Starting phenix.real_space_refine on Fri Dec 8 16:34:36 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vfi_21173/12_2023/6vfi_21173.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vfi_21173/12_2023/6vfi_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_2023/6vfi_21173.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vfi_21173/12_2023/6vfi_21173.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vfi_21173/12_2023/6vfi_21173.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vfi_21173/12_2023/6vfi_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: 0.18s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 22.76, per 1000 atoms: 0.39 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: 18.95 Conformation dependent library (CDL) restraints added in 7.9 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: 3.92 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: 20.01 Time building geometry restraints manager: 20.65 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: 1.000 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: 0.040 Extract box with map and model: 8.130 Check model and map are aligned: 0.680 Set scattering table: 0.420 Process input model: 119.240 Find NCS groups from input model: 3.200 Set up NCS constraints: 0.610 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:2.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 135.800 ------------------------------------------------------------------------------- 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 : 0.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 0.1861 time to fit residues: 7.2676 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: 0.1082 Evaluate side-chains 87 residues out of total 166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.143 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: 0.1091 time to fit residues: 10.5896 Evaluate side-chains 32 residues out of total 166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 0.139 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1823 ------------------------------------------------------------------------------- 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: 0.6980 overall best weight: 2.0586 ------------------------------------------------------------------------------- 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: 0.8092 moved from start: 0.4736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 59064 Z= 0.244 Angle : 0.723 12.441 79944 Z= 0.367 Chirality : 0.043 0.358 9648 Planarity : 0.004 0.021 10128 Dihedral : 4.036 13.721 8424 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 15.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.39 % Allowed : 2.72 % Favored : 96.89 % 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: 2.23 (0.09), residues: 7464 helix: 1.80 (0.06), residues: 6648 sheet: None (None), residues: 0 loop : -1.09 (0.24), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP 0 40 PHE 0.003 0.001 PHE 1 149 TYR 0.012 0.002 TYR i 19 ARG 0.001 0.000 ARG h 83 *********************** 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 : 0.115 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.1559 time to fit residues: 4.6987 Evaluate side-chains 14 residues out of total 91 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 0.086 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1120 Evaluate side-chains 48 residues out of total 166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 47 time to evaluate : 0.138 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 47 average time/residue: 0.0915 time to fit residues: 5.0003 Evaluate side-chains 28 residues out of total 166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.139 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 363 optimal weight: 0.0270 chunk 202 optimal weight: 7.9990 chunk 544 optimal weight: 2.9990 chunk 445 optimal weight: 8.9990 chunk 180 optimal weight: 10.0000 chunk 655 optimal weight: 10.0000 chunk 707 optimal weight: 30.0000 chunk 583 optimal weight: 8.9990 chunk 649 optimal weight: 7.9990 chunk 223 optimal weight: 3.9990 chunk 525 optimal weight: 10.0000 overall best weight: 4.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle 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: 0.8186 moved from start: 0.5551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 59064 Z= 0.249 Angle : 0.680 8.934 79944 Z= 0.362 Chirality : 0.040 0.218 9648 Planarity : 0.004 0.039 10128 Dihedral : 4.361 21.609 8424 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 15.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % 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: 1.42 (0.09), residues: 7464 helix: 1.31 (0.06), residues: 6648 sheet: None (None), residues: 0 loop : -1.79 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP 2 40 PHE 0.004 0.001 PHE V 149 TYR 0.023 0.002 TYR A 49 ARG 0.006 0.001 ARG 5 40 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14074 Ramachandran restraints generated. 7037 Oldfield, 0 Emsley, 7037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14074 Ramachandran restraints generated. 