Starting phenix.real_space_refine on Mon Mar 11 09:20:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a8e_15230/03_2024/8a8e_15230.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a8e_15230/03_2024/8a8e_15230.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a8e_15230/03_2024/8a8e_15230.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a8e_15230/03_2024/8a8e_15230.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a8e_15230/03_2024/8a8e_15230.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a8e_15230/03_2024/8a8e_15230.pdb" } resolution = 2.9 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= 0.003 sd= 0.014 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: 4 Type Number sf(0) Gaussians S 264 5.16 5 C 35832 2.51 5 N 10032 2.21 5 O 10440 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 37": "OE1" <-> "OE2" Residue "A GLU 57": "OE1" <-> "OE2" Residue "A GLU 65": "OE1" <-> "OE2" Residue "A PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 90": "OE1" <-> "OE2" Residue "A GLU 98": "OE1" <-> "OE2" Residue "A GLU 121": "OE1" <-> "OE2" Residue "A GLU 167": "OE1" <-> "OE2" Residue "A GLU 217": "OE1" <-> "OE2" Residue "A GLU 225": "OE1" <-> "OE2" Residue "A GLU 247": "OE1" <-> "OE2" Residue "A ARG 283": "NH1" <-> "NH2" Residue "A GLU 289": "OE1" <-> "OE2" Residue "A GLU 290": "OE1" <-> "OE2" Residue "A GLU 296": "OE1" <-> "OE2" Residue "B GLU 37": "OE1" <-> "OE2" Residue "B GLU 57": "OE1" <-> "OE2" Residue "B GLU 65": "OE1" <-> "OE2" Residue "B PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 90": "OE1" <-> "OE2" Residue "B GLU 98": "OE1" <-> "OE2" Residue "B GLU 121": "OE1" <-> "OE2" Residue "B GLU 167": "OE1" <-> "OE2" Residue "B GLU 217": "OE1" <-> "OE2" Residue "B GLU 225": "OE1" <-> "OE2" Residue "B GLU 247": "OE1" <-> "OE2" Residue "B ARG 283": "NH1" <-> "NH2" Residue "B GLU 289": "OE1" <-> "OE2" Residue "B GLU 290": "OE1" <-> "OE2" Residue "B GLU 296": "OE1" <-> "OE2" Residue "C GLU 37": "OE1" <-> "OE2" Residue "C GLU 57": "OE1" <-> "OE2" Residue "C GLU 65": "OE1" <-> "OE2" Residue "C PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 90": "OE1" <-> "OE2" Residue "C GLU 98": "OE1" <-> "OE2" Residue "C GLU 121": "OE1" <-> "OE2" Residue "C GLU 167": "OE1" <-> "OE2" Residue "C GLU 217": "OE1" <-> "OE2" Residue "C GLU 225": "OE1" <-> "OE2" Residue "C GLU 247": "OE1" <-> "OE2" Residue "C ARG 283": "NH1" <-> "NH2" Residue "C GLU 289": "OE1" <-> "OE2" Residue "C GLU 290": "OE1" <-> "OE2" Residue "C GLU 296": "OE1" <-> "OE2" Residue "D GLU 37": "OE1" <-> "OE2" Residue "D GLU 57": "OE1" <-> "OE2" Residue "D GLU 65": "OE1" <-> "OE2" Residue "D PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 90": "OE1" <-> "OE2" Residue "D GLU 98": "OE1" <-> "OE2" Residue "D GLU 121": "OE1" <-> "OE2" Residue "D GLU 167": "OE1" <-> "OE2" Residue "D GLU 217": "OE1" <-> "OE2" Residue "D GLU 225": "OE1" <-> "OE2" Residue "D GLU 247": "OE1" <-> "OE2" Residue "D ARG 283": "NH1" <-> "NH2" Residue "D GLU 289": "OE1" <-> "OE2" Residue "D GLU 290": "OE1" <-> "OE2" Residue "D GLU 296": "OE1" <-> "OE2" Residue "E GLU 37": "OE1" <-> "OE2" Residue "E GLU 57": "OE1" <-> "OE2" Residue "E GLU 65": "OE1" <-> "OE2" Residue "E PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 90": "OE1" <-> "OE2" Residue "E GLU 98": "OE1" <-> "OE2" Residue "E GLU 121": "OE1" <-> "OE2" Residue "E GLU 167": "OE1" <-> "OE2" Residue "E GLU 217": "OE1" <-> "OE2" Residue "E GLU 225": "OE1" <-> "OE2" Residue "E GLU 247": "OE1" <-> "OE2" Residue "E ARG 283": "NH1" <-> "NH2" Residue "E GLU 289": "OE1" <-> "OE2" Residue "E GLU 290": "OE1" <-> "OE2" Residue "E GLU 296": "OE1" <-> "OE2" Residue "F GLU 37": "OE1" <-> "OE2" Residue "F GLU 57": "OE1" <-> "OE2" Residue "F GLU 65": "OE1" <-> "OE2" Residue "F PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 90": "OE1" <-> "OE2" Residue "F GLU 98": "OE1" <-> "OE2" Residue "F GLU 121": "OE1" <-> "OE2" Residue "F GLU 167": "OE1" <-> "OE2" Residue "F GLU 217": "OE1" <-> "OE2" Residue "F GLU 225": "OE1" <-> "OE2" Residue "F GLU 247": "OE1" <-> "OE2" Residue "F ARG 283": "NH1" <-> "NH2" Residue "F GLU 289": "OE1" <-> "OE2" Residue "F GLU 290": "OE1" <-> "OE2" Residue "F GLU 296": "OE1" <-> "OE2" Residue "G GLU 37": "OE1" <-> "OE2" Residue "G GLU 57": "OE1" <-> "OE2" Residue "G GLU 65": "OE1" <-> "OE2" Residue "G PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 90": "OE1" <-> "OE2" Residue "G GLU 98": "OE1" <-> "OE2" Residue "G GLU 121": "OE1" <-> "OE2" Residue "G GLU 167": "OE1" <-> "OE2" Residue "G GLU 217": "OE1" <-> "OE2" Residue "G GLU 225": "OE1" <-> "OE2" Residue "G GLU 247": "OE1" <-> "OE2" Residue "G ARG 283": "NH1" <-> "NH2" Residue "G GLU 289": "OE1" <-> "OE2" Residue "G GLU 290": "OE1" <-> "OE2" Residue "G GLU 296": "OE1" <-> "OE2" Residue "H GLU 37": "OE1" <-> "OE2" Residue "H GLU 57": "OE1" <-> "OE2" Residue "H GLU 65": "OE1" <-> "OE2" Residue "H PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 90": "OE1" <-> "OE2" Residue "H GLU 98": "OE1" <-> "OE2" Residue "H GLU 121": "OE1" <-> "OE2" Residue "H GLU 167": "OE1" <-> "OE2" Residue "H GLU 217": "OE1" <-> "OE2" Residue "H GLU 225": "OE1" <-> "OE2" Residue "H GLU 247": "OE1" <-> "OE2" Residue "H ARG 283": "NH1" <-> "NH2" Residue "H GLU 289": "OE1" <-> "OE2" Residue "H GLU 290": "OE1" <-> "OE2" Residue "H GLU 296": "OE1" <-> "OE2" Residue "I GLU 37": "OE1" <-> "OE2" Residue "I GLU 57": "OE1" <-> "OE2" Residue "I GLU 65": "OE1" <-> "OE2" Residue "I PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 90": "OE1" <-> "OE2" Residue "I GLU 98": "OE1" <-> "OE2" Residue "I GLU 121": "OE1" <-> "OE2" Residue "I GLU 167": "OE1" <-> "OE2" Residue "I GLU 217": "OE1" <-> "OE2" Residue "I GLU 225": "OE1" <-> "OE2" Residue "I GLU 247": "OE1" <-> "OE2" Residue "I ARG 283": "NH1" <-> "NH2" Residue "I GLU 289": "OE1" <-> "OE2" Residue "I GLU 290": "OE1" <-> "OE2" Residue "I GLU 296": "OE1" <-> "OE2" Residue "J GLU 37": "OE1" <-> "OE2" Residue "J GLU 57": "OE1" <-> "OE2" Residue "J GLU 65": "OE1" <-> "OE2" Residue "J PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 90": "OE1" <-> "OE2" Residue "J GLU 98": "OE1" <-> "OE2" Residue "J GLU 121": "OE1" <-> "OE2" Residue "J GLU 167": "OE1" <-> "OE2" Residue "J GLU 217": "OE1" <-> "OE2" Residue "J GLU 225": "OE1" <-> "OE2" Residue "J GLU 247": "OE1" <-> "OE2" Residue "J ARG 283": "NH1" <-> "NH2" Residue "J GLU 289": "OE1" <-> "OE2" Residue "J GLU 290": "OE1" <-> "OE2" Residue "J GLU 296": "OE1" <-> "OE2" Residue "K GLU 37": "OE1" <-> "OE2" Residue "K GLU 57": "OE1" <-> "OE2" Residue "K GLU 65": "OE1" <-> "OE2" Residue "K PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 90": "OE1" <-> "OE2" Residue "K GLU 98": "OE1" <-> "OE2" Residue "K GLU 121": "OE1" <-> "OE2" Residue "K GLU 167": "OE1" <-> "OE2" Residue "K GLU 217": "OE1" <-> "OE2" Residue "K GLU 225": "OE1" <-> "OE2" Residue "K GLU 247": "OE1" <-> "OE2" Residue "K ARG 283": "NH1" <-> "NH2" Residue "K GLU 289": "OE1" <-> "OE2" Residue "K GLU 290": "OE1" <-> "OE2" Residue "K GLU 296": "OE1" <-> "OE2" Residue "L GLU 37": "OE1" <-> "OE2" Residue "L GLU 57": "OE1" <-> "OE2" Residue "L GLU 65": "OE1" <-> "OE2" Residue "L PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 90": "OE1" <-> "OE2" Residue "L GLU 98": "OE1" <-> "OE2" Residue "L GLU 121": "OE1" <-> "OE2" Residue "L GLU 167": "OE1" <-> "OE2" Residue "L GLU 217": "OE1" <-> "OE2" Residue "L GLU 225": "OE1" <-> "OE2" Residue "L GLU 247": "OE1" <-> "OE2" Residue "L ARG 283": "NH1" <-> "NH2" Residue "L GLU 289": "OE1" <-> "OE2" Residue "L GLU 290": "OE1" <-> "OE2" Residue "L GLU 296": "OE1" <-> "OE2" Residue "M GLU 37": "OE1" <-> "OE2" Residue "M GLU 57": "OE1" <-> "OE2" Residue "M GLU 65": "OE1" <-> "OE2" Residue "M PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 90": "OE1" <-> "OE2" Residue "M GLU 98": "OE1" <-> "OE2" Residue "M GLU 121": "OE1" <-> "OE2" Residue "M GLU 167": "OE1" <-> "OE2" Residue "M GLU 217": "OE1" <-> "OE2" Residue "M GLU 225": "OE1" <-> "OE2" Residue "M GLU 247": "OE1" <-> "OE2" Residue "M ARG 283": "NH1" <-> "NH2" Residue "M GLU 289": "OE1" <-> "OE2" Residue "M GLU 290": "OE1" <-> "OE2" Residue "M GLU 296": "OE1" <-> "OE2" Residue "N GLU 37": "OE1" <-> "OE2" Residue "N GLU 57": "OE1" <-> "OE2" Residue "N GLU 65": "OE1" <-> "OE2" Residue "N PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 90": "OE1" <-> "OE2" Residue "N GLU 98": "OE1" <-> "OE2" Residue "N GLU 121": "OE1" <-> "OE2" Residue "N GLU 167": "OE1" <-> "OE2" Residue "N GLU 217": "OE1" <-> "OE2" Residue "N GLU 225": "OE1" <-> "OE2" Residue "N GLU 247": "OE1" <-> "OE2" Residue "N ARG 283": "NH1" <-> "NH2" Residue "N GLU 289": "OE1" <-> "OE2" Residue "N GLU 290": "OE1" <-> "OE2" Residue "N GLU 296": "OE1" <-> "OE2" Residue "O GLU 37": "OE1" <-> "OE2" Residue "O GLU 57": "OE1" <-> "OE2" Residue "O GLU 65": "OE1" <-> "OE2" Residue "O PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 90": "OE1" <-> "OE2" Residue "O GLU 98": "OE1" <-> "OE2" Residue "O GLU 121": "OE1" <-> "OE2" Residue "O GLU 167": "OE1" <-> "OE2" Residue "O GLU 217": "OE1" <-> "OE2" Residue "O GLU 225": "OE1" <-> "OE2" Residue "O GLU 247": "OE1" <-> "OE2" Residue "O ARG 283": "NH1" <-> "NH2" Residue "O GLU 289": "OE1" <-> "OE2" Residue "O GLU 290": "OE1" <-> "OE2" Residue "O GLU 296": "OE1" <-> "OE2" Residue "P GLU 37": "OE1" <-> "OE2" Residue "P GLU 57": "OE1" <-> "OE2" Residue "P GLU 65": "OE1" <-> "OE2" Residue "P PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 90": "OE1" <-> "OE2" Residue "P GLU 98": "OE1" <-> "OE2" Residue "P GLU 121": "OE1" <-> "OE2" Residue "P GLU 167": "OE1" <-> "OE2" Residue "P GLU 217": "OE1" <-> "OE2" Residue "P GLU 225": "OE1" <-> "OE2" Residue "P GLU 247": "OE1" <-> "OE2" Residue "P ARG 283": "NH1" <-> "NH2" Residue "P GLU 289": "OE1" <-> "OE2" Residue "P GLU 290": "OE1" <-> "OE2" Residue "P GLU 296": "OE1" <-> "OE2" Residue "Q GLU 37": "OE1" <-> "OE2" Residue "Q GLU 57": "OE1" <-> "OE2" Residue "Q GLU 65": "OE1" <-> "OE2" Residue "Q PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 90": "OE1" <-> "OE2" Residue "Q GLU 98": "OE1" <-> "OE2" Residue "Q GLU 121": "OE1" <-> "OE2" Residue "Q GLU 167": "OE1" <-> "OE2" Residue "Q GLU 217": "OE1" <-> "OE2" Residue "Q GLU 225": "OE1" <-> "OE2" Residue "Q GLU 247": "OE1" <-> "OE2" Residue "Q ARG 283": "NH1" <-> "NH2" Residue "Q GLU 289": "OE1" <-> "OE2" Residue "Q GLU 290": "OE1" <-> "OE2" Residue "Q GLU 296": "OE1" <-> "OE2" Residue "R GLU 37": "OE1" <-> "OE2" Residue "R GLU 57": "OE1" <-> "OE2" Residue "R GLU 65": "OE1" <-> "OE2" Residue "R PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 90": "OE1" <-> "OE2" Residue "R GLU 98": "OE1" <-> "OE2" Residue "R GLU 121": "OE1" <-> "OE2" Residue "R GLU 167": "OE1" <-> "OE2" Residue "R GLU 217": "OE1" <-> "OE2" Residue "R GLU 225": "OE1" <-> "OE2" Residue "R GLU 247": "OE1" <-> "OE2" Residue "R ARG 283": "NH1" <-> "NH2" Residue "R GLU 289": "OE1" <-> "OE2" Residue "R GLU 290": "OE1" <-> "OE2" Residue "R GLU 296": "OE1" <-> "OE2" Residue "S GLU 37": "OE1" <-> "OE2" Residue "S GLU 57": "OE1" <-> "OE2" Residue "S GLU 65": "OE1" <-> "OE2" Residue "S PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 90": "OE1" <-> "OE2" Residue "S GLU 98": "OE1" <-> "OE2" Residue "S GLU 121": "OE1" <-> "OE2" Residue "S GLU 167": "OE1" <-> "OE2" Residue "S GLU 217": "OE1" <-> "OE2" Residue "S GLU 225": "OE1" <-> "OE2" Residue "S GLU 247": "OE1" <-> "OE2" Residue "S ARG 283": "NH1" <-> "NH2" Residue "S GLU 289": "OE1" <-> "OE2" Residue "S GLU 290": "OE1" <-> "OE2" Residue "S GLU 296": "OE1" <-> "OE2" Residue "T GLU 37": "OE1" <-> "OE2" Residue "T GLU 57": "OE1" <-> "OE2" Residue "T GLU 65": "OE1" <-> "OE2" Residue "T PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 90": "OE1" <-> "OE2" Residue "T GLU 98": "OE1" <-> "OE2" Residue "T GLU 121": "OE1" <-> "OE2" Residue "T GLU 167": "OE1" <-> "OE2" Residue "T GLU 217": "OE1" <-> "OE2" Residue "T GLU 225": "OE1" <-> "OE2" Residue "T GLU 247": "OE1" <-> "OE2" Residue "T ARG 283": "NH1" <-> "NH2" Residue "T GLU 289": "OE1" <-> "OE2" Residue "T GLU 290": "OE1" <-> "OE2" Residue "T GLU 296": "OE1" <-> "OE2" Residue "U GLU 37": "OE1" <-> "OE2" Residue "U GLU 57": "OE1" <-> "OE2" Residue "U GLU 65": "OE1" <-> "OE2" Residue "U PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 90": "OE1" <-> "OE2" Residue "U GLU 98": "OE1" <-> "OE2" Residue "U GLU 121": "OE1" <-> "OE2" Residue "U GLU 167": "OE1" <-> "OE2" Residue "U GLU 217": "OE1" <-> "OE2" Residue "U GLU 225": "OE1" <-> "OE2" Residue "U GLU 247": "OE1" <-> "OE2" Residue "U ARG 283": "NH1" <-> "NH2" Residue "U GLU 289": "OE1" <-> "OE2" Residue "U GLU 290": "OE1" <-> "OE2" Residue "U GLU 296": "OE1" <-> "OE2" Residue "V GLU 37": "OE1" <-> "OE2" Residue "V GLU 57": "OE1" <-> "OE2" Residue "V GLU 65": "OE1" <-> "OE2" Residue "V PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 90": "OE1" <-> "OE2" Residue "V GLU 98": "OE1" <-> "OE2" Residue "V GLU 121": "OE1" <-> "OE2" Residue "V GLU 167": "OE1" <-> "OE2" Residue "V GLU 217": "OE1" <-> "OE2" Residue "V GLU 225": "OE1" <-> "OE2" Residue "V GLU 247": "OE1" <-> "OE2" Residue "V ARG 283": "NH1" <-> "NH2" Residue "V GLU 289": "OE1" <-> "OE2" Residue "V GLU 290": "OE1" <-> "OE2" Residue "V GLU 296": "OE1" <-> "OE2" Residue "W GLU 37": "OE1" <-> "OE2" Residue "W GLU 57": "OE1" <-> "OE2" Residue "W GLU 65": "OE1" <-> "OE2" Residue "W PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 90": "OE1" <-> "OE2" Residue "W GLU 98": "OE1" <-> "OE2" Residue "W GLU 121": "OE1" <-> "OE2" Residue "W GLU 167": "OE1" <-> "OE2" Residue "W GLU 217": "OE1" <-> "OE2" Residue "W GLU 225": "OE1" <-> "OE2" Residue "W GLU 247": "OE1" <-> "OE2" Residue "W ARG 283": "NH1" <-> "NH2" Residue "W GLU 289": "OE1" <-> "OE2" Residue "W GLU 290": "OE1" <-> "OE2" Residue "W GLU 296": "OE1" <-> "OE2" Residue "X GLU 37": "OE1" <-> "OE2" Residue "X GLU 57": "OE1" <-> "OE2" Residue "X GLU 65": "OE1" <-> "OE2" Residue "X PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 90": "OE1" <-> "OE2" Residue "X GLU 98": "OE1" <-> "OE2" Residue "X GLU 121": "OE1" <-> "OE2" Residue "X GLU 167": "OE1" <-> "OE2" Residue "X GLU 217": "OE1" <-> "OE2" Residue "X GLU 225": "OE1" <-> "OE2" Residue "X GLU 247": "OE1" <-> "OE2" Residue "X ARG 283": "NH1" <-> "NH2" Residue "X GLU 289": "OE1" <-> "OE2" Residue "X GLU 290": "OE1" <-> "OE2" Residue "X GLU 296": "OE1" <-> "OE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 56568 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 2357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2357 Classifications: {'peptide': 302} Link IDs: {'PTRANS': 17, 'TRANS': 284} Chain: "B" Number of atoms: 2357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2357 Classifications: {'peptide': 302} Link IDs: {'PTRANS': 17, 'TRANS': 284} Chain: "C" Number of atoms: 2357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2357 Classifications: {'peptide': 302} Link IDs: {'PTRANS': 17, 'TRANS': 284} Chain: "D" Number of atoms: 2357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2357 Classifications: {'peptide': 302} Link IDs: {'PTRANS': 17, 'TRANS': 284} Chain: "E" Number of atoms: 2357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2357 Classifications: {'peptide': 302} Link IDs: {'PTRANS': 17, 'TRANS': 284} Chain: "F" Number of atoms: 2357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2357 Classifications: {'peptide': 302} Link IDs: {'PTRANS': 17, 'TRANS': 284} Chain: "G" Number of atoms: 2357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2357 Classifications: {'peptide': 302} Link IDs: {'PTRANS': 17, 'TRANS': 284} Chain: "H" Number of atoms: 2357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2357 Classifications: {'peptide': 302} Link IDs: {'PTRANS': 17, 'TRANS': 284} Chain: "I" Number of atoms: 2357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2357 Classifications: {'peptide': 302} Link IDs: {'PTRANS': 17, 'TRANS': 284} Chain: "J" Number of atoms: 2357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2357 Classifications: {'peptide': 302} Link IDs: {'PTRANS': 17, 'TRANS': 284} Chain: "K" Number of atoms: 2357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2357 Classifications: {'peptide': 302} Link IDs: {'PTRANS': 17, 'TRANS': 284} Chain: "L" Number of atoms: 2357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2357 Classifications: {'peptide': 302} Link IDs: {'PTRANS': 17, 'TRANS': 284} Chain: "M" Number of atoms: 2357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2357 Classifications: {'peptide': 302} Link IDs: {'PTRANS': 17, 'TRANS': 284} Chain: "N" Number of atoms: 2357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2357 Classifications: {'peptide': 302} Link IDs: {'PTRANS': 17, 'TRANS': 284} Chain: "O" Number of atoms: 2357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2357 Classifications: {'peptide': 302} Link IDs: {'PTRANS': 17, 'TRANS': 284} Chain: "P" Number of atoms: 2357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2357 Classifications: {'peptide': 302} Link IDs: {'PTRANS': 17, 'TRANS': 284} Chain: "Q" Number of atoms: 2357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2357 Classifications: {'peptide': 302} Link IDs: {'PTRANS': 17, 'TRANS': 284} Chain: "R" Number of atoms: 2357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2357 Classifications: {'peptide': 302} Link IDs: {'PTRANS': 17, 'TRANS': 284} Chain: "S" Number of atoms: 2357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2357 Classifications: {'peptide': 302} Link IDs: {'PTRANS': 17, 'TRANS': 284} Chain: "T" Number of atoms: 2357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2357 Classifications: {'peptide': 302} Link IDs: {'PTRANS': 17, 'TRANS': 284} Chain: "U" Number of atoms: 2357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2357 Classifications: {'peptide': 302} Link IDs: {'PTRANS': 17, 'TRANS': 284} Chain: "V" Number of atoms: 2357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2357 Classifications: {'peptide': 302} Link IDs: {'PTRANS': 17, 'TRANS': 284} Chain: "W" Number of atoms: 2357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2357 Classifications: {'peptide': 302} Link IDs: {'PTRANS': 17, 'TRANS': 284} Chain: "X" Number of atoms: 2357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2357 Classifications: {'peptide': 302} Link IDs: {'PTRANS': 17, 'TRANS': 284} Time building chain proxies: 21.45, per 1000 atoms: 0.38 Number of scatterers: 56568 At special positions: 0 Unit cell: (165, 165, 165, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 264 16.00 O 10440 8.00 N 10032 7.00 C 35832 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: 15.61 Conformation dependent library (CDL) restraints added in 8.0 seconds 14400 Ramachandran restraints generated. 