Starting phenix.real_space_refine on Thu Jan 18 12:42:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vfi_21173/01_2024/6vfi_21173.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vfi_21173/01_2024/6vfi_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_21173/01_2024/6vfi_21173.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vfi_21173/01_2024/6vfi_21173.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vfi_21173/01_2024/6vfi_21173.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vfi_21173/01_2024/6vfi_21173.pdb" } resolution = 4.54 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= 0.001 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 Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 216 5.16 5 C 37008 2.51 5 N 9768 2.21 5 O 11496 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped 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 "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" 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" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 58488 Number of models: 1 Model: "" Number of chains: 48 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: "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} 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} Time building chain proxies: 21.42, per 1000 atoms: 0.37 Number of scatterers: 58488 At special positions: 0 Unit cell: (188.49, 188.49, 188.49, 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 216 16.00 O 11496 8.00 N 9768 7.00 C 37008 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 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 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 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 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: 18.78 Conformation dependent library (CDL) restraints added in 7.7 seconds 14928 Ramachandran restraints generated. 7464 Oldfield, 0 Emsley, 7464 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14400 Finding SS restraints... Secondary structure from input PDB file: 360 helices and 0 sheets defined 90.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.48 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 5328 hydrogen bonds defined for protein. 15984 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: 18.22 Time building geometry restraints manager: 20.61 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: 12192 1.32 - 1.45: 16056 1.45 - 1.57: 30264 1.57 - 1.70: 264 1.70 - 1.82: 288 Bond restraints: 59064 Sorted by residual: bond pdb=" CA ILE Z 102 " pdb=" C ILE Z 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 J 102 " pdb=" C ILE J 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 5 102 " pdb=" C ILE 5 102 " 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 H 102 " pdb=" C ILE H 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 ... (remaining 59059 not shown) Histogram of bond angle deviations from ideal: 100.78 - 107.35: 1416 107.35 - 113.92: 32928 113.92 - 120.50: 28032 120.50 - 127.07: 17328 127.07 - 133.64: 240 Bond angle restraints: 79944 Sorted by residual: angle pdb=" N SER R 97 " pdb=" CA SER R 97 " pdb=" C SER R 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 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 h 97 " pdb=" CA SER h 97 " pdb=" C SER h 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 3 97 " pdb=" CA SER 3 97 " pdb=" C SER 3 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 D 97 " pdb=" CA SER D 97 " pdb=" C SER D 97 " ideal model delta sigma weight residual 110.53 121.44 -10.91 1.29e+00 6.01e-01 7.16e+01 ... (remaining 79939 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.84: 34896 15.84 - 31.69: 1008 31.69 - 47.53: 408 47.53 - 63.38: 192 63.38 - 79.22: 24 Dihedral angle restraints: 36528 sinusoidal: 14184 harmonic: 22344 Sorted by residual: dihedral pdb=" CA ASP 8 86 " pdb=" CB ASP 8 86 " pdb=" CG ASP 8 86 " pdb=" OD1 ASP 8 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 e 86 " pdb=" CB ASP e 86 " pdb=" CG ASP e 86 " pdb=" OD1 ASP e 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 36525 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 5544 0.073 - 0.145: 3144 0.145 - 0.218: 840 0.218 - 0.291: 96 0.291 - 0.364: 24 Chirality restraints: 9648 Sorted by residual: chirality pdb=" CA ASN 0 76 " pdb=" N ASN 0 76 " pdb=" C ASN 0 76 " pdb=" CB ASN 0 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 O 76 " pdb=" N ASN O 76 " pdb=" C ASN O 76 " pdb=" CB ASN O 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 a 76 " pdb=" N ASN a 76 " pdb=" C ASN a 76 " pdb=" CB ASN a 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 9645 not shown) Planarity restraints: 10128 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR c 47 " 0.039 2.00e-02 2.50e+03 2.07e-02 8.58e+00 pdb=" CG TYR c 47 " -0.013 2.00e-02 2.50e+03 pdb=" CD1 