Starting phenix.real_space_refine (version: dev) on Mon Dec 19 00:21:44 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vfi_21173/12_2022/6vfi_21173.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vfi_21173/12_2022/6vfi_21173.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vfi_21173/12_2022/6vfi_21173.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vfi_21173/12_2022/6vfi_21173.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vfi_21173/12_2022/6vfi_21173.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vfi_21173/12_2022/6vfi_21173.pdb" } resolution = 4.54 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "C TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 55": "OE1" <-> "OE2" Residue "C TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 55": "OE1" <-> "OE2" Residue "B TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 55": "OE1" <-> "OE2" Residue "E TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 55": "OE1" <-> "OE2" Residue "G TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 55": "OE1" <-> "OE2" Residue "I TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 55": "OE1" <-> "OE2" Residue "K TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 55": "OE1" <-> "OE2" Residue "M TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 55": "OE1" <-> "OE2" Residue "O TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 55": "OE1" <-> "OE2" Residue "Q TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 55": "OE1" <-> "OE2" Residue "S TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 55": "OE1" <-> "OE2" Residue "U TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 55": "OE1" <-> "OE2" Residue "W TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 55": "OE1" <-> "OE2" Residue "Y TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 GLU 55": "OE1" <-> "OE2" Residue "0 TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 55": "OE1" <-> "OE2" Residue "2 TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 55": "OE1" <-> "OE2" Residue "4 TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 GLU 55": "OE1" <-> "OE2" Residue "6 TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 GLU 55": "OE1" <-> "OE2" Residue "8 TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 55": "OE1" <-> "OE2" Residue "a TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 55": "OE1" <-> "OE2" Residue "c TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 55": "OE1" <-> "OE2" Residue "e TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 55": "OE1" <-> "OE2" Residue "g TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i GLU 55": "OE1" <-> "OE2" Residue "i TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k GLU 55": "OE1" <-> "OE2" Residue "k TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m GLU 55": "OE1" <-> "OE2" Residue "m TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 60925 Number of models: 1 Model: "" Number of chains: 50 Chain: "C" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 959 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "D" Number of atoms: 1478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1478 Classifications: {'peptide': 197} Link IDs: {'TRANS': 196} Chain: "B" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 959 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "A" Number of atoms: 1478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1478 Classifications: {'peptide': 197} Link IDs: {'TRANS': 196} Chain: "E" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 959 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "F" Number of atoms: 1478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1478 Classifications: {'peptide': 197} Link IDs: {'TRANS': 196} Chain: "G" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 959 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "H" Number of atoms: 1478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1478 Classifications: {'peptide': 197} Link IDs: {'TRANS': 196} Chain: "I" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 959 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "J" Number of atoms: 1478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1478 Classifications: {'peptide': 197} Link IDs: {'TRANS': 196} Chain: "K" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 959 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "L" Number of atoms: 1478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1478 Classifications: {'peptide': 197} Link IDs: {'TRANS': 196} Chain: "M" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 959 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "N" Number of atoms: 1478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1478 Classifications: {'peptide': 197} Link IDs: {'TRANS': 196} Chain: "O" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 959 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "P" Number of atoms: 1478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1478 Classifications: {'peptide': 197} Link IDs: {'TRANS': 196} Chain: "Q" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 959 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "R" Number of atoms: 1478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1478 Classifications: {'peptide': 197} Link IDs: {'TRANS': 196} Chain: "S" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 959 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "T" Number of atoms: 1478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1478 Classifications: {'peptide': 197} Link IDs: {'TRANS': 196} Chain: "U" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 959 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "V" Number of atoms: 1478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1478 Classifications: {'peptide': 197} Link IDs: {'TRANS': 196} Chain: "W" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 959 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "X" Number of atoms: 1478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1478 Classifications: {'peptide': 197} Link IDs: {'TRANS': 196} Chain: "Y" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 959 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "Z" Number of atoms: 1478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1478 Classifications: {'peptide': 197} Link IDs: {'TRANS': 196} Chain: "0" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 959 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "1" Number of atoms: 1478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1478 Classifications: {'peptide': 197} Link IDs: {'TRANS': 196} Chain: "2" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 