7200 Oldfield, 0 Emsley, 7200 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13392 Finding SS restraints... Secondary structure from input PDB file: 408 helices and 24 sheets defined 59.9% alpha, 10.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.65 Creating SS restraints... Processing helix chain 'A' and resid 20 through 25 Processing helix chain 'A' and resid 36 through 41 Processing helix chain 'A' and resid 46 through 54 Processing helix chain 'A' and resid 55 through 74 removed outlier: 3.956A pdb=" N LEU A 59 " --> pdb=" O LYS A 55 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL A 70 " --> pdb=" O GLY A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 91 Processing helix chain 'A' and resid 105 through 109 removed outlier: 3.823A pdb=" N GLY A 109 " --> pdb=" O PRO A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 119 removed outlier: 3.694A pdb=" N ARG A 115 " --> pdb=" O ARG A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 135 removed outlier: 4.537A pdb=" N LEU A 123 " --> pdb=" O GLN A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 164 removed outlier: 3.944A pdb=" N ILE A 154 " --> pdb=" O HIS A 150 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL A 164 " --> pdb=" O ILE A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 186 Processing helix chain 'A' and resid 186 through 192 removed outlier: 3.726A pdb=" N LEU A 190 " --> pdb=" O ILE A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 211 Processing helix chain 'A' and resid 219 through 223 removed outlier: 3.517A pdb=" N LEU A 222 " --> pdb=" O VAL A 219 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR A 223 " --> pdb=" O ALA A 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 219 through 223' Processing helix chain 'A' and resid 227 through 245 Processing helix chain 'A' and resid 253 through 256 removed outlier: 3.511A pdb=" N SER A 256 " --> pdb=" O GLN A 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 253 through 256' Processing helix chain 'A' and resid 257 through 268 Processing helix chain 'A' and resid 278 through 302 Processing helix chain 'B' and resid 20 through 25 Processing helix chain 'B' and resid 36 through 41 Processing helix chain 'B' and resid 46 through 54 Processing helix chain 'B' and resid 55 through 74 removed outlier: 3.956A pdb=" N LEU B 59 " --> pdb=" O LYS B 55 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL B 70 " --> pdb=" O GLY B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 91 Processing helix chain 'B' and resid 105 through 109 removed outlier: 3.823A pdb=" N GLY B 109 " --> pdb=" O PRO B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 119 removed outlier: 3.694A pdb=" N ARG B 115 " --> pdb=" O ARG B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 135 removed outlier: 4.537A pdb=" N LEU B 123 " --> pdb=" O GLN B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 164 removed outlier: 3.944A pdb=" N ILE B 154 " --> pdb=" O HIS B 150 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL B 164 " --> pdb=" O ILE B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 186 Processing helix chain 'B' and resid 186 through 192 removed outlier: 3.726A pdb=" N LEU B 190 " --> pdb=" O ILE B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 211 Processing helix chain 'B' and resid 219 through 223 removed outlier: 3.517A pdb=" N LEU B 222 " --> pdb=" O VAL B 219 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR B 223 " --> pdb=" O ALA B 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 219 through 223' Processing helix chain 'B' and resid 227 through 245 Processing helix chain 'B' and resid 253 through 256 removed outlier: 3.511A pdb=" N SER B 256 " --> pdb=" O GLN B 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 253 through 256' Processing helix chain 'B' and resid 257 through 268 Processing helix chain 'B' and resid 278 through 302 Processing helix chain 'C' and resid 20 through 25 Processing helix chain 'C' and resid 36 through 41 Processing helix chain 'C' and resid 46 through 54 Processing helix chain 'C' and resid 55 through 74 removed outlier: 3.956A pdb=" N LEU C 59 " --> pdb=" O LYS C 55 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL C 70 " --> pdb=" O GLY C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 91 Processing helix chain 'C' and resid 105 through 109 removed outlier: 3.823A pdb=" N GLY C 109 " --> pdb=" O PRO C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 119 removed outlier: 3.694A pdb=" N ARG C 115 " --> pdb=" O ARG C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 135 removed outlier: 4.537A pdb=" N LEU C 123 " --> pdb=" O GLN C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 164 removed outlier: 3.944A pdb=" N ILE C 154 " --> pdb=" O HIS C 150 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL C 164 " --> pdb=" O ILE C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 186 Processing helix chain 'C' and resid 186 through 192 removed outlier: 3.726A pdb=" N LEU C 190 " --> pdb=" O ILE C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 211 Processing helix chain 'C' and resid 219 through 223 removed outlier: 3.517A pdb=" N LEU C 222 " --> pdb=" O VAL C 219 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR C 223 " --> pdb=" O ALA C 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 219 through 223' Processing helix chain 'C' and resid 227 through 245 Processing helix chain 'C' and resid 253 through 256 removed outlier: 3.511A pdb=" N SER C 256 " --> pdb=" O GLN C 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 253 through 256' Processing helix chain 'C' and resid 257 through 268 Processing helix chain 'C' and resid 278 through 302 Processing helix chain 'D' and resid 20 through 25 Processing helix chain 'D' and resid 36 through 41 Processing helix chain 'D' and resid 46 through 54 Processing helix chain 'D' and resid 55 through 74 removed outlier: 3.956A pdb=" N LEU D 59 " --> pdb=" O LYS D 55 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL D 70 " --> pdb=" O GLY D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'D' and resid 105 through 109 removed outlier: 3.823A pdb=" N GLY D 109 " --> pdb=" O PRO D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 119 removed outlier: 3.694A pdb=" N ARG D 115 " --> pdb=" O ARG D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 135 removed outlier: 4.537A pdb=" N LEU D 123 " --> pdb=" O GLN D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 164 removed outlier: 3.944A pdb=" N ILE D 154 " --> pdb=" O HIS D 150 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL D 164 " --> pdb=" O ILE D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 186 Processing helix chain 'D' and resid 186 through 192 removed outlier: 3.726A pdb=" N LEU D 190 " --> pdb=" O ILE D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 211 Processing helix chain 'D' and resid 219 through 223 removed outlier: 3.517A pdb=" N LEU D 222 " --> pdb=" O VAL D 219 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR D 223 " --> pdb=" O ALA D 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 219 through 223' Processing helix chain 'D' and resid 227 through 245 Processing helix chain 'D' and resid 253 through 256 removed outlier: 3.511A pdb=" N SER D 256 " --> pdb=" O GLN D 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 253 through 256' Processing helix chain 'D' and resid 257 through 268 Processing helix chain 'D' and resid 278 through 302 Processing helix chain 'E' and resid 20 through 25 Processing helix chain 'E' and resid 36 through 41 Processing helix chain 'E' and resid 46 through 54 Processing helix chain 'E' and resid 55 through 74 removed outlier: 3.956A pdb=" N LEU E 59 " --> pdb=" O LYS E 55 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL E 70 " --> pdb=" O GLY E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'E' and resid 105 through 109 removed outlier: 3.823A pdb=" N GLY E 109 " --> pdb=" O PRO E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 119 removed outlier: 3.694A pdb=" N ARG E 115 " --> pdb=" O ARG E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 119 through 135 removed outlier: 4.537A pdb=" N LEU E 123 " --> pdb=" O GLN E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 150 through 164 removed outlier: 3.944A pdb=" N ILE E 154 " --> pdb=" O HIS E 150 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL E 164 " --> pdb=" O ILE E 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 180 through 186 Processing helix chain 'E' and resid 186 through 192 removed outlier: 3.726A pdb=" N LEU E 190 " --> pdb=" O ILE E 186 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 211 Processing helix chain 'E' and resid 219 through 223 removed outlier: 3.517A pdb=" N LEU E 222 " --> pdb=" O VAL E 219 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR E 223 " --> pdb=" O ALA E 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 219 through 223' Processing helix chain 'E' and resid 227 through 245 Processing helix chain 'E' and resid 253 through 256 removed outlier: 3.511A pdb=" N SER E 256 " --> pdb=" O GLN E 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 253 through 256' Processing helix chain 'E' and resid 257 through 268 Processing helix chain 'E' and resid 278 through 302 Processing helix chain 'F' and resid 20 through 25 Processing helix chain 'F' and resid 36 through 41 Processing helix chain 'F' and resid 46 through 54 Processing helix chain 'F' and resid 55 through 74 removed outlier: 3.956A pdb=" N LEU F 59 " --> pdb=" O LYS F 55 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL F 70 " --> pdb=" O GLY F 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 91 Processing helix chain 'F' and resid 105 through 109 removed outlier: 3.823A pdb=" N GLY F 109 " --> pdb=" O PRO F 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 119 removed outlier: 3.694A pdb=" N ARG F 115 " --> pdb=" O ARG F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 119 through 135 removed outlier: 4.537A pdb=" N LEU F 123 " --> pdb=" O GLN F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 150 through 164 removed outlier: 3.944A pdb=" N ILE F 154 " --> pdb=" O HIS F 150 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL F 164 " --> pdb=" O ILE F 160 " (cutoff:3.500A) Processing helix chain 'F' and resid 180 through 186 Processing helix chain 'F' and resid 186 through 192 removed outlier: 3.726A pdb=" N LEU F 190 " --> pdb=" O ILE F 186 " (cutoff:3.500A) Processing helix chain 'F' and resid 202 through 211 Processing helix chain 'F' and resid 219 through 223 removed outlier: 3.517A pdb=" N LEU F 222 " --> pdb=" O VAL F 219 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR F 223 " --> pdb=" O ALA F 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 219 through 223' Processing helix chain 'F' and resid 227 through 245 Processing helix chain 'F' and resid 253 through 256 removed outlier: 3.511A pdb=" N SER F 256 " --> pdb=" O GLN F 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 253 through 256' Processing helix chain 'F' and resid 257 through 268 Processing helix chain 'F' and resid 278 through 302 Processing helix chain 'G' and resid 20 through 25 Processing helix chain 'G' and resid 36 through 41 Processing helix chain 'G' and resid 46 through 54 Processing helix chain 'G' and resid 55 through 74 removed outlier: 3.956A pdb=" N LEU G 59 " --> pdb=" O LYS G 55 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL G 70 " --> pdb=" O GLY G 66 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 91 Processing helix chain 'G' and resid 105 through 109 removed outlier: 3.823A pdb=" N GLY G 109 " --> pdb=" O PRO G 106 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 119 removed outlier: 3.694A pdb=" N ARG G 115 " --> pdb=" O ARG G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 119 through 135 removed outlier: 4.537A pdb=" N LEU G 123 " --> pdb=" O GLN G 119 " (cutoff:3.500A) Processing helix chain 'G' and resid 150 through 164 removed outlier: 3.944A pdb=" N ILE G 154 " --> pdb=" O HIS G 150 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL G 164 " --> pdb=" O ILE G 160 " (cutoff:3.500A) Processing helix chain 'G' and resid 180 through 186 Processing helix chain 'G' and resid 186 through 192 removed outlier: 3.726A pdb=" N LEU G 190 " --> pdb=" O ILE G 186 " (cutoff:3.500A) Processing helix chain 'G' and resid 202 through 211 Processing helix chain 'G' and resid 219 through 223 removed outlier: 3.517A pdb=" N LEU G 222 " --> pdb=" O VAL G 219 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR G 223 " --> pdb=" O ALA G 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 219 through 223' Processing helix chain 'G' and resid 227 through 245 Processing helix chain 'G' and resid 253 through 256 removed outlier: 3.511A pdb=" N SER G 256 " --> pdb=" O GLN G 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 253 through 256' Processing helix chain 'G' and resid 257 through 268 Processing helix chain 'G' and resid 278 through 302 Processing helix chain 'H' and resid 20 through 25 Processing helix chain 'H' and resid 36 through 41 Processing helix chain 'H' and resid 46 through 54 Processing helix chain 'H' and resid 55 through 74 removed outlier: 3.956A pdb=" N LEU H 59 " --> pdb=" O LYS H 55 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL H 70 " --> pdb=" O GLY H 66 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 105 through 109 removed outlier: 3.823A pdb=" N GLY H 109 " --> pdb=" O PRO H 106 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 119 removed outlier: 3.694A pdb=" N ARG H 115 " --> pdb=" O ARG H 111 " (cutoff:3.500A) Processing helix chain 'H' and resid 119 through 135 removed outlier: 4.537A pdb=" N LEU H 123 " --> pdb=" O GLN H 119 " (cutoff:3.500A) Processing helix chain 'H' and resid 150 through 164 removed outlier: 3.944A pdb=" N ILE H 154 " --> pdb=" O HIS H 150 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL H 164 " --> pdb=" O ILE H 160 " (cutoff:3.500A) Processing helix chain 'H' and resid 180 through 186 Processing helix chain 'H' and resid 186 through 192 removed outlier: 3.726A pdb=" N LEU H 190 " --> pdb=" O ILE H 186 " (cutoff:3.500A) Processing helix chain 'H' and resid 202 through 211 Processing helix chain 'H' and resid 219 through 223 removed outlier: 3.517A pdb=" N LEU H 222 " --> pdb=" O VAL H 219 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR H 223 " --> pdb=" O ALA H 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 219 through 223' Processing helix chain 'H' and resid 227 through 245 Processing helix chain 'H' and resid 253 through 256 removed outlier: 3.511A pdb=" N SER H 256 " --> pdb=" O GLN H 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 253 through 256' Processing helix chain 'H' and resid 257 through 268 Processing helix chain 'H' and resid 278 through 302 Processing helix chain 'I' and resid 20 through 25 Processing helix chain 'I' and resid 36 through 41 Processing helix chain 'I' and resid 46 through 54 Processing helix chain 'I' and resid 55 through 74 removed outlier: 3.956A pdb=" N LEU I 59 " --> pdb=" O LYS I 55 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL I 70 " --> pdb=" O GLY I 66 " (cutoff:3.500A) Processing helix chain 'I' and resid 87 through 91 Processing helix chain 'I' and resid 105 through 109 removed outlier: 3.823A pdb=" N GLY I 109 " --> pdb=" O PRO I 106 " (cutoff:3.500A) Processing helix chain 'I' and resid 111 through 119 removed outlier: 3.694A pdb=" N ARG I 115 " --> pdb=" O ARG I 111 " (cutoff:3.500A) Processing helix chain 'I' and resid 119 through 135 removed outlier: 4.537A pdb=" N LEU I 123 " --> pdb=" O GLN I 119 " (cutoff:3.500A) Processing helix chain 'I' and resid 150 through 164 removed outlier: 3.944A pdb=" N ILE I 154 " --> pdb=" O HIS I 150 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL I 164 " --> pdb=" O ILE I 160 " (cutoff:3.500A) Processing helix chain 'I' and resid 180 through 186 Processing helix chain 'I' and resid 186 through 192 removed outlier: 3.726A pdb=" N LEU I 190 " --> pdb=" O ILE I 186 " (cutoff:3.500A) Processing helix chain 'I' and resid 202 through 211 Processing helix chain 'I' and resid 219 through 223 removed outlier: 3.517A pdb=" N LEU I 222 " --> pdb=" O VAL I 219 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR I 223 " --> pdb=" O ALA I 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 219 through 223' Processing helix chain 'I' and resid 227 through 245 Processing helix chain 'I' and resid 253 through 256 removed outlier: 3.511A pdb=" N SER I 256 " --> pdb=" O GLN I 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 253 through 256' Processing helix chain 'I' and resid 257 through 268 Processing helix chain 'I' and resid 278 through 302 Processing helix chain 'J' and resid 20 through 25 Processing helix chain 'J' and resid 36 through 41 Processing helix chain 'J' and resid 46 through 54 Processing helix chain 'J' and resid 55 through 74 removed outlier: 3.956A pdb=" N LEU J 59 " --> pdb=" O LYS J 55 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL J 70 " --> pdb=" O GLY J 66 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 91 Processing helix chain 'J' and resid 105 through 109 removed outlier: 3.823A pdb=" N GLY J 109 " --> pdb=" O PRO J 106 " (cutoff:3.500A) Processing helix chain 'J' and resid 111 through 119 removed outlier: 3.694A pdb=" N ARG J 115 " --> pdb=" O ARG J 111 " (cutoff:3.500A) Processing helix chain 'J' and resid 119 through 135 removed outlier: 4.537A pdb=" N LEU J 123 " --> pdb=" O GLN J 119 " (cutoff:3.500A) Processing helix chain 'J' and resid 150 through 164 removed outlier: 3.944A pdb=" N ILE J 154 " --> pdb=" O HIS J 150 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL J 164 " --> pdb=" O ILE J 160 " (cutoff:3.500A) Processing helix chain 'J' and resid 180 through 186 Processing helix chain 'J' and resid 186 through 192 removed outlier: 3.726A pdb=" N LEU J 190 " --> pdb=" O ILE J 186 " (cutoff:3.500A) Processing helix chain 'J' and resid 202 through 211 Processing helix chain 'J' and resid 219 through 223 removed outlier: 3.517A pdb=" N LEU J 222 " --> pdb=" O VAL J 219 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR J 223 " --> pdb=" O ALA J 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 219 through 223' Processing helix chain 'J' and resid 227 through 245 Processing helix chain 'J' and resid 253 through 256 removed outlier: 3.511A pdb=" N SER J 256 " --> pdb=" O GLN J 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 253 through 256' Processing helix chain 'J' and resid 257 through 268 Processing helix chain 'J' and resid 278 through 302 