TYR c 47 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR c 47 " -0.018 2.00e-02 2.50e+03 pdb=" CE1 TYR c 47 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR c 47 " -0.010 2.00e-02 2.50e+03 pdb=" CZ TYR c 47 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR c 47 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR M 47 " -0.039 2.00e-02 2.50e+03 2.07e-02 8.58e+00 pdb=" CG TYR M 47 " 0.013 2.00e-02 2.50e+03 pdb=" CD1 TYR M 47 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR M 47 " 0.018 2.00e-02 2.50e+03 pdb=" CE1 TYR M 47 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR M 47 " 0.010 2.00e-02 2.50e+03 pdb=" CZ TYR M 47 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR M 47 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR 8 47 " -0.039 2.00e-02 2.50e+03 2.07e-02 8.58e+00 pdb=" CG TYR 8 47 " 0.013 2.00e-02 2.50e+03 pdb=" CD1 TYR 8 47 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR 8 47 " 0.018 2.00e-02 2.50e+03 pdb=" CE1 TYR 8 47 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR 8 47 " 0.010 2.00e-02 2.50e+03 pdb=" CZ TYR 8 47 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR 8 47 " -0.030 2.00e-02 2.50e+03 ... (remaining 10125 not shown) Histogram of nonbonded interaction distances: 2.45 - 2.94: 28656 2.94 - 3.43: 67872 3.43 - 3.92: 99384 3.92 - 4.41: 123504 4.41 - 4.90: 176136 Nonbonded interactions: 495552 Sorted by model distance: nonbonded pdb=" O LEU O 117 " pdb=" C THR O 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 4 117 " pdb=" C THR 4 118 " model vdw 2.449 3.270 nonbonded pdb=" O LEU W 117 " pdb=" C THR W 118 " model vdw 2.449 3.270 nonbonded pdb=" O LEU G 117 " pdb=" C THR G 118 " model vdw 2.449 3.270 ... (remaining 495547 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' } 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' } 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' } 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' } Set refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.610 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: 0.040 Extract box with map and model: 7.900 Check model and map are aligned: 0.630 Set scattering table: 0.390 Process input model: 112.090 Find NCS groups from input model: 3.000 Set up NCS constraints: 0.600 Set refine NCS operators: 0.000 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:2.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 128.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 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 59064 Z= 1.191 Angle : 1.468 10.913 79944 Z= 1.037 Chirality : 0.089 0.364 9648 Planarity : 0.008 0.029 10128 Dihedral : 10.928 79.219 21984 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 % Allowed : 0.78 % Favored : 99.22 % 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: 1.21 (0.08), residues: 7464 helix: 1.06 (0.05), residues: 6816 sheet: None (None), residues: 0 loop : -1.24 (0.26), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.009 TRP S 40 PHE 0.008 0.004 PHE j 149 TYR 0.039 0.007 TYR M 47 ARG 0.005 0.001 ARG 4 24 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14928 Ramachandran restraints generated. 7464 Oldfield, 0 Emsley, 7464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14928 Ramachandran restraints generated. 7464 Oldfield, 0 Emsley, 7464 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 : 0.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 12 LEU cc_start: 0.9600 (tp) cc_final: 0.9388 (tt) REVERT: 0 101 ASP cc_start: 0.8115 (t0) cc_final: 0.7864 (m-30) REVERT: 0 117 LEU cc_start: 0.8238 (mt) cc_final: 0.8032 (mp) outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 0.1807 time to fit residues: 7.0599 Evaluate side-chains 21 residues out of total 91 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.078 Evaluate side-chains 87 residues out of total 166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 91 THR cc_start: 0.8899 (m) cc_final: 0.8592 (p) REVERT: 1 129 LEU cc_start: 0.9087 (tp) cc_final: 0.8869 (mt) REVERT: 1 155 CYS cc_start: 0.8074 (m) cc_final: 0.7787 (t) REVERT: 1 162 GLU cc_start: 0.8299 (tp30) cc_final: 0.7956 (tt0) REVERT: 1 164 ILE cc_start: 0.8837 (mt) cc_final: 0.8615 (mt) REVERT: 1 167 LEU cc_start: 0.9349 (mt) cc_final: 0.9115 (mm) REVERT: 1 172 THR cc_start: 0.8188 (m) cc_final: 0.7719 (m) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.1049 time to fit residues: 10.1811 Evaluate side-chains 33 residues out of total 166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 607 optimal weight: 2.9990 chunk 545 optimal weight: 9.9990 chunk 302 optimal weight: 8.9990 chunk 186 optimal weight: 0.5980 chunk 368 optimal weight: 6.9990 chunk 291 optimal weight: 2.9990 chunk 564 optimal weight: 3.9990 chunk 218 optimal weight: 8.9990 chunk 343 optimal weight: 2.9990 chunk 420 optimal weight: 10.0000 chunk 653 optimal weight: 0.0980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 50 GLN O 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: 0.8090 moved from start: 0.4377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 59064 Z= 0.249 Angle : 0.723 12.673 79944 Z= 0.369 Chirality : 0.042 0.306 9648 Planarity : 0.004 0.024 10128 Dihedral : 4.001 13.118 8424 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 15.