959 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "3" Number of atoms: 1478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1478 Classifications: {'peptide': 197} Link IDs: {'TRANS': 196} Chain: "4" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 959 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "5" Number of atoms: 1478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1478 Classifications: {'peptide': 197} Link IDs: {'TRANS': 196} Chain: "6" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 959 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "7" Number of atoms: 1478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1478 Classifications: {'peptide': 197} Link IDs: {'TRANS': 196} Chain: "8" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 959 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "9" Number of atoms: 1478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1478 Classifications: {'peptide': 197} Link IDs: {'TRANS': 196} Chain: "a" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 959 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "b" Number of atoms: 1478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1478 Classifications: {'peptide': 197} Link IDs: {'TRANS': 196} Chain: "c" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 959 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "d" Number of atoms: 1478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1478 Classifications: {'peptide': 197} Link IDs: {'TRANS': 196} Chain: "e" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 959 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "f" Number of atoms: 1478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1478 Classifications: {'peptide': 197} Link IDs: {'TRANS': 196} Chain: "g" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 959 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "h" Number of atoms: 1478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1478 Classifications: {'peptide': 197} Link IDs: {'TRANS': 196} Chain: "i" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 959 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "j" Number of atoms: 1478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1478 Classifications: {'peptide': 197} Link IDs: {'TRANS': 196} Chain: "k" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 959 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "l" Number of atoms: 1478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1478 Classifications: {'peptide': 197} Link IDs: {'TRANS': 196} Chain: "m" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 959 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "n" Number of atoms: 1478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1478 Classifications: {'peptide': 197} Link IDs: {'TRANS': 196} Time building chain proxies: 24.89, per 1000 atoms: 0.41 Number of scatterers: 60925 At special positions: 0 Unit cell: (206, 259.56, 257.5, 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 225 16.00 O 11975 8.00 N 10175 7.00 C 38550 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=50, symmetry=0 Simple disulfide: pdb=" SG CYS D 3 " - pdb=" SG CYS D 55 " distance=2.04 Simple disulfide: pdb=" SG CYS D 103 " - pdb=" SG CYS D 155 " distance=2.02 Simple disulfide: pdb=" SG CYS A 3 " - pdb=" SG CYS A 55 " distance=2.04 Simple disulfide: pdb=" SG CYS A 103 " - pdb=" SG CYS A 155 " distance=2.02 Simple disulfide: pdb=" SG CYS F 3 " - pdb=" SG CYS F 55 " distance=2.04 Simple disulfide: pdb=" SG CYS F 103 " - pdb=" SG CYS F 155 " distance=2.02 Simple disulfide: pdb=" SG CYS H 3 " - pdb=" SG CYS H 55 " distance=2.04 Simple disulfide: pdb=" SG CYS H 103 " - pdb=" SG CYS H 155 " distance=2.02 Simple disulfide: pdb=" SG CYS J 3 " - pdb=" SG CYS J 55 " distance=2.04 Simple disulfide: pdb=" SG CYS J 103 " - pdb=" SG CYS J 155 " distance=2.02 Simple disulfide: pdb=" SG CYS L 3 " - pdb=" SG CYS L 55 " distance=2.04 Simple disulfide: pdb=" SG CYS L 103 " - pdb=" SG CYS L 155 " distance=2.02 Simple disulfide: pdb=" SG CYS N 3 " - pdb=" SG CYS N 55 " distance=2.04 Simple disulfide: pdb=" SG CYS N 103 " - pdb=" SG CYS N 155 " distance=2.02 Simple disulfide: pdb=" SG CYS P 3 " - pdb=" SG CYS P 55 " distance=2.04 Simple disulfide: pdb=" SG CYS P 103 " - pdb=" SG CYS P 155 " distance=2.02 Simple disulfide: pdb=" SG CYS R 3 " - pdb=" SG CYS R 55 " distance=2.04 Simple disulfide: pdb=" SG CYS R 103 " - pdb=" SG CYS R 155 " distance=2.02 Simple disulfide: pdb=" SG CYS T 3 " - pdb=" SG CYS T 55 " distance=2.04 Simple disulfide: pdb=" SG CYS T 103 " - pdb=" SG CYS T 155 " distance=2.02 Simple disulfide: pdb=" SG CYS V 3 " - pdb=" SG CYS V 55 " distance=2.04 Simple disulfide: pdb=" SG CYS V 103 " - pdb=" SG CYS V 155 " distance=2.02 Simple disulfide: pdb=" SG CYS X 3 " - pdb=" SG CYS X 55 " distance=2.04 Simple disulfide: pdb=" SG CYS X 103 " - pdb=" SG CYS X 155 " distance=2.02 Simple disulfide: pdb=" SG CYS Z 3 " - pdb=" SG CYS Z 55 " distance=2.04 Simple disulfide: pdb=" SG CYS Z 103 " - pdb=" SG CYS Z 155 " distance=2.02 Simple disulfide: pdb=" SG CYS 1 3 " - pdb=" SG CYS 1 55 " distance=2.04 Simple disulfide: pdb=" SG CYS 1 103 " - pdb=" SG CYS 1 155 " distance=2.02 Simple disulfide: pdb=" SG CYS 3 3 " - pdb=" SG CYS 3 55 " distance=2.04 Simple disulfide: pdb=" SG CYS 3 103 " - pdb=" SG CYS 3 155 " distance=2.02 Simple disulfide: pdb=" SG CYS 5 3 " - pdb=" SG CYS 5 55 " distance=2.04 Simple disulfide: pdb=" SG CYS 5 103 " - pdb=" SG CYS 5 155 " distance=2.02 Simple disulfide: pdb=" SG CYS 7 3 " - pdb=" SG CYS 7 55 " distance=2.04 Simple disulfide: pdb=" SG CYS 7 103 " - pdb=" SG CYS 7 155 " distance=2.02 Simple disulfide: pdb=" SG CYS 9 3 " - pdb=" SG CYS 9 55 " distance=2.04 Simple disulfide: pdb=" SG CYS 9 103 " - pdb=" SG CYS 9 155 " distance=2.02 Simple disulfide: pdb=" SG CYS b 3 " - pdb=" SG CYS b 55 " distance=2.04 Simple disulfide: pdb=" SG CYS b 103 " - pdb=" SG CYS b 155 " distance=2.02 Simple disulfide: pdb=" SG CYS d 3 " - pdb=" SG CYS d 55 " distance=2.04 Simple disulfide: pdb=" SG CYS d 103 " - pdb=" SG CYS d 155 " distance=2.02 Simple disulfide: pdb=" SG CYS f 3 " - pdb=" SG CYS f 55 " distance=2.04 Simple disulfide: pdb=" SG CYS f 103 " - pdb=" SG CYS f 155 " distance=2.02 Simple disulfide: pdb=" SG CYS h 3 " - pdb=" SG CYS h 55 " distance=2.04 Simple disulfide: pdb=" SG CYS h 103 " - pdb=" SG CYS h 155 " distance=2.02 Simple disulfide: pdb=" SG CYS j 3 " - pdb=" SG CYS j 55 " distance=2.04 Simple disulfide: pdb=" SG CYS j 103 " - pdb=" SG CYS j 155 " distance=2.02 Simple disulfide: pdb=" SG CYS l 3 " - pdb=" SG CYS l 55 " distance=2.04 Simple disulfide: pdb=" SG CYS l 103 " - pdb=" SG CYS l 155 " distance=2.02 Simple disulfide: pdb=" SG CYS n 3 " - pdb=" SG CYS n 55 " distance=2.04 Simple disulfide: pdb=" SG CYS n 103 " - pdb=" SG CYS n 155 " distance=2.02 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: 20.06 Conformation dependent library (CDL) restraints added in 6.9 seconds 15550 Ramachandran restraints generated. 