Processing helix chain 'K' and resid 20 through 25 Processing helix chain 'K' and resid 36 through 41 Processing helix chain 'K' and resid 46 through 54 Processing helix chain 'K' and resid 55 through 74 removed outlier: 3.956A pdb=" N LEU K 59 " --> pdb=" O LYS K 55 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL K 70 " --> pdb=" O GLY K 66 " (cutoff:3.500A) Processing helix chain 'K' and resid 87 through 91 Processing helix chain 'K' and resid 105 through 109 removed outlier: 3.823A pdb=" N GLY K 109 " --> pdb=" O PRO K 106 " (cutoff:3.500A) Processing helix chain 'K' and resid 111 through 119 removed outlier: 3.694A pdb=" N ARG K 115 " --> pdb=" O ARG K 111 " (cutoff:3.500A) Processing helix chain 'K' and resid 119 through 135 removed outlier: 4.537A pdb=" N LEU K 123 " --> pdb=" O GLN K 119 " (cutoff:3.500A) Processing helix chain 'K' and resid 150 through 164 removed outlier: 3.944A pdb=" N ILE K 154 " --> pdb=" O HIS K 150 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL K 164 " --> pdb=" O ILE K 160 " (cutoff:3.500A) Processing helix chain 'K' and resid 180 through 186 Processing helix chain 'K' and resid 186 through 192 removed outlier: 3.726A pdb=" N LEU K 190 " --> pdb=" O ILE K 186 " (cutoff:3.500A) Processing helix chain 'K' and resid 202 through 211 Processing helix chain 'K' and resid 219 through 223 removed outlier: 3.517A pdb=" N LEU K 222 " --> pdb=" O VAL K 219 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR K 223 " --> pdb=" O ALA K 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 219 through 223' Processing helix chain 'K' and resid 227 through 245 Processing helix chain 'K' and resid 253 through 256 removed outlier: 3.511A pdb=" N SER K 256 " --> pdb=" O GLN K 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 253 through 256' Processing helix chain 'K' and resid 257 through 268 Processing helix chain 'K' and resid 278 through 302 Processing helix chain 'L' and resid 20 through 25 Processing helix chain 'L' and resid 36 through 41 Processing helix chain 'L' and resid 46 through 54 Processing helix chain 'L' and resid 55 through 74 removed outlier: 3.956A pdb=" N LEU L 59 " --> pdb=" O LYS L 55 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL L 70 " --> pdb=" O GLY L 66 " (cutoff:3.500A) Processing helix chain 'L' and resid 87 through 91 Processing helix chain 'L' and resid 105 through 109 removed outlier: 3.823A pdb=" N GLY L 109 " --> pdb=" O PRO L 106 " (cutoff:3.500A) Processing helix chain 'L' and resid 111 through 119 removed outlier: 3.694A pdb=" N ARG L 115 " --> pdb=" O ARG L 111 " (cutoff:3.500A) Processing helix chain 'L' and resid 119 through 135 removed outlier: 4.537A pdb=" N LEU L 123 " --> pdb=" O GLN L 119 " (cutoff:3.500A) Processing helix chain 'L' and resid 150 through 164 removed outlier: 3.944A pdb=" N ILE L 154 " --> pdb=" O HIS L 150 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL L 164 " --> pdb=" O ILE L 160 " (cutoff:3.500A) Processing helix chain 'L' and resid 180 through 186 Processing helix chain 'L' and resid 186 through 192 removed outlier: 3.726A pdb=" N LEU L 190 " --> pdb=" O ILE L 186 " (cutoff:3.500A) Processing helix chain 'L' and resid 202 through 211 Processing helix chain 'L' and resid 219 through 223 removed outlier: 3.517A pdb=" N LEU L 222 " --> pdb=" O VAL L 219 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR L 223 " --> pdb=" O ALA L 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 219 through 223' Processing helix chain 'L' and resid 227 through 245 Processing helix chain 'L' and resid 253 through 256 removed outlier: 3.511A pdb=" N SER L 256 " --> pdb=" O GLN L 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 253 through 256' Processing helix chain 'L' and resid 257 through 268 Processing helix chain 'L' and resid 278 through 302 Processing helix chain 'M' and resid 20 through 25 Processing helix chain 'M' and resid 36 through 41 Processing helix chain 'M' and resid 46 through 54 Processing helix chain 'M' and resid 55 through 74 removed outlier: 3.956A pdb=" N LEU M 59 " --> pdb=" O LYS M 55 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL M 70 " --> pdb=" O GLY M 66 " (cutoff:3.500A) Processing helix chain 'M' and resid 87 through 91 Processing helix chain 'M' and resid 105 through 109 removed outlier: 3.823A pdb=" N GLY M 109 " --> pdb=" O PRO M 106 " (cutoff:3.500A) Processing helix chain 'M' and resid 111 through 119 removed outlier: 3.694A pdb=" N ARG M 115 " --> pdb=" O ARG M 111 " (cutoff:3.500A) Processing helix chain 'M' and resid 119 through 135 removed outlier: 4.537A pdb=" N LEU M 123 " --> pdb=" O GLN M 119 " (cutoff:3.500A) Processing helix chain 'M' and resid 150 through 164 removed outlier: 3.944A pdb=" N ILE M 154 " --> pdb=" O HIS M 150 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL M 164 " --> pdb=" O ILE M 160 " (cutoff:3.500A) Processing helix chain 'M' and resid 180 through 186 Processing helix chain 'M' and resid 186 through 192 removed outlier: 3.726A pdb=" N LEU M 190 " --> pdb=" O ILE M 186 " (cutoff:3.500A) Processing helix chain 'M' and resid 202 through 211 Processing helix chain 'M' and resid 219 through 223 removed outlier: 3.517A pdb=" N LEU M 222 " --> pdb=" O VAL M 219 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR M 223 " --> pdb=" O ALA M 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 219 through 223' Processing helix chain 'M' and resid 227 through 245 Processing helix chain 'M' and resid 253 through 256 removed outlier: 3.511A pdb=" N SER M 256 " --> pdb=" O GLN M 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 253 through 256' Processing helix chain 'M' and resid 257 through 268 Processing helix chain 'M' and resid 278 through 302 Processing helix chain 'N' and resid 20 through 25 Processing helix chain 'N' and resid 36 through 41 Processing helix chain 'N' and resid 46 through 54 Processing helix chain 'N' and resid 55 through 74 removed outlier: 3.956A pdb=" N LEU N 59 " --> pdb=" O LYS N 55 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL N 70 " --> pdb=" O GLY N 66 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'N' and resid 105 through 109 removed outlier: 3.823A pdb=" N GLY N 109 " --> pdb=" O PRO N 106 " (cutoff:3.500A) Processing helix chain 'N' and resid 111 through 119 removed outlier: 3.694A pdb=" N ARG N 115 " --> pdb=" O ARG N 111 " (cutoff:3.500A) Processing helix chain 'N' and resid 119 through 135 removed outlier: 4.537A pdb=" N LEU N 123 " --> pdb=" O GLN N 119 " (cutoff:3.500A) Processing helix chain 'N' and resid 150 through 164 removed outlier: 3.944A pdb=" N ILE N 154 " --> pdb=" O HIS N 150 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL N 164 " --> pdb=" O ILE N 160 " (cutoff:3.500A) Processing helix chain 'N' and resid 180 through 186 Processing helix chain 'N' and resid 186 through 192 removed outlier: 3.726A pdb=" N LEU N 190 " --> pdb=" O ILE N 186 " (cutoff:3.500A) Processing helix chain 'N' and resid 202 through 211 Processing helix chain 'N' and resid 219 through 223 removed outlier: 3.517A pdb=" N LEU N 222 " --> pdb=" O VAL N 219 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR N 223 " --> pdb=" O ALA N 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 219 through 223' Processing helix chain 'N' and resid 227 through 245 Processing helix chain 'N' and resid 253 through 256 removed outlier: 3.511A pdb=" N SER N 256 " --> pdb=" O GLN N 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 253 through 256' Processing helix chain 'N' and resid 257 through 268 Processing helix chain 'N' and resid 278 through 302 Processing helix chain 'O' and resid 20 through 25 Processing helix chain 'O' and resid 36 through 41 Processing helix chain 'O' and resid 46 through 54 Processing helix chain 'O' and resid 55 through 74 removed outlier: 3.956A pdb=" N LEU O 59 " --> pdb=" O LYS O 55 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL O 70 " --> pdb=" O GLY O 66 " (cutoff:3.500A) Processing helix chain 'O' and resid 87 through 91 Processing helix chain 'O' and resid 105 through 109 removed outlier: 3.823A pdb=" N GLY O 109 " --> pdb=" O PRO O 106 " (cutoff:3.500A) Processing helix chain 'O' and resid 111 through 119 removed outlier: 3.694A pdb=" N ARG O 115 " --> pdb=" O ARG O 111 " (cutoff:3.500A) Processing helix chain 'O' and resid 119 through 135 removed outlier: 4.537A pdb=" N LEU O 123 " --> pdb=" O GLN O 119 " (cutoff:3.500A) Processing helix chain 'O' and resid 150 through 164 removed outlier: 3.944A pdb=" N ILE O 154 " --> pdb=" O HIS O 150 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL O 164 " --> pdb=" O ILE O 160 " (cutoff:3.500A) Processing helix chain 'O' and resid 180 through 186 Processing helix chain 'O' and resid 186 through 192 removed outlier: 3.726A pdb=" N LEU O 190 " --> pdb=" O ILE O 186 " (cutoff:3.500A) Processing helix chain 'O' and resid 202 through 211 Processing helix chain 'O' and resid 219 through 223 removed outlier: 3.517A pdb=" N LEU O 222 " --> pdb=" O VAL O 219 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR O 223 " --> pdb=" O ALA O 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 219 through 223' Processing helix chain 'O' and resid 227 through 245 Processing helix chain 'O' and resid 253 through 256 removed outlier: 3.511A pdb=" N SER O 256 " --> pdb=" O GLN O 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 253 through 256' Processing helix chain 'O' and resid 257 through 268 Processing helix chain 'O' and resid 278 through 302 Processing helix chain 'P' and resid 20 through 25 Processing helix chain 'P' and resid 36 through 41 Processing helix chain 'P' and resid 46 through 54 Processing helix chain 'P' and resid 55 through 74 removed outlier: 3.956A pdb=" N LEU P 59 " --> pdb=" O LYS P 55 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL P 70 " --> pdb=" O GLY P 66 " (cutoff:3.500A) Processing helix chain 'P' and resid 87 through 91 Processing helix chain 'P' and resid 105 through 109 removed outlier: 3.823A pdb=" N GLY P 109 " --> pdb=" O PRO P 106 " (cutoff:3.500A) Processing helix chain 'P' and resid 111 through 119 removed outlier: 3.694A pdb=" N ARG P 115 " --> pdb=" O ARG P 111 " (cutoff:3.500A) Processing helix chain 'P' and resid 119 through 135 removed outlier: 4.537A pdb=" N LEU P 123 " --> pdb=" O GLN P 119 " (cutoff:3.500A) Processing helix chain 'P' and resid 150 through 164 removed outlier: 3.944A pdb=" N ILE P 154 " --> pdb=" O HIS P 150 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL P 164 " --> pdb=" O ILE P 160 " (cutoff:3.500A) Processing helix chain 'P' and resid 180 through 186 Processing helix chain 'P' and resid 186 through 192 removed outlier: 3.726A pdb=" N LEU P 190 " --> pdb=" O ILE P 186 " (cutoff:3.500A) Processing helix chain 'P' and resid 202 through 211 Processing helix chain 'P' and resid 219 through 223 removed outlier: 3.517A pdb=" N LEU P 222 " --> pdb=" O VAL P 219 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR P 223 " --> pdb=" O ALA P 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 219 through 223' Processing helix chain 'P' and resid 227 through 245 Processing helix chain 'P' and resid 253 through 256 removed outlier: 3.511A pdb=" N SER P 256 " --> pdb=" O GLN P 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 253 through 256' Processing helix chain 'P' and resid 257 through 268 Processing helix chain 'P' and resid 278 through 302 Processing helix chain 'Q' and resid 20 through 25 Processing helix chain 'Q' and resid 36 through 41 Processing helix chain 'Q' and resid 46 through 54 Processing helix chain 'Q' and resid 55 through 74 removed outlier: 3.956A pdb=" N LEU Q 59 " --> pdb=" O LYS Q 55 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL Q 70 " --> pdb=" O GLY Q 66 " (cutoff:3.500A) Processing helix chain 'Q' and resid 87 through 91 Processing helix chain 'Q' and resid 105 through 109 removed outlier: 3.823A pdb=" N GLY Q 109 " --> pdb=" O PRO Q 106 " (cutoff:3.500A) Processing helix chain 'Q' and resid 111 through 119 removed outlier: 3.694A pdb=" N ARG Q 115 " --> pdb=" O ARG Q 111 " (cutoff:3.500A) Processing helix chain 'Q' and resid 119 through 135 removed outlier: 4.537A pdb=" N LEU Q 123 " --> pdb=" O GLN Q 119 " (cutoff:3.500A) Processing helix chain 'Q' and resid 150 through 164 removed outlier: 3.944A pdb=" N ILE Q 154 " --> pdb=" O HIS Q 150 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL Q 164 " --> pdb=" O ILE Q 160 " (cutoff:3.500A) Processing helix chain 'Q' and resid 180 through 186 Processing helix chain 'Q' and resid 186 through 192 removed outlier: 3.726A pdb=" N LEU Q 190 " --> pdb=" O ILE Q 186 " (cutoff:3.500A) Processing helix chain 'Q' and resid 202 through 211 Processing helix chain 'Q' and resid 219 through 223 removed outlier: 3.517A pdb=" N LEU Q 222 " --> pdb=" O VAL Q 219 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR Q 223 " --> pdb=" O ALA Q 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 219 through 223' Processing helix chain 'Q' and resid 227 through 245 Processing helix chain 'Q' and resid 253 through 256 removed outlier: 3.511A pdb=" N SER Q 256 " --> pdb=" O GLN Q 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 253 through 256' Processing helix chain 'Q' and resid 257 through 268 Processing helix chain 'Q' and resid 278 through 302 Processing helix chain 'R' and resid 20 through 25 Processing helix chain 'R' and resid 36 through 41 Processing helix chain 'R' and resid 46 through 54 Processing helix chain 'R' and resid 55 through 74 removed outlier: 3.956A pdb=" N LEU R 59 " --> pdb=" O LYS R 55 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL R 70 " --> pdb=" O GLY R 66 " (cutoff:3.500A) Processing helix chain 'R' and resid 87 through 91 Processing helix chain 'R' and resid 105 through 109 removed outlier: 3.823A pdb=" N GLY R 109 " --> pdb=" O PRO R 106 " (cutoff:3.500A) Processing helix chain 'R' and resid 111 through 119 removed outlier: 3.694A pdb=" N ARG R 115 " --> pdb=" O ARG R 111 " (cutoff:3.500A) Processing helix chain 'R' and resid 119 through 135 removed outlier: 4.537A pdb=" N LEU R 123 " --> pdb=" O GLN R 119 " (cutoff:3.500A) Processing helix chain 'R' and resid 150 through 164 removed outlier: 3.944A pdb=" N ILE R 154 " --> pdb=" O HIS R 150 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL R 164 " --> pdb=" O ILE R 160 " (cutoff:3.500A) Processing helix chain 'R' and resid 180 through 186 Processing helix chain 'R' and resid 186 through 192 removed outlier: 3.726A pdb=" N LEU R 190 " --> pdb=" O ILE R 186 " (cutoff:3.500A) Processing helix chain 'R' and resid 202 through 211 Processing helix chain 'R' and resid 219 through 223 removed outlier: 3.517A pdb=" N LEU R 222 " --> pdb=" O VAL R 219 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR R 223 " --> pdb=" O ALA R 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 219 through 223' Processing helix chain 'R' and resid 227 through 245 Processing helix chain 'R' and resid 253 through 256 removed outlier: 3.511A pdb=" N SER R 256 " --> pdb=" O GLN R 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 253 through 256' Processing helix chain 'R' and resid 257 through 268 Processing helix chain 'R' and resid 278 through 302 Processing helix chain 'S' and resid 20 through 25 Processing helix chain 'S' and resid 36 through 41 Processing helix chain 'S' and resid 46 through 54 Processing helix chain 'S' and resid 55 through 74 removed outlier: 3.956A pdb=" N LEU S 59 " --> pdb=" O LYS S 55 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL S 70 " --> pdb=" O GLY S 66 " (cutoff:3.500A) Processing helix chain 'S' and resid 87 through 91 Processing helix chain 'S' and resid 105 through 109 removed outlier: 3.823A pdb=" N GLY S 109 " --> pdb=" O PRO S 106 " (cutoff:3.500A) Processing helix chain 'S' and resid 111 through 119 removed outlier: 3.694A pdb=" N ARG S 115 " --> pdb=" O ARG S 111 " (cutoff:3.500A) Processing helix chain 'S' and resid 119 through 135 removed outlier: 4.537A pdb=" N LEU S 123 " --> pdb=" O GLN S 119 " (cutoff:3.500A) Processing helix chain 'S' and resid 150 through 164 removed outlier: 3.944A pdb=" N ILE S 154 " --> pdb=" O HIS S 150 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL S 164 " --> pdb=" O ILE S 160 " (cutoff:3.500A) Processing helix chain 'S' and resid 180 through 186 Processing helix chain 'S' and resid 186 through 192 removed outlier: 3.726A pdb=" N LEU S 190 " --> pdb=" O ILE S 186 " (cutoff:3.500A) Processing helix chain 'S' and resid 202 through 211 Processing helix chain 'S' and resid 219 through 223 removed outlier: 3.517A pdb=" N LEU S 222 " --> pdb=" O VAL S 219 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR S 223 " --> pdb=" O ALA S 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 219 through 223' Processing helix chain 'S' and resid 227 through 245 Processing helix chain 'S' and resid 253 through 256 removed outlier: 3.511A pdb=" N SER S 256 " --> pdb=" O GLN S 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 253 through 256' Processing helix chain 'S' and resid 257 through 268 Processing helix chain 'S' and resid 278 through 302 Processing helix chain 'T' and resid 20 through 25 Processing helix chain 'T' and resid 36 through 41 Processing helix chain 'T' and resid 46 through 54 Processing helix chain 'T' and resid 55 through 74 removed outlier: 3.956A pdb=" N LEU T 59 " --> pdb=" O LYS T 55 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL T 70 " --> pdb=" O GLY T 66 " (cutoff:3.500A) Processing helix chain 'T' and resid 87 through 91 Processing helix chain 'T' and resid 105 through 109 removed outlier: 3.823A pdb=" N GLY T 109 " --> pdb=" O PRO T 106 " (cutoff:3.500A) Processing helix chain 'T' and resid 111 through 119 removed outlier: 3.694A pdb=" N ARG T 115 " --> pdb=" O ARG T 111 " (cutoff:3.500A) Processing helix chain 'T' and resid 119 through 135 removed outlier: 4.537A pdb=" N LEU T 123 " --> pdb=" O GLN T 119 " (cutoff:3.500A) Processing helix chain 'T' and resid 150 through 164 removed outlier: 3.944A pdb=" N ILE T 154 " --> pdb=" O HIS T 150 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL T 164 " --> pdb=" O ILE T 160 " (cutoff:3.500A) Processing helix chain 'T' and resid 180 through 186 Processing helix chain 'T' and resid 186 through 192 removed outlier: 3.726A pdb=" N LEU T 190 " --> pdb=" O ILE T 186 " (cutoff:3.500A) Processing helix chain 'T' and resid 202 through 211 Processing helix chain 'T' and resid 219 through 223 removed outlier: 3.517A pdb=" N LEU T 222 " --> pdb=" O VAL T 219 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR T 223 " --> pdb=" O ALA T 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 219 through 