER Chi-restraints excluded: chain W residue 183 SER Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 8 GLU Chi-restraints excluded: chain J residue 27 ASP Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain J residue 98 LYS Chi-restraints excluded: chain J residue 316 ASP Chi-restraints excluded: chain J residue 366 MET Chi-restraints excluded: chain J residue 396 ASP Chi-restraints excluded: chain J residue 433 ASP Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 316 ASP Chi-restraints excluded: chain D residue 396 ASP Chi-restraints excluded: chain D residue 421 GLU Chi-restraints excluded: chain D residue 469 THR Chi-restraints excluded: chain D residue 565 LEU Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 316 ASP Chi-restraints excluded: chain F residue 396 ASP Chi-restraints excluded: chain H residue 27 ASP Chi-restraints excluded: chain H residue 98 LYS Chi-restraints excluded: chain H residue 311 GLU Chi-restraints excluded: chain H residue 319 MET Chi-restraints excluded: chain H residue 391 LYS Chi-restraints excluded: chain H residue 396 ASP Chi-restraints excluded: chain H residue 537 GLU Chi-restraints excluded: chain L residue 27 ASP Chi-restraints excluded: chain L residue 60 ASN Chi-restraints excluded: chain L residue 276 GLU Chi-restraints excluded: chain L residue 316 ASP Chi-restraints excluded: chain L residue 396 ASP Chi-restraints excluded: chain N residue 27 ASP Chi-restraints excluded: chain N residue 212 GLU Chi-restraints excluded: chain N residue 240 LYS Chi-restraints excluded: chain N residue 316 ASP Chi-restraints excluded: chain N residue 366 MET Chi-restraints excluded: chain N residue 396 ASP Chi-restraints excluded: chain N residue 421 GLU Chi-restraints excluded: chain N residue 444 VAL Chi-restraints excluded: chain N residue 469 THR Chi-restraints excluded: chain N residue 537 GLU Chi-restraints excluded: chain P residue 51 LEU Chi-restraints excluded: chain P residue 276 GLU Chi-restraints excluded: chain P residue 319 MET Chi-restraints excluded: chain P residue 366 MET Chi-restraints excluded: chain P residue 396 ASP Chi-restraints excluded: chain P residue 421 GLU Chi-restraints excluded: chain P residue 477 GLU Chi-restraints excluded: chain P residue 565 LEU Chi-restraints excluded: chain R residue 37 THR Chi-restraints excluded: chain R residue 212 GLU Chi-restraints excluded: chain R residue 319 MET Chi-restraints excluded: chain R residue 391 LYS Chi-restraints excluded: chain R residue 396 ASP Chi-restraints excluded: chain R residue 517 LYS Chi-restraints excluded: chain R residue 537 GLU Chi-restraints excluded: chain R residue 565 LEU Chi-restraints excluded: chain T residue 51 LEU Chi-restraints excluded: chain T residue 98 LYS Chi-restraints excluded: chain T residue 240 LYS Chi-restraints excluded: chain T residue 396 ASP Chi-restraints excluded: chain T residue 421 GLU Chi-restraints excluded: chain T residue 477 GLU Chi-restraints excluded: chain V residue 51 LEU Chi-restraints excluded: chain V residue 276 GLU Chi-restraints excluded: chain V residue 314 HIS Chi-restraints excluded: chain V residue 338 ARG Chi-restraints excluded: chain V residue 396 ASP Chi-restraints excluded: chain V residue 421 GLU Chi-restraints excluded: chain V residue 444 VAL Chi-restraints excluded: chain V residue 565 LEU Chi-restraints excluded: chain X residue 8 GLU Chi-restraints excluded: chain X residue 51 LEU Chi-restraints excluded: chain X residue 236 ASP Chi-restraints excluded: chain X residue 396 ASP Chi-restraints excluded: chain X residue 555 LYS Chi-restraints excluded: chain X residue 565 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 948 random chunks: chunk 884 optimal weight: 0.7980 chunk 103 optimal weight: 4.9990 chunk 522 optimal weight: 3.9990 chunk 669 optimal weight: 10.0000 chunk 518 optimal weight: 0.1980 chunk 772 optimal weight: 6.9990 chunk 512 optimal weight: 10.0000 chunk 913 optimal weight: 0.9980 chunk 571 optimal weight: 7.9990 chunk 557 optimal weight: 10.0000 chunk 421 optimal weight: 20.0000 overall best weight: 2.1984 ------------------------------------------------------------------------------- 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 F 34 HIS F 333 GLN H 34 HIS 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 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 314 HIS V 333 GLN V 539 ASN V 544 HIS X 309 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.2147 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= 0.224 Angle : 0.528 9.167 102348 Z= 0.286 Chirality : 0.046 0.215 11400 Planarity : 0.004 0.048 13404 Dihedral : 4.954 44.738 10359 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.18 % Allowed : 12.67 % Favored : 85.15 % 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: 0.33 (0.08), residues: 9600 helix: 1.13 (0.10), residues: 2892 sheet: 0.79 (0.15), residues: 1140 loop : -0.36 (0.08), residues: 5568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP P 181 HIS 0.006 0.001 HIS X 248 PHE 0.019 0.002 PHE O 198 TYR 0.023 0.002 TYR I 15 ARG 0.009 0.000 ARG O 21 *********************** 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 1201 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 1029 time to evaluate : 6.697 Fit side-chains revert: symmetry clash REVERT: A 58 MET cc_start: 0.7785 (mtt) cc_final: 0.7358 (mtm) REVERT: A 66 LYS cc_start: 0.8247 (OUTLIER) cc_final: 0.7924 (mttm) REVERT: A 80 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7751 (pt0) REVERT: A 130 LYS cc_start: 0.8160 (OUTLIER) cc_final: 0.7859 (tptm) REVERT: A 219 LYS cc_start: 0.8558 (OUTLIER) cc_final: 0.8137 (tppt) REVERT: C 80 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7732 (pt0) REVERT: C 110 GLU cc_start: 0.7953 (tt0) cc_final: 0.7625 (tt0) REVERT: C 155 ASP cc_start: 0.8317 (t0) cc_final: 0.8091 (t0) REVERT: E 125 LYS cc_start: 0.8033 (mmmt) cc_final: 0.7767 (mmtm) REVERT: G 51 LYS cc_start: 0.8631 (OUTLIER) cc_final: 0.7752 (mptp) REVERT: G 80 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7496 (pt0) REVERT: I 21 ARG cc_start: 0.7304 (OUTLIER) cc_final: 0.6883 (ttp-170) REVERT: I 58 MET cc_start: 0.7974 (mtm) cc_final: 0.7720 (mtm) REVERT: K 77 MET cc_start: 0.8519 (mtp) cc_final: 0.8295 (mtp) REVERT: K 80 