7775 Oldfield, 0 Emsley, 7775 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15000 Finding SS restraints... Secondary structure from input PDB file: 375 helices and 0 sheets defined 90.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.75 Creating SS restraints... Processing helix chain 'B' and resid 1 through 16 Processing helix chain 'B' and resid 18 through 33 Processing helix chain 'B' and resid 36 through 50 Processing helix chain 'B' and resid 52 through 67 Processing helix chain 'B' and resid 71 through 84 Processing helix chain 'B' and resid 86 through 101 Processing helix chain 'B' and resid 104 through 117 Processing helix chain 'A' and resid 2 through 21 Processing helix chain 'A' and resid 23 through 45 removed outlier: 4.007A pdb=" N LEU A 44 " --> pdb=" O ARG A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 70 removed outlier: 4.178A pdb=" N GLU A 54 " --> pdb=" O GLU A 50 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N SER A 70 " --> pdb=" O ALA A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 96 Processing helix chain 'A' and resid 101 through 120 Processing helix chain 'A' and resid 123 through 146 Processing helix chain 'A' and resid 148 through 170 Processing helix chain 'A' and resid 173 through 194 Processing helix chain 'C' and resid 1 through 16 Processing helix chain 'C' and resid 18 through 33 Processing helix chain 'C' and resid 36 through 50 Processing helix chain 'C' and resid 52 through 67 Processing helix chain 'C' and resid 71 through 84 Processing helix chain 'C' and resid 86 through 101 Processing helix chain 'C' and resid 104 through 117 Processing helix chain 'D' and resid 2 through 21 Processing helix chain 'D' and resid 23 through 45 removed outlier: 4.007A pdb=" N LEU D 44 " --> pdb=" O ARG D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 70 removed outlier: 4.178A pdb=" N GLU D 54 " --> pdb=" O GLU D 50 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N SER D 70 " --> pdb=" O ALA D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 96 Processing helix chain 'D' and resid 101 through 120 Processing helix chain 'D' and resid 123 through 146 Processing helix chain 'D' and resid 148 through 170 Processing helix chain 'D' and resid 173 through 194 Processing helix chain 'E' and resid 1 through 16 Processing helix chain 'E' and resid 18 through 33 Processing helix chain 'E' and resid 36 through 50 Processing helix chain 'E' and resid 52 through 67 Processing helix chain 'E' and resid 71 through 84 Processing helix chain 'E' and resid 86 through 101 Processing helix chain 'E' and resid 104 through 117 Processing helix chain 'F' and resid 2 through 21 Processing helix chain 'F' and resid 23 through 45 removed outlier: 4.007A pdb=" N LEU F 44 " --> pdb=" O ARG F 40 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 70 removed outlier: 4.178A pdb=" N GLU F 54 " --> pdb=" O GLU F 50 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N SER F 70 " --> pdb=" O ALA F 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 96 Processing helix chain 'F' and resid 101 through 120 Processing helix chain 'F' and resid 123 through 146 Processing helix chain 'F' and resid 148 through 170 Processing helix chain 'F' and resid 173 through 194 Processing helix chain 'G' and resid 1 through 16 Processing helix chain 'G' and resid 18 through 33 Processing helix chain 'G' and resid 36 through 50 Processing helix chain 'G' and resid 52 through 67 Processing helix chain 'G' and resid 71 through 84 Processing helix chain 'G' and resid 86 through 101 Processing helix chain 'G' and resid 104 through 117 Processing helix chain 'H' and resid 2 through 21 Processing helix chain 'H' and resid 23 through 45 removed outlier: 4.007A pdb=" N LEU H 44 " --> pdb=" O ARG H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 48 through 70 removed outlier: 4.178A pdb=" N GLU H 54 " --> pdb=" O GLU H 50 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N SER H 70 " --> pdb=" O ALA H 66 " (cutoff:3.500A) Processing helix chain 'H' and resid 74 through 96 Processing helix chain 'H' and resid 101 through 120 Processing helix chain 'H' and resid 123 through 146 Processing helix chain 'H' and resid 148 through 170 Processing helix chain 'H' and resid 173 through 194 Processing helix chain 'I' and resid 1 through 16 Processing helix chain 'I' and resid 18 through 33 Processing helix chain 'I' and resid 36 through 50 Processing helix chain 'I' and resid 52 through 67 Processing helix chain 'I' and resid 71 through 84 Processing helix chain 'I' and resid 86 through 101 Processing helix chain 'I' and resid 104 through 117 Processing helix chain 'J' and resid 2 through 21 Processing helix chain 'J' and resid 23 through 45 removed outlier: 4.007A pdb=" N LEU J 44 " --> pdb=" O ARG J 40 " (cutoff:3.500A) Processing helix chain 'J' and resid 48 through 70 removed outlier: 4.178A pdb=" N GLU J 54 " --> pdb=" O GLU J 50 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N SER J 70 " --> pdb=" O ALA J 66 " (cutoff:3.500A) Processing helix chain 'J' and resid 74 through 96 Processing helix chain 'J' and resid 101 through 120 Processing helix chain 'J' and resid 123 through 146 Processing helix chain 'J' and resid 148 through 170 Processing helix chain 'J' and resid 173 through 194 Processing helix chain 'K' and resid 1 through 16 Processing helix chain 'K' and resid 18 through 33 Processing helix chain 'K' and resid 36 through 50 Processing helix chain 'K' and resid 52 through 67 Processing helix chain 'K' and resid 71 through 84 Processing helix chain 'K' and resid 86 through 101 Processing helix chain 'K' and resid 104 through 117 Processing helix chain 'L' and resid 2 through 21 Processing helix chain 'L' and resid 23 through 45 removed outlier: 4.007A pdb=" N LEU L 44 " --> pdb=" O ARG L 40 " (cutoff:3.500A) Processing helix chain 'L' and resid 48 through 70 removed outlier: 4.178A pdb=" N GLU L 54 " --> pdb=" O GLU L 50 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N SER L 70 " --> pdb=" O ALA L 66 " (cutoff:3.500A) Processing helix chain 'L' and resid 74 through 96 Processing helix chain 'L' and resid 101 through 120 Processing helix chain 'L' and resid 123 through 146 Processing helix chain 'L' and resid 148 through 170 Processing helix chain 'L' and resid 173 through 194 Processing