223' Processing helix chain 'T' and resid 227 through 245 Processing helix chain 'T' and resid 253 through 256 removed outlier: 3.511A pdb=" N SER T 256 " --> pdb=" O GLN T 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 253 through 256' Processing helix chain 'T' and resid 257 through 268 Processing helix chain 'T' and resid 278 through 302 Processing helix chain 'U' and resid 20 through 25 Processing helix chain 'U' and resid 36 through 41 Processing helix chain 'U' and resid 46 through 54 Processing helix chain 'U' and resid 55 through 74 removed outlier: 3.956A pdb=" N LEU U 59 " --> pdb=" O LYS U 55 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL U 70 " --> pdb=" O GLY U 66 " (cutoff:3.500A) Processing helix chain 'U' and resid 87 through 91 Processing helix chain 'U' and resid 105 through 109 removed outlier: 3.823A pdb=" N GLY U 109 " --> pdb=" O PRO U 106 " (cutoff:3.500A) Processing helix chain 'U' and resid 111 through 119 removed outlier: 3.694A pdb=" N ARG U 115 " --> pdb=" O ARG U 111 " (cutoff:3.500A) Processing helix chain 'U' and resid 119 through 135 removed outlier: 4.537A pdb=" N LEU U 123 " --> pdb=" O GLN U 119 " (cutoff:3.500A) Processing helix chain 'U' and resid 150 through 164 removed outlier: 3.944A pdb=" N ILE U 154 " --> pdb=" O HIS U 150 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL U 164 " --> pdb=" O ILE U 160 " (cutoff:3.500A) Processing helix chain 'U' and resid 180 through 186 Processing helix chain 'U' and resid 186 through 192 removed outlier: 3.726A pdb=" N LEU U 190 " --> pdb=" O ILE U 186 " (cutoff:3.500A) Processing helix chain 'U' and resid 202 through 211 Processing helix chain 'U' and resid 219 through 223 removed outlier: 3.517A pdb=" N LEU U 222 " --> pdb=" O VAL U 219 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR U 223 " --> pdb=" O ALA U 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 219 through 223' Processing helix chain 'U' and resid 227 through 245 Processing helix chain 'U' and resid 253 through 256 removed outlier: 3.511A pdb=" N SER U 256 " --> pdb=" O GLN U 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 253 through 256' Processing helix chain 'U' and resid 257 through 268 Processing helix chain 'U' and resid 278 through 302 Processing helix chain 'V' and resid 20 through 25 Processing helix chain 'V' and resid 36 through 41 Processing helix chain 'V' and resid 46 through 54 Processing helix chain 'V' and resid 55 through 74 removed outlier: 3.956A pdb=" N LEU V 59 " --> pdb=" O LYS V 55 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL V 70 " --> pdb=" O GLY V 66 " (cutoff:3.500A) Processing helix chain 'V' and resid 87 through 91 Processing helix chain 'V' and resid 105 through 109 removed outlier: 3.823A pdb=" N GLY V 109 " --> pdb=" O PRO V 106 " (cutoff:3.500A) Processing helix chain 'V' and resid 111 through 119 removed outlier: 3.694A pdb=" N ARG V 115 " --> pdb=" O ARG V 111 " (cutoff:3.500A) Processing helix chain 'V' and resid 119 through 135 removed outlier: 4.537A pdb=" N LEU V 123 " --> pdb=" O GLN V 119 " (cutoff:3.500A) Processing helix chain 'V' and resid 150 through 164 removed outlier: 3.944A pdb=" N ILE V 154 " --> pdb=" O HIS V 150 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL V 164 " --> pdb=" O ILE V 160 " (cutoff:3.500A) Processing helix chain 'V' and resid 180 through 186 Processing helix chain 'V' and resid 186 through 192 removed outlier: 3.726A pdb=" N LEU V 190 " --> pdb=" O ILE V 186 " (cutoff:3.500A) Processing helix chain 'V' and resid 202 through 211 Processing helix chain 'V' and resid 219 through 223 removed outlier: 3.517A pdb=" N LEU V 222 " --> pdb=" O VAL V 219 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR V 223 " --> pdb=" O ALA V 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 219 through 223' Processing helix chain 'V' and resid 227 through 245 Processing helix chain 'V' and resid 253 through 256 removed outlier: 3.511A pdb=" N SER V 256 " --> pdb=" O GLN V 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 253 through 256' Processing helix chain 'V' and resid 257 through 268 Processing helix chain 'V' and resid 278 through 302 Processing helix chain 'W' and resid 20 through 25 Processing helix chain 'W' and resid 36 through 41 Processing helix chain 'W' and resid 46 through 54 Processing helix chain 'W' and resid 55 through 74 removed outlier: 3.956A pdb=" N LEU W 59 " --> pdb=" O LYS W 55 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL W 70 " --> pdb=" O GLY W 66 " (cutoff:3.500A) Processing helix chain 'W' and resid 87 through 91 Processing helix chain 'W' and resid 105 through 109 removed outlier: 3.823A pdb=" N GLY W 109 " --> pdb=" O PRO W 106 " (cutoff:3.500A) Processing helix chain 'W' and resid 111 through 119 removed outlier: 3.694A pdb=" N ARG W 115 " --> pdb=" O ARG W 111 " (cutoff:3.500A) Processing helix chain 'W' and resid 119 through 135 removed outlier: 4.537A pdb=" N LEU W 123 " --> pdb=" O GLN W 119 " (cutoff:3.500A) Processing helix chain 'W' and resid 150 through 164 removed outlier: 3.944A pdb=" N ILE W 154 " --> pdb=" O HIS W 150 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL W 164 " --> pdb=" O ILE W 160 " (cutoff:3.500A) Processing helix chain 'W' and resid 180 through 186 Processing helix chain 'W' and resid 186 through 192 removed outlier: 3.726A pdb=" N LEU W 190 " --> pdb=" O ILE W 186 " (cutoff:3.500A) Processing helix chain 'W' and resid 202 through 211 Processing helix chain 'W' and resid 219 through 223 removed outlier: 3.517A pdb=" N LEU W 222 " --> pdb=" O VAL W 219 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR W 223 " --> pdb=" O ALA W 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 219 through 223' Processing helix chain 'W' and resid 227 through 245 Processing helix chain 'W' and resid 253 through 256 removed outlier: 3.511A pdb=" N SER W 256 " --> pdb=" O GLN W 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 253 through 256' Processing helix chain 'W' and resid 257 through 268 Processing helix chain 'W' and resid 278 through 302 Processing helix chain 'X' and resid 20 through 25 Processing helix chain 'X' and resid 36 through 41 Processing helix chain 'X' and resid 46 through 54 Processing helix chain 'X' and resid 55 through 74 removed outlier: 3.956A pdb=" N LEU X 59 " --> pdb=" O LYS X 55 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL X 70 " --> pdb=" O GLY X 66 " (cutoff:3.500A) Processing helix chain 'X' and resid 87 through 91 Processing helix chain 'X' and resid 105 through 109 removed outlier: 3.823A pdb=" N GLY X 109 " --> pdb=" O PRO X 106 " (cutoff:3.500A) Processing helix chain 'X' and resid 111 through 119 removed outlier: 3.694A pdb=" N ARG X 115 " --> pdb=" O ARG X 111 " (cutoff:3.500A) Processing helix chain 'X' and resid 119 through 135 removed outlier: 4.537A pdb=" N LEU X 123 " --> pdb=" O GLN X 119 " (cutoff:3.500A) Processing helix chain 'X' and resid 150 through 164 removed outlier: 3.944A pdb=" N ILE X 154 " --> pdb=" O HIS X 150 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL X 164 " --> pdb=" O ILE X 160 " (cutoff:3.500A) Processing helix chain 'X' and resid 180 through 186 Processing helix chain 'X' and resid 186 through 192 removed outlier: 3.726A pdb=" N LEU X 190 " --> pdb=" O ILE X 186 " (cutoff:3.500A) Processing helix chain 'X' and resid 202 through 211 Processing helix chain 'X' and resid 219 through 223 removed outlier: 3.517A pdb=" N LEU X 222 " --> pdb=" O VAL X 219 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR X 223 " --> pdb=" O ALA X 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 219 through 223' Processing helix chain 'X' and resid 227 through 245 Processing helix chain 'X' and resid 253 through 256 removed outlier: 3.511A pdb=" N SER X 256 " --> pdb=" O GLN X 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 253 through 256' Processing helix chain 'X' and resid 257 through 268 Processing helix chain 'X' and resid 278 through 302 Processing sheet with id=AA1, first strand: chain 'A' and resid 247 through 251 removed outlier: 3.603A pdb=" N PHE A 197 " --> pdb=" O TRP A 174 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N GLY A 32 " --> pdb=" O TRP A 80 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ARG A 82 " --> pdb=" O GLY A 32 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LEU A 34 " --> pdb=" O ARG A 82 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N GLY A 32 " --> pdb=" O VAL A 10 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N VAL A 12 " --> pdb=" O GLY A 32 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU A 34 " --> pdb=" O VAL A 12 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N VAL A 14 " --> pdb=" O LEU A 34 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 247 through 251 removed outlier: 3.603A pdb=" N PHE B 197 " --> pdb=" O TRP B 174 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N GLY B 32 " --> pdb=" O TRP B 80 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ARG B 82 " --> pdb=" O GLY B 32 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LEU B 34 " --> pdb=" O ARG B 82 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N GLY B 32 " --> pdb=" O VAL B 10 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N VAL B 12 " --> pdb=" O GLY B 32 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU B 34 " --> pdb=" O VAL B 12 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N VAL B 14 " --> pdb=" O LEU B 34 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 247 through 251 removed outlier: 3.603A pdb=" N PHE C 197 " --> pdb=" O TRP C 174 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N GLY C 32 " --> pdb=" O TRP C 80 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ARG C 82 " --> pdb=" O GLY C 32 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LEU C 34 " --> pdb=" O ARG C 82 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N GLY C 32 " --> pdb=" O VAL C 10 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N VAL C 12 " --> pdb=" O GLY C 32 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU C 34 " --> pdb=" O VAL C 12 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N VAL C 14 " --> pdb=" O LEU C 34 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 247 through 251 removed outlier: 3.603A pdb=" N PHE D 197 " --> pdb=" O TRP D 174 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N GLY D 32 " --> pdb=" O TRP D 80 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ARG D 82 " --> pdb=" O GLY D 32 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LEU D 34 " --> pdb=" O ARG D 82 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N GLY D 32 " --> pdb=" O VAL D 10 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N VAL D 12 " --> pdb=" O GLY D 32 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU D 34 " --> pdb=" O VAL D 12 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N VAL D 14 " --> pdb=" O LEU D 34 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 247 through 251 removed outlier: 3.603A pdb=" N PHE E 197 " --> pdb=" O TRP E 174 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N GLY E 32 " --> pdb=" O TRP E 80 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ARG E 82 " --> pdb=" O GLY E 32 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LEU E 34 " --> pdb=" O ARG E 82 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N GLY E 32 " --> pdb=" O VAL E 10 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N VAL E 12 " --> pdb=" O GLY E 32 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU E 34 " --> pdb=" O VAL E 12 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N VAL E 14 " --> pdb=" O LEU E 34 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 247 through 251 removed outlier: 3.603A pdb=" N PHE F 197 " --> pdb=" O TRP F 174 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N GLY F 32 " --> pdb=" O TRP F 80 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ARG F 82 " --> pdb=" O GLY F 32 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LEU F 34 " --> pdb=" O ARG F 82 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N GLY F 32 " --> pdb=" O VAL F 10 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N VAL F 12 " --> pdb=" O GLY F 32 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU F 34 " --> pdb=" O VAL F 12 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N VAL F 14 " --> pdb=" O LEU F 34 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 247 through 251 removed outlier: 3.603A pdb=" N PHE G 197 " --> pdb=" O TRP G 174 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N GLY G 32 " --> pdb=" O TRP G 80 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ARG G 82 " --> pdb=" O GLY G 32 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LEU G 34 " --> pdb=" O ARG G 82 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N GLY G 32 " --> pdb=" O VAL G 10 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N VAL G 12 " --> pdb=" O GLY G 32 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU G 34 " --> pdb=" O VAL G 12 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N VAL G 14 " --> pdb=" O LEU G 34 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 247 through 251 removed outlier: 3.603A pdb=" N PHE H 197 " --> pdb=" O TRP H 174 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N GLY H 32 " --> pdb=" O TRP H 80 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ARG H 82 " --> pdb=" O GLY H 32 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LEU H 34 " --> pdb=" O ARG H 82 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N GLY H 32 " --> pdb=" O VAL H 10 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N VAL H 12 " --> pdb=" O GLY H 32 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU H 34 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N VAL H 14 " --> pdb=" O LEU H 34 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 247 through 251 removed outlier: 3.603A pdb=" N PHE I 197 " --> pdb=" O TRP I 174 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N GLY I 32 " --> pdb=" O TRP I 80 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ARG I 82 " --> pdb=" O GLY I 32 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LEU I 34 " --> pdb=" O ARG I 82 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N GLY I 32 " --> pdb=" O VAL I 10 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N VAL I 12 " --> pdb=" O GLY I 32 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU I 34 " --> pdb=" O VAL I 12 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N VAL I 14 " --> pdb=" O LEU I 34 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 247 through 251 removed outlier: 3.603A pdb=" N PHE J 197 " --> pdb=" O TRP J 174 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N GLY J 32 " --> pdb=" O TRP J 80 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ARG J 82 " --> pdb=" O GLY J 32 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LEU J 34 " --> pdb=" O ARG J 82 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N GLY J 32 " --> pdb=" O VAL J 10 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N VAL J 12 " --> pdb=" O GLY J 32 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU J 34 " --> pdb=" O VAL J 12 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N VAL J 14 " --> pdb=" O LEU J 34 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 247 through 251 removed outlier: 3.603A pdb=" N PHE K 197 " --> pdb=" O TRP K 174 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N GLY K 32 " --> pdb=" O TRP K 80 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ARG K 82 " --> pdb=" O GLY K 32 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LEU K 34 " --> pdb=" O ARG K 82 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N GLY K 32 " --> pdb=" O VAL K 10 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N VAL K 12 " --> pdb=" O GLY K 32 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU K 34 " --> pdb=" O VAL K 12 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N VAL K 14 " --> pdb=" O LEU K 34 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 247 through 251 removed outlier: 3.603A pdb=" N PHE L 197 " --> pdb=" O TRP L 174 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N GLY L 32 " --> pdb=" O TRP L 80 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ARG L 82 " --> pdb=" O GLY L 32 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LEU L 34 " --> pdb=" O ARG L 82 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N GLY L 32 " --> pdb=" O VAL L 10 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N VAL L 12 " --> pdb=" O GLY L 32 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU L 34 " --> pdb=" O VAL L 12 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N VAL L 14 " --> pdb=" O LEU L 34 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'M' and resid 247 through 251 removed outlier: 3.603A pdb=" N PHE M 197 " --> pdb=" O TRP M 174 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N GLY M 32 " --> pdb=" O TRP M 80 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ARG M 82 " --> pdb=" O GLY M 32 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LEU M 34 " --> pdb=" O ARG M 82 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N GLY M 32 " --> pdb=" O VAL M 10 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N VAL M 12 " --> pdb=" O GLY M 32 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU M 34 " --> pdb=" O VAL M 12 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N VAL M 14 " --> pdb=" O LEU M 34 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'N' and resid 247 through 251 removed outlier: 3.603A pdb=" N PHE N 197 " --> pdb=" O TRP N 174 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N GLY N 32 " --> pdb=" O TRP N 80 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ARG N 82 " --> pdb=" O GLY N 32 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LEU N 34 " --> pdb=" O ARG N 82 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N GLY N 32 " --> pdb=" O VAL N 10 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N VAL N 12 " --> pdb=" O GLY N 32 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU N 34 " --> pdb=" O VAL N 12 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N VAL N 14 " --> pdb=" O LEU N 34 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'O' and resid 247 through 251 removed outlier: 3.603A pdb=" N PHE O 197 " --> pdb=" O TRP O 174 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N GLY O 32 " --> pdb=" O TRP O 80 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ARG O 82 " --> pdb=" O GLY O 32 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LEU O 34 " --> pdb=" O ARG O 82 