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7621 (pt0) REVERT: K 125 LYS cc_start: 0.8232 (OUTLIER) cc_final: 0.7805 (mmmt) REVERT: M 71 MET cc_start: 0.8794 (mtp) cc_final: 0.8109 (mtp) REVERT: M 130 LYS cc_start: 0.8360 (OUTLIER) cc_final: 0.7887 (ttmm) REVERT: O 72 ASP cc_start: 0.8219 (t0) cc_final: 0.7897 (t0) REVERT: Q 58 MET cc_start: 0.7996 (mtm) cc_final: 0.7763 (mtt) REVERT: Q 60 GLU cc_start: 0.7892 (tt0) cc_final: 0.7670 (tt0) REVERT: Q 71 MET cc_start: 0.8815 (mtp) cc_final: 0.8525 (mtp) REVERT: Q 80 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7560 (pt0) REVERT: S 29 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.7894 (mtmt) REVERT: S 132 LYS cc_start: 0.8703 (OUTLIER) cc_final: 0.8483 (tttp) REVERT: U 116 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.7113 (mm-30) REVERT: U 209 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7910 (tp30) REVERT: J 1 MET cc_start: 0.6901 (OUTLIER) cc_final: 0.6094 (tmt) REVERT: J 8 GLU cc_start: 0.7465 (OUTLIER) cc_final: 0.7244 (pt0) REVERT: J 51 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8146 (tt) REVERT: J 60 ASN cc_start: 0.8290 (m110) cc_final: 0.8049 (m110) REVERT: J 103 ASP cc_start: 0.7927 (m-30) cc_final: 0.7686 (m-30) REVERT: D 565 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8568 (tt) REVERT: F 1 MET cc_start: 0.6780 (OUTLIER) cc_final: 0.6137 (tmt) REVERT: F 559 LYS cc_start: 0.8211 (OUTLIER) cc_final: 0.7995 (tttp) REVERT: H 65 GLU cc_start: 0.7706 (tt0) cc_final: 0.7491 (tt0) REVERT: H 98 LYS cc_start: 0.8021 (OUTLIER) cc_final: 0.6979 (tttm) REVERT: H 182 MET cc_start: 0.8896 (mmm) cc_final: 0.8549 (mmm) REVERT: H 311 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.6839 (tt0) REVERT: H 319 MET cc_start: 0.6926 (OUTLIER) cc_final: 0.6715 (mpt) REVERT: H 353 MET cc_start: 0.8452 (mtp) cc_final: 0.8136 (mtp) REVERT: H 537 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.7338 (mm-30) REVERT: L 262 MET cc_start: 0.8503 (mmm) cc_final: 0.8214 (mmm) REVERT: L 340 ARG cc_start: 0.8343 (mtm-85) cc_final: 0.8096 (mtm180) REVERT: L 366 MET cc_start: 0.7076 (ptp) cc_final: 0.6619 (ptp) REVERT: L 478 MET cc_start: 0.8665 (mmt) cc_final: 0.8255 (mmt) REVERT: L 550 LYS cc_start: 0.8268 (mtpp) cc_final: 0.7951 (mtmt) REVERT: L 555 LYS cc_start: 0.8262 (ptpt) cc_final: 0.7891 (mttt) REVERT: N 98 LYS cc_start: 0.7955 (OUTLIER) cc_final: 0.6507 (tttm) REVERT: N 182 MET cc_start: 0.8799 (mmm) cc_final: 0.8501 (mmm) REVERT: N 317 MET cc_start: 0.7664 (ttm) cc_final: 0.7353 (ttp) REVERT: N 319 MET cc_start: 0.6657 (mmm) cc_final: 0.6098 (tpp) REVERT: N 396 ASP cc_start: 0.7516 (OUTLIER) cc_final: 0.7205 (t70) REVERT: N 537 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.7110 (mm-30) REVERT: P 98 LYS cc_start: 0.7958 (OUTLIER) cc_final: 0.6727 (tmtm) REVERT: P 276 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7262 (pm20) REVERT: P 319 MET cc_start: 0.6948 (OUTLIER) cc_final: 0.6665 (mpp) REVERT: P 396 ASP cc_start: 0.7470 (OUTLIER) cc_final: 0.7152 (t70) REVERT: P 421 GLU cc_start: 0.7593 (OUTLIER) cc_final: 0.7237 (pt0) REVERT: P 537 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7385 (mt-10) REVERT: R 27 ASP cc_start: 0.7774 (OUTLIER) cc_final: 0.7537 (m-30) REVERT: R 98 LYS cc_start: 0.7963 (OUTLIER) cc_final: 0.7633 (tptp) REVERT: R 182 MET cc_start: 0.8850 (mmm) cc_final: 0.8575 (mmm) REVERT: R 319 MET cc_start: 0.6610 (OUTLIER) cc_final: 0.6046 (tpp) REVERT: R 478 MET cc_start: 0.8728 (mmt) cc_final: 0.8357 (mmp) REVERT: R 537 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.7255 (mt-10) REVERT: T 1 MET cc_start: 0.6706 (tmm) cc_final: 0.6378 (tmm) REVERT: T 319 MET cc_start: 0.7016 (OUTLIER) cc_final: 0.6807 (mtt) REVERT: T 396 ASP cc_start: 0.7555 (OUTLIER) cc_final: 0.7288 (t70) REVERT: V 537 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7333 (mt-10) REVERT: X 385 LYS cc_start: 0.8008 (mttp) cc_final: 0.7801 (mmtp) REVERT: X 555 LYS cc_start: 0.8285 (OUTLIER) cc_final: 0.7755 (ptpt) outliers start: 172 outliers final: 98 residues processed: 1105 average time/residue: 1.8291 time to fit residues: 2598.0951 Evaluate side-chains 1148 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 1007 time to evaluate : 6.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 62 ARG Chi-restraints excluded: chain A residue 66 LYS Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 130 LYS Chi-restraints excluded: chain A residue 219 LYS Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 503 ILE Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain G residue 51 LYS Chi-restraints excluded: chain G residue 80 GLU Chi-restraints excluded: chain G residue 128 SER Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 183 SER Chi-restraints excluded: chain I residue 21 ARG Chi-restraints excluded: chain I residue 128 SER Chi-restraints excluded: chain I residue 170 SER Chi-restraints excluded: chain I residue 183 SER Chi-restraints excluded: chain K residue 80 GLU Chi-restraints excluded: chain K residue 125 LYS Chi-restraints excluded: chain K residue 183 SER Chi-restraints excluded: chain M residue 21 ARG Chi-restraints excluded: chain M residue 80 GLU Chi-restraints excluded: chain M residue 130 LYS Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 44 MET Chi-restraints excluded: chain O residue 128 SER Chi-restraints excluded: chain O residue 170 SER Chi-restraints excluded: chain Q residue 68 ASP Chi-restraints excluded: chain Q residue 80 GLU Chi-restraints excluded: chain Q residue 86 MET Chi-restraints excluded: chain Q residue 128 SER Chi-restraints excluded: chain Q residue 136 ASP Chi-restraints excluded: chain Q residue 170 SER Chi-restraints excluded: chain S residue 29 LYS Chi-restraints excluded: chain S residue 52 LYS Chi-restraints excluded: chain S residue 128 SER Chi-restraints excluded: chain S residue 132 LYS Chi-restraints excluded: chain S residue 170 SER Chi-restraints excluded: chain U residue 44 MET Chi-restraints excluded: chain U residue 116 GLU Chi-restraints excluded: chain U residue 183 SER Chi-restraints excluded: chain U residue 209 GLU Chi-restraints excluded: chain W residue 128 SER Chi-restraints excluded: chain W residue 183 SER Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 8 GLU Chi-restraints excluded: chain J residue 27 