helix chain 'M' and resid 1 through 16 Processing helix chain 'M' and resid 18 through 33 Processing helix chain 'M' and resid 36 through 50 Processing helix chain 'M' and resid 52 through 67 Processing helix chain 'M' and resid 71 through 84 Processing helix chain 'M' and resid 86 through 101 Processing helix chain 'M' and resid 104 through 117 Processing helix chain 'N' and resid 2 through 21 Processing helix chain 'N' and resid 23 through 45 removed outlier: 4.007A pdb=" N LEU N 44 " --> pdb=" O ARG N 40 " (cutoff:3.500A) Processing helix chain 'N' and resid 48 through 70 removed outlier: 4.178A pdb=" N GLU N 54 " --> pdb=" O GLU N 50 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N SER N 70 " --> pdb=" O ALA N 66 " (cutoff:3.500A) Processing helix chain 'N' and resid 74 through 96 Processing helix chain 'N' and resid 101 through 120 Processing helix chain 'N' and resid 123 through 146 Processing helix chain 'N' and resid 148 through 170 Processing helix chain 'N' and resid 173 through 194 Processing helix chain 'O' and resid 1 through 16 Processing helix chain 'O' and resid 18 through 33 Processing helix chain 'O' and resid 36 through 50 Processing helix chain 'O' and resid 52 through 67 Processing helix chain 'O' and resid 71 through 84 Processing helix chain 'O' and resid 86 through 101 Processing helix chain 'O' and resid 104 through 117 Processing helix chain 'P' and resid 2 through 21 Processing helix chain 'P' and resid 23 through 45 removed outlier: 4.007A pdb=" N LEU P 44 " --> pdb=" O ARG P 40 " (cutoff:3.500A) Processing helix chain 'P' and resid 48 through 70 removed outlier: 4.178A pdb=" N GLU P 54 " --> pdb=" O GLU P 50 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N SER P 70 " --> pdb=" O ALA P 66 " (cutoff:3.500A) Processing helix chain 'P' and resid 74 through 96 Processing helix chain 'P' and resid 101 through 120 Processing helix chain 'P' and resid 123 through 146 Processing helix chain 'P' and resid 148 through 170 Processing helix chain 'P' and resid 173 through 194 Processing helix chain 'Q' and resid 1 through 16 Processing helix chain 'Q' and resid 18 through 33 Processing helix chain 'Q' and resid 36 through 50 Processing helix chain 'Q' and resid 52 through 67 Processing helix chain 'Q' and resid 71 through 84 Processing helix chain 'Q' and resid 86 through 101 Processing helix chain 'Q' and resid 104 through 117 Processing helix chain 'R' and resid 2 through 21 Processing helix chain 'R' and resid 23 through 45 removed outlier: 4.007A pdb=" N LEU R 44 " --> pdb=" O ARG R 40 " (cutoff:3.500A) Processing helix chain 'R' and resid 48 through 70 removed outlier: 4.178A pdb=" N GLU R 54 " --> pdb=" O GLU R 50 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N SER R 70 " --> pdb=" O ALA R 66 " (cutoff:3.500A) Processing helix chain 'R' and resid 74 through 96 Processing helix chain 'R' and resid 101 through 120 Processing helix chain 'R' and resid 123 through 146 Processing helix chain 'R' and resid 148 through 170 Processing helix chain 'R' and resid 173 through 194 Processing helix chain 'S' and resid 1 through 16 Processing helix chain 'S' and resid 18 through 33 Processing helix chain 'S' and resid 36 through 50 Processing helix chain 'S' and resid 52 through 67 Processing helix chain 'S' and resid 71 through 84 Processing helix chain 'S' and resid 86 through 101 Processing helix chain 'S' and resid 104 through 117 Processing helix chain 'T' and resid 2 through 21 Processing helix chain 'T' and resid 23 through 45 removed outlier: 4.007A pdb=" N LEU T 44 " --> pdb=" O ARG T 40 " (cutoff:3.500A) Processing helix chain 'T' and resid 48 through 70 removed outlier: 4.178A pdb=" N GLU T 54 " --> pdb=" O GLU T 50 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N SER T 70 " --> pdb=" O ALA T 66 " (cutoff:3.500A) Processing helix chain 'T' and resid 74 through 96 Processing helix chain 'T' and resid 101 through 120 Processing helix chain 'T' and resid 123 through 146 Processing helix chain 'T' and resid 148 through 170 Processing helix chain 'T' and resid 173 through 194 Processing helix chain 'U' and resid 1 through 16 Processing helix chain 'U' and resid 18 through 33 Processing helix chain 'U' and resid 36 through 50 Processing helix chain 'U' and resid 52 through 67 Processing helix chain 'U' and resid 71 through 84 Processing helix chain 'U' and resid 86 through 101 Processing helix chain 'U' and resid 104 through 117 Processing helix chain 'V' and resid 2 through 21 Processing helix chain 'V' and resid 23 through 45 removed outlier: 4.007A pdb=" N LEU V 44 " --> pdb=" O ARG V 40 " (cutoff:3.500A) Processing helix chain 'V' and resid 48 through 70 removed outlier: 4.178A pdb=" N GLU V 54 " --> pdb=" O GLU V 50 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N SER V 70 " --> pdb=" O ALA V 66 " (cutoff:3.500A) Processing helix chain 'V' and resid 74 through 96 Processing helix chain 'V' and resid 101 through 120 Processing helix chain 'V' and resid 123 through 146 Processing helix chain 'V' and resid 148 through 170 Processing helix chain 'V' and resid 173 through 194 Processing helix chain 'W' and resid 1 through 16 Processing helix chain 'W' and resid 18 through 33 Processing helix chain 'W' and resid 36 through 50 Processing helix chain 'W' and resid 52 through 67 Processing helix chain 'W' and resid 71 through 84 Processing helix chain 'W' and resid 86 through 101 Processing helix chain 'W' and resid 104 through 117 Processing helix chain 'X' and resid 2 through 21 Processing helix chain 'X' and resid 23 through 45 removed outlier: 4.007A pdb=" N LEU X 44 " --> pdb=" O ARG X 40 " (cutoff:3.500A) Processing helix chain 'X' and resid 48 through 70 removed outlier: 4.178A pdb=" N GLU X 54 " --> pdb=" O GLU X 50 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N SER X 70 " --> pdb=" O ALA X 66 " (cutoff:3.500A) Processing helix chain 'X' and resid 74 through 96 Processing helix chain 'X' and resid 101 through 120 Processing helix chain 'X' and resid 123 through 146 Processing helix chain 'X' and resid 148 through 170 Processing helix chain 'X' and resid 173 through 194 Processing helix chain 'Y' and resid 1 through 16 Processing helix chain 'Y' and resid 18 through 33 Processing helix chain 'Y' and resid 36 through 50 Processing helix chain 'Y' and resid 52 through 67 Processing helix chain 'Y' and resid 71 through 84 Processing helix chain 'Y' and resid 86 through 101 Processing helix chain 'Y' and resid 104 through 117 Processing helix chain 'Z' and resid 2 through 21 Processing helix chain 'Z' and resid 23 through 45 removed outlier: 4.007A pdb=" N LEU Z 44 " --> pdb=" O ARG Z 40 " (cutoff:3.500A) Processing