7037 Oldfield, 0 Emsley, 7037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 91 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.091 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.1069 time to fit residues: 2.5215 Evaluate side-chains 16 residues out of total 91 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.086 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1091 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 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.0648 time to fit residues: 2.7753 Evaluate side-chains 25 residues out of total 166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.139 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 647 optimal weight: 6.9990 chunk 492 optimal weight: 0.0870 chunk 339 optimal weight: 0.9990 chunk 72 optimal weight: 5.9990 chunk 312 optimal weight: 5.9990 chunk 439 optimal weight: 4.9990 chunk 657 optimal weight: 1.9990 chunk 695 optimal weight: 6.9990 chunk 343 optimal weight: 0.1980 chunk 623 optimal weight: 0.0270 chunk 187 optimal weight: 0.5980 overall best weight: 0.3818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 110 ASN Total number of N/Q/H flips: 1 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: 0.8132 moved from start: 0.5819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 59064 Z= 0.185 Angle : 0.660 8.056 79944 Z= 0.342 Chirality : 0.040 0.220 9648 Planarity : 0.004 0.030 10128 Dihedral : 4.270 22.180 8424 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.39 % Allowed : 2.72 % Favored : 96.89 % 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: 1.43 (0.09), residues: 7464 helix: 1.34 (0.06), residues: 6648 sheet: None (None), residues: 0 loop : -2.06 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP 2 40 PHE 0.003 0.001 PHE P 149 TYR 0.024 0.002 TYR W 19 ARG 0.007 0.000 ARG P 40 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13684 Ramachandran restraints generated. 6842 Oldfield, 0 Emsley, 6842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13684 Ramachandran restraints generated. 6842 Oldfield, 0 Emsley, 6842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 91 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 22 time to evaluate : 0.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 22 average time/residue: 0.1073 time to fit residues: 2.6504 Evaluate side-chains 18 residues out of total 91 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 17 time to evaluate : 0.088 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0143 time to fit residues: 0.1319 Evaluate side-chains 41 residues out of total 166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.142 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.0805 time to fit residues: 3.9491 Evaluate side-chains 26 residues out of total 166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.141 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 579 optimal weight: 1.9990 chunk 395 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 518 optimal weight: 6.9990 chunk 287 optimal weight: 5.9990 chunk 593 optimal weight: 30.0000 chunk 481 optimal weight: 8.9990 chunk 0 optimal weight: 10.9990 chunk 355 optimal weight: 0.0060 chunk 624 optimal weight: 4.9990 chunk 175 optimal weight: 0.4980 overall best weight: 1.0400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 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: 0.8143 moved from start: 0.5862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 59064 Z= 0.185 Angle : 0.660 8.056 79944 Z= 0.342 Chirality : 0.040 0.220 9648 Planarity : 0.004 0.030 10128 Dihedral : 4.270 22.180 8424 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 28.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 1.43 (0.09), residues: 7464 helix: 1.34 (0.06), residues: 6648 sheet: None (None), residues: 0 loop : -2.06 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP 4 40 PHE 0.003 0.001 PHE F 149 TYR 0.024 0.002 TYR W 19 ARG 0.007 0.000 ARG P 40 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13684 Ramachandran restraints generated. 6842 Oldfield, 0 Emsley, 6842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13684 Ramachandran restraints generated. 6842 Oldfield, 0 Emsley, 6842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 91 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.1151 time to fit residues: 2.4489 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: 0.1086 Evaluate side-chains 36 residues out of total 166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 0.139 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.0639 time to fit residues: 2.8845 Evaluate side-chains 26 residues out of total 166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.157 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 234 optimal weight: 40.0000 chunk 626 optimal weight: 4.9990 chunk 137 optimal weight: 8.9990 chunk 408 optimal weight: 5.9990 chunk 171 optimal weight: 3.9990 chunk 696 optimal weight: 2.9990 chunk 578 optimal weight: 0.3980 chunk 322 optimal weight: 6.9990 chunk 57 optimal weight: 4.9990 chunk 230 optimal weight: 0.1980 chunk 365 optimal weight: 0.1980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 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: 0.8143 moved from start: 0.5863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 59064 Z= 0.185 Angle : 0.660 8.056 79944 Z= 0.342 Chirality : 0.040 0.220 9648 Planarity : 0.004 0.030 10128 Dihedral : 4.270 22.180 8424 Min Nonbonded Distance : 1.654 Molprobity Statistics. All-atom Clashscore : 28.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 1.43 (0.09), residues: 7464 helix: 1.34 (0.06), residues: 6648 sheet: None (None), residues: 0 loop : -2.06 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP Y 40 PHE 0.003 0.001 PHE D 149 TYR 0.024 0.002 TYR S 19 ARG 0.007 0.000 ARG P 40 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13684 Ramachandran restraints generated. 