ASP Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain J residue 316 ASP Chi-restraints excluded: chain J residue 366 MET Chi-restraints excluded: chain J residue 396 ASP Chi-restraints excluded: chain J residue 433 ASP Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 316 ASP Chi-restraints excluded: chain D residue 396 ASP Chi-restraints excluded: chain D residue 421 GLU Chi-restraints excluded: chain D residue 469 THR Chi-restraints excluded: chain D residue 565 LEU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 55 MET Chi-restraints excluded: chain F residue 316 ASP Chi-restraints excluded: chain F residue 396 ASP Chi-restraints excluded: chain F residue 559 LYS Chi-restraints excluded: chain H residue 27 ASP Chi-restraints excluded: chain H residue 98 LYS Chi-restraints excluded: chain H residue 311 GLU Chi-restraints excluded: chain H residue 319 MET Chi-restraints excluded: chain H residue 391 LYS Chi-restraints excluded: chain H residue 396 ASP Chi-restraints excluded: chain H residue 421 GLU Chi-restraints excluded: chain H residue 537 GLU Chi-restraints excluded: chain L residue 27 ASP Chi-restraints excluded: chain L residue 51 LEU Chi-restraints excluded: chain L residue 60 ASN Chi-restraints excluded: chain L residue 276 GLU Chi-restraints excluded: chain L residue 316 ASP Chi-restraints excluded: chain L residue 396 ASP Chi-restraints excluded: chain N residue 27 ASP Chi-restraints excluded: chain N residue 98 LYS Chi-restraints excluded: chain N residue 212 GLU Chi-restraints excluded: chain N residue 240 LYS Chi-restraints excluded: chain N residue 316 ASP Chi-restraints excluded: chain N residue 366 MET Chi-restraints excluded: chain N residue 396 ASP Chi-restraints excluded: chain N residue 421 GLU Chi-restraints excluded: chain N residue 444 VAL Chi-restraints excluded: chain N residue 469 THR Chi-restraints excluded: chain N residue 537 GLU Chi-restraints excluded: chain P residue 51 LEU Chi-restraints excluded: chain P residue 98 LYS Chi-restraints excluded: chain P residue 276 GLU Chi-restraints excluded: chain P residue 319 MET Chi-restraints excluded: chain P residue 366 MET Chi-restraints excluded: chain P residue 396 ASP Chi-restraints excluded: chain P residue 421 GLU Chi-restraints excluded: chain P residue 477 GLU Chi-restraints excluded: chain P residue 537 GLU Chi-restraints excluded: chain P residue 559 LYS Chi-restraints excluded: chain P residue 565 LEU Chi-restraints excluded: chain R residue 27 ASP Chi-restraints excluded: chain R residue 37 THR Chi-restraints excluded: chain R residue 98 LYS Chi-restraints excluded: chain R residue 212 GLU Chi-restraints excluded: chain R residue 319 MET Chi-restraints excluded: chain R residue 391 LYS Chi-restraints excluded: chain R residue 396 ASP Chi-restraints excluded: chain R residue 517 LYS Chi-restraints excluded: chain R residue 537 GLU Chi-restraints excluded: chain R residue 565 LEU Chi-restraints excluded: chain T residue 51 LEU Chi-restraints excluded: chain T residue 240 LYS Chi-restraints excluded: chain T residue 319 MET Chi-restraints excluded: chain T residue 396 ASP Chi-restraints excluded: chain T residue 421 GLU Chi-restraints excluded: chain T residue 477 GLU Chi-restraints excluded: chain V residue 51 LEU Chi-restraints excluded: chain V residue 276 GLU Chi-restraints excluded: chain V residue 319 MET Chi-restraints excluded: chain V residue 338 ARG Chi-restraints excluded: chain V residue 396 ASP Chi-restraints excluded: chain V residue 421 GLU Chi-restraints excluded: chain V residue 444 VAL Chi-restraints excluded: chain V residue 537 GLU Chi-restraints excluded: chain V residue 565 LEU Chi-restraints excluded: chain X residue 8 GLU Chi-restraints excluded: chain X residue 51 LEU Chi-restraints excluded: chain X residue 236 ASP Chi-restraints excluded: chain X residue 396 ASP Chi-restraints excluded: chain X residue 555 LYS Chi-restraints excluded: chain X residue 565 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 948 random chunks: chunk 565 optimal weight: 6.9990 chunk 364 optimal weight: 0.9990 chunk 545 optimal weight: 0.9990 chunk 275 optimal weight: 10.0000 chunk 179 optimal weight: 0.5980 chunk 177 optimal weight: 10.0000 chunk 580 optimal weight: 7.9990 chunk 622 optimal weight: 6.9990 chunk 451 optimal weight: 5.9990 chunk 85 optimal weight: 10.0000 chunk 718 optimal weight: 6.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- 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 D 309 ASN F 34 HIS F 333 GLN H 34 HIS 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 383 ASN R 535 HIS T 34 HIS T 60 ASN T 314 HIS V 34 HIS V 314 HIS V 333 GLN V 544 HIS X 309 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 75888 Z= 0.293 Angle : 0.572 9.962 102348 Z= 0.309 Chirality : 0.048 0.218 11400 Planarity : 0.004 0.048 13404 Dihedral : 5.123 42.894 10359 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.15 % Allowed : 12.87 % Favored : 84.98 % 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: 0.21 (0.08), residues: 9600 helix: 0.95 (0.09), residues: 2904 sheet: 0.81 (0.16), residues: 1068 loop : -0.40 (0.08), residues: 5628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP F 377 HIS 0.007 0.001 HIS X 248 PHE 0.022 0.002 PHE S 198 TYR 0.025 0.002 TYR C 15 ARG 0.011 0.001 ARG W 21 *********************** 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 1179 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 1009 time to evaluate : 6.