helix chain 'Z' and resid 48 through 70 removed outlier: 4.178A pdb=" N GLU Z 54 " --> pdb=" O GLU Z 50 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N SER Z 70 " --> pdb=" O ALA Z 66 " (cutoff:3.500A) Processing helix chain 'Z' and resid 74 through 96 Processing helix chain 'Z' and resid 101 through 120 Processing helix chain 'Z' and resid 123 through 146 Processing helix chain 'Z' and resid 148 through 170 Processing helix chain 'Z' and resid 173 through 194 Processing helix chain '0' and resid 1 through 16 Processing helix chain '0' and resid 18 through 33 Processing helix chain '0' and resid 36 through 50 Processing helix chain '0' and resid 52 through 67 Processing helix chain '0' and resid 71 through 84 Processing helix chain '0' and resid 86 through 101 Processing helix chain '0' and resid 104 through 117 Processing helix chain '1' and resid 2 through 21 Processing helix chain '1' and resid 23 through 45 removed outlier: 4.007A pdb=" N LEU 1 44 " --> pdb=" O ARG 1 40 " (cutoff:3.500A) Processing helix chain '1' and resid 48 through 70 removed outlier: 4.178A pdb=" N GLU 1 54 " --> pdb=" O GLU 1 50 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N SER 1 70 " --> pdb=" O ALA 1 66 " (cutoff:3.500A) Processing helix chain '1' and resid 74 through 96 Processing helix chain '1' and resid 101 through 120 Processing helix chain '1' and resid 123 through 146 Processing helix chain '1' and resid 148 through 170 Processing helix chain '1' and resid 173 through 194 Processing helix chain '2' and resid 1 through 16 Processing helix chain '2' and resid 18 through 33 Processing helix chain '2' and resid 36 through 50 Processing helix chain '2' and resid 52 through 67 Processing helix chain '2' and resid 71 through 84 Processing helix chain '2' and resid 86 through 101 Processing helix chain '2' and resid 104 through 117 Processing helix chain '3' and resid 2 through 21 Processing helix chain '3' and resid 23 through 45 removed outlier: 4.007A pdb=" N LEU 3 44 " --> pdb=" O ARG 3 40 " (cutoff:3.500A) Processing helix chain '3' and resid 48 through 70 removed outlier: 4.178A pdb=" N GLU 3 54 " --> pdb=" O GLU 3 50 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N SER 3 70 " --> pdb=" O ALA 3 66 " (cutoff:3.500A) Processing helix chain '3' and resid 74 through 96 Processing helix chain '3' and resid 101 through 120 Processing helix chain '3' and resid 123 through 146 Processing helix chain '3' and resid 148 through 170 Processing helix chain '3' and resid 173 through 194 Processing helix chain '4' and resid 1 through 16 Processing helix chain '4' and resid 18 through 33 Processing helix chain '4' and resid 36 through 50 Processing helix chain '4' and resid 52 through 67 Processing helix chain '4' and resid 71 through 84 Processing helix chain '4' and resid 86 through 101 Processing helix chain '4' and resid 104 through 117 Processing helix chain '5' and resid 2 through 21 Processing helix chain '5' and resid 23 through 45 removed outlier: 4.007A pdb=" N LEU 5 44 " --> pdb=" O ARG 5 40 " (cutoff:3.500A) Processing helix chain '5' and resid 48 through 70 removed outlier: 4.178A pdb=" N GLU 5 54 " --> pdb=" O GLU 5 50 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N SER 5 70 " --> pdb=" O ALA 5 66 " (cutoff:3.500A) Processing helix chain '5' and resid 74 through 96 Processing helix chain '5' and resid 101 through 120 Processing helix chain '5' and resid 123 through 146 Processing helix chain '5' and resid 148 through 170 Processing helix chain '5' and resid 173 through 194 Processing helix chain '6' and resid 1 through 16 Processing helix chain '6' and resid 18 through 33 Processing helix chain '6' and resid 36 through 50 Processing helix chain '6' and resid 52 through 67 Processing helix chain '6' and resid 71 through 84 Processing helix chain '6' and resid 86 through 101 Processing helix chain '6' and resid 104 through 117 Processing helix chain '7' and resid 2 through 21 Processing helix chain '7' and resid 23 through 45 removed outlier: 4.007A pdb=" N LEU 7 44 " --> pdb=" O ARG 7 40 " (cutoff:3.500A) Processing helix chain '7' and resid 48 through 70 removed outlier: 4.178A pdb=" N GLU 7 54 " --> pdb=" O GLU 7 50 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N SER 7 70 " --> pdb=" O ALA 7 66 " (cutoff:3.500A) Processing helix chain '7' and resid 74 through 96 Processing helix chain '7' and resid 101 through 120 Processing helix chain '7' and resid 123 through 146 Processing helix chain '7' and resid 148 through 170 Processing helix chain '7' and resid 173 through 194 Processing helix chain '8' and resid 1 through 16 Processing helix chain '8' and resid 18 through 33 Processing helix chain '8' and resid 36 through 50 Processing helix chain '8' and resid 52 through 67 Processing helix chain '8' and resid 71 through 84 Processing helix chain '8' and resid 86 through 101 Processing helix chain '8' and resid 104 through 117 Processing helix chain '9' and resid 2 through 21 Processing helix chain '9' and resid 23 through 45 removed outlier: 4.007A pdb=" N LEU 9 44 " --> pdb=" O ARG 9 40 " (cutoff:3.500A) Processing helix chain '9' and resid 48 through 70 removed outlier: 4.178A pdb=" N GLU 9 54 " --> pdb=" O GLU 9 50 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N SER 9 70 " --> pdb=" O ALA 9 66 " (cutoff:3.500A) Processing helix chain '9' and resid 74 through 96 Processing helix chain '9' and resid 101 through 120 Processing helix chain '9' and resid 123 through 146 Processing helix chain '9' and resid 148 through 170 Processing helix chain '9' and resid 173 through 194 Processing helix chain 'a' and resid 1 through 16 Processing helix chain 'a' and resid 18 through 33 Processing helix chain 'a' and resid 36 through 50 Processing helix chain 'a' and resid 52 through 67 Processing helix chain 'a' and resid 71 through 84 Processing helix chain 'a' and resid 86 through 101 Processing helix chain 'a' and resid 104 through 117 Processing helix chain 'b' and resid 2 through 21 Processing helix chain 'b' and resid 23 through 45 removed outlier: 4.007A pdb=" N LEU b 44 " --> pdb=" O ARG b 40 " (cutoff:3.500A) Processing helix chain 'b' and resid 48 through 70 removed outlier: 4.178A pdb=" N GLU b 54 " --> pdb=" O GLU b 50 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N SER b 70 " --> pdb=" O ALA b 66 " (cutoff:3.500A) Processing helix chain 'b' and resid 74 through 96 Processing helix chain 'b' and resid 101 through 120 Processing helix chain 'b' and resid 123 through 146 Processing helix chain 'b' and resid 148 through 170 Processing helix chain 'b' and resid 173 through 194 Processing helix chain 'c' and resid 1 through 16 Processing helix chain 