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N GLY O 32 " --> pdb=" O VAL O 10 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N VAL O 12 " --> pdb=" O GLY O 32 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU O 34 " --> pdb=" O VAL O 12 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N VAL O 14 " --> pdb=" O LEU O 34 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'P' and resid 247 through 251 removed outlier: 3.603A pdb=" N PHE P 197 " --> pdb=" O TRP P 174 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N GLY P 32 " --> pdb=" O TRP P 80 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ARG P 82 " --> pdb=" O GLY P 32 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LEU P 34 " --> pdb=" O ARG P 82 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N GLY P 32 " --> pdb=" O VAL P 10 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N VAL P 12 " --> pdb=" O GLY P 32 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU P 34 " --> pdb=" O VAL P 12 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N VAL P 14 " --> pdb=" O LEU P 34 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'Q' and resid 247 through 251 removed outlier: 3.603A pdb=" N PHE Q 197 " --> pdb=" O TRP Q 174 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N GLY Q 32 " --> pdb=" O TRP Q 80 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ARG Q 82 " --> pdb=" O GLY Q 32 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LEU Q 34 " --> pdb=" O ARG Q 82 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N GLY Q 32 " --> pdb=" O VAL Q 10 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N VAL Q 12 " --> pdb=" O GLY Q 32 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU Q 34 " --> pdb=" O VAL Q 12 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N VAL Q 14 " --> pdb=" O LEU Q 34 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'R' and resid 247 through 251 removed outlier: 3.603A pdb=" N PHE R 197 " --> pdb=" O TRP R 174 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N GLY R 32 " --> pdb=" O TRP R 80 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ARG R 82 " --> pdb=" O GLY R 32 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LEU R 34 " --> pdb=" O ARG R 82 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N GLY R 32 " --> pdb=" O VAL R 10 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N VAL R 12 " --> pdb=" O GLY R 32 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU R 34 " --> pdb=" O VAL R 12 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N VAL R 14 " --> pdb=" O LEU R 34 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'S' and resid 247 through 251 removed outlier: 3.603A pdb=" N PHE S 197 " --> pdb=" O TRP S 174 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N GLY S 32 " --> pdb=" O TRP S 80 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ARG S 82 " --> pdb=" O GLY S 32 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LEU S 34 " --> pdb=" O ARG S 82 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N GLY S 32 " --> pdb=" O VAL S 10 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N VAL S 12 " --> pdb=" O GLY S 32 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU S 34 " --> pdb=" O VAL S 12 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N VAL S 14 " --> pdb=" O LEU S 34 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'T' and resid 247 through 251 removed outlier: 3.603A pdb=" N PHE T 197 " --> pdb=" O TRP T 174 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N GLY T 32 " --> pdb=" O TRP T 80 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ARG T 82 " --> pdb=" O GLY T 32 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LEU T 34 " --> pdb=" O ARG T 82 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N GLY T 32 " --> pdb=" O VAL T 10 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N VAL T 12 " --> pdb=" O GLY T 32 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU T 34 " --> pdb=" O VAL T 12 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N VAL T 14 " --> pdb=" O LEU T 34 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'U' and resid 247 through 251 removed outlier: 3.603A pdb=" N PHE U 197 " --> pdb=" O TRP U 174 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N GLY U 32 " --> pdb=" O TRP U 80 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ARG U 82 " --> pdb=" O GLY U 32 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LEU U 34 " --> pdb=" O ARG U 82 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N GLY U 32 " --> pdb=" O VAL U 10 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N VAL U 12 " --> pdb=" O GLY U 32 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU U 34 " --> pdb=" O VAL U 12 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N VAL U 14 " --> pdb=" O LEU U 34 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'V' and resid 247 through 251 removed outlier: 3.603A pdb=" N PHE V 197 " --> pdb=" O TRP V 174 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N GLY V 32 " --> pdb=" O TRP V 80 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ARG V 82 " --> pdb=" O GLY V 32 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LEU V 34 " --> pdb=" O ARG V 82 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N GLY V 32 " --> pdb=" O VAL V 10 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N VAL V 12 " --> pdb=" O GLY V 32 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU V 34 " --> pdb=" O VAL V 12 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N VAL V 14 " --> pdb=" O LEU V 34 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'W' and resid 247 through 251 removed outlier: 3.603A pdb=" N PHE W 197 " --> pdb=" O TRP W 174 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N GLY W 32 " --> pdb=" O TRP W 80 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ARG W 82 " --> pdb=" O GLY W 32 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LEU W 34 " --> pdb=" O ARG W 82 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N GLY W 32 " --> pdb=" O VAL W 10 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N VAL W 12 " --> pdb=" O GLY W 32 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU W 34 " --> pdb=" O VAL W 12 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N VAL W 14 " --> pdb=" O LEU W 34 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'X' and resid 247 through 251 removed outlier: 3.603A pdb=" N PHE X 197 " --> pdb=" O TRP X 174 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N GLY X 32 " --> pdb=" O TRP X 80 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ARG X 82 " --> pdb=" O GLY X 32 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LEU X 34 " --> pdb=" O ARG X 82 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N GLY X 32 " --> pdb=" O VAL X 10 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N VAL X 12 " --> pdb=" O GLY X 32 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU X 34 " --> pdb=" O VAL X 12 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N VAL X 14 " --> pdb=" O LEU X 34 " (cutoff:3.500A) 3024 hydrogen bonds defined for protein. 8784 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: 22.70 Time building geometry restraints manager: 17.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 19200 1.34 - 1.46: 8016 1.46 - 1.58: 29832 1.58 - 1.70: 0 1.70 - 1.81: 480 Bond restraints: 57528 Sorted by residual: bond pdb=" C MET T 94 " pdb=" N PRO T 95 " ideal model delta sigma weight residual 1.332 1.357 -0.025 1.12e-02 7.97e+03 4.87e+00 bond pdb=" C MET W 94 " pdb=" N PRO W 95 " ideal model delta sigma weight residual 1.332 1.357 -0.025 1.12e-02 7.97e+03 4.87e+00 bond pdb=" C MET G 94 " pdb=" N PRO G 95 " ideal model delta sigma weight residual 1.332 1.357 -0.025 1.12e-02 7.97e+03 4.87e+00 bond pdb=" C MET X 94 " pdb=" N PRO X 95 " ideal model delta sigma weight residual 1.332 1.357 -0.025 1.12e-02 7.97e+03 4.87e+00 bond pdb=" C MET H 94 " pdb=" N PRO H 95 " ideal model delta sigma weight residual 1.332 1.357 -0.025 1.12e-02 7.97e+03 4.87e+00 ... (remaining 57523 not shown) Histogram of bond angle deviations from ideal: 100.04 - 106.85: 1992 106.85 - 113.66: 32448 113.66 - 120.46: 22968 120.46 - 127.27: 19824 127.27 - 134.08: 480 Bond angle restraints: 77712 Sorted by residual: angle pdb=" C TYR V 75 " pdb=" N PRO V 76 " pdb=" CA PRO V 76 " ideal model delta sigma weight residual 119.84 111.56 8.28 1.25e+00 6.40e-01 4.39e+01 angle pdb=" C TYR J 75 " pdb=" N PRO J 76 " pdb=" CA PRO J 76 " ideal model delta sigma weight residual 119.84 111.56 8.28 1.25e+00 6.40e-01 4.39e+01 angle pdb=" C TYR W 75 " pdb=" N PRO W 76 " pdb=" CA PRO W 76 " ideal model delta sigma weight residual 119.84 111.56 8.28 1.25e+00 6.40e-01 4.39e+01 angle pdb=" C TYR G 75 " pdb=" N PRO G 76 " pdb=" CA PRO G 76 " ideal model delta sigma weight residual 119.84 111.56 8.28 1.25e+00 6.40e-01 4.39e+01 angle pdb=" C TYR I 75 " pdb=" N PRO I 76 " pdb=" CA PRO I 76 " ideal model delta sigma weight residual 119.84 111.56 8.28 1.25e+00 6.40e-01 4.39e+01 ... (remaining 77707 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 31464 17.90 - 35.80: 3240 35.80 - 53.70: 768 53.70 - 71.59: 192 71.59 - 89.49: 48 Dihedral angle restraints: 35712 sinusoidal: 14952 harmonic: 20760 Sorted by residual: dihedral pdb=" CB GLU V 37 " pdb=" CG GLU V 37 " pdb=" CD GLU V 37 " pdb=" OE1 GLU V 37 " ideal model delta sinusoidal sigma weight residual 0.00 89.49 -89.49 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU U 37 " pdb=" CG GLU U 37 " pdb=" CD GLU U 37 " pdb=" OE1 GLU U 37 " ideal model delta sinusoidal sigma weight residual 0.00 89.49 -89.49 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU B 37 " pdb=" CG GLU B 37 " pdb=" CD GLU B 37 " pdb=" OE1 GLU B 37 " ideal model delta sinusoidal sigma weight residual 0.00 89.49 -89.49 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 35709 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 6696 0.054 - 0.108: 1800 0.108 - 0.162: 264 0.162 - 0.216: 0 0.216 - 0.270: 24 Chirality restraints: 8784 Sorted by residual: chirality pdb=" CA TYR A 75 " pdb=" N TYR A 75 " pdb=" C TYR A 75 " pdb=" CB TYR A 75 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" CA TYR U 75 " pdb=" N TYR U 75 " pdb=" C TYR U 75 " pdb=" CB TYR U 75 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" CA TYR M 75 " pdb=" N TYR M 75 " pdb=" C TYR M 75 " pdb=" CB TYR M 75 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.82e+00 ... (remaining 8781 not shown) Planarity restraints: 10152 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET H 16 " 0.041 5.00e-02 4.00e+02 6.18e-02 6.11e+00 pdb=" N PRO H 17 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO H 17 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO H 17 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET X 16 " 0.041 5.00e-02 4.00e+02 6.18e-02 6.11e+00 pdb=" N PRO X 17 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO X 17 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO X 17 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET K 16 " 0.041 5.00e-02 4.00e+02 6.18e-02 6.11e+00 pdb=" N PRO K 17 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO K 17 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO K 17 " 0.034 5.00e-02 4.00e+02 ... (remaining 10149 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 18828 2.86 - 3.37: 50352 3.37 - 3.88: 86580 3.88 - 4.39: 100116 4.39 - 4.90: 172368 Nonbonded interactions: 428244 Sorted by model distance: nonbonded pdb=" O ALA K 23 " pdb=" OG1 THR K 26 " model vdw 2.353 2.440 nonbonded pdb=" O ALA Q 23 " pdb=" OG1 THR Q 26 " model vdw 2.353 2.440 nonbonded pdb=" O ALA C 23 " pdb=" OG1 THR C 26 " model vdw 2.353 2.440 nonbonded pdb=" O ALA N 23 " pdb=" OG1 THR N 26 " model vdw 2.353 2.440 nonbonded pdb=" O ALA R 23 " pdb=" OG1 THR R 26 " model vdw 2.353 2.440 ... (remaining 428239 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' 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: 0.710 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: 0.030 Extract box with map and model: 5.350 Check model and map are aligned: 0.640 Set scattering table: 0.400 Process input model: 114.710 Find NCS groups from input model: 2.980 Set up NCS constraints: 0.410 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:11.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 137.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 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 : 0.005 0.046 57528 Z= 0.349 Angle : 0.790 9.080 77712 Z= 0.500 Chirality : 0.049 0.270 8784 Planarity : 0.007 0.062 10152 Dihedral : 15.948 89.493 22320 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 2.81 % Allowed : 12.45 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.84 (0.08), residues: 7200 helix: -1.38 (0.07), residues: 3720 sheet: -0.89 (0.17), residues: 720 loop : -2.74 (0.09), residues: 2760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP O 80 HIS 0.005 0.002 HIS G 227 PHE 0.020 0.003 PHE R 74 TYR 0.016 0.002 TYR P 75 ARG 0.003 0.000 ARG O 262 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14400 Ramachandran restraints generated. 7200 Oldfield, 0 Emsley, 7200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14400 Ramachandran restraints generated. 7200 Oldfield, 0 Emsley, 7200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 5976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 408 time to evaluate : 5.214 Fit side-chains REVERT: A 177 MET cc_start: 0.8456 (mtp) cc_final: 0.8145 (mmm) REVERT: B 177 MET cc_start: 0.8460 (mtp) cc_final: 0.8144 (mmm) REVERT: C 177 MET cc_start: 0.8463 (mtp) cc_final: 0.8147 (mmm) REVERT: D 177 MET cc_start: 0.8462 (mtp) cc_final: 0.8145 (mmm) REVERT: E 177 MET cc_start: 0.8462 (mtp) cc_final: 0.8146 (mmm) REVERT: F 177 MET cc_start: 0.8464 (mtp) cc_final: 0.8145 (mmm) REVERT: G 177 MET cc_start: 0.8469 (mtp) cc_final: 0.8148 (mmm) REVERT: H 177 MET cc_start: 0.8468 (mtp) cc_final: 0.8150 (mmm) REVERT: I 177 MET cc_start: 0.8464 (mtp) cc_final: 0.8145 (mmm) REVERT: J 177 MET cc_start: 0.8469 (mtp) cc_final: 0.8148 (mmm) REVERT: K 177 MET cc_start: 0.8468 (mtp) cc_final: 0.8150 (mmm) REVERT: L 177 MET cc_start: 0.8462 (mtp) cc_final: 0.8146 (mmm) REVERT: M 177 MET cc_start: 0.8460 (mtp) cc_final: 0.8144 (mmm) REVERT: N 177 MET cc_start: 0.8463 (mtp) cc_final: 0.8147 (mmm) REVERT: O 177 MET cc_start: 0.8462 (mtp) cc_final: 0.8145 (mmm) REVERT: P 177 MET cc_start: 0.8456 (mtp) cc_final: 0.8145 (mmm) REVERT: Q 177 MET cc_start: 0.8462 (mtp) cc_final: 0.8145 (mmm) REVERT: R 177 MET cc_start: 0.8456 (mtp) cc_final: 0.8145 (mmm) REVERT: S 177 MET cc_start: 0.8460 (mtp) cc_final: 0.8144 (mmm) REVERT: T 177 MET cc_start: 0.8463 (mtp) cc_final: 0.8147 (mmm) REVERT: U 177 MET cc_start: 0.8462 (mtp) cc_final: 0.8146 (mmm) REVERT: V 177 MET cc_start: 0.8464 (mtp) cc_final: 0.8145 (mmm) REVERT: W 177 MET cc_start: 0.8469 (mtp) cc_final: 0.8148 (mmm) REVERT: X 177 MET cc_start: 0.8468 (mtp) cc_final: 0.8150 (mmm) outliers start: 168 outliers final: 96 residues processed: 576 average time/residue: 1.7049 time to fit residues: 1191.1731 Evaluate side-chains 336 residues out of total 5976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 240 time to evaluate : 5.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 74 PHE Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 74 PHE Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 74 PHE Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 74 PHE Chi-restraints excluded: chain D residue 163 GLU Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 74 PHE Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain E residue 212 ILE Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 74 PHE Chi-restraints excluded: chain F residue 163 GLU Chi-restraints excluded: chain F residue 212 ILE Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 74 PHE Chi-restraints excluded: chain G residue 163 GLU Chi-restraints excluded: chain G residue 212 ILE Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 74 PHE Chi-restraints excluded: chain H residue 163 GLU Chi-restraints excluded: chain H residue 212 ILE Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 74 PHE Chi-restraints excluded: chain I residue 163 GLU Chi-restraints excluded: chain I residue 212 ILE Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 74 PHE Chi-restraints excluded: chain J residue 163 GLU Chi-restraints excluded: chain J residue 212 ILE Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 74 PHE Chi-restraints excluded: chain K residue 163 GLU Chi-restraints excluded: chain K residue 212 ILE Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 74 PHE Chi-restraints excluded: chain L residue 163 GLU Chi-restraints excluded: chain L residue 212 ILE Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 74 PHE Chi-restraints excluded: chain M residue 163 GLU Chi-restraints excluded: chain M residue 212 ILE Chi-restraints excluded: chain N residue 5 VAL Chi-restraints excluded: chain N residue 74 PHE Chi-restraints excluded: chain N residue 163 GLU Chi-restraints excluded: chain N residue 212 ILE Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 74 PHE Chi-restraints excluded: chain O residue 163 GLU Chi-restraints excluded: chain O residue 212 ILE Chi-restraints excluded: chain P residue 5 VAL Chi-restraints excluded: chain P residue 74 PHE Chi-restraints excluded: chain P residue 163 GLU Chi-restraints excluded: chain P residue 212 ILE Chi-restraints excluded: chain Q residue 5 VAL Chi-restraints excluded: chain Q residue 74 PHE Chi-restraints excluded: chain Q residue 163 GLU Chi-restraints excluded: chain Q residue 212 ILE Chi-restraints excluded: chain R residue 5 VAL Chi-restraints excluded: chain R residue 74 PHE Chi-restraints excluded: chain R residue 163 GLU Chi-restraints excluded: chain R residue 212 ILE Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 74 PHE Chi-restraints excluded: chain S residue 163 GLU Chi-restraints excluded: chain S residue 212 ILE Chi-restraints excluded: chain T residue 5 VAL Chi-restraints excluded: chain T residue 74 PHE Chi-restraints excluded: chain T residue 163 GLU Chi-restraints excluded: chain T residue 212 ILE Chi-restraints excluded: chain U residue 5 VAL Chi-restraints excluded: chain U residue 74 PHE Chi-restraints excluded: chain U residue 163 GLU Chi-restraints excluded: chain U residue 212 ILE Chi-restraints excluded: chain V residue 5 VAL Chi-restraints excluded: chain V residue 74 PHE Chi-restraints excluded: chain V residue 163 GLU Chi-restraints excluded: chain V residue 212 ILE Chi-restraints excluded: chain W residue 5 VAL Chi-restraints excluded: chain W residue 74 PHE Chi-restraints excluded: chain W residue 163 GLU Chi-restraints excluded: chain W residue 212 ILE Chi-restraints excluded: chain X residue 5 VAL Chi-restraints excluded: chain X residue 74 PHE Chi-restraints excluded: chain X residue 163 GLU Chi-restraints excluded: chain X residue 212 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 607 optimal weight: 0.5980 chunk 545 optimal weight: 5.9990 chunk 302 optimal weight: 1.9990 chunk 186 optimal weight: 6.9990 chunk 368 optimal weight: 1.9990 chunk 291 optimal weight: 10.0000 chunk 564 optimal weight: 0.1980 chunk 218 optimal weight: 8.9990 chunk 343 optimal weight: 2.9990 chunk 420 optimal weight: 0.0060 chunk 653 optimal weight: 3.9990 overall best weight: 0.9600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 ASN A 207 GLN B 203 ASN B 207 GLN C 203 ASN C 207 GLN D 203 ASN D 207 GLN E 203 ASN E 207 GLN F 203 ASN F 207 GLN G 203 ASN G 207 GLN H 203 ASN H 207 GLN I 203 ASN I 207 GLN J 203 ASN J 207 GLN K 203 ASN K 207 GLN L 203 ASN L 207 GLN M 203 ASN M 207 GLN N 203 ASN N 207 GLN O 203 ASN O 207 GLN P 203 ASN P 207 GLN Q 203 ASN Q 207 GLN R 203 ASN R 207 GLN S 203 ASN S 207 GLN T 203 ASN T 207 GLN U 203 ASN U 207 GLN V 203 ASN V 207 GLN W 203 ASN W 207 GLN X 203 ASN X 207 GLN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 57528 Z= 0.145 Angle : 0.473 4.287 77712 Z= 0.256 Chirality : 0.042 0.140 8784 Planarity : 0.005 0.039 10152 Dihedral : 5.321 53.634 8064 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.41 % Allowed : 16.06 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.09), residues: 7200 helix: 0.83 (0.09), residues: 3624 sheet: -0.35 (0.18), residues: 744 loop : -2.19 (0.09), residues: 2832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 110 HIS 0.001 0.000 HIS B 150 PHE 0.019 0.002 PHE D 74 TYR 0.011 0.001 TYR E 75 ARG 0.005 0.000 ARG E 104 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14400 Ramachandran restraints generated. 