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 MET cc_start: 0.7793 (mtt) cc_final: 0.7370 (mtm) REVERT: A 66 LYS cc_start: 0.8263 (OUTLIER) cc_final: 0.7938 (mttm) REVERT: A 80 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7771 (pt0) REVERT: A 130 LYS cc_start: 0.8188 (OUTLIER) cc_final: 0.7893 (tptm) REVERT: A 219 LYS cc_start: 0.8567 (OUTLIER) cc_final: 0.8174 (tppt) REVERT: B 550 LYS cc_start: 0.8244 (mtpp) cc_final: 0.7944 (mtmt) REVERT: C 80 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7721 (pt0) REVERT: C 110 GLU cc_start: 0.7951 (tt0) cc_final: 0.7616 (tt0) REVERT: C 130 LYS cc_start: 0.7975 (ttmm) cc_final: 0.7715 (mtpt) REVERT: C 155 ASP cc_start: 0.8322 (t0) cc_final: 0.8100 (t0) REVERT: E 125 LYS cc_start: 0.8042 (mmmt) cc_final: 0.7777 (mmtm) REVERT: G 51 LYS cc_start: 0.8623 (OUTLIER) cc_final: 0.7716 (mptp) REVERT: G 80 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7515 (pt0) REVERT: I 21 ARG cc_start: 0.7403 (OUTLIER) cc_final: 0.7122 (ttp-170) REVERT: I 58 MET cc_start: 0.7960 (mtm) cc_final: 0.7696 (mtm) REVERT: K 77 MET cc_start: 0.8511 (mtp) cc_final: 0.8136 (mtp) REVERT: K 80 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.7632 (pt0) REVERT: K 125 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.7805 (mmmt) REVERT: M 71 MET cc_start: 0.8816 (mtp) cc_final: 0.8089 (mtp) REVERT: M 130 LYS cc_start: 0.8391 (OUTLIER) cc_final: 0.7933 (ttmm) REVERT: O 72 ASP cc_start: 0.8235 (t0) cc_final: 0.7896 (t0) REVERT: Q 60 GLU cc_start: 0.7878 (tt0) cc_final: 0.7654 (tt0) REVERT: Q 71 MET cc_start: 0.8807 (mtp) cc_final: 0.8542 (mtp) REVERT: Q 80 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7553 (pt0) REVERT: S 29 LYS cc_start: 0.8269 (OUTLIER) cc_final: 0.7931 (mtmt) REVERT: U 116 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.7108 (mm-30) REVERT: U 181 GLU cc_start: 0.7500 (tt0) cc_final: 0.7229 (tt0) REVERT: U 209 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7868 (tp30) REVERT: J 1 MET cc_start: 0.6939 (OUTLIER) cc_final: 0.6184 (tmt) REVERT: J 8 GLU cc_start: 0.7507 (OUTLIER) cc_final: 0.7268 (pt0) REVERT: J 51 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8238 (tt) REVERT: J 60 ASN cc_start: 0.8327 (m110) cc_final: 0.8100 (m110) REVERT: J 103 ASP cc_start: 0.7933 (m-30) cc_final: 0.7707 (m-30) REVERT: D 565 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8619 (tt) REVERT: F 1 MET cc_start: 0.6778 (OUTLIER) cc_final: 0.6145 (tmt) REVERT: F 559 LYS cc_start: 0.8214 (OUTLIER) cc_final: 0.8009 (tttp) REVERT: H 65 GLU cc_start: 0.7751 (tt0) cc_final: 0.7541 (tt0) REVERT: H 98 LYS cc_start: 0.8016 (OUTLIER) cc_final: 0.6964 (tttm) REVERT: H 182 MET cc_start: 0.8885 (mmm) cc_final: 0.8515 (mmm) REVERT: H 311 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.6852 (tt0) REVERT: H 353 MET cc_start: 0.8441 (mtp) cc_final: 0.8159 (mtp) REVERT: H 537 GLU cc_start: 0.7642 (OUTLIER) cc_final: 0.7343 (mm-30) REVERT: L 340 ARG cc_start: 0.8372 (mtm-85) cc_final: 0.8117 (mtm180) REVERT: L 366 MET cc_start: 0.7204 (ptp) cc_final: 0.6824 (ptp) REVERT: L 478 MET cc_start: 0.8687 (mmt) cc_final: 0.7998 (mmt) REVERT: L 550 LYS cc_start: 0.8283 (mtpp) cc_final: 0.7956 (mtmt) REVERT: L 555 LYS cc_start: 0.8263 (OUTLIER) cc_final: 0.7894 (mttt) REVERT: N 98 LYS cc_start: 0.7973 (OUTLIER) cc_final: 0.6599 (tttm) REVERT: N 182 MET cc_start: 0.8766 (mmm) cc_final: 0.8441 (mmm) REVERT: N 319 MET cc_start: 0.6694 (mmm) cc_final: 0.6118 (tpp) REVERT: N 396 ASP cc_start: 0.7580 (OUTLIER) cc_final: 0.7246 (t70) REVERT: N 537 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.7094 (mm-30) REVERT: P 98 LYS cc_start: 0.7927 (OUTLIER) cc_final: 0.6703 (tmtm) REVERT: P 276 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7307 (pm20) REVERT: P 319 MET cc_start: 0.6954 (OUTLIER) cc_final: 0.6678 (mpp) REVERT: P 396 ASP cc_start: 0.7531 (OUTLIER) cc_final: 0.7197 (t70) REVERT: P 421 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.7244 (pt0) REVERT: P 537 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7382 (mt-10) REVERT: R 27 ASP cc_start: 0.7810 (OUTLIER) cc_final: 0.7564 (m-30) REVERT: R 98 LYS cc_start: 0.7979 (OUTLIER) cc_final: 0.7639 (tptp) REVERT: R 182 MET cc_start: 0.8848 (mmm) cc_final: 0.8558 (mmm) REVERT: R 478 MET cc_start: 0.8757 (mmt) cc_final: 0.8486 (mmp) REVERT: R 537 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.7226 (mt-10) REVERT: T 1 MET cc_start: 0.6704 (tmm) cc_final: 0.6367 (tmm) REVERT: T 98 LYS cc_start: 0.8123 (OUTLIER) cc_final: 0.7717 (tmtm) REVERT: T 396 ASP cc_start: 0.7570 (OUTLIER) cc_final: 0.7305 (t70) REVERT: T 559 LYS cc_start: 0.8309 (OUTLIER) cc_final: 0.8018 (tttm) REVERT: V 537 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7336 (mt-10) REVERT: X 385 LYS cc_start: 0.8072 (mttp) cc_final: 0.7859 (mmtp) REVERT: X 555 LYS cc_start: 0.8291 (OUTLIER) cc_final: 0.7763 (ptpt) outliers start: 170 outliers final: 96 residues processed: 1079 average time/residue: 1.8425 time to fit residues: 2549.2718 Evaluate side-chains 1139 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 1001 time to evaluate : 6.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 62 ARG Chi-restraints excluded: chain A residue 66 LYS Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 130 LYS Chi-restraints excluded: chain A residue 219 LYS Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 503 ILE Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain E residue 21 ARG Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain G residue 51 LYS Chi-restraints excluded: chain G residue 80 GLU Chi-restraints excluded: chain G residue 128 SER Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 183 SER Chi-restraints excluded: chain I residue 21 ARG Chi-restraints excluded: chain I residue 44 MET Chi-restraints excluded: chain I residue 125 LYS Chi-restraints excluded: chain I residue 128 SER Chi-restraints excluded: chain I residue 170 SER Chi-restraints excluded: chain I residue 183 SER Chi-restraints excluded: chain K residue 80 GLU Chi-restraints excluded: chain K residue 125 LYS Chi-restraints excluded: chain K residue 183 SER Chi-restraints excluded: chain M residue 21 ARG Chi-restraints excluded: chain M residue 80 GLU Chi-restraints excluded: chain M residue 130 LYS Chi-restraints excluded: chain O residue 128 SER Chi-restraints excluded: chain O residue 170 SER Chi-restraints excluded: chain O residue 210 SER Chi-restraints excluded: chain Q residue 68 ASP Chi-restraints excluded: chain Q residue 80 GLU Chi-restraints excluded: chain Q residue 128 SER Chi-restraints excluded: chain Q residue 136 ASP Chi-restraints excluded: chain Q residue 170 SER Chi-restraints excluded: chain S residue 29 LYS Chi-restraints excluded: chain S residue 52 LYS Chi-restraints excluded: chain S residue 128 SER Chi-restraints excluded: chain S residue 170 SER Chi-restraints excluded: chain U residue 44 MET Chi-restraints excluded: chain U residue 116 GLU Chi-restraints excluded: chain U residue 183 SER Chi-restraints excluded: chain U residue 209 GLU Chi-restraints excluded: chain W residue 128 SER Chi-restraints