'c' and resid 18 through 33 Processing helix chain 'c' and resid 36 through 50 Processing helix chain 'c' and resid 52 through 67 Processing helix chain 'c' and resid 71 through 84 Processing helix chain 'c' and resid 86 through 101 Processing helix chain 'c' and resid 104 through 117 Processing helix chain 'd' and resid 2 through 21 Processing helix chain 'd' and resid 23 through 45 removed outlier: 4.007A pdb=" N LEU d 44 " --> pdb=" O ARG d 40 " (cutoff:3.500A) Processing helix chain 'd' and resid 48 through 70 removed outlier: 4.178A pdb=" N GLU d 54 " --> pdb=" O GLU d 50 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N SER d 70 " --> pdb=" O ALA d 66 " (cutoff:3.500A) Processing helix chain 'd' and resid 74 through 96 Processing helix chain 'd' and resid 101 through 120 Processing helix chain 'd' and resid 123 through 146 Processing helix chain 'd' and resid 148 through 170 Processing helix chain 'd' and resid 173 through 194 Processing helix chain 'e' and resid 1 through 16 Processing helix chain 'e' and resid 18 through 33 Processing helix chain 'e' and resid 36 through 50 Processing helix chain 'e' and resid 52 through 67 Processing helix chain 'e' and resid 71 through 84 Processing helix chain 'e' and resid 86 through 101 Processing helix chain 'e' and resid 104 through 117 Processing helix chain 'f' and resid 2 through 21 Processing helix chain 'f' and resid 23 through 45 removed outlier: 4.007A pdb=" N LEU f 44 " --> pdb=" O ARG f 40 " (cutoff:3.500A) Processing helix chain 'f' and resid 48 through 70 removed outlier: 4.178A pdb=" N GLU f 54 " --> pdb=" O GLU f 50 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N SER f 70 " --> pdb=" O ALA f 66 " (cutoff:3.500A) Processing helix chain 'f' and resid 74 through 96 Processing helix chain 'f' and resid 101 through 120 Processing helix chain 'f' and resid 123 through 146 Processing helix chain 'f' and resid 148 through 170 Processing helix chain 'f' and resid 173 through 194 Processing helix chain 'g' and resid 1 through 16 Processing helix chain 'g' and resid 18 through 33 Processing helix chain 'g' and resid 36 through 50 Processing helix chain 'g' and resid 52 through 67 Processing helix chain 'g' and resid 71 through 84 Processing helix chain 'g' and resid 86 through 101 Processing helix chain 'g' and resid 104 through 117 Processing helix chain 'h' and resid 2 through 21 Processing helix chain 'h' and resid 23 through 45 removed outlier: 4.007A pdb=" N LEU h 44 " --> pdb=" O ARG h 40 " (cutoff:3.500A) Processing helix chain 'h' and resid 48 through 70 removed outlier: 4.178A pdb=" N GLU h 54 " --> pdb=" O GLU h 50 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N SER h 70 " --> pdb=" O ALA h 66 " (cutoff:3.500A) Processing helix chain 'h' and resid 74 through 96 Processing helix chain 'h' and resid 101 through 120 Processing helix chain 'h' and resid 123 through 146 Processing helix chain 'h' and resid 148 through 170 Processing helix chain 'h' and resid 173 through 194 Processing helix chain 'i' and resid 1 through 16 Processing helix chain 'i' and resid 18 through 33 Processing helix chain 'i' and resid 36 through 50 Processing helix chain 'i' and resid 52 through 67 Processing helix chain 'i' and resid 71 through 84 Processing helix chain 'i' and resid 86 through 101 Processing helix chain 'i' and resid 104 through 117 Processing helix chain 'j' and resid 2 through 21 Processing helix chain 'j' and resid 23 through 45 removed outlier: 4.007A pdb=" N LEU j 44 " --> pdb=" O ARG j 40 " (cutoff:3.500A) Processing helix chain 'j' and resid 48 through 70 removed outlier: 4.178A pdb=" N GLU j 54 " --> pdb=" O GLU j 50 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N SER j 70 " --> pdb=" O ALA j 66 " (cutoff:3.500A) Processing helix chain 'j' and resid 74 through 96 Processing helix chain 'j' and resid 101 through 120 Processing helix chain 'j' and resid 123 through 146 Processing helix chain 'j' and resid 148 through 170 Processing helix chain 'j' and resid 173 through 194 Processing helix chain 'k' and resid 1 through 16 Processing helix chain 'k' and resid 18 through 33 Processing helix chain 'k' and resid 36 through 50 Processing helix chain 'k' and resid 52 through 67 Processing helix chain 'k' and resid 71 through 84 Processing helix chain 'k' and resid 86 through 101 Processing helix chain 'k' and resid 104 through 117 Processing helix chain 'l' and resid 2 through 21 Processing helix chain 'l' and resid 23 through 45 removed outlier: 4.007A pdb=" N LEU l 44 " --> pdb=" O ARG l 40 " (cutoff:3.500A) Processing helix chain 'l' and resid 48 through 70 removed outlier: 4.178A pdb=" N GLU l 54 " --> pdb=" O GLU l 50 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N SER l 70 " --> pdb=" O ALA l 66 " (cutoff:3.500A) Processing helix chain 'l' and resid 74 through 96 Processing helix chain 'l' and resid 101 through 120 Processing helix chain 'l' and resid 123 through 146 Processing helix chain 'l' and resid 148 through 170 Processing helix chain 'l' and resid 173 through 194 Processing helix chain 'm' and resid 1 through 16 Processing helix chain 'm' and resid 18 through 33 Processing helix chain 'm' and resid 36 through 50 Processing helix chain 'm' and resid 52 through 67 Processing helix chain 'm' and resid 71 through 84 Processing helix chain 'm' and resid 86 through 101 Processing helix chain 'm' and resid 104 through 117 Processing helix chain 'n' and resid 2 through 21 Processing helix chain 'n' and resid 23 through 45 removed outlier: 4.007A pdb=" N LEU n 44 " --> pdb=" O ARG n 40 " (cutoff:3.500A) Processing helix chain 'n' and resid 48 through 70 removed outlier: 4.178A pdb=" N GLU n 54 " --> pdb=" O GLU n 50 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N SER n 70 " --> pdb=" O ALA n 66 " (cutoff:3.500A) Processing helix chain 'n' and resid 74 through 96 Processing helix chain 'n' and resid 101 through 120 Processing helix chain 'n' and resid 123 through 146 Processing helix chain 'n' and resid 148 through 170 Processing helix chain 'n' and resid 173 through 194 5550 hydrogen bonds defined for protein. 16650 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: 19.28 Time building geometry restraints manager: 21.