7200 Oldfield, 0 Emsley, 7200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14400 Ramachandran restraints generated. 7200 Oldfield, 0 Emsley, 7200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 5976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 336 time to evaluate : 7.233 Fit side-chains REVERT: B 177 MET cc_start: 0.8340 (mtp) cc_final: 0.7999 (mmm) REVERT: C 177 MET cc_start: 0.8338 (mtp) cc_final: 0.7997 (mmm) REVERT: E 177 MET cc_start: 0.8338 (mtp) cc_final: 0.7996 (mmm) REVERT: F 177 MET cc_start: 0.8340 (mtp) cc_final: 0.8000 (mmm) REVERT: G 177 MET cc_start: 0.8336 (mtp) cc_final: 0.7997 (mmm) REVERT: H 177 MET cc_start: 0.8342 (mtp) cc_final: 0.7996 (mmm) REVERT: I 177 MET cc_start: 0.8340 (mtp) cc_final: 0.8000 (mmm) REVERT: J 177 MET cc_start: 0.8336 (mtp) cc_final: 0.7997 (mmm) REVERT: K 177 MET cc_start: 0.8342 (mtp) cc_final: 0.7996 (mmm) REVERT: L 177 MET cc_start: 0.8338 (mtp) cc_final: 0.7996 (mmm) REVERT: M 177 MET cc_start: 0.8340 (mtp) cc_final: 0.7999 (mmm) REVERT: N 177 MET cc_start: 0.8338 (mtp) cc_final: 0.7997 (mmm) REVERT: S 177 MET cc_start: 0.8340 (mtp) cc_final: 0.7999 (mmm) REVERT: T 177 MET cc_start: 0.8338 (mtp) cc_final: 0.7997 (mmm) REVERT: U 177 MET cc_start: 0.8338 (mtp) cc_final: 0.7996 (mmm) REVERT: V 177 MET cc_start: 0.8340 (mtp) cc_final: 0.8000 (mmm) REVERT: W 177 MET cc_start: 0.8336 (mtp) cc_final: 0.7997 (mmm) REVERT: X 177 MET cc_start: 0.8342 (mtp) cc_final: 0.7996 (mmm) outliers start: 144 outliers final: 24 residues processed: 480 average time/residue: 1.3267 time to fit residues: 814.1748 Evaluate side-chains 288 residues out of total 5976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 264 time to evaluate : 5.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain B residue 55 LYS Chi-restraints excluded: chain C residue 55 LYS Chi-restraints excluded: chain D residue 55 LYS Chi-restraints excluded: chain E residue 55 LYS Chi-restraints excluded: chain F residue 55 LYS Chi-restraints excluded: chain G residue 55 LYS Chi-restraints excluded: chain H residue 55 LYS Chi-restraints excluded: chain I residue 55 LYS Chi-restraints excluded: chain J residue 55 LYS Chi-restraints excluded: chain K residue 55 LYS Chi-restraints excluded: chain L residue 55 LYS Chi-restraints excluded: chain M residue 55 LYS Chi-restraints excluded: chain N residue 55 LYS Chi-restraints excluded: chain O residue 55 LYS Chi-restraints excluded: chain P residue 55 LYS Chi-restraints excluded: chain Q residue 55 LYS Chi-restraints excluded: chain R residue 55 LYS Chi-restraints excluded: chain S residue 55 LYS Chi-restraints excluded: chain T residue 55 LYS Chi-restraints excluded: chain U residue 55 LYS Chi-restraints excluded: chain V residue 55 LYS Chi-restraints excluded: chain W residue 55 LYS Chi-restraints excluded: chain X residue 55 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 363 optimal weight: 10.0000 chunk 202 optimal weight: 10.0000 chunk 544 optimal weight: 5.9990 chunk 445 optimal weight: 3.9990 chunk 180 optimal weight: 0.0060 chunk 655 optimal weight: 5.9990 chunk 707 optimal weight: 6.9990 chunk 583 optimal weight: 10.0000 chunk 649 optimal weight: 3.9990 chunk 223 optimal weight: 8.9990 chunk 525 optimal weight: 20.0000 overall best weight: 4.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 57528 Z= 0.237 Angle : 0.573 8.553 77712 Z= 0.304 Chirality : 0.045 0.149 8784 Planarity : 0.007 0.076 10152 Dihedral : 3.896 12.935 7872 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.41 % Allowed : 16.37 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.09), residues: 7200 helix: 1.19 (0.09), residues: 3672 sheet: -0.40 (0.18), residues: 744 loop : -1.97 (0.10), residues: 2784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP Q 80 HIS 0.003 0.001 HIS S 236 PHE 0.023 0.003 PHE W 74 TYR 0.031 0.002 TYR F 75 ARG 0.002 0.000 ARG H 262 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14400 Ramachandran restraints generated. 7200 Oldfield, 0 Emsley, 7200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14400 Ramachandran restraints generated. 7200 Oldfield, 0 Emsley, 7200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 5976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 288 time to evaluate : 5.322 Fit side-chains REVERT: B 177 MET cc_start: 0.8431 (mtp) cc_final: 0.8062 (mmm) REVERT: C 177 MET cc_start: 0.8434 (mtp) cc_final: 0.8059 (mmm) REVERT: E 177 MET cc_start: 0.8427 (mtp) cc_final: 0.8057 (mmm) REVERT: F 177 MET cc_start: 0.8427 (mtp) cc_final: 0.8055 (mmm) REVERT: G 177 MET cc_start: 0.8435 (mtp) cc_final: 0.8058 (mmm) REVERT: H 177 MET cc_start: 0.8433 (mtp) cc_final: 0.8056 (mmm) REVERT: I 177 MET cc_start: 0.8427 (mtp) cc_final: 0.8055 (mmm) REVERT: J 177 MET cc_start: 0.8435 (mtp) cc_final: 0.8058 (mmm) REVERT: K 177 MET cc_start: 0.8433 (mtp) cc_final: 0.8056 (mmm) REVERT: L 177 MET cc_start: 0.8427 (mtp) cc_final: 0.8057 (mmm) REVERT: M 177 MET cc_start: 0.8431 (mtp) cc_final: 0.8062 (mmm) REVERT: N 177 MET cc_start: 0.8434 (mtp) cc_final: 0.8059 (mmm) REVERT: S 177 MET cc_start: 0.8431 (mtp) cc_final: 0.8062 (mmm) REVERT: T 177 MET cc_start: 0.8434 (mtp) cc_final: 0.8059 (mmm) REVERT: U 177 MET cc_start: 0.8427 (mtp) cc_final: 0.8057 (mmm) REVERT: V 177 MET cc_start: 0.8427 (mtp) cc_final: 0.8055 (mmm) REVERT: W 177 MET cc_start: 0.8435 (mtp) cc_final: 0.8058 (mmm) REVERT: X 177 MET cc_start: 0.8433 (mtp) cc_final: 0.8056 (mmm) outliers start: 144 outliers final: 96 residues processed: 384 average time/residue: 1.4544 time to fit residues: 702.0813 Evaluate side-chains 384 residues out of total 5976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 288 time to evaluate : 5.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain B residue 55 LYS Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain C residue 55 LYS Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 107 MET Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 55 LYS Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 107 MET Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain E residue 55 LYS Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 107 MET Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain F residue 55 LYS Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 107 MET Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain G residue 55 LYS Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 107 MET Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 55 LYS Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain H residue 107 MET Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain I residue 55 LYS Chi-restraints excluded: chain I residue 59 LEU Chi-restraints excluded: chain I residue 107 MET Chi-restraints excluded: chain I residue 108 LEU Chi-restraints excluded: chain J residue 55 LYS Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 107 MET Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain K residue 55 LYS Chi-restraints excluded: chain K residue 59 LEU Chi-restraints excluded: chain K residue 107 MET Chi-restraints excluded: chain K residue 108 LEU Chi-restraints excluded: chain L residue 55 LYS Chi-restraints excluded: chain L residue 59 LEU Chi-restraints excluded: chain L residue 107 MET Chi-restraints excluded: chain L residue 108 LEU Chi-restraints excluded: chain M residue 55 LYS Chi-restraints excluded: chain M residue 59 LEU Chi-restraints excluded: chain M residue 107 MET Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain N residue 55 LYS Chi-restraints excluded: chain N residue 59 LEU Chi-restraints excluded: chain N residue 107 MET Chi-restraints excluded: chain N residue 108 LEU Chi-restraints excluded: chain O residue 55 LYS Chi-restraints excluded: chain O residue 59 LEU Chi-restraints excluded: chain O residue 107 MET Chi-restraints excluded: chain O residue 108 LEU Chi-restraints excluded: chain P residue 55 LYS Chi-restraints excluded: chain P residue 59 LEU Chi-restraints excluded: chain P residue 107 MET Chi-restraints excluded: chain P residue 108 LEU Chi-restraints excluded: chain Q residue 55 LYS Chi-restraints excluded: chain Q residue 59 LEU Chi-restraints excluded: chain Q residue 107 MET Chi-restraints excluded: chain Q residue 108 LEU Chi-restraints excluded: chain R residue 55 LYS Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 107 MET Chi-restraints excluded: chain R residue 108 LEU Chi-restraints excluded: chain S residue 55 LYS Chi-restraints excluded: chain S residue 59 LEU Chi-restraints excluded: chain S residue 107 MET Chi-restraints excluded: chain S residue 108 LEU Chi-restraints excluded: chain T residue 55 LYS Chi-restraints excluded: chain T residue 59 LEU Chi-restraints excluded: chain T residue 107 MET Chi-restraints excluded: chain T residue 108 LEU Chi-restraints excluded: chain U residue 55 LYS Chi-restraints excluded: chain U residue 59 LEU Chi-restraints excluded: chain U residue 107 MET Chi-restraints excluded: chain U residue 108 LEU Chi-restraints excluded: chain V residue 55 LYS Chi-restraints excluded: chain V residue 59 LEU Chi-restraints excluded: chain V residue 107 MET Chi-restraints excluded: chain V residue 108 LEU Chi-restraints excluded: chain W residue 55 LYS Chi-restraints excluded: chain W residue 59 LEU Chi-restraints excluded: chain W residue 107 MET Chi-restraints excluded: chain W residue 108 LEU Chi-restraints excluded: chain X residue 55 LYS Chi-restraints excluded: chain X residue 59 LEU Chi-restraints excluded: chain X residue 107 MET Chi-restraints excluded: chain X residue 108 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 647 optimal weight: 5.9990 chunk 492 optimal weight: 5.9990 chunk 339 optimal weight: 0.7980 chunk 72 optimal weight: 4.9990 chunk 312 optimal weight: 5.9990 chunk 439 optimal weight: 2.9990 chunk 657 optimal weight: 10.0000 chunk 695 optimal weight: 20.0000 chunk 343 optimal weight: 9.9990 chunk 623 optimal weight: 2.9990 chunk 187 optimal weight: 6.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 57528 Z= 0.211 Angle : 0.539 6.853 77712 Z= 0.284 Chirality : 0.044 0.128 8784 Planarity : 0.006 0.066 10152 Dihedral : 3.786 13.149 7872 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 3.06 % Allowed : 16.42 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.09), residues: 7200 helix: 1.52 (0.09), residues: 3624 sheet: -0.22 (0.18), residues: 744 loop : -1.81 (0.09), residues: 2832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP N 110 HIS 0.003 0.001 HIS Q 236 PHE 0.022 0.003 PHE A 74 TYR 0.021 0.002 TYR P 75 ARG 0.002 0.000 ARG B 262 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14400 Ramachandran restraints generated. 7200 Oldfield, 0 Emsley, 7200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14400 Ramachandran restraints generated. 7200 Oldfield, 0 Emsley, 7200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 5976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 288 time to evaluate : 5.249 Fit side-chains REVERT: B 177 MET cc_start: 0.8412 (mtp) cc_final: 0.8080 (mmm) REVERT: C 177 MET cc_start: 0.8416 (mtp) cc_final: 0.8081 (mmm) REVERT: E 177 MET cc_start: 0.8412 (mtp) cc_final: 0.8080 (mmm) REVERT: F 177 MET cc_start: 0.8411 (mtp) cc_final: 0.8078 (mmm) REVERT: G 177 MET cc_start: 0.8418 (mtp) cc_final: 0.8084 (mmm) REVERT: H 177 MET cc_start: 0.8415 (mtp) cc_final: 0.8078 (mmm) REVERT: I 177 MET cc_start: 0.8411 (mtp) cc_final: 0.8078 (mmm) REVERT: J 177 MET cc_start: 0.8418 (mtp) cc_final: 0.8084 (mmm) REVERT: K 177 MET cc_start: 0.8415 (mtp) cc_final: 0.8078 (mmm) REVERT: L 177 MET cc_start: 0.8412 (mtp) cc_final: 0.8080 (mmm) REVERT: M 177 MET cc_start: 0.8412 (mtp) cc_final: 0.8080 (mmm) REVERT: N 177 MET cc_start: 0.8416 (mtp) cc_final: 0.8081 (mmm) REVERT: S 177 MET cc_start: 0.8412 (mtp) cc_final: 0.8080 (mmm) REVERT: T 177 MET cc_start: 0.8416 (mtp) cc_final: 0.8081 (mmm) REVERT: U 177 MET cc_start: 0.8412 (mtp) cc_final: 0.8080 (mmm) REVERT: V 177 MET cc_start: 0.8411 (mtp) cc_final: 0.8078 (mmm) REVERT: W 177 MET cc_start: 0.8418 (mtp) cc_final: 0.8084 (mmm) REVERT: X 177 MET cc_start: 0.8415 (mtp) cc_final: 0.8078 (mmm) outliers start: 183 outliers final: 123 residues processed: 423 average time/residue: 1.4278 time to fit residues: 760.0618 Evaluate side-chains 411 residues out of total 5976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 288 time to evaluate : 5.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 MET Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain C residue 16 MET Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 107 MET Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain D residue 16 MET Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 107 MET Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 277 ASP Chi-restraints excluded: chain E residue 16 MET Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 107 MET Chi-restraints excluded: chain E residue 212 ILE Chi-restraints excluded: chain E residue 277 ASP Chi-restraints excluded: chain F residue 16 MET Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 107 MET Chi-restraints excluded: chain F residue 212 ILE Chi-restraints excluded: chain F residue 277 ASP Chi-restraints excluded: chain G residue 16 MET Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 107 MET Chi-restraints excluded: chain G residue 212 ILE Chi-restraints excluded: chain G residue 277 ASP Chi-restraints excluded: chain H residue 16 MET Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain H residue 107 MET Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain H residue 212 ILE Chi-restraints excluded: chain H residue 277 ASP Chi-restraints excluded: chain I residue 16 MET Chi-restraints excluded: chain I residue 59 LEU Chi-restraints excluded: chain I residue 107 MET Chi-restraints excluded: chain I residue 212 ILE Chi-restraints excluded: chain I residue 277 ASP Chi-restraints excluded: chain J residue 16 MET Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 107 MET Chi-restraints excluded: chain J residue 212 ILE Chi-restraints excluded: chain J residue 277 ASP Chi-restraints excluded: chain K residue 16 MET Chi-restraints excluded: chain K residue 59 LEU Chi-restraints excluded: chain K residue 107 MET Chi-restraints excluded: chain K residue 108 LEU Chi-restraints excluded: chain K residue 212 ILE Chi-restraints excluded: chain K residue 277 ASP Chi-restraints excluded: chain L residue 16 MET Chi-restraints excluded: chain L residue 59 LEU Chi-restraints excluded: chain L residue 107 MET Chi-restraints excluded: chain L residue 212 ILE Chi-restraints excluded: chain L residue 277 ASP Chi-restraints excluded: chain M residue 16 MET Chi-restraints excluded: chain M residue 59 LEU Chi-restraints excluded: chain M residue 107 MET Chi-restraints excluded: chain M residue 212 ILE Chi-restraints excluded: chain M residue 277 ASP Chi-restraints excluded: chain N residue 16 MET Chi-restraints excluded: chain N residue 59 LEU Chi-restraints excluded: chain N residue 107 MET Chi-restraints excluded: chain N residue 212 ILE Chi-restraints excluded: chain N residue 277 ASP Chi-restraints excluded: chain O residue 16 MET Chi-restraints excluded: chain O residue 59 LEU Chi-restraints excluded: chain O residue 107 MET Chi-restraints excluded: chain O residue 212 ILE Chi-restraints excluded: chain O residue 277 ASP Chi-restraints excluded: chain P residue 16 MET Chi-restraints excluded: chain P residue 59 LEU Chi-restraints excluded: chain P residue 107 MET Chi-restraints excluded: chain P residue 212 ILE Chi-restraints excluded: chain P residue 277 ASP Chi-restraints excluded: chain Q residue 16 MET Chi-restraints excluded: chain Q residue 59 LEU Chi-restraints excluded: chain Q residue 107 MET Chi-restraints excluded: chain Q residue 212 ILE Chi-restraints excluded: chain Q residue 277 ASP Chi-restraints excluded: chain R residue 16 MET Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 107 MET Chi-restraints excluded: chain R residue 212 ILE Chi-restraints excluded: chain R residue 277 ASP Chi-restraints excluded: chain S residue 16 MET Chi-restraints excluded: chain S residue 59 LEU Chi-restraints excluded: chain S residue 107 MET Chi-restraints excluded: chain S residue 212 ILE Chi-restraints excluded: chain S residue 277 ASP Chi-restraints excluded: chain T residue 16 MET Chi-restraints excluded: chain T residue 59 LEU Chi-restraints excluded: chain T residue 107 MET Chi-restraints excluded: chain T residue 212 ILE Chi-restraints excluded: chain T residue 277 ASP Chi-restraints excluded: chain U residue 16 MET Chi-restraints excluded: chain U residue 59 LEU Chi-restraints excluded: chain U residue 107 MET Chi-restraints excluded: chain U residue 212 ILE Chi-restraints excluded: chain U residue 277 ASP Chi-restraints excluded: chain V residue 16 MET Chi-restraints excluded: chain V residue 59 LEU Chi-restraints excluded: chain V residue 107 MET Chi-restraints excluded: chain V residue 212 ILE Chi-restraints excluded: chain V residue 277 ASP Chi-restraints excluded: chain W residue 16 MET Chi-restraints excluded: chain W residue 59 LEU Chi-restraints excluded: chain W residue 107 MET Chi-restraints excluded: chain W residue 212 ILE Chi-restraints excluded: chain W residue 277 ASP Chi-restraints excluded: chain X residue 16 MET Chi-restraints excluded: chain X residue 59 LEU Chi-restraints excluded: chain X residue 107 MET Chi-restraints excluded: chain X residue 108 LEU Chi-restraints excluded: chain X residue 212 ILE Chi-restraints excluded: chain X residue 277 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 579 optimal weight: 0.3980 chunk 395 optimal weight: 20.0000 chunk 10 optimal weight: 0.9990 chunk 518 optimal weight: 9.9990 chunk 287 optimal weight: 5.9990 chunk 593 optimal weight: 2.9990 chunk 481 optimal weight: 0.0670 chunk 0 optimal weight: 20.0000 chunk 355 optimal weight: 0.2980 chunk 624 optimal weight: 7.9990 chunk 175 optimal weight: 0.0010 overall best weight: 0.3526 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 57528 Z= 0.109 Angle : 0.412 4.682 77712 Z= 0.213 Chirality : 0.041 0.124 8784 Planarity : 0.005 0.057 10152 Dihedral : 3.225 11.920 7872 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.31 % Allowed : 17.97 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.10), residues: 7200 helix: 1.90 (0.09), residues: 3696 sheet: 0.18 (0.18), residues: 744 loop : -1.61 (0.10), residues: 2760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP N 110 HIS 0.001 0.000 HIS I 46 PHE 0.006 0.001 PHE Q 197 TYR 0.006 0.001 TYR O 81 ARG 0.001 0.000 ARG M 92 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14400 Ramachandran restraints generated. 