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.39 % Allowed : 1.56 % Favored : 98.05 % 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: 2.39 (0.09), residues: 7464 helix: 1.90 (0.06), residues: 6648 sheet: None (None), residues: 0 loop : -0.98 (0.24), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP 0 40 PHE 0.005 0.002 PHE f 149 TYR 0.016 0.002 TYR d 99 ARG 0.007 0.000 ARG i 24 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14696 Ramachandran restraints generated. 7348 Oldfield, 0 Emsley, 7348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14696 Ramachandran restraints generated. 7348 Oldfield, 0 Emsley, 7348 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 : 0.086 Fit side-chains revert: symmetry clash REVERT: O 95 GLN cc_start: 0.9076 (tm-30) cc_final: 0.7978 (tm-30) REVERT: O 101 ASP cc_start: 0.8092 (t0) cc_final: 0.7627 (m-30) REVERT: O 110 ASN cc_start: 0.8019 (m-40) cc_final: 0.7691 (t0) outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.1255 time to fit residues: 3.8437 Evaluate side-chains 17 residues out of total 91 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.083 Evaluate side-chains 49 residues out of total 166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 48 time to evaluate : 0.133 Fit side-chains revert: symmetry clash REVERT: l 26 GLU cc_start: 0.8594 (mt-10) cc_final: 0.8272 (mm-30) REVERT: l 91 THR cc_start: 0.9059 (m) cc_final: 0.8838 (p) REVERT: l 93 LYS cc_start: 0.8659 (pptt) cc_final: 0.8284 (tptt) REVERT: l 172 THR cc_start: 0.8104 (m) cc_final: 0.7334 (m) outliers start: 1 outliers final: 0 residues processed: 48 average time/residue: 0.0916 time to fit residues: 5.1047 Evaluate side-chains 28 residues out of total 166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.135 ------------------------------------------------------------------------------- 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-1.21-5211/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-1.21-5211/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 798, in minimization_ncs ncs_groups = ncs_groups) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/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-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/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-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/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: 63.677 > 50: distance: 4 - 5: 10.319 distance: 5 - 6: 21.318 distance: 5 - 8: 32.887 distance: 6 - 7: 20.417 distance: 6 - 9: 26.585 distance: 7 - 38: 36.794 distance: 9 - 10: 15.638 distance: 10 - 13: 16.304 distance: 11 - 12: 30.327 distance: 11 - 17: 19.322 distance: 12 - 50: 20.037 distance: 13 - 14: 7.995 distance: 13 - 15: 11.524 distance: 14 - 16: 9.600 distance: 17 - 18: 8.306 distance: 18 - 19: 14.401 distance: 18 - 21: 23.580 distance: 19 - 20: 36.063 distance: 19 - 26: 17.033 distance: 20 - 59: 35.581 distance: 21 - 22: 12.163 distance: 22 - 23: 18.395 distance: 23 - 24: 26.097 distance: 23 - 25: 19.039 distance: 26 - 27: 22.331 distance: 27 - 28: 31.488 distance: 27 - 30: 31.204 distance: 28 - 29: 11.381 distance: 28 - 38: 38.311 distance: 29 - 68: 24.536 distance: 30 - 31: 25.362 distance: 31 - 32: 31.752 distance: 31 - 33: 40.147 distance: 32 - 34: 19.782 distance: 33 - 35: 9.410 distance: 34 - 36: 17.899 distance: 35 - 36: 31.148 distance: 36 - 37: 35.716 distance: 38 - 39: 32.503 distance: 39 - 40: 23.275 distance: 39 - 42: 16.840 distance: 40 - 41: 24.306 distance: 40 - 50: 17.670 distance: 41 - 73: 28.008 distance: 42 - 43: 11.371 distance: 43 - 44: 22.261 distance: 43 - 45: 18.497 distance: 44 - 46: 19.615 distance: 45 - 47: 25.978 distance: 46 - 48: 31.127 distance: 47 - 48: 11.058 distance: 48 - 49: 24.038 distance: 50 - 51: 16.902 distance: 51 - 52: 12.741 distance: 51 - 54: 30.588 distance: 52 - 53: 25.303 distance: 52 - 59: 16.442 distance: 54 - 55: 12.928 distance: 55 - 56: 11.993 distance: 56 - 57: 12.923 distance: 56 - 58: 15.773 distance: 59 - 60: 8.900 distance: 60 - 61: 19.741 distance: 61 - 62: 33.205 distance: 61 - 68: 29.590 distance: 63 - 64: 14.153 distance: 64 - 65: 9.813 distance: 65 - 66: 24.780 distance: 66 - 67: 13.603 distance: 68 - 69: 14.430 distance: 69 - 70: 10.397 distance: 69 - 72: 11.774 distance: 70 - 71: 16.608 distance: 70 - 73: 5.771 distance: 73 - 74: 5.852 distance: 74 - 75: 7.407 distance: 75 - 76: 4.403