excluded: chain W residue 183 SER Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 8 GLU Chi-restraints excluded: chain J residue 27 ASP Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain J residue 316 ASP Chi-restraints excluded: chain J residue 366 MET Chi-restraints excluded: chain J residue 396 ASP Chi-restraints excluded: chain J residue 433 ASP Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain D residue 316 ASP Chi-restraints excluded: chain D residue 366 MET Chi-restraints excluded: chain D residue 396 ASP Chi-restraints excluded: chain D residue 421 GLU Chi-restraints excluded: chain D residue 469 THR Chi-restraints excluded: chain D residue 565 LEU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 316 ASP Chi-restraints excluded: chain F residue 396 ASP Chi-restraints excluded: chain F residue 559 LYS Chi-restraints excluded: chain H residue 27 ASP Chi-restraints excluded: chain H residue 98 LYS Chi-restraints excluded: chain H residue 311 GLU Chi-restraints excluded: chain H residue 391 LYS Chi-restraints excluded: chain H residue 396 ASP Chi-restraints excluded: chain H residue 537 GLU Chi-restraints excluded: chain L residue 27 ASP Chi-restraints excluded: chain L residue 51 LEU Chi-restraints excluded: chain L residue 60 ASN Chi-restraints excluded: chain L residue 276 GLU Chi-restraints excluded: chain L residue 316 ASP Chi-restraints excluded: chain L residue 396 ASP Chi-restraints excluded: chain L residue 503 ILE Chi-restraints excluded: chain L residue 555 LYS Chi-restraints excluded: chain N residue 27 ASP Chi-restraints excluded: chain N residue 98 LYS Chi-restraints excluded: chain N residue 212 GLU Chi-restraints excluded: chain N residue 240 LYS Chi-restraints excluded: chain N residue 316 ASP Chi-restraints excluded: chain N residue 366 MET Chi-restraints excluded: chain N residue 396 ASP Chi-restraints excluded: chain N residue 421 GLU Chi-restraints excluded: chain N residue 469 THR Chi-restraints excluded: chain N residue 537 GLU Chi-restraints excluded: chain P residue 51 LEU Chi-restraints excluded: chain P residue 98 LYS Chi-restraints excluded: chain P residue 276 GLU Chi-restraints excluded: chain P residue 319 MET Chi-restraints excluded: chain P residue 366 MET Chi-restraints excluded: chain P residue 396 ASP Chi-restraints excluded: chain P residue 421 GLU Chi-restraints excluded: chain P residue 477 GLU Chi-restraints excluded: chain P residue 537 GLU Chi-restraints excluded: chain P residue 559 LYS Chi-restraints excluded: chain R residue 27 ASP Chi-restraints excluded: chain R residue 37 THR Chi-restraints excluded: chain R residue 98 LYS Chi-restraints excluded: chain R residue 212 GLU Chi-restraints excluded: chain R residue 391 LYS Chi-restraints excluded: chain R residue 396 ASP Chi-restraints excluded: chain R residue 517 LYS Chi-restraints excluded: chain R residue 537 GLU Chi-restraints excluded: chain R residue 565 LEU Chi-restraints excluded: chain T residue 51 LEU Chi-restraints excluded: chain T residue 98 LYS Chi-restraints excluded: chain T residue 240 LYS Chi-restraints excluded: chain T residue 396 ASP Chi-restraints excluded: chain T residue 421 GLU Chi-restraints excluded: chain T residue 477 GLU Chi-restraints excluded: chain T residue 559 LYS Chi-restraints excluded: chain V residue 38 ILE Chi-restraints excluded: chain V residue 51 LEU Chi-restraints excluded: chain V residue 276 GLU Chi-restraints excluded: chain V residue 338 ARG Chi-restraints excluded: chain V residue 396 ASP Chi-restraints excluded: chain V residue 421 GLU Chi-restraints excluded: chain V residue 444 VAL Chi-restraints excluded: chain V residue 537 GLU Chi-restraints excluded: chain V residue 565 LEU Chi-restraints excluded: chain X residue 8 GLU Chi-restraints excluded: chain X residue 51 LEU Chi-restraints excluded: chain X residue 236 ASP Chi-restraints excluded: chain X residue 396 ASP Chi-restraints excluded: chain X residue 555 LYS Chi-restraints excluded: chain X residue 565 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 948 random chunks: chunk 831 optimal weight: 1.9990 chunk 875 optimal weight: 0.7980 chunk 798 optimal weight: 0.7980 chunk 851 optimal weight: 10.0000 chunk 512 optimal weight: 9.9990 chunk 370 optimal weight: 5.9990 chunk 668 optimal weight: 8.9990 chunk 261 optimal weight: 8.9990 chunk 769 optimal weight: 0.9980 chunk 805 optimal weight: 0.8980 chunk 848 optimal weight: 8.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 HIS B 539 ASN S 31 ASN W 208 ASN J 309 ASN D 309 ASN D 383 ASN F 34 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 314 HIS N 333 GLN P 333 GLN R 34 HIS R 383 ASN R 512 GLN T 34 HIS V 34 HIS ** V 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 314 HIS V 333 GLN V 539 ASN V 544 HIS X 309 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 75888 Z= 0.153 Angle : 0.486 8.581 102348 Z= 0.262 Chirality : 0.044 0.218 11400 Planarity : 0.004 0.050 13404 Dihedral : 4.796 46.366 10359 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.54 % Allowed : 13.63 % Favored : 84.83 % 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: 0.42 (0.08), residues: 9600 helix: 1.31 (0.10), residues: 2880 sheet: 0.65 (0.15), residues: 1044 loop : -0.30 (0.08), residues: 5676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP P 181 HIS 0.005 0.001 HIS B 248 PHE 0.019 0.001 PHE E 198 TYR 0.019 0.001 TYR I 15 ARG 0.009 0.000 ARG W 21 *********************** 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 1170 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 1048 time to evaluate : 6.816 Fit side-chains revert: symmetry clash REVERT: A 58 MET cc_start: 0.7733 (mtt) cc_final: 0.7338 (mtm) REVERT: A 66 LYS cc_start: 0.8250 (OUTLIER) cc_final: 0.7922 (mttm) REVERT: A 80 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7594 (pt0) REVERT: A 219 LYS cc_start: 0.8536 (OUTLIER) cc_final: 0.8103 (tppt) REVERT: B 550 LYS cc_start: 0.8243 (mtpp) cc_final: 0.7941 (mtmt) REVERT: C 80 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7696 (pt0) REVERT: C 110 GLU cc_start: 0.7901 (tt0) cc_final: 0.7577 (tt0) REVERT: C 130 LYS cc_start: 0.7913 (ttmm) cc_final: 0.7654 (mtpt) REVERT: C 155 ASP cc_start: 0.8314 (t0) cc_final: 0.8087 (t0) REVERT: E 125 LYS cc_start: 0.7904 (mmmt) cc_final: 