7200 Oldfield, 0 Emsley, 7200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14400 Ramachandran restraints generated. 7200 Oldfield, 0 Emsley, 7200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 5976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 306 time to evaluate : 5.254 Fit side-chains REVERT: B 177 MET cc_start: 0.8047 (mtp) cc_final: 0.7797 (mmm) REVERT: C 177 MET cc_start: 0.8042 (mtp) cc_final: 0.7795 (mmm) REVERT: E 177 MET cc_start: 0.8044 (mtp) cc_final: 0.7795 (mmm) REVERT: F 177 MET cc_start: 0.8044 (mtp) cc_final: 0.7794 (mmm) REVERT: G 177 MET cc_start: 0.8040 (mtp) cc_final: 0.7791 (mmm) REVERT: H 177 MET cc_start: 0.8042 (mtp) cc_final: 0.7793 (mmm) REVERT: I 177 MET cc_start: 0.8044 (mtp) cc_final: 0.7794 (mmm) REVERT: J 177 MET cc_start: 0.8040 (mtp) cc_final: 0.7791 (mmm) REVERT: K 177 MET cc_start: 0.8042 (mtp) cc_final: 0.7793 (mmm) REVERT: L 177 MET cc_start: 0.8044 (mtp) cc_final: 0.7795 (mmm) REVERT: M 177 MET cc_start: 0.8047 (mtp) cc_final: 0.7797 (mmm) REVERT: N 177 MET cc_start: 0.8042 (mtp) cc_final: 0.7795 (mmm) REVERT: S 177 MET cc_start: 0.8047 (mtp) cc_final: 0.7797 (mmm) REVERT: T 177 MET cc_start: 0.8042 (mtp) cc_final: 0.7795 (mmm) REVERT: U 177 MET cc_start: 0.8044 (mtp) cc_final: 0.7795 (mmm) REVERT: V 177 MET cc_start: 0.8044 (mtp) cc_final: 0.7794 (mmm) REVERT: W 177 MET cc_start: 0.8040 (mtp) cc_final: 0.7791 (mmm) REVERT: X 177 MET cc_start: 0.8042 (mtp) cc_final: 0.7793 (mmm) outliers start: 78 outliers final: 24 residues processed: 360 average time/residue: 1.2942 time to fit residues: 607.7734 Evaluate side-chains 306 residues out of total 5976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 282 time to evaluate : 5.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain I residue 108 LEU Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain K residue 108 LEU Chi-restraints excluded: chain L residue 108 LEU Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain N residue 108 LEU Chi-restraints excluded: chain O residue 108 LEU Chi-restraints excluded: chain P residue 108 LEU Chi-restraints excluded: chain Q residue 108 LEU Chi-restraints excluded: chain R residue 108 LEU Chi-restraints excluded: chain S residue 108 LEU Chi-restraints excluded: chain T residue 108 LEU Chi-restraints excluded: chain U residue 108 LEU Chi-restraints excluded: chain V residue 108 LEU Chi-restraints excluded: chain W residue 108 LEU Chi-restraints excluded: chain X residue 108 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 234 optimal weight: 7.9990 chunk 626 optimal weight: 9.9990 chunk 137 optimal weight: 3.9990 chunk 408 optimal weight: 10.0000 chunk 171 optimal weight: 20.0000 chunk 696 optimal weight: 6.9990 chunk 578 optimal weight: 10.0000 chunk 322 optimal weight: 0.0970 chunk 57 optimal weight: 7.9990 chunk 230 optimal weight: 9.9990 chunk 365 optimal weight: 20.0000 overall best weight: 5.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 57528 Z= 0.300 Angle : 0.596 9.076 77712 Z= 0.316 Chirality : 0.047 0.130 8784 Planarity : 0.006 0.055 10152 Dihedral : 3.826 12.669 7872 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 2.46 % Allowed : 17.97 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.09), residues: 7200 helix: 1.31 (0.08), residues: 3816 sheet: 0.31 (0.19), residues: 720 loop : -1.49 (0.10), residues: 2664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP T 80 HIS 0.004 0.001 HIS W 236 PHE 0.029 0.003 PHE N 74 TYR 0.022 0.002 TYR Q 75 ARG 0.003 0.000 ARG B 262 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14400 Ramachandran restraints generated. 7200 Oldfield, 0 Emsley, 7200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14400 Ramachandran restraints generated. 7200 Oldfield, 0 Emsley, 7200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 5976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 306 time to evaluate : 5.438 Fit side-chains REVERT: B 177 MET cc_start: 0.8339 (mtp) cc_final: 0.8037 (mmm) REVERT: C 177 MET cc_start: 0.8340 (mtp) cc_final: 0.8037 (mmm) REVERT: E 177 MET cc_start: 0.8339 (mtp) cc_final: 0.8040 (mmm) REVERT: F 177 MET cc_start: 0.8342 (mtp) cc_final: 0.8041 (mmm) REVERT: G 177 MET cc_start: 0.8346 (mtp) cc_final: 0.8042 (mmm) REVERT: H 177 MET cc_start: 0.8340 (mtp) cc_final: 0.8040 (mmm) REVERT: I 177 MET cc_start: 0.8342 (mtp) cc_final: 0.8041 (mmm) REVERT: J 177 MET cc_start: 0.8346 (mtp) cc_final: 0.8042 (mmm) REVERT: K 177 MET cc_start: 0.8340 (mtp) cc_final: 0.8040 (mmm) REVERT: L 177 MET cc_start: 0.8339 (mtp) cc_final: 0.8040 (mmm) REVERT: M 177 MET cc_start: 0.8339 (mtp) cc_final: 0.8037 (mmm) REVERT: N 177 MET cc_start: 0.8340 (mtp) cc_final: 0.8037 (mmm) REVERT: S 177 MET cc_start: 0.8339 (mtp) cc_final: 0.8037 (mmm) REVERT: T 177 MET cc_start: 0.8340 (mtp) cc_final: 0.8037 (mmm) REVERT: U 177 MET cc_start: 0.8339 (mtp) cc_final: 0.8040 (mmm) REVERT: V 177 MET cc_start: 0.8342 (mtp) cc_final: 0.8041 (mmm) REVERT: W 177 MET cc_start: 0.8346 (mtp) cc_final: 0.8042 (mmm) REVERT: X 177 MET cc_start: 0.8340 (mtp) cc_final: 0.8040 (mmm) outliers start: 147 outliers final: 93 residues processed: 405 average time/residue: 1.3161 time to fit residues: 682.5200 Evaluate side-chains 399 residues out of total 5976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 306 time to evaluate : 5.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 107 MET Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 107 MET Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 107 MET Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 212 ILE Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 107 MET Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 212 ILE Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 107 MET Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 212 ILE Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain H residue 107 MET Chi-restraints excluded: chain H residue 212 ILE Chi-restraints excluded: chain I residue 59 LEU Chi-restraints excluded: chain I residue 107 MET Chi-restraints excluded: chain I residue 108 LEU Chi-restraints excluded: chain I residue 212 ILE Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 107 MET Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain J residue 212 ILE Chi-restraints excluded: chain K residue 59 LEU Chi-restraints excluded: chain K residue 107 MET Chi-restraints excluded: chain K residue 212 ILE Chi-restraints excluded: chain L residue 59 LEU Chi-restraints excluded: chain L residue 107 MET Chi-restraints excluded: chain L residue 108 LEU Chi-restraints excluded: chain L residue 212 ILE Chi-restraints excluded: chain M residue 59 LEU Chi-restraints excluded: chain M residue 107 MET Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain M residue 212 ILE Chi-restraints excluded: chain N residue 59 LEU Chi-restraints excluded: chain N residue 107 MET Chi-restraints excluded: chain N residue 108 LEU Chi-restraints excluded: chain N residue 212 ILE Chi-restraints excluded: chain O residue 59 LEU Chi-restraints excluded: chain O residue 107 MET Chi-restraints excluded: chain O residue 108 LEU Chi-restraints excluded: chain O residue 212 ILE Chi-restraints excluded: chain P residue 59 LEU Chi-restraints excluded: chain P residue 107 MET Chi-restraints excluded: chain P residue 108 LEU Chi-restraints excluded: chain P residue 212 ILE Chi-restraints excluded: chain Q residue 59 LEU Chi-restraints excluded: chain Q residue 107 MET Chi-restraints excluded: chain Q residue 108 LEU Chi-restraints excluded: chain Q residue 212 ILE Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 107 MET Chi-restraints excluded: chain R residue 108 LEU Chi-restraints excluded: chain R residue 212 ILE Chi-restraints excluded: chain S residue 59 LEU Chi-restraints excluded: chain S residue 107 MET Chi-restraints excluded: chain S residue 108 LEU Chi-restraints excluded: chain S residue 212 ILE Chi-restraints excluded: chain T residue 59 LEU Chi-restraints excluded: chain T residue 107 MET Chi-restraints excluded: chain T residue 108 LEU Chi-restraints excluded: chain T residue 212 ILE Chi-restraints excluded: chain U residue 59 LEU Chi-restraints excluded: chain U residue 107 MET Chi-restraints excluded: chain U residue 108 LEU Chi-restraints excluded: chain U residue 212 ILE Chi-restraints excluded: chain V residue 59 LEU Chi-restraints excluded: chain V residue 107 MET Chi-restraints excluded: chain V residue 108 LEU Chi-restraints excluded: chain V residue 212 ILE Chi-restraints excluded: chain W residue 59 LEU Chi-restraints excluded: chain W residue 107 MET Chi-restraints excluded: chain W residue 108 LEU Chi-restraints excluded: chain W residue 212 ILE Chi-restraints excluded: chain X residue 59 LEU Chi-restraints excluded: chain X residue 107 MET Chi-restraints excluded: chain X residue 212 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 671 optimal weight: 7.9990 chunk 78 optimal weight: 0.0980 chunk 396 optimal weight: 8.9990 chunk 508 optimal weight: 2.9990 chunk 394 optimal weight: 8.9990 chunk 586 optimal weight: 8.9990 chunk 389 optimal weight: 6.9990 chunk 693 optimal weight: 5.9990 chunk 434 optimal weight: 8.9990 chunk 423 optimal weight: 7.9990 chunk 320 optimal weight: 8.9990 overall best weight: 4.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 57528 Z= 0.271 Angle : 0.589 9.030 77712 Z= 0.309 Chirality : 0.046 0.133 8784 Planarity : 0.006 0.040 10152 Dihedral : 3.884 13.120 7872 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 2.51 % Allowed : 19.48 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.09), residues: 7200 helix: 1.31 (0.08), residues: 3768 sheet: 0.32 (0.19), residues: 720 loop : -1.42 (0.10), residues: 2712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP V 110 HIS 0.003 0.001 HIS L 236 PHE 0.026 0.003 PHE D 74 TYR 0.020 0.002 TYR R 75 ARG 0.003 0.000 ARG B 262 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14400 Ramachandran restraints generated. 7200 Oldfield, 0 Emsley, 7200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14400 Ramachandran restraints generated. 7200 Oldfield, 0 Emsley, 7200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 5976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 306 time to evaluate : 5.208 Fit side-chains REVERT: B 177 MET cc_start: 0.8359 (mtp) cc_final: 0.8038 (mmm) REVERT: C 177 MET cc_start: 0.8361 (mtp) cc_final: 0.8040 (mmm) REVERT: E 177 MET cc_start: 0.8356 (mtp) cc_final: 0.8035 (mmm) REVERT: F 177 MET cc_start: 0.8361 (mtp) cc_final: 0.8038 (mmm) REVERT: G 177 MET cc_start: 0.8366 (mtp) cc_final: 0.8043 (mmm) REVERT: H 177 MET cc_start: 0.8361 (mtp) cc_final: 0.8040 (mmm) REVERT: I 177 MET cc_start: 0.8361 (mtp) cc_final: 0.8038 (mmm) REVERT: J 177 MET cc_start: 0.8366 (mtp) cc_final: 0.8043 (mmm) REVERT: K 177 MET cc_start: 0.8361 (mtp) cc_final: 0.8040 (mmm) REVERT: L 177 MET cc_start: 0.8356 (mtp) cc_final: 0.8035 (mmm) REVERT: M 177 MET cc_start: 0.8359 (mtp) cc_final: 0.8038 (mmm) REVERT: N 177 MET cc_start: 0.8361 (mtp) cc_final: 0.8040 (mmm) REVERT: S 177 MET cc_start: 0.8359 (mtp) cc_final: 0.8038 (mmm) REVERT: T 177 MET cc_start: 0.8361 (mtp) cc_final: 0.8040 (mmm) REVERT: U 177 MET cc_start: 0.8356 (mtp) cc_final: 0.8035 (mmm) REVERT: V 177 MET cc_start: 0.8361 (mtp) cc_final: 0.8038 (mmm) REVERT: W 177 MET cc_start: 0.8366 (mtp) cc_final: 0.8043 (mmm) REVERT: X 177 MET cc_start: 0.8361 (mtp) cc_final: 0.8040 (mmm) outliers start: 150 outliers final: 96 residues processed: 432 average time/residue: 1.3897 time to fit residues: 760.8858 Evaluate side-chains 402 residues out of total 5976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 306 time to evaluate : 5.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 107 MET Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 107 MET Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 107 MET Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 212 ILE Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 107 MET Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 212 ILE Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 107 MET Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 212 ILE Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain H residue 107 MET Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain H residue 212 ILE Chi-restraints excluded: chain I residue 59 LEU Chi-restraints excluded: chain I residue 107 MET Chi-restraints excluded: chain I residue 108 LEU Chi-restraints excluded: chain I residue 212 ILE Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 107 MET Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain J residue 212 ILE Chi-restraints excluded: chain K residue 59 LEU Chi-restraints excluded: chain K residue 107 MET Chi-restraints excluded: chain K residue 108 LEU Chi-restraints excluded: chain K residue 212 ILE Chi-restraints excluded: chain L residue 59 LEU Chi-restraints excluded: chain L residue 107 MET Chi-restraints excluded: chain L residue 108 LEU Chi-restraints excluded: chain L residue 212 ILE Chi-restraints excluded: chain M residue 59 LEU Chi-restraints excluded: chain M residue 107 MET Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain M residue 212 ILE Chi-restraints excluded: chain N residue 59 LEU Chi-restraints excluded: chain N residue 107 MET Chi-restraints excluded: chain N residue 108 LEU Chi-restraints excluded: chain N residue 212 ILE Chi-restraints excluded: chain O residue 59 LEU Chi-restraints excluded: chain O residue 107 MET Chi-restraints excluded: chain O residue 108 LEU Chi-restraints excluded: chain O residue 212 ILE Chi-restraints excluded: chain P residue 59 LEU Chi-restraints excluded: chain P residue 107 MET Chi-restraints excluded: chain P residue 108 LEU Chi-restraints excluded: chain P residue 212 ILE Chi-restraints excluded: chain Q residue 59 LEU Chi-restraints excluded: chain Q residue 107 MET Chi-restraints excluded: chain Q residue 108 LEU Chi-restraints excluded: chain Q residue 212 ILE Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 107 MET Chi-restraints excluded: chain R residue 108 LEU Chi-restraints excluded: chain R residue 212 ILE Chi-restraints excluded: chain S residue 59 LEU Chi-restraints excluded: chain S residue 107 MET Chi-restraints excluded: chain S residue 108 LEU Chi-restraints excluded: chain S residue 212 ILE Chi-restraints excluded: chain T residue 59 LEU Chi-restraints excluded: chain T residue 107 MET Chi-restraints excluded: chain T residue 108 LEU Chi-restraints excluded: chain T residue 212 ILE Chi-restraints excluded: chain U residue 59 LEU Chi-restraints excluded: chain U residue 107 MET Chi-restraints excluded: chain U residue 108 LEU Chi-restraints excluded: chain U residue 212 ILE Chi-restraints excluded: chain V residue 59 LEU Chi-restraints excluded: chain V residue 107 MET Chi-restraints excluded: chain V residue 108 LEU Chi-restraints excluded: chain V residue 212 ILE Chi-restraints excluded: chain W residue 59 LEU Chi-restraints excluded: chain W residue 107 MET Chi-restraints excluded: chain W residue 108 LEU Chi-restraints excluded: chain W residue 212 ILE Chi-restraints excluded: chain X residue 59 LEU Chi-restraints excluded: chain X residue 107 MET Chi-restraints excluded: chain X residue 108 LEU Chi-restraints excluded: chain X residue 212 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 429 optimal weight: 10.0000 chunk 277 optimal weight: 5.9990 chunk 414 optimal weight: 9.9990 chunk 209 optimal weight: 2.9990 chunk 136 optimal weight: 9.9990 chunk 134 optimal weight: 6.9990 chunk 441 optimal weight: 5.9990 chunk 472 optimal weight: 0.4980 chunk 343 optimal weight: 9.9990 chunk 64 optimal weight: 7.9990 chunk 545 optimal weight: 0.4980 overall best weight: 3.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 57528 Z= 0.196 Angle : 0.526 7.577 77712 Z= 0.275 Chirality : 0.044 0.128 8784 Planarity : 0.005 0.036 10152 Dihedral : 3.690 12.961 7872 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 1.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 1.61 % Allowed : 20.48 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.10), residues: 7200 helix: 1.67 (0.09), residues: 3672 sheet: 0.07 (0.18), residues: 744 loop : -1.42 (0.10), residues: 2784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 110 HIS 0.002 0.001 HIS A 236 PHE 0.020 0.002 PHE A 74 TYR 0.013 0.002 TYR E 75 ARG 0.002 0.000 ARG P 92 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14400 Ramachandran restraints generated. 7200 Oldfield, 0 Emsley, 7200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14400 Ramachandran restraints generated. 