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 12700 1.32 - 1.45: 16725 1.45 - 1.57: 31525 1.57 - 1.70: 275 1.70 - 1.82: 300 Bond restraints: 61525 Sorted by residual: bond pdb=" CA ILE X 102 " pdb=" C ILE X 102 " ideal model delta sigma weight residual 1.524 1.476 0.048 1.23e-02 6.61e+03 1.53e+01 bond pdb=" CA ILE n 102 " pdb=" C ILE n 102 " ideal model delta sigma weight residual 1.524 1.476 0.048 1.23e-02 6.61e+03 1.53e+01 bond pdb=" CA ILE 3 102 " pdb=" C ILE 3 102 " ideal model delta sigma weight residual 1.524 1.476 0.048 1.23e-02 6.61e+03 1.53e+01 bond pdb=" CA ILE 1 102 " pdb=" C ILE 1 102 " ideal model delta sigma weight residual 1.524 1.476 0.048 1.23e-02 6.61e+03 1.53e+01 bond pdb=" CA ILE D 102 " pdb=" C ILE D 102 " ideal model delta sigma weight residual 1.524 1.476 0.048 1.23e-02 6.61e+03 1.53e+01 ... (remaining 61520 not shown) Histogram of bond angle deviations from ideal: 100.78 - 107.35: 1475 107.35 - 113.92: 34300 113.92 - 120.50: 29200 120.50 - 127.07: 18050 127.07 - 133.64: 250 Bond angle restraints: 83275 Sorted by residual: angle pdb=" N SER j 97 " pdb=" CA SER j 97 " pdb=" C SER j 97 " ideal model delta sigma weight residual 110.53 121.44 -10.91 1.29e+00 6.01e-01 7.16e+01 angle pdb=" N SER T 97 " pdb=" CA SER T 97 " pdb=" C SER T 97 " ideal model delta sigma weight residual 110.53 121.44 -10.91 1.29e+00 6.01e-01 7.16e+01 angle pdb=" N SER Z 97 " pdb=" CA SER Z 97 " pdb=" C SER Z 97 " ideal model delta sigma weight residual 110.53 121.44 -10.91 1.29e+00 6.01e-01 7.16e+01 angle pdb=" N SER l 97 " pdb=" CA SER l 97 " pdb=" C SER l 97 " ideal model delta sigma weight residual 110.53 121.44 -10.91 1.29e+00 6.01e-01 7.16e+01 angle pdb=" N SER L 97 " pdb=" CA SER L 97 " pdb=" C SER L 97 " ideal model delta sigma weight residual 110.53 121.44 -10.91 1.29e+00 6.01e-01 7.16e+01 ... (remaining 83270 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.84: 36350 15.84 - 31.69: 1050 31.69 - 47.53: 425 47.53 - 63.38: 200 63.38 - 79.22: 25 Dihedral angle restraints: 38050 sinusoidal: 14775 harmonic: 23275 Sorted by residual: dihedral pdb=" CA ASP W 86 " pdb=" CB ASP W 86 " pdb=" CG ASP W 86 " pdb=" OD1 ASP W 86 " ideal model delta sinusoidal sigma weight residual -30.00 -88.78 58.78 1 2.00e+01 2.50e-03 1.16e+01 dihedral pdb=" CA ASP c 86 " pdb=" CB ASP c 86 " pdb=" CG ASP c 86 " pdb=" OD1 ASP c 86 " ideal model delta sinusoidal sigma weight residual -30.00 -88.78 58.78 1 2.00e+01 2.50e-03 1.16e+01 dihedral pdb=" CA ASP M 86 " pdb=" CB ASP M 86 " pdb=" CG ASP M 86 " pdb=" OD1 ASP M 86 " ideal model delta sinusoidal sigma weight residual -30.00 -88.78 58.78 1 2.00e+01 2.50e-03 1.16e+01 ... (remaining 38047 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 5775 0.073 - 0.145: 3275 0.145 - 0.218: 875 0.218 - 0.291: 100 0.291 - 0.364: 25 Chirality restraints: 10050 Sorted by residual: chirality pdb=" CA ASN 8 76 " pdb=" N ASN 8 76 " pdb=" C ASN 8 76 " pdb=" CB ASN 8 76 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.31e+00 chirality pdb=" CA ASN 4 76 " pdb=" N ASN 4 76 " pdb=" C ASN 4 76 " pdb=" CB ASN 4 76 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.31e+00 chirality pdb=" CA ASN B 76 " pdb=" N ASN B 76 " pdb=" C ASN B 76 " pdb=" CB ASN B 76 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.31e+00 ... (remaining 10047 not shown) Planarity restraints: 10550 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR e 47 " 0.039 2.00e-02 2.50e+03 2.07e-02 8.58e+00 pdb=" CG TYR e 47 " -0.013 2.00e-02 2.50e+03 pdb=" CD1 TYR e 47 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR e 47 " -0.018 2.00e-02 2.50e+03 pdb=" CE1 TYR e 47 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR e 47 " -0.010 2.00e-02 2.50e+03 pdb=" CZ TYR e 47 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR e 47 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR S 47 " 0.039 2.00e-02 2.50e+03 2.07e-02 8.58e+00 pdb=" CG TYR S 47 " -0.013 2.00e-02 2.50e+03 pdb=" CD1 TYR S 47 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR S 47 " -0.018 2.00e-02 2.50e+03 pdb=" CE1 TYR S 47 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR S 47 " -0.010 2.00e-02 2.50e+03 pdb=" CZ TYR S 47 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR S 47 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR k 47 " 0.039 2.00e-02 2.50e+03 2.07e-02 8.58e+00 pdb=" CG TYR k 47 " -0.013 2.00e-02 2.50e+03 pdb=" CD1 TYR k 47 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR k 47 " -0.018 2.00e-02 2.50e+03 pdb=" CE1 TYR k 47 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR k 47 " -0.010 2.00e-02 2.50e+03 pdb=" CZ TYR k 47 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR k 47 " 0.030 2.00e-02 2.50e+03 ... (remaining 10547 not shown) Histogram of nonbonded interaction distances: 2.45 - 2.94: 29846 2.94 - 3.43: 70692 3.43 - 3.92: 103462 3.92 - 4.41: 128511 4.41 - 4.90: 183278 Nonbonded interactions: 515789 Sorted by model distance: nonbonded pdb=" O LEU i 117 " pdb=" C THR i 118 " model vdw 2.449 3.270 nonbonded pdb=" O LEU Y 117 " pdb=" C THR Y 118 " model vdw 2.449 3.270 nonbonded pdb=" O LEU 6 117 " pdb=" C THR 6 118 " model vdw 2.449 3.270 nonbonded pdb=" O LEU Q 117 " pdb=" C THR Q 118 " model vdw 2.449 3.270 nonbonded pdb=" O LEU I 117 " pdb=" C THR I 118 " model vdw 2.449 3.270 ... (remaining 515784 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 '0' selection = chain '2' selection = chain '4' selection = chain '6' selection = chain '8' selection = chain 'B' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'U' selection = chain 'W' selection = chain 'Y' selection = chain 'a' selection = chain 'c' selection = chain 'e' selection = chain 'g' selection = chain 'i' selection = chain 'k' selection = chain 'm' } ncs_group { reference = chain '1' selection = chain '3' selection = chain '5' selection = chain '7' selection = chain '9' selection = chain 'A' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'V' selection = chain 'X' selection = chain 'Z' selection = chain 'b' selection = chain 'd' selection = chain 'f' selection = chain 'h' selection = chain 'j' selection = chain 'l' selection = chain 'n' } Set up NCS constraints Number of NCS constrained groups: 2 pdb_interpretation.ncs_group { reference = chain '0' selection = chain '2' selection = chain '4' selection = chain '6' selection = chain '8' selection = chain 'B' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'U' selection = chain 'W' selection = chain 'Y' selection = chain 'a' selection = chain 'c' selection = chain 'e' selection = chain 'g' selection = chain 'i' selection = chain 'k' selection = chain 'm' } pdb_interpretation.ncs_group { reference = chain '1' selection = chain '3' selection = chain '5' selection = chain '7' selection = chain '9' selection = chain 'A' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'V' selection = chain 'X' selection = chain 'Z' selection = chain 'b' selection = chain 'd' selection = chain 'f' selection = chain 'h' selection = chain 'j' selection = chain 'l' selection = chain 'n' } Set refine NCS operators NCS operators will be refined. Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 225 5.16 5 C 38550 2.51 5 N 10175 2.21 5 O 11975 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 10.920 Check model and map are aligned: 0.790 Convert atoms to be neutral: 0.390 Process input model: 120.060 Find NCS groups from input model: 3.220 Set up NCS constraints: 0.610 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.020 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 139.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 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 : 0.018 0.078 61525 Z= 1.191 Angle : 1.468 10.913 83275 Z= 1.037 Chirality : 0.089 0.364 10050 Planarity : 0.008 0.029 10550 Dihedral : 10.928 79.219 22900 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 0.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.08), residues: 7775 helix: 1.06 (0.05), residues: 7100 sheet: None (None), residues: 0 loop : -1.24 (0.25), residues: 675 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15550 Ramachandran restraints generated. 7775 Oldfield, 0 Emsley, 7775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15550 Ramachandran restraints generated. 7775 Oldfield, 0 Emsley, 7775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 91 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 0.1683 time to fit residues: 6.6086 Evaluate side-chains 20 residues out of total 91 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.085 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1098 Evaluate side-chains 87 residues out of total 166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.1029 time to fit residues: 10.0230 Evaluate side-chains 33 residues out of total 166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 0.138 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 750 random chunks: chunk 633 optimal weight: 0.0980 chunk 568 optimal weight: 0.4980 chunk 315 optimal weight: 2.9990 chunk 194 optimal weight: 0.9990 chunk 383 optimal weight: 0.6980 chunk 303 optimal weight: 0.6980 chunk 587 optimal weight: 5.9990 chunk 227 optimal weight: 6.9990 chunk 357 optimal weight: 10.0000 chunk 437 optimal weight: 5.9990 chunk 681 optimal weight: 4.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 50 GLN K 76 ASN Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.4637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 61525 Z= 0.245 Angle : 0.741 12.607 83275 Z= 0.369 Chirality : 0.042 0.323 10050 Planarity : 0.004 0.020 10550 Dihedral : 4.037 13.519 8775 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 15.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer Outliers : 0.39 % 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: 2.25 (0.09), residues: 7775 helix: 1.81 (0.05), residues: 6925 sheet: None (None), residues: 0 loop : -1.08 (0.24), residues: 850 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15318 Ramachandran restraints generated. 7659 Oldfield, 0 Emsley, 7659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15318 Ramachandran restraints generated. 7659 Oldfield, 0 Emsley, 7659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 91 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.088 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.1449 time to fit residues: 4.3844 Evaluate side-chains 16 residues out of total 91 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.087 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1143 Evaluate side-chains 49 residues out of total 166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 48 time to evaluate : 0.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 48 average time/residue: 0.0895 time to fit residues: 5.0066 Evaluate side-chains 34 residues out of total 166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.141 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/iotbx/cli_parser.py", line 864, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 675, in refine_xyz self.minimization_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 770, in minimization_ncs ncs_groups = ncs_groups) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 400, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 133, in refine refine_sites = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 434, in __init__ ignore_line_search_failed_maxfev=True)) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 459, in compute_functional_and_gradients x=self.x) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 248, in target_and_gradients grad = g_data) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 112, in restraints_target_and_grads compute_gradients = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 55.5606 > 50: distance: 1 - 2: 14.458 distance: 2 - 3: 15.877 distance: 2 - 5: 15.011 distance: 3 - 4: 29.372 distance: 3 - 6: 24.745 distance: 6 - 7: 6.369 distance: 7 - 8: 35.633 distance: 8 - 9: 21.274 distance: 8 - 10: 31.084 distance: 10 - 11: 19.809 distance: 11 - 12: 24.666 distance: 11 - 14: 22.430 distance: 12 - 13: 9.601 distance: 12 - 17: 13.794 distance: 14 - 16: 7.549 distance: 17 - 18: 4.168 distance: 18 - 19: 34.692 distance: 18 - 21: 25.128 distance: 19 - 20: 17.073 distance: 19 - 23: 4.104 distance: 20 - 49: 28.836 distance: 21 - 22: 18.281 distance: 23 - 24: 13.050 distance: 24 - 25: 14.335 distance: 24 - 27: 11.149 distance: 25 - 26: 7.177 distance: 26 - 57: 17.371 distance: 27 - 28: 7.245 distance: 28 - 29: 12.156 distance: 29 - 30: 4.278 distance: 29 - 31: 5.389 distance: 32 - 33: 7.377 distance: 33 - 34: 6.714 distance: 33 - 36: 5.355 distance: 34 - 35: 6.073 distance: 34 - 40: 8.603 distance: 35 - 62: 10.369 distance: 36 - 37: 13.137 distance: 37 - 38: 9.421 distance: 37 - 39: 5.010 distance: 40 - 41: 6.500 distance: 41 - 42: 8.805 distance: 41 - 44: 25.748 distance: 42 - 43: 4.055 distance: 42 - 49: 14.146 distance: 43 - 71: 43.131 distance: 44 - 45: 24.531 distance: 45 - 46: 17.315 distance: 46 - 47: 25.670 distance: 46 - 48: 11.310 distance: 49 - 50: 13.665 distance: 50 - 51: 17.644 distance: 50 - 53: 18.977 distance: 51 - 57: 22.938 distance: 52 - 77: 22.546 distance: 53 - 54: 21.327 distance: 53 - 55: 16.615 distance: 54 - 56: 26.029 distance: 57 - 58: 4.638 distance: 58 - 59: 15.959 distance: 58 - 61: 23.844 distance: 59 - 60: 17.218 distance: 59 - 62: 4.882 distance: 62 - 63: 18.321 distance: 63 - 64: 11.615 distance: 63 - 66: 17.344 distance: 64 - 65: 14.303 distance: 64 - 71: 4.728 distance: 66 - 67: 28.110 distance: 67 - 68: 11.071 distance: 68 - 69: 17.563 distance: 68 - 70: 10.377 distance: 71 - 72: 17.976 distance: 72 - 73: 18.575 distance: 72 - 75: 22.550 distance: 73 - 74: 15.438 distance: 73 - 77: 14.465 distance: 75 - 76: 15.359 distance: 77 - 78: 27.962 distance: 78 - 79: 35.821 distance: 79 - 80: 28.920