0.7644 (mmtm) REVERT: G 51 LYS cc_start: 0.8600 (OUTLIER) cc_final: 0.7716 (mptp) REVERT: G 80 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7466 (pt0) REVERT: I 21 ARG cc_start: 0.7353 (OUTLIER) cc_final: 0.6957 (ttp-170) REVERT: I 58 MET cc_start: 0.7907 (mtm) cc_final: 0.7652 (mtm) REVERT: K 77 MET cc_start: 0.8482 (mtp) cc_final: 0.8192 (mtp) REVERT: K 125 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.7816 (mmmt) REVERT: M 21 ARG cc_start: 0.7460 (OUTLIER) cc_final: 0.7240 (tmm160) REVERT: M 71 MET cc_start: 0.8760 (mtp) cc_final: 0.8077 (mtp) REVERT: M 130 LYS cc_start: 0.8350 (OUTLIER) cc_final: 0.7871 (ttmm) REVERT: O 72 ASP cc_start: 0.8225 (t0) cc_final: 0.7869 (t0) REVERT: Q 58 MET cc_start: 0.7929 (mtm) cc_final: 0.7711 (mtt) REVERT: Q 60 GLU cc_start: 0.7833 (tt0) cc_final: 0.7615 (tt0) REVERT: Q 71 MET cc_start: 0.8799 (mtp) cc_final: 0.8498 (mtp) REVERT: Q 80 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7592 (pt0) REVERT: Q 134 VAL cc_start: 0.8091 (OUTLIER) cc_final: 0.7884 (t) REVERT: S 29 LYS cc_start: 0.8189 (OUTLIER) cc_final: 0.7831 (mtmt) REVERT: U 116 GLU cc_start: 0.7530 (OUTLIER) cc_final: 0.7028 (mm-30) REVERT: U 181 GLU cc_start: 0.7392 (tt0) cc_final: 0.7171 (tt0) REVERT: U 209 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7835 (tp30) REVERT: J 1 MET cc_start: 0.6829 (OUTLIER) cc_final: 0.6047 (tmt) REVERT: J 8 GLU cc_start: 0.7397 (OUTLIER) cc_final: 0.7182 (pt0) REVERT: J 60 ASN cc_start: 0.8290 (m110) cc_final: 0.8052 (m110) REVERT: J 85 ASP cc_start: 0.7458 (m-30) cc_final: 0.7163 (m-30) REVERT: J 103 ASP cc_start: 0.7935 (m-30) cc_final: 0.7700 (m-30) REVERT: D 85 ASP cc_start: 0.7686 (m-30) cc_final: 0.7472 (m-30) REVERT: D 565 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8453 (tt) REVERT: F 550 LYS cc_start: 0.8219 (mtpp) cc_final: 0.7840 (mtpt) REVERT: H 65 GLU cc_start: 0.7757 (tt0) cc_final: 0.7556 (tt0) REVERT: H 182 MET cc_start: 0.8899 (mmm) cc_final: 0.8591 (mmm) REVERT: H 311 GLU cc_start: 0.7490 (OUTLIER) cc_final: 0.6792 (tt0) REVERT: L 340 ARG cc_start: 0.8306 (mtm-85) cc_final: 0.8051 (mtm180) REVERT: L 366 MET cc_start: 0.7093 (ptp) cc_final: 0.6611 (ptp) REVERT: L 550 LYS cc_start: 0.8247 (mtpp) cc_final: 0.7963 (mtmt) REVERT: L 555 LYS cc_start: 0.8227 (OUTLIER) cc_final: 0.7948 (mttt) REVERT: N 182 MET cc_start: 0.8834 (mmm) cc_final: 0.8553 (mmm) REVERT: N 319 MET cc_start: 0.6631 (mmm) cc_final: 0.6059 (tpp) REVERT: N 396 ASP cc_start: 0.7520 (OUTLIER) cc_final: 0.7214 (t70) REVERT: P 276 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.7244 (pm20) REVERT: P 319 MET cc_start: 0.6944 (OUTLIER) cc_final: 0.6663 (mpp) REVERT: P 396 ASP cc_start: 0.7503 (OUTLIER) cc_final: 0.7173 (t70) REVERT: P 421 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.7231 (pt0) REVERT: R 182 MET cc_start: 0.8840 (mmm) cc_final: 0.8527 (mmm) REVERT: R 478 MET cc_start: 0.8659 (mmt) cc_final: 0.8296 (mmp) REVERT: R 550 LYS cc_start: 0.8245 (mtpp) cc_final: 0.7841 (tttt) REVERT: T 1 MET cc_start: 0.6687 (tmm) cc_final: 0.6370 (tmm) REVERT: T 396 ASP cc_start: 0.7491 (OUTLIER) cc_final: 0.7230 (t70) REVERT: X 385 LYS cc_start: 0.8007 (mttp) cc_final: 0.7799 (mmtp) REVERT: X 478 MET cc_start: 0.8685 (mmt) cc_final: 0.7863 (mmt) REVERT: X 555 LYS cc_start: 0.8209 (OUTLIER) cc_final: 0.7726 (ptpt) outliers start: 122 outliers final: 61 residues processed: 1096 average time/residue: 1.8134 time to fit residues: 2568.0034 Evaluate side-chains 1113 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 1025 time to evaluate : 6.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ARG Chi-restraints excluded: chain A residue 66 LYS Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 219 LYS Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 503 ILE Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain G residue 51 LYS Chi-restraints excluded: chain G residue 80 GLU Chi-restraints excluded: chain G residue 128 SER Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain I residue 21 ARG Chi-restraints excluded: chain I residue 128 SER Chi-restraints excluded: chain I residue 170 SER Chi-restraints excluded: chain I residue 183 SER Chi-restraints excluded: chain K residue 125 LYS Chi-restraints excluded: chain M residue 21 ARG Chi-restraints excluded: chain M residue 130 LYS Chi-restraints excluded: chain O residue 128 SER Chi-restraints excluded: chain O residue 170 SER Chi-restraints excluded: chain Q residue 80 GLU Chi-restraints excluded: chain Q residue 128 SER Chi-restraints excluded: chain Q residue 134 VAL Chi-restraints excluded: chain Q residue 170 SER Chi-restraints excluded: chain S residue 29 LYS Chi-restraints excluded: chain S residue 62 ARG Chi-restraints excluded: chain S residue 128 SER Chi-restraints excluded: chain S residue 170 SER Chi-restraints excluded: chain U residue 44 MET Chi-restraints excluded: chain U residue 116 GLU Chi-restraints excluded: chain U residue 209 GLU Chi-restraints excluded: chain W residue 128 SER Chi-restraints excluded: chain W residue 183 SER Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 8 GLU Chi-restraints excluded: chain J residue 27 ASP Chi-restraints excluded: chain J residue 396 ASP Chi-restraints excluded: chain J residue 433 ASP Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 396 ASP Chi-restraints excluded: chain D residue 421 GLU Chi-restraints excluded: chain D residue 469 THR Chi-restraints excluded: chain D residue 565 LEU Chi-restraints excluded: chain F residue 55 MET Chi-restraints excluded: chain F residue 316 ASP Chi-restraints excluded: chain F residue 396 ASP Chi-restraints excluded: chain H residue 27 ASP Chi-restraints excluded: chain H residue 311 GLU Chi-restraints excluded: chain H residue 396 ASP Chi-restraints excluded: chain L residue 27 ASP Chi-restraints excluded: chain L residue 60 ASN Chi-restraints excluded: chain L residue 276 GLU Chi-restraints excluded: chain L residue 396 ASP Chi-restraints excluded: chain L residue 555 LYS Chi-restraints excluded: chain N residue 27 ASP Chi-restraints excluded: chain N residue 212 GLU Chi-restraints excluded: chain N residue 240 LYS Chi-restraints excluded: chain N residue 316 ASP Chi-restraints excluded: chain N residue 396 ASP Chi-restraints excluded: chain N residue 421 