7200 Oldfield, 0 Emsley, 7200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 5976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 306 time to evaluate : 5.216 Fit side-chains REVERT: B 177 MET cc_start: 0.8251 (mtp) cc_final: 0.7914 (mmm) REVERT: C 177 MET cc_start: 0.8254 (mtp) cc_final: 0.7915 (mmm) REVERT: E 177 MET cc_start: 0.8248 (mtp) cc_final: 0.7911 (mmm) REVERT: F 177 MET cc_start: 0.8254 (mtp) cc_final: 0.7914 (mmm) REVERT: G 177 MET cc_start: 0.8257 (mtp) cc_final: 0.7918 (mmm) REVERT: H 177 MET cc_start: 0.8254 (mtp) cc_final: 0.7914 (mmm) REVERT: I 177 MET cc_start: 0.8254 (mtp) cc_final: 0.7914 (mmm) REVERT: J 177 MET cc_start: 0.8257 (mtp) cc_final: 0.7918 (mmm) REVERT: K 177 MET cc_start: 0.8254 (mtp) cc_final: 0.7914 (mmm) REVERT: L 177 MET cc_start: 0.8248 (mtp) cc_final: 0.7911 (mmm) REVERT: M 177 MET cc_start: 0.8251 (mtp) cc_final: 0.7914 (mmm) REVERT: N 177 MET cc_start: 0.8254 (mtp) cc_final: 0.7915 (mmm) REVERT: S 177 MET cc_start: 0.8251 (mtp) cc_final: 0.7914 (mmm) REVERT: T 177 MET cc_start: 0.8254 (mtp) cc_final: 0.7915 (mmm) REVERT: U 177 MET cc_start: 0.8248 (mtp) cc_final: 0.7911 (mmm) REVERT: V 177 MET cc_start: 0.8254 (mtp) cc_final: 0.7914 (mmm) REVERT: W 177 MET cc_start: 0.8257 (mtp) cc_final: 0.7918 (mmm) REVERT: X 177 MET cc_start: 0.8254 (mtp) cc_final: 0.7914 (mmm) outliers start: 96 outliers final: 66 residues processed: 378 average time/residue: 1.2329 time to fit residues: 606.3142 Evaluate side-chains 372 residues out of total 5976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 306 time to evaluate : 5.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain C residue 107 MET Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain D residue 107 MET Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain E residue 107 MET Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain F residue 107 MET Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain G residue 107 MET Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 143 VAL Chi-restraints excluded: chain H residue 107 MET Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain I residue 107 MET Chi-restraints excluded: chain I residue 108 LEU Chi-restraints excluded: chain I residue 143 VAL Chi-restraints excluded: chain J residue 107 MET Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain J residue 143 VAL Chi-restraints excluded: chain K residue 107 MET Chi-restraints excluded: chain K residue 108 LEU Chi-restraints excluded: chain K residue 143 VAL Chi-restraints excluded: chain L residue 107 MET Chi-restraints excluded: chain L residue 108 LEU Chi-restraints excluded: chain L residue 143 VAL Chi-restraints excluded: chain M residue 107 MET Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain M residue 143 VAL Chi-restraints excluded: chain N residue 107 MET Chi-restraints excluded: chain N residue 108 LEU Chi-restraints excluded: chain N residue 143 VAL Chi-restraints excluded: chain O residue 107 MET Chi-restraints excluded: chain O residue 108 LEU Chi-restraints excluded: chain P residue 107 MET Chi-restraints excluded: chain P residue 108 LEU Chi-restraints excluded: chain Q residue 107 MET Chi-restraints excluded: chain Q residue 108 LEU Chi-restraints excluded: chain R residue 107 MET Chi-restraints excluded: chain R residue 108 LEU Chi-restraints excluded: chain S residue 107 MET Chi-restraints excluded: chain S residue 108 LEU Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain T residue 107 MET Chi-restraints excluded: chain T residue 108 LEU Chi-restraints excluded: chain T residue 143 VAL Chi-restraints excluded: chain U residue 107 MET Chi-restraints excluded: chain U residue 108 LEU Chi-restraints excluded: chain U residue 143 VAL Chi-restraints excluded: chain V residue 107 MET Chi-restraints excluded: chain V residue 108 LEU Chi-restraints excluded: chain V residue 143 VAL Chi-restraints excluded: chain W residue 107 MET Chi-restraints excluded: chain W residue 108 LEU Chi-restraints excluded: chain W residue 143 VAL Chi-restraints excluded: chain X residue 107 MET Chi-restraints excluded: chain X residue 108 LEU Chi-restraints excluded: chain X residue 143 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 631 optimal weight: 4.9990 chunk 664 optimal weight: 6.9990 chunk 606 optimal weight: 7.9990 chunk 646 optimal weight: 7.9990 chunk 389 optimal weight: 7.9990 chunk 281 optimal weight: 10.0000 chunk 507 optimal weight: 10.0000 chunk 198 optimal weight: 2.9990 chunk 584 optimal weight: 7.9990 chunk 611 optimal weight: 5.9990 chunk 644 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 57528 Z= 0.316 Angle : 0.635 9.832 77712 Z= 0.333 Chirality : 0.047 0.133 8784 Planarity : 0.006 0.039 10152 Dihedral : 3.994 13.070 7872 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 1.76 % Allowed : 20.33 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.09), residues: 7200 helix: 1.23 (0.08), residues: 3768 sheet: 0.31 (0.19), residues: 720 loop : -1.33 (0.10), residues: 2712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 110 HIS 0.004 0.002 HIS J 236 PHE 0.028 0.003 PHE L 74 TYR 0.018 0.002 TYR G 75 ARG 0.003 0.000 ARG Q 262 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14400 Ramachandran restraints generated. 7200 Oldfield, 0 Emsley, 7200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14400 Ramachandran restraints generated. 7200 Oldfield, 0 Emsley, 7200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 5976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 306 time to evaluate : 5.231 Fit side-chains REVERT: B 49 LYS cc_start: 0.6622 (OUTLIER) cc_final: 0.6134 (ttmm) REVERT: B 177 MET cc_start: 0.8342 (mtp) cc_final: 0.8017 (mmm) REVERT: C 49 LYS cc_start: 0.6631 (OUTLIER) cc_final: 0.6144 (ttmm) REVERT: C 177 MET cc_start: 0.8347 (mtp) cc_final: 0.8018 (mmm) REVERT: E 49 LYS cc_start: 0.6632 (OUTLIER) cc_final: 0.6142 (ttmm) REVERT: E 177 MET cc_start: 0.8343 (mtp) cc_final: 0.8017 (mmm) REVERT: F 49 LYS cc_start: 0.6625 (OUTLIER) cc_final: 0.6137 (ttmm) REVERT: F 177 MET cc_start: 0.8347 (mtp) cc_final: 0.8021 (mmm) REVERT: G 49 LYS cc_start: 0.6606 (OUTLIER) cc_final: 0.6122 (ttmm) REVERT: G 177 MET cc_start: 0.8350 (mtp) cc_final: 0.8023 (mmm) REVERT: H 49 LYS cc_start: 0.6612 (OUTLIER) cc_final: 0.6125 (ttmm) REVERT: H 177 MET cc_start: 0.8345 (mtp) cc_final: 0.8019 (mmm) REVERT: I 49 LYS cc_start: 0.6625 (OUTLIER) cc_final: 0.6137 (ttmm) REVERT: I 177 MET cc_start: 0.8347 (mtp) cc_final: 0.8021 (mmm) REVERT: J 49 LYS cc_start: 0.6606 (OUTLIER) cc_final: 0.6122 (ttmm) REVERT: J 177 MET cc_start: 0.8350 (mtp) cc_final: 0.8023 (mmm) REVERT: K 49 LYS cc_start: 0.6612 (OUTLIER) cc_final: 0.6125 (ttmm) REVERT: K 177 MET cc_start: 0.8345 (mtp) cc_final: 0.8019 (mmm) REVERT: L 49 LYS cc_start: 0.6632 (OUTLIER) cc_final: 0.6142 (ttmm) REVERT: L 177 MET cc_start: 0.8343 (mtp) cc_final: 0.8017 (mmm) REVERT: M 49 LYS cc_start: 0.6622 (OUTLIER) cc_final: 0.6134 (ttmm) REVERT: M 177 MET cc_start: 0.8342 (mtp) cc_final: 0.8017 (mmm) REVERT: N 49 LYS cc_start: 0.6631 (OUTLIER) cc_final: 0.6144 (ttmm) REVERT: N 177 MET cc_start: 0.8347 (mtp) cc_final: 0.8018 (mmm) REVERT: S 49 LYS cc_start: 0.6622 (OUTLIER) cc_final: 0.6134 (ttmm) REVERT: S 177 MET cc_start: 0.8342 (mtp) cc_final: 0.8017 (mmm) REVERT: T 49 LYS cc_start: 0.6631 (OUTLIER) cc_final: 0.6144 (ttmm) REVERT: T 177 MET cc_start: 0.8347 (mtp) cc_final: 0.8018 (mmm) REVERT: U 49 LYS cc_start: 0.6632 (OUTLIER) cc_final: 0.6142 (ttmm) REVERT: U 177 MET cc_start: 0.8343 (mtp) cc_final: 0.8017 (mmm) REVERT: V 49 LYS cc_start: 0.6625 (OUTLIER) cc_final: 0.6137 (ttmm) REVERT: V 177 MET cc_start: 0.8347 (mtp) cc_final: 0.8021 (mmm) REVERT: W 49 LYS cc_start: 0.6606 (OUTLIER) cc_final: 0.6122 (ttmm) REVERT: W 177 MET cc_start: 0.8350 (mtp) cc_final: 0.8023 (mmm) REVERT: X 49 LYS cc_start: 0.6612 (OUTLIER) cc_final: 0.6125 (ttmm) REVERT: X 177 MET cc_start: 0.8345 (mtp) cc_final: 0.8019 (mmm) outliers start: 105 outliers final: 75 residues processed: 387 average time/residue: 1.4621 time to fit residues: 709.8130 Evaluate side-chains 399 residues out of total 5976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 306 time to evaluate : 5.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain B residue 49 LYS Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 107 MET Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 107 MET Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain E residue 49 LYS Chi-restraints excluded: chain E residue 103 GLU Chi-restraints excluded: chain E residue 107 MET Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain F residue 49 LYS Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 107 MET Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain G residue 49 LYS Chi-restraints excluded: chain G residue 103 GLU Chi-restraints excluded: chain G residue 107 MET Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 49 LYS Chi-restraints excluded: chain H residue 103 GLU Chi-restraints excluded: chain H residue 107 MET Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain H residue 212 ILE Chi-restraints excluded: chain I residue 49 LYS Chi-restraints excluded: chain I residue 103 GLU Chi-restraints excluded: chain I residue 107 MET Chi-restraints excluded: chain I residue 108 LEU Chi-restraints excluded: chain J residue 49 LYS Chi-restraints excluded: chain J residue 103 GLU Chi-restraints excluded: chain J residue 107 MET Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain K residue 49 LYS Chi-restraints excluded: chain K residue 103 GLU Chi-restraints excluded: chain K residue 107 MET Chi-restraints excluded: chain K residue 108 LEU Chi-restraints excluded: chain K residue 212 ILE Chi-restraints excluded: chain L residue 49 LYS Chi-restraints excluded: chain L residue 103 GLU Chi-restraints excluded: chain L residue 107 MET Chi-restraints excluded: chain L residue 108 LEU Chi-restraints excluded: chain M residue 49 LYS Chi-restraints excluded: chain M residue 103 GLU Chi-restraints excluded: chain M residue 107 MET Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain N residue 49 LYS Chi-restraints excluded: chain N residue 103 GLU Chi-restraints excluded: chain N residue 107 MET Chi-restraints excluded: chain N residue 108 LEU Chi-restraints excluded: chain O residue 103 GLU Chi-restraints excluded: chain O residue 107 MET Chi-restraints excluded: chain O residue 108 LEU Chi-restraints excluded: chain P residue 103 GLU Chi-restraints excluded: chain P residue 107 MET Chi-restraints excluded: chain P residue 108 LEU Chi-restraints excluded: chain Q residue 103 GLU Chi-restraints excluded: chain Q residue 107 MET Chi-restraints excluded: chain Q residue 108 LEU Chi-restraints excluded: chain R residue 103 GLU Chi-restraints excluded: chain R residue 107 MET Chi-restraints excluded: chain R residue 108 LEU Chi-restraints excluded: chain S residue 49 LYS Chi-restraints excluded: chain S residue 103 GLU Chi-restraints excluded: chain S residue 107 MET Chi-restraints excluded: chain S residue 108 LEU Chi-restraints excluded: chain T residue 49 LYS Chi-restraints excluded: chain T residue 103 GLU Chi-restraints excluded: chain T residue 107 MET Chi-restraints excluded: chain T residue 108 LEU Chi-restraints excluded: chain U residue 49 LYS Chi-restraints excluded: chain U residue 103 GLU Chi-restraints excluded: chain U residue 107 MET Chi-restraints excluded: chain U residue 108 LEU Chi-restraints excluded: chain V residue 49 LYS Chi-restraints excluded: chain V residue 103 GLU Chi-restraints excluded: chain V residue 107 MET Chi-restraints excluded: chain V residue 108 LEU Chi-restraints excluded: chain W residue 49 LYS Chi-restraints excluded: chain W residue 103 GLU Chi-restraints excluded: chain W residue 107 MET Chi-restraints excluded: chain W residue 108 LEU Chi-restraints excluded: chain X residue 49 LYS Chi-restraints excluded: chain X residue 103 GLU Chi-restraints excluded: chain X residue 107 MET Chi-restraints excluded: chain X residue 108 LEU Chi-restraints excluded: chain X residue 212 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 424 optimal weight: 8.9990 chunk 683 optimal weight: 5.9990 chunk 417 optimal weight: 9.9990 chunk 324 optimal weight: 6.9990 chunk 475 optimal weight: 8.9990 chunk 717 optimal weight: 10.0000 chunk 660 optimal weight: 0.6980 chunk 571 optimal weight: 10.0000 chunk 59 optimal weight: 0.6980 chunk 441 optimal weight: 4.9990 chunk 350 optimal weight: 9.9990 overall best weight: 3.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 57528 Z= 0.229 Angle : 0.566 8.575 77712 Z= 0.295 Chirality : 0.045 0.129 8784 Planarity : 0.005 0.038 10152 Dihedral : 3.836 13.080 7872 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 1.66 % Allowed : 20.38 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.09), residues: 7200 helix: 1.54 (0.08), residues: 3672 sheet: 0.13 (0.18), residues: 744 loop : -1.42 (0.10), residues: 2784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP V 110 HIS 0.003 0.001 HIS Q 236 PHE 0.022 0.003 PHE R 74 TYR 0.014 0.002 TYR C 75 ARG 0.002 0.000 ARG O 262 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14400 Ramachandran restraints generated. 7200 Oldfield, 0 Emsley, 7200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14400 Ramachandran restraints generated. 7200 Oldfield, 0 Emsley, 7200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 5976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 306 time to evaluate : 5.181 Fit side-chains outliers start: 99 outliers final: 99 residues processed: 381 average time/residue: 1.2642 time to fit residues: 626.5113 Evaluate side-chains 405 residues out of total 5976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 306 time to evaluate : 5.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 107 MET Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 107 MET Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 107 MET Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 212 ILE Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 107 MET Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 212 ILE Chi-restraints excluded: chain G residue 55 LYS Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 107 MET Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 212 ILE Chi-restraints excluded: chain H residue 55 LYS Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain H residue 107 MET Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain I residue 59 LEU Chi-restraints excluded: chain I residue 107 MET Chi-restraints excluded: chain I residue 108 LEU Chi-restraints excluded: chain I residue 212 ILE Chi-restraints excluded: chain J residue 55 LYS Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 107 MET Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain J residue 212 ILE Chi-restraints excluded: chain K residue 55 LYS Chi-restraints excluded: chain K residue 59 LEU Chi-restraints excluded: chain K residue 107 MET Chi-restraints excluded: chain K residue 108 LEU Chi-restraints excluded: chain L residue 59 LEU Chi-restraints excluded: chain L residue 107 MET Chi-restraints excluded: chain L residue 108 LEU Chi-restraints excluded: chain L residue 212 ILE Chi-restraints excluded: chain M residue 59 LEU Chi-restraints excluded: chain M residue 107 MET Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain M residue 212 ILE Chi-restraints excluded: chain N residue 59 LEU Chi-restraints excluded: chain N residue 107 MET Chi-restraints excluded: chain N residue 108 LEU Chi-restraints excluded: chain N residue 212 ILE Chi-restraints excluded: chain O residue 59 LEU Chi-restraints excluded: chain O residue 107 MET Chi-restraints excluded: chain O residue 108 LEU Chi-restraints excluded: chain O residue 212 ILE Chi-restraints excluded: chain P residue 59 LEU Chi-restraints excluded: chain P residue 107 MET Chi-restraints excluded: chain P residue 108 LEU Chi-restraints excluded: chain P residue 212 ILE Chi-restraints excluded: chain Q residue 59 LEU Chi-restraints excluded: chain Q residue 107 MET Chi-restraints excluded: chain Q residue 108 LEU Chi-restraints excluded: chain Q residue 212 ILE Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 107 MET Chi-restraints excluded: chain R residue 108 LEU Chi-restraints excluded: chain R residue 212 ILE Chi-restraints excluded: chain S residue 59 LEU Chi-restraints excluded: chain S residue 107 MET Chi-restraints excluded: chain S residue 108 LEU Chi-restraints excluded: chain S residue 212 ILE Chi-restraints excluded: chain T residue 59 LEU Chi-restraints excluded: chain T residue 107 MET Chi-restraints excluded: chain T residue 108 LEU Chi-restraints excluded: chain T residue 212 ILE Chi-restraints excluded: chain U residue 59 LEU Chi-restraints excluded: chain U residue 107 MET Chi-restraints excluded: chain U residue 108 LEU Chi-restraints excluded: chain U residue 212 ILE Chi-restraints excluded: chain V residue 59 LEU Chi-restraints excluded: chain V residue 107 MET Chi-restraints excluded: chain V residue 108 LEU Chi-restraints excluded: chain V residue 212 ILE Chi-restraints excluded: chain W residue 55 LYS Chi-restraints excluded: chain W residue 59 LEU Chi-restraints excluded: chain W residue 107 MET Chi-restraints excluded: chain W residue 108 LEU Chi-restraints excluded: chain W residue 212 ILE Chi-restraints excluded: chain X residue 55 LYS Chi-restraints excluded: chain X residue 59 LEU Chi-restraints excluded: chain X residue 107 MET Chi-restraints excluded: chain X residue 108 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 453 optimal weight: 7.9990 chunk 608 optimal weight: 8.9990 chunk 174 optimal weight: 8.9990 chunk 526 optimal weight: 6.9990 chunk 84 optimal weight: 9.9990 chunk 158 optimal weight: 10.0000 chunk 572 optimal weight: 1.9990 chunk 239 optimal weight: 0.9980 chunk 587 optimal weight: 6.9990 chunk 72 optimal weight: 9.9990 chunk 105 optimal weight: 4.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.113067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.090383 restraints weight = 104897.682| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 1.88 r_work: 0.3190 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 57528 Z= 0.251 Angle : 0.583 8.763 77712 Z= 0.305 Chirality : 0.045 0.132 8784 Planarity : 0.005 0.037 10152 Dihedral : 3.877 12.898 7872 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 2.06 % Allowed : 19.93 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.09), residues: 7200 helix: 1.51 (0.08), residues: 3672 sheet: 0.10 (0.18), residues: 744 loop : -1.40 (0.10), residues: 2784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP V 110 HIS 0.003 0.001 HIS H 236 PHE 0.025 0.003 PHE H 74 TYR 0.016 0.002 TYR A 75 ARG 0.003 0.000 ARG E 262 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12672.11 seconds wall clock time: 222 minutes 40.69 seconds (13360.69 seconds total)