6842 Oldfield, 0 Emsley, 6842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13684 Ramachandran restraints generated. 6842 Oldfield, 0 Emsley, 6842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 91 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.1180 time to fit residues: 2.5065 Evaluate side-chains 16 residues out of total 91 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.086 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1092 Evaluate side-chains 36 residues out of total 166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 0.153 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.0661 time to fit residues: 2.9750 Evaluate side-chains 26 residues out of total 166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.142 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 671 optimal weight: 8.9990 chunk 78 optimal weight: 5.9990 chunk 396 optimal weight: 1.9990 chunk 508 optimal weight: 6.9990 chunk 394 optimal weight: 10.0000 chunk 586 optimal weight: 5.9990 chunk 389 optimal weight: 9.9990 chunk 693 optimal weight: 0.0010 chunk 434 optimal weight: 4.9990 chunk 423 optimal weight: 1.9990 chunk 320 optimal weight: 7.9990 overall best weight: 2.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 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: 0.8143 moved from start: 0.5863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 59064 Z= 0.185 Angle : 0.660 8.056 79944 Z= 0.342 Chirality : 0.040 0.220 9648 Planarity : 0.004 0.030 10128 Dihedral : 4.270 22.180 8424 Min Nonbonded Distance : 1.654 Molprobity Statistics. All-atom Clashscore : 28.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 1.43 (0.09), residues: 7464 helix: 1.34 (0.06), residues: 6648 sheet: None (None), residues: 0 loop : -2.06 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP 4 40 PHE 0.003 0.001 PHE N 149 TYR 0.024 0.002 TYR Q 19 ARG 0.007 0.000 ARG T 40 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13294 Ramachandran restraints generated. 6647 Oldfield, 0 Emsley, 6647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13294 Ramachandran restraints generated. 6647 Oldfield, 0 Emsley, 6647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 91 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.1168 time to fit residues: 2.4823 Evaluate side-chains 16 residues out of total 91 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.084 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1089 Evaluate side-chains 36 residues out of total 166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 0.139 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.0647 time to fit residues: 2.9457 Evaluate side-chains 26 residues out of total 166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.138 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 429 optimal weight: 2.9990 chunk 277 optimal weight: 0.8980 chunk 414 optimal weight: 6.9990 chunk 209 optimal weight: 5.9990 chunk 136 optimal weight: 3.9990 chunk 134 optimal weight: 0.9990 chunk 441 optimal weight: 0.7980 chunk 472 optimal weight: 5.9990 chunk 343 optimal weight: 1.9990 chunk 64 optimal weight: 10.0000 chunk 545 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 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: 0.8143 moved from start: 0.5863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 59064 Z= 0.185 Angle : 0.660 8.056 79944 Z= 0.342 Chirality : 0.040 0.220 9648 Planarity : 0.004 0.030 10128 Dihedral : 4.270 22.180 8424 Min Nonbonded Distance : 1.654 Molprobity Statistics. All-atom Clashscore : 28.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 1.43 (0.09), residues: 7464 helix: 1.34 (0.06), residues: 6648 sheet: None (None), residues: 0 loop : -2.06 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP 4 40 PHE 0.003 0.001 PHE H 149 TYR 0.024 0.002 TYR O 19 ARG 0.007 0.000 ARG A 40 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13294 Ramachandran restraints generated. 6647 Oldfield, 0 Emsley, 6647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13294 Ramachandran restraints generated. 6647 Oldfield, 0 Emsley, 6647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 91 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.1191 time to fit residues: 2.5339 Evaluate side-chains 16 residues out of total 91 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.086 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1095 Evaluate side-chains 36 residues out of total 166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 0.140 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.0643 time to fit residues: 2.8980 Evaluate side-chains 26 residues out of total 166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.141 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 631 optimal weight: 0.9980 chunk 664 optimal weight: 9.9990 chunk 606 optimal weight: 0.1980 chunk 646 optimal weight: 6.9990 chunk 389 optimal weight: 5.9990 chunk 281 optimal weight: 5.9990 chunk 507 optimal weight: 2.9990 chunk 198 optimal weight: 3.9990 chunk 584 optimal weight: 10.0000 chunk 611 optimal weight: 4.9990 chunk 644 optimal weight: 10.0000 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 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: 0.8143 moved from start: 0.5863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 59064 Z= 0.185 Angle : 0.660 8.056 79944 Z= 0.342 Chirality : 0.040 0.220 9648 Planarity : 0.004 0.030 10128 Dihedral : 4.270 22.180 8424 Min Nonbonded Distance : 1.654 Molprobity Statistics. All-atom Clashscore : 28.