GLU Chi-restraints excluded: chain N residue 444 VAL Chi-restraints excluded: chain N residue 469 THR Chi-restraints excluded: chain P residue 276 GLU Chi-restraints excluded: chain P residue 319 MET Chi-restraints excluded: chain P residue 366 MET Chi-restraints excluded: chain P residue 396 ASP Chi-restraints excluded: chain P residue 421 GLU Chi-restraints excluded: chain P residue 477 GLU Chi-restraints excluded: chain R residue 391 LYS Chi-restraints excluded: chain R residue 396 ASP Chi-restraints excluded: chain T residue 240 LYS Chi-restraints excluded: chain T residue 396 ASP Chi-restraints excluded: chain V residue 276 GLU Chi-restraints excluded: chain V residue 338 ARG Chi-restraints excluded: chain V residue 396 ASP Chi-restraints excluded: chain V residue 421 GLU Chi-restraints excluded: chain V residue 444 VAL Chi-restraints excluded: chain X residue 236 ASP Chi-restraints excluded: chain X residue 396 ASP Chi-restraints excluded: chain X residue 555 LYS Chi-restraints excluded: chain X residue 565 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 948 random chunks: chunk 559 optimal weight: 0.5980 chunk 900 optimal weight: 9.9990 chunk 549 optimal weight: 0.3980 chunk 427 optimal weight: 7.9990 chunk 625 optimal weight: 7.9990 chunk 944 optimal weight: 3.9990 chunk 869 optimal weight: 4.9990 chunk 752 optimal weight: 9.9990 chunk 78 optimal weight: 20.0000 chunk 580 optimal weight: 9.9990 chunk 461 optimal weight: 7.9990 overall best weight: 3.5986 ------------------------------------------------------------------------------- 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 D 309 ASN D 383 ASN F 34 HIS F 309 ASN F 333 GLN F 383 ASN H 34 HIS H 309 ASN L 34 HIS L 309 ASN L 314 HIS N 34 HIS P 309 ASN P 333 GLN R 34 HIS R 60 ASN R 383 ASN ** R 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 34 HIS T 60 ASN T 314 HIS V 34 HIS V 314 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: 0.8403 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 75888 Z= 0.329 Angle : 0.589 10.332 102348 Z= 0.318 Chirality : 0.049 0.225 11400 Planarity : 0.005 0.048 13404 Dihedral : 5.122 43.236 10359 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.45 % Allowed : 13.87 % Favored : 84.67 % 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: 0.21 (0.08), residues: 9600 helix: 0.97 (0.09), residues: 2892 sheet: 0.80 (0.16), residues: 1068 loop : -0.41 (0.08), residues: 5640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP J 377 HIS 0.008 0.001 HIS J 417 PHE 0.022 0.002 PHE S 198 TYR 0.026 0.002 TYR C 15 ARG 0.010 0.001 ARG W 21 ********************** 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 1122 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 1007 time to evaluate : 6.698 Fit side-chains revert: symmetry clash REVERT: A 58 MET cc_start: 0.7785 (mtt) cc_final: 0.7361 (mtm) REVERT: A 66 LYS cc_start: 0.8282 (OUTLIER) cc_final: 0.7947 (mttm) REVERT: A 80 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7782 (pt0) REVERT: A 219 LYS cc_start: 0.8563 (OUTLIER) cc_final: 0.8159 (tppt) REVERT: B 550 LYS cc_start: 0.8248 (mtpp) cc_final: 0.7927 (mtmt) REVERT: C 80 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7717 (pt0) REVERT: C 110 GLU cc_start: 0.7948 (tt0) cc_final: 0.7598 (tt0) REVERT: C 130 LYS cc_start: 0.7949 (ttmm) cc_final: 0.7692 (mtpt) REVERT: C 155 ASP cc_start: 0.8326 (t0) cc_final: 0.8106 (t0) REVERT: E 125 LYS cc_start: 0.8056 (mmmt) cc_final: 0.7792 (mmtm) REVERT: G 51 LYS cc_start: 0.8620 (OUTLIER) cc_final: 0.7734 (mptp) REVERT: G 80 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7513 (pt0) REVERT: I 21 ARG cc_start: 0.7319 (OUTLIER) cc_final: 0.6963 (ttp-170) REVERT: I 58 MET cc_start: 0.7952 (mtm) cc_final: 0.7660 (mtm) REVERT: K 77 MET cc_start: 0.8500 (mtp) cc_final: 0.8132 (mtp) REVERT: K 80 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7628 (pt0) REVERT: K 125 LYS cc_start: 0.8236 (OUTLIER) cc_final: 0.7804 (mmmt) REVERT: M 71 MET cc_start: 0.8810 (mtp) cc_final: 0.8086 (mtp) REVERT: M 130 LYS cc_start: 0.8395 (OUTLIER) cc_final: 0.7936 (ttmm) REVERT: O 72 ASP cc_start: 0.8242 (t0) cc_final: 0.7897 (t0) REVERT: Q 60 GLU cc_start: 0.7876 (tt0) cc_final: 0.7622 (tt0) REVERT: Q 71 MET cc_start: 0.8807 (mtp) cc_final: 0.8557 (mtp) REVERT: Q 80 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.7557 (pt0) REVERT: S 29 LYS cc_start: 0.8266 (OUTLIER) cc_final: 0.7925 (mtmt) REVERT: U 116 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.7105 (mm-30) REVERT: U 209 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7877 (tp30) REVERT: J 1 MET cc_start: 0.6943 (OUTLIER) cc_final: 0.6195 (tmt) REVERT: J 8 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.7277 (pt0) REVERT: J 60 ASN cc_start: 0.8338 (m110) cc_final: 0.8108 (m110) REVERT: J 103 ASP cc_start: 0.7926 (m-30) cc_final: 0.7694 (m-30) REVERT: D 537 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7403 (mt-10) REVERT: F 550 LYS cc_start: 0.8233 (mtpp) cc_final: 0.7865 (mtpt) REVERT: F 559 LYS cc_start: 0.8204 (OUTLIER) cc_final: 0.8000 (tttp) REVERT: H 65 GLU cc_start: 0.7754 (tt0) cc_final: 0.7543 (tt0) REVERT: H 182 MET cc_start: 0.8883 (mmm) cc_final: 0.8516 (mmm) REVERT: H 311 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.6855 (tt0) REVERT: L 340 ARG cc_start: 0.8345 (mtm-85) cc_final: 0.8099 (mtm180) REVERT: L 366 MET cc_start: 0.7244 (ptp) cc_final: 0.6772 (ptp) REVERT: L 478 MET cc_start: 0.8640 (mmt) cc_final: 0.8201 (mmt) REVERT: L 550 LYS cc_start: 0.8274 (mtpp) cc_final: 0.7957 (mtmt) REVERT: L 555 LYS cc_start: 0.8269 (OUTLIER) cc_final: 0.7898 (mttt) REVERT: N 98 LYS cc_start: 0.7946 (OUTLIER) cc_final: 0.6571 (tttm) REVERT: N 319 MET cc_start: 0.6710 (mmm) cc_final: 0.6189 (tpp) REVERT: N 396 ASP cc_start: 0.7534 (OUTLIER) cc_final: 0.7200 (t70) REVERT: P 98 LYS cc_start: 0.7918 (OUTLIER) cc_final: 0.6686 (tmtm) REVERT: P 276 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7245 (pm20) REVERT: P 319 MET cc_start: 0.6976 (OUTLIER) cc_final: 0.6699 (mpp) REVERT: P 396 ASP cc_start: 0.7487 (OUTLIER) cc_final: 0.7176 (t70) REVERT: P 421 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.7251 (pt0) REVERT: R 98 LYS cc_start: 0.7985 (OUTLIER) cc_final: 0.7636 (tptp) REVERT: R 182 MET cc_start: 0.8832 (mmm) cc_final: 0.8534 (mmm) REVERT: R 478 MET cc_start: 0.8784 (mmt) cc_final: 0.8529 (mmp) REVERT: T 1 MET cc_start: 0.6711 (tmm) cc_final: 0.6392 (tmm) REVERT: T 98 LYS cc_start: 0.8149 (OUTLIER) cc_final: 0.7673 (tmtm) REVERT: T 396 ASP cc_start: 0.7561 (OUTLIER) cc_final: 0.7286 (t70) REVERT: X 385 LYS cc_start: 0.8048 (mttp) cc_final: 0.7838 (mmtp) REVERT: X 555 LYS cc_start: 0.8303 (OUTLIER) cc_final: 0.7773 (ptpt) outliers start: 115 outliers final: 60 residues processed: 1050 average time/residue: 1.8201 time to fit residues: 2449.2163 Evaluate side-chains 1089 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 998 time to evaluate : 6.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ARG Chi-restraints excluded: chain A residue 66 LYS Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 219 LYS Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 503 ILE Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain G residue 51 LYS Chi-restraints excluded: chain G residue 80 GLU Chi-restraints excluded: chain G residue 128 SER Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain I residue 21 ARG Chi-restraints excluded: chain I residue 128 SER Chi-restraints excluded: chain I residue 170 SER Chi-restraints excluded: chain I residue 183 SER Chi-restraints excluded: chain K residue 80 GLU Chi-restraints excluded: chain K residue 125 LYS Chi-restraints excluded: chain M residue 21 ARG Chi-restraints excluded: chain M residue 130 LYS Chi-restraints excluded: chain O residue 128 SER Chi-restraints excluded: chain O residue 170 SER Chi-restraints excluded: chain Q residue 68 ASP Chi-restraints excluded: chain Q residue 80 GLU Chi-restraints excluded: chain Q residue 128 SER Chi-restraints excluded: chain Q residue 170 SER Chi-restraints excluded: chain S residue 29 LYS Chi-restraints excluded: chain S residue 44 MET Chi-restraints excluded: chain S residue 62 ARG Chi-restraints excluded: chain S residue 128 SER Chi-restraints excluded: chain S residue 170 SER Chi-restraints excluded: chain U residue 44 MET Chi-restraints excluded: chain U residue 116 GLU Chi-restraints excluded: chain U residue 209 GLU Chi-restraints excluded: chain W residue 128 SER Chi-restraints excluded: chain W residue 183 SER Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 8 GLU Chi-restraints excluded: chain J residue 27 ASP Chi-restraints excluded: chain J residue 396 ASP Chi-restraints excluded: chain J residue 433 ASP Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain D residue 396 ASP Chi-restraints excluded: chain D residue 421 GLU Chi-restraints excluded: chain D residue 469 THR Chi-restraints excluded: chain D residue 537 GLU Chi-restraints excluded: chain F residue 316 ASP Chi-restraints excluded: chain F residue 396 ASP Chi-restraints excluded: chain F residue 559 LYS Chi-restraints excluded: chain H residue 27 ASP Chi-restraints excluded: chain H residue 311 GLU Chi-restraints excluded: chain H residue 396 ASP Chi-restraints excluded: chain L residue 27 ASP Chi-restraints excluded: chain L residue 60 ASN Chi-restraints excluded: chain L residue 276 GLU Chi-restraints excluded: chain L residue 396 ASP Chi-restraints excluded: chain L residue 555 LYS Chi-restraints excluded: chain N residue 27 ASP Chi-restraints excluded: chain N residue 98 LYS Chi-restraints excluded: chain N residue 212 GLU Chi-restraints excluded: chain N residue 240 LYS Chi-restraints excluded: chain N residue 316 ASP Chi-restraints excluded: chain N residue 396 ASP Chi-restraints excluded: chain N residue 421 GLU Chi-restraints excluded: chain P residue 98 LYS Chi-restraints excluded: chain P residue 276 GLU Chi-restraints excluded: chain P residue 319 MET Chi-restraints excluded: chain P residue 366 MET Chi-restraints excluded: chain P residue 396 ASP Chi-restraints excluded: chain P residue 421 GLU Chi-restraints excluded: chain R residue 98 LYS Chi-restraints excluded: chain R residue 212 GLU Chi-restraints excluded: chain R residue 391 LYS Chi-restraints excluded: chain R residue 396 ASP Chi-restraints excluded: chain T residue 98 LYS Chi-restraints excluded: chain T residue 240 LYS Chi-restraints excluded: chain T residue 396 ASP Chi-restraints excluded: chain V residue 276 GLU Chi-restraints excluded: chain V residue 338 ARG Chi-restraints excluded: chain V residue 396 ASP Chi-restraints excluded: chain V residue 421 GLU Chi-restraints excluded: chain V residue 444 VAL Chi-restraints excluded: chain X residue 236 ASP Chi-restraints excluded: chain X residue 396 ASP Chi-restraints excluded: chain X residue 555 LYS Chi-restraints excluded: chain X residue 565 LEU 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: 0.9990 chunk 693 optimal weight: 0.2980 chunk 111 optimal weight: 6.9990 chunk 208 optimal weight: 6.9990 chunk 753 optimal weight: 5.9990 chunk 315 optimal weight: 10.0000 chunk 773 optimal weight: 0.0980 chunk 95 optimal weight: 10.0000 chunk 138 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 D 383 ASN F 34 HIS F 309 ASN F 333 GLN F 383 ASN H 34 HIS H 309 ASN L 34 HIS L 309 ASN L 314 HIS N 34 HIS R 34 HIS R 60 ASN R 383 ASN ** R 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 34 HIS T 314 HIS V 34 HIS ** V 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 314 HIS V 333 GLN V 539 ASN V 544 HIS X 309 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.126009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.100695 restraints weight = 76149.890| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 1.42 r_work: 0.3110 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 75888 Z= 0.158 Angle : 0.503 9.371 102348 Z= 0.271 Chirality : 0.045 0.231 11400 Planarity : 0.004 0.049 13404 Dihedral : 4.879 45.468 10359 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.34 % Allowed : 14.15 % Favored : 84.51 % 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: 0.35 (0.08), residues: 9600 helix: 1.22 (0.10), residues: 2880 sheet: 0.62 (0.15), residues: 1044 loop : -0.32 (0.08), residues: 5676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP P 181 HIS 0.006 0.001 HIS B 248 PHE 0.019 0.001 PHE A 198 TYR 0.022 0.001 TYR C 15 ARG 0.010 0.000 ARG S 21 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 33420.10 seconds wall clock time: 580 minutes 30.24 seconds (34830.24 seconds total)