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 1.43 (0.09), residues: 7464 helix: 1.34 (0.06), residues: 6648 sheet: None (None), residues: 0 loop : -2.06 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP 2 40 PHE 0.003 0.001 PHE b 149 TYR 0.024 0.002 TYR S 19 ARG 0.007 0.000 ARG H 40 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13294 Ramachandran restraints generated. 6647 Oldfield, 0 Emsley, 6647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13294 Ramachandran restraints generated. 6647 Oldfield, 0 Emsley, 6647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 91 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.1281 time to fit residues: 2.7117 Evaluate side-chains 16 residues out of total 91 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.086 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1100 Evaluate side-chains 36 residues out of total 166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 0.140 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.0644 time to fit residues: 2.8996 Evaluate side-chains 26 residues out of total 166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.139 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 424 optimal weight: 8.9990 chunk 683 optimal weight: 0.7980 chunk 417 optimal weight: 0.7980 chunk 324 optimal weight: 7.9990 chunk 475 optimal weight: 0.5980 chunk 717 optimal weight: 0.0170 chunk 660 optimal weight: 10.0000 chunk 571 optimal weight: 5.9990 chunk 59 optimal weight: 6.9990 chunk 441 optimal weight: 1.9990 chunk 350 optimal weight: 5.9990 overall best weight: 0.8420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 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: 0.8143 moved from start: 0.5863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 59064 Z= 0.185 Angle : 0.660 8.056 79944 Z= 0.342 Chirality : 0.040 0.220 9648 Planarity : 0.004 0.030 10128 Dihedral : 4.270 22.180 8424 Min Nonbonded Distance : 1.654 Molprobity Statistics. All-atom Clashscore : 28.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 1.43 (0.09), residues: 7464 helix: 1.34 (0.06), residues: 6648 sheet: None (None), residues: 0 loop : -2.06 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP Y 40 PHE 0.003 0.001 PHE N 149 TYR 0.024 0.002 TYR U 19 ARG 0.007 0.000 ARG Z 40 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13294 Ramachandran restraints generated. 6647 Oldfield, 0 Emsley, 6647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13294 Ramachandran restraints generated. 6647 Oldfield, 0 Emsley, 6647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 91 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.1218 time to fit residues: 2.5912 Evaluate side-chains 16 residues out of total 91 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.086 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1094 Evaluate side-chains 36 residues out of total 166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 0.140 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.0657 time to fit residues: 2.9775 Evaluate side-chains 26 residues out of total 166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.156 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 453 optimal weight: 2.9990 chunk 608 optimal weight: 7.9990 chunk 174 optimal weight: 6.9990 chunk 526 optimal weight: 5.9990 chunk 84 optimal weight: 7.9990 chunk 158 optimal weight: 3.9990 chunk 572 optimal weight: 4.9990 chunk 239 optimal weight: 0.0060 chunk 587 optimal weight: 8.9990 chunk 72 optimal weight: 0.8980 chunk 105 optimal weight: 4.9990 overall best weight: 2.5802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.052107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.045239 restraints weight = 5392.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.046603 restraints weight = 3507.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.047727 restraints weight = 2505.233| |-----------------------------------------------------------------------------| r_work (final): 0.3016 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.073173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.060930 restraints weight = 6257.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.062705 restraints weight = 4203.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.064044 restraints weight = 3113.936| |-----------------------------------------------------------------------------| r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.5863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 59064 Z= 0.185 Angle : 0.660 8.056 79944 Z= 0.342 Chirality : 0.040 0.220 9648 Planarity : 0.004 0.030 10128 Dihedral : 4.270 22.180 8424 Min Nonbonded Distance : 1.654 Molprobity Statistics. All-atom Clashscore : 28.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 1.43 (0.09), residues: 7464 helix: 1.34 (0.06), residues: 6648 sheet: None (None), residues: 0 loop : -2.06 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP 2 40 PHE 0.003 0.001 PHE F 149 TYR 0.024 0.002 TYR S 19 ARG 0.007 0.000 ARG h 40 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4774.17 seconds wall clock time: 